*** This is the DRAFT VERSION 0.3 ALPHA of the Minimum Common Oncology Data Elements (mCODE™) implementation guide. ***
+ ++ +
Tumor and molecular markers are key prognostic factors in calculating cancer staging, identifying treatment options, and monitoring progression of disease. This IG distinguishes tumor marker from genomics as follows:
+mCODE identifies a dedicated FHIR profile called TumorMarker for the identification of cancer tumor markers.
+mCODE focuses on cancer genomics - the study of the totality of DNA sequence and gene expression differences between tumour cells and normal host cells. It aims to understand the genetic basis of tumour cell proliferation and the evolution of the cancer genome under mutation and selection by the body environment, the immune system and therapeutic interventions (source: Nature).
+mCODE will only include the minimal set of genetic related elements relevant to capture in an EHR to drive treatment options.
+mCODE aligns with the Sync for Genes approach to adopting a layered-based adoption model. With mCODE's initial emphasis on a minimal set of elements to drive treatment, there is no immediate need to model and store whole sequence reads that would be sent from an NGS labs. Rather, only the relevant genetics labs test results and variant names and interpretation, noted by Sync for Genes as levels 1 and 2, would suffice. Subsequently, the mCODE implementation mapped to the observation-genetics profile as much as possible.
+ +mCODE aligns with the Genetic Test Registry (GTR) as the primary source for identifying genetic tests, assigning the relevant GTR ID to the GeneticMarkerAnalysisResult.code element.
+ +The GeneticMarkerAnalysisResult profile provides an extensible value set of genetic tests related to cancer-linked molecular markers. The initial terms in this value set were curated based on the following filter criteria in the GTR TestVersion data:
+The geneticsGene attribute is not bound to a cancer-specific value set at this time. Nevertheless, we provide a recommended value set of cancer-related genes in the CancerGeneVS value set.
+The CancerGeneVS value set includes the HUGO approved symbol rather than the full representation of the Gene ID (in the format approved_symbol:identifier). This choice was pragmatic since a certain number of systems store the symbol rather than the non-semantic identifier assigned by HUGO. Nevertheless, the approved symbol for the gene is unique so it is possible to derive the identifier from the HUGO dataset if needed.
+ +References used in the mCODE biomarker model include:
++ \ No newline at end of file diff --git a/spec/IndexFolder_Oncocore/index.html b/spec/IndexFolder_Oncocore/index.html new file mode 100644 index 00000000..caf2ff7a --- /dev/null +++ b/spec/IndexFolder_Oncocore/index.html @@ -0,0 +1,47 @@ +
*** This is a DRAFT VERSION of the Minimum Common Oncology Data Elements (mCODE™) implementation guide. ***
+ ++ +
+ +
According to the National Cancer Institute, 38.5 percent of men and women will be diagnosed with cancer at some point during their lifetimes. In 2014, an estimated 14.7M people were living with cancer in the United States. While numbers for cancer and other major diseases are staggering in terms of human suffering, such large figures also provide a place to look for potential solutions. The ultimate goal is to establish data models, technologies, and methods that result in research-quality real-world EHR data for every patient that drives evidence-based and data-driven treatment and analytics for high-quality health outcomes. The intent is that this research-quality real-world data would allow the information gathered from all cancers patient to contribute substantially to improving care for all future cancer patients.
+ +Under the leadership of the American Society of Clinical Oncology (ASCO) and in partnership with CancerLinQ and MITRE, a committee of leading clinical experts in oncology is developing mCODE (minimal Common Oncology Data Elements). mCODE consists of a core set of structured data elements necessary to support clinical care and oncology research across all cancers.
+ ++ +
+ + +
Domain content was provided by the ASCO/CancerLinQ team with additional research from the MITRE Corporation. Help, guidance, and wisdom was generously provided by all members of the ASCO/CancerLinQ team, especially the Dr. Robert Miller and Dr. Wendy Rubenstein.
+This IG was authored by the MITRE Corporation using the Clinical Information Modeling and Profiling Language (CIMPL), a free, open source toolchain from MITRE Corporation.
+ + ++ \ No newline at end of file diff --git a/spec/IndexFolder_Oncocore/mCodeDiagram.png b/spec/IndexFolder_Oncocore/mCodeDiagram.png new file mode 100644 index 00000000..ade7aa24 Binary files /dev/null and b/spec/IndexFolder_Oncocore/mCodeDiagram.png differ diff --git a/spec/IndexFolder_Oncocore/modeling.html b/spec/IndexFolder_Oncocore/modeling.html new file mode 100644 index 00000000..5c3bf780 --- /dev/null +++ b/spec/IndexFolder_Oncocore/modeling.html @@ -0,0 +1,28 @@ +
*** This is the DRAFT VERSION 0.3 ALPHA of the Minimum Common Oncology Data Elements (mCODE™) implementation guide. ***
+ ++ +
+
++ +
Specifications consulted for the development of this IG include:
+TBD.
+ ++ diff --git a/spec/IndexFolder_Oncocore/terminology.html b/spec/IndexFolder_Oncocore/terminology.html new file mode 100644 index 00000000..a4c0bf21 --- /dev/null +++ b/spec/IndexFolder_Oncocore/terminology.html @@ -0,0 +1,48 @@ +
*** This is the DRAFT VERSION 0.3 ALPHA of the Minimum Common Oncology Data Elements (mCODE™) implementation guide. ***
+ ++ +
+ +
This implementation guide supplies terminology bindings drawn primarily from LOINC for "observables", and SNOMED-CT for values, results and findings. There are a few exceptions to this:
++ +
Value sets from the FHIR specification are reused to the extent possible. In addition to the FHIR shr.base specification (DSTU2, DSTU3 and R4), Argonaut Data Query Implementation Guide, and the US Core Implementation Guide were also considered.
+ +There may be differences across these specifications in the value sets used, as well as binding strength. This guide addresses these discrepancies by using the lowest common denominator amongst the specifications. This approach is not without challenges, as there cases where different value sets are required by different specifications, which leaves no choice but to opt for one value set over another.
+ ++ +
This guide includes multiple value sets created specifically to support the terminology needs of the models. These value sets where created only when no known existing value sets were deemed to be fit for purpose, or when existing value needs needed to be extended.
+ +NOTE:There is a known issue with HL7's FHIR implementation guide publisher that causes an error in the expansion of local value sets in the implementation guide. While this prevents the value sets from being shown in the value set pages, the content of the value sets is correctly expanded in json and xml, which readers can access from the indivual value set pages.
+ ++ +
FHIR structurally separates missing value reasons (exception values) from answer sets. For example, FHIR uses two attributes, Observation.value and Observation.dataAbsentReason. For this reason, when LOINC answer lists included missing value explanations, those answers were separated and placed in a separate value set. However, we note that LOINC answer sets are not very consistent with regard to missing value reasons, and possibly incomplete. This leaves open a question on what a cross-cutting normative set of missing value reasons or exception values might be.
+ ++ +
The AJCC staging system is recognized as one of the most widely-used standards for cancer staging. However, this guide does not include any AJCC terminology due to unresolved copyright issues. As such, elements related to staging may not currently include required terminology bindings.
+ ++ \ No newline at end of file diff --git a/spec/IndexFolder_Oncocore/treatment.html b/spec/IndexFolder_Oncocore/treatment.html new file mode 100644 index 00000000..bc5f25c4 --- /dev/null +++ b/spec/IndexFolder_Oncocore/treatment.html @@ -0,0 +1,47 @@ +
*** This is the DRAFT VERSION 0.3 ALPHA of the Minimum Common Oncology Data Elements (mCODE™) implementation guide. ***
+ ++ +
The Treatment domain includes procedures and medications administered in the treatment of a cancer patient.
+The following profiles are relevant to cancer treatment:
+The CourseOfTreatmentPerformed profile embeds elements which comprise a course of treatment. These include surgical, radiation, imaging, and medication therapies. These are further described below.
+ +Procedures are further categorized as:
++ +
Medication therapies in mCODE are further categorized as:
+Chemotherapy and hormone therapy agents are not specified as constraints within the profile. Rather, we provide a means of deriving the list of relevant drug integredients pertaining to the therapeutic drug class (as Rxnorm RXCUIs) on-demand using RXCLASS.
++ + \ No newline at end of file diff --git a/spec/LandingPageBreastCancer.html b/spec/LandingPageBreastCancer.html index 90774391..3eb7fbda 100644 --- a/spec/LandingPageBreastCancer.html +++ b/spec/LandingPageBreastCancer.html @@ -14,12 +14,12 @@
This section provides orientation to the ballot materials.
-There are several representations of the same content in the ballot materials. Different representations will be useful to different audiences:
The sponsoring work groups and the Cancer Interoperability Group are seeking both general and specific comments regarding this material.
@@ -47,7 +47,7 @@CIMI develops several class hierarchies. The first is the ClinicalStatement hierarchy, exemplified by the BreastCancerHistologicGrade hierarchy, above. A clinical statement represents a fact, opinion, or observation that relates to a patient, for example, "the patient has a diagnosis of congestive heart failure" or "patient has an order for physical therapy" [CIMI Modeling and Quality Guide].
-However, ClinicalStatement is not the only class needed to construct a clinical statement. The clinical statement itself has no clinical content; to gain content, the ClinicalStatement class must reference a topic and a context. The topic is the clinical entity being described by the Clinical Statement, for example, a laboratory test. The context describes the circumstance applied to the topic. For example, we can speak of "blood pressure of 120/80" as an observation or a goal; similarly, we can speak of a procedure as recommended, ordered, planned, performed, or not performed. Both the topic and context are defined in class hierarchies of their own. For example, for the BreastCancerHistologicGrade, the topic hierarchy is as follows:
+CIMI develops several class hierarchies. The first is the ConditionOrObservation hierarchy, exemplified by the BreastCancerHistologicGrade hierarchy, above. A clinical statement represents a fact, opinion, or observation that relates to a patient, for example, "the patient has a diagnosis of congestive heart failure" or "patient has an order for physical therapy" [CIMI Modeling and Quality Guide].
+However, ConditionOrObservation is not the only class needed to construct a clinical statement. The clinical statement itself has no clinical content; to gain content, the ConditionOrObservation class must reference a topic and a context. The topic is the clinical entity being described by the Clinical ConditionOrObservation, for example, a laboratory test. The context describes the circumstance applied to the topic. For example, we can speak of "blood pressure of 120/80" as an observation or a goal; similarly, we can speak of a procedure as recommended, ordered, planned, performed, or not performed. Both the topic and context are defined in class hierarchies of their own. For example, for the BreastCancerHistologicGrade, the topic hierarchy is as follows:
It is important to understand the both the benefits and costs of this design choice. Separating topic and context increases consistency and reuse. For example, the same procedure topic can be used whether the context is recommending the procedure, planning the procedure, or performing the procedure. In addition, by reusing the contexts, each recommendation will have the same set of recommendation-related attributes, courtesy of the shared context. The same is true for each plan or performance, regardless of topic.
Under the topic-context pattern, creating one new domain class can require creating multiple classes. For example, the BreastCancerStage observation requires two new classes: a BreastCancerStageTopic class, where the StageTiming attribute is added, and the BreastCancerStage class itself, which extends and constrains Observation. In the ADL/BMM serialization, the BreastCancerStageTopic properties would form a new class in the BMM, extending the reference model, and the terminology and other constraints would be applied in an archetype. Modelers must weave three threads together form new classes. It is possible that the right user-friendly tooling could mitigate the resulting "what-goes-where?" and "what-comes-from-where?" problems, but tooling cannot decide which of the three hierarchies should be extended. Even in CIMI circles, this is frequently a gray area.
-Exploration of alternatives is beyond the scope of this IG, but we briefly method that there is a potential simplification that could retain the key benefits of the topic-context pattern, while greatly simplifying the class hierarchy by eliminating the separate topic and context hierarchies. This involves extending the clinical statement hierarchy with classes that represent different contexts, creating, for example, OrderedStatement, ActionPerformedStatement, ActionNotPerformedStatement, ObservationStatement, etc. This approach creates a fixed set of classes from which all other classes derive.
+Exploration of alternatives is beyond the scope of this IG, but we briefly method that there is a potential simplification that could retain the key benefits of the topic-context pattern, while greatly simplifying the class hierarchy by eliminating the separate topic and context hierarchies. This involves extending the clinical statement hierarchy with classes that represent different contexts, creating, for example, OrderedStatement, ActionPerformed, ActionNotPerformedStatement, ObservationStatement, etc. This approach creates a fixed set of classes from which all other classes derive.
- This is a preliminary version of the CIMI Health Level 7 (HL7) Fast Healthcare
- Interoperability Resources (FHIR) profiles, extensions, value sets, and code systems.
-
-Lorem ipsum dolor sit amet, consectetur adipiscing elit. Sed non lacus tellus. Mauris in luctus ex. Donec nec leo mauris. Suspendisse nec velit ullamcorper, condimentum neque vel, consequat massa. Ut mattis fermentum facilisis. Etiam ut tortor tortor. Nam eget egestas dolor. Pellentesque dignissim purus mauris, id auctor purus iaculis sit amet. -
--Quisque sagittis viverra lorem eget blandit. Morbi laoreet nulla ac metus accumsan, ac tristique urna molestie. Aenean ut tortor vitae nulla luctus suscipit. Proin augue risus, laoreet sed fringilla a, cursus sollicitudin ligula. Donec sed accumsan magna. Duis at molestie ex. Sed id condimentum massa. Nam quis metus et orci tincidunt aliquam at ac ipsum. Aliquam nec enim diam. Donec ante metus, fermentum eu massa ac, lobortis mattis velit. -
--Cras pellentesque efficitur consectetur. Duis sed tristique lorem. Fusce ultrices neque eu euismod rhoncus. Etiam scelerisque vehicula lacus ut faucibus. Fusce arcu lacus, tempus venenatis massa sit amet, dictum lobortis purus. In nunc nisi, consectetur semper magna sit amet, fermentum pulvinar dui. Nulla mollis dolor a diam condimentum sollicitudin. Sed egestas urna a leo ullamcorper molestie. Vestibulum accumsan, lorem ac volutpat viverra, ex felis lacinia felis, condimentum pharetra magna ex ut elit. Class aptent taciti sociosqu ad litora torquent per conubia nostra, per inceptos himenaeos. Phasellus semper accumsan eros, id congue turpis malesuada ac. Donec eget porta felis. Phasellus eu massa massa. Vestibulum sem erat, imperdiet sed feugiat et, tempus nec turpis. Ut consectetur urna nec eros pharetra, consectetur feugiat ligula facilisis. -
--Sed ligula justo, vehicula eu purus et, porttitor congue nibh. Aliquam efficitur eros a nulla varius, in lacinia augue bibendum. In mi erat, rutrum id eleifend eget, scelerisque a arcu. Cras vel posuere urna. Mauris condimentum nunc orci, ut lacinia sem placerat sit amet. Suspendisse congue egestas ipsum quis efficitur. Aliquam justo est, mollis vel semper sit amet, consequat eu lorem. Phasellus vitae nunc in nisi hendrerit porttitor. Class aptent taciti sociosqu ad litora torquent per conubia nostra, per inceptos himenaeos. Ut viverra lacinia consequat. Fusce eget dui sed ex rhoncus mattis. Duis dignissim ut massa consequat tristique. Cras sollicitudin maximus eros at pulvinar. -
diff --git a/exampleIndexContent.html b/spec/LandingPageExample.html similarity index 100% rename from exampleIndexContent.html rename to spec/LandingPageExample.html diff --git a/spec/LandingPageOccupation.html b/spec/LandingPageOccupation.html index 9d929ecf..27f23535 100644 --- a/spec/LandingPageOccupation.html +++ b/spec/LandingPageOccupation.html @@ -1,29 +1,259 @@ +
- This is a preliminary version of the Occupational Data Health Level 7 (HL7) Fast Healthcare
- Interoperability Resources (FHIR) Implementation Guide.
-
- Lorem ipsum dolor sit amet, consectetur adipiscing elit. Sed non lacus tellus. Mauris in luctus ex. Donec nec leo mauris. Suspendisse nec velit ullamcorper, condimentum neque vel, consequat massa. Ut mattis fermentum facilisis. Etiam ut tortor tortor. Nam eget egestas dolor. Pellentesque dignissim purus mauris, id auctor purus iaculis sit amet. + This Implementation Guide contains guidance, new logical models, profiles and extensions to implement support for Occupational Data for Health (ODH). ODH is primarily designed to facilitate clinical care, including population health; ODH also can be used to support public health reporting, population health, and similar value-based care. ODH is not designed to support billing activities. This STU Ballot for the Occupational Data for Health (ODH) Implementation Guide (IG) is sponsored by the National Institute of Safety and Health (NIOSH), a federal agency responsible for conducting research and making recommendations for the prevention of work-related injury and illness. NIOSH is a part of the Centers for Disease and Prevention (CDC). The project to define ODH was done with a group representing a variety of stakeholders including NIOSH subject matter experts, epidemiologists, occupational health providers, and vendors.
- Quisque sagittis viverra lorem eget blandit. Morbi laoreet nulla ac metus accumsan, ac tristique urna molestie. Aenean ut tortor vitae nulla luctus suscipit. Proin augue risus, laoreet sed fringilla a, cursus sollicitudin ligula. Donec sed accumsan magna. Duis at molestie ex. Sed id condimentum massa. Nam quis metus et orci tincidunt aliquam at ac ipsum. Aliquam nec enim diam. Donec ante metus, fermentum eu massa ac, lobortis mattis velit. -
+ The majority of adults in the U.S. spend more than half their waking hours at work. Therefore, health and work are inextricably inter-related. For example, the management of chronic conditions requires taking the patient’s work environment into consideration. Furthermore, the recognition of new conditions related to previously unknown workplace hazards has often come from astute clinicians, which requires knowledge of the patients’ work-setting. ONC has indicated recognition of the value of work information for health care. +The incorporation of self-reported ODH into Electronic Health Records (EHRs) and other IT healthcare systems provides an opportunity to improve health in relation to work. ODH has not been broadly recognized as a social determinant of health and has not yet been a priority for inclusion in IT healthcare systems in a structured way that fully supports direct patient care and occupational public health activities.
+Though research has been conducted and guidance is available to support clinicians, the IT healthcare systems they work in are unable to efficiently identify patients that would benefit the most from this knowledge.
+This project seeks to address this gap of system and awareness by modeling ODH in a way so that it supports diagnosis, treatment, research and surveillance of work-related injury and illness.
- Cras pellentesque efficitur consectetur. Duis sed tristique lorem. Fusce ultrices neque eu euismod rhoncus. Etiam scelerisque vehicula lacus ut faucibus. Fusce arcu lacus, tempus venenatis massa sit amet, dictum lobortis purus. In nunc nisi, consectetur semper magna sit amet, fermentum pulvinar dui. Nulla mollis dolor a diam condimentum sollicitudin. Sed egestas urna a leo ullamcorper molestie.
- + The Occupational Data for Health (ODH) FHIR IG covers information about a patient’s work or a patient's family member's work. ODH is designed for the social history section of a medical record, to facilitate clinical care in most/all disciplines and delivery environments. ODH also can be used to support public health reporting, population health activities, clinical decision support, and similar value-based care. ODH is not designed to support billing activities. The scope of the work information includes: +- Sed ligula justo, vehicula eu purus et, porttitor congue nibh. Aliquam efficitur eros a nulla varius, in lacinia augue bibendum. In mi erat, rutrum id eleifend eget, scelerisque a arcu. Cras vel posuere urna. Mauris condimentum nunc orci, ut lacinia sem placerat sit amet. Suspendisse congue egestas ipsum quis efficitur. -
-- Aliquam justo est, mollis vel semper sit amet, consequat eu lorem. Phasellus vitae nunc in nisi hendrerit porttitor. Class aptent taciti sociosqu ad litora torquent per conubia nostra, per inceptos himenaeos. Ut viverra lacinia consequat. Fusce eget dui sed ex rhoncus mattis. Duis dignissim ut massa consequat tristique. Cras sollicitudin maximus eros at pulvinar. -
+This IG includes more extensive occupational data than typically collected in current systems. The content and structure of this IG is intended to inform clinical care, support population health and contribute to public health activities. While there may be some overlap with administrative and billing information maintained by some systems, the information in this IG is not designed to support billing and administrative needs.
+This profile is specified as a composition resource, but it is not intended to be used as a stand-alone composition. Rather, the content should be included in broader health information summary and other compositions, and available as a response to requests for occupational data for health information.
+Some of the value sets in this IG are preliminary. If no code exists for a given concept (e.g. a new occupation), text should be used to describe the concept and the coded value should be omitted.
+A value set for combat zone location that meets the purpose of supporting patient care, population health, and public health needs has not been identified. Therefore, only start and end dates are included.
+Retirement date is captured as how it relates to a person, not to a specific job.
+- Aliquam justo est, mollis vel semper sit amet, consequat eu lorem. Phasellus vitae nunc in nisi hendrerit porttitor. Class aptent taciti sociosqu ad litora torquent per conubia nostra, per inceptos himenaeos. Ut viverra lacinia consequat. Fusce eget dui sed ex rhoncus mattis. Duis dignissim ut massa consequat tristique. Cras sollicitudin maximus eros at pulvinar. -
- \ No newline at end of file +Both general and specific comments regarding this material are invited.
+While this profile is specified for the US Realm, the design is intended to support international needs. Three of the referenced value sets supporting Occupation, Industry, and Supervisory Level are necessarily US specific, and the remaining three supporting Work Schedule, Employment Status, and Work Classification are defined to support international concepts. Input is requested regarding whether these should be specified as ‘extensible’, ‘required’ (using ‘text only’ where a concept does not yet exist such as a new occupation), or as an ‘example’ for those US specific concepts.
++
+
|
+ Co-Editor: + |
+
+ Genevieve Barkocy Luensman +CDC/NIOSH/RHD/SB +Respiratory Health Division (RHD), National Institute for Occupational Safety and Health (NIOSH) + + |
+
+ Co-Editor: + |
+
+ Eileen Storey +AECOM/Professional Staffing Partners Plus Contractor + |
+
|
+ Co-Editor: + |
+
+ Barbara Wallace +AECOM/Professional Staffing Partners Plus Contractor + + |
+
+ Co-Editor: + |
+
+ Margaret S. Filios +Respiratory Health Division (RHD), National Institute for Occupational Safety and Health (NIOSH) + |
+
|
+ Co-Editor: + |
+
+ Stacey Marovich, MHI, MS, PMP, MCTS +CDC/NIOSH/DSHEFS + + |
+
+ Co-Editor: + |
+
+ Marie Haring Sweeney +Division of Surveillance, Hazard Evaluation, and Field Studies (DSHEFS), National Institute for Occupational Safety and Health (NIOSH) + |
+
|
+ Co-Editor: + |
+
+ Angela C. Crovetti + Sr. Consultant, Attain/CDC/NIOSH/WTCHP + + |
+
+ Co-Editor: + |
+
+ John Myers +Division of Safety Research (DSR), National Institute for Occupational Safety and Health (NIOSH) + |
+
|
+ Co-Editor: + |
+
+ Lori Reed-Fourquet +e-HealthSign, LLC + + |
+
+ Co-Editor: + |
+
+ Kerry Souza +Division of Surveillance, Hazard Evaluation, and Field Studies (DSHEFS), National Institute for Occupational Safety and Health (NIOSH) + |
+
|
+ Co-Editor: + |
+
+ Rob Hausam +Hausam Consulting + + |
+
+ Co-Editor: + |
+
+ Christina Socias-Morales +Division of Safety Research (DSR), National Institute for Occupational Safety and Health (NIOSH) + |
+
|
+ Co-Editor: + |
+
+ Mark Kramer +MITRE + + |
+
+ Co-Editor: + |
+
+ Sherry Baron +DSHEFS, NIOSH. Currently Queens College, City University of New York, Flushing NY USA + |
+
+
Contributors include participants HL7 HIR Management Group, Structured Documents Work Group, Patient Administration Workgroup, Orders and Observations Work Group and the Public Health Workgroup:
++
|
+ Douglas Trout + |
+
+ Division of Surveillance, Hazard Evaluation, and Field Studies (DSHEFS), National Institute for Occupational Safety and Health (NIOSH) + |
+
|
+ Kristin Yeoman + |
+
+ Western States Division (WSD), National Institute for Occupational Safety and Health (NIOSH) + |
+
|
+ Sara Luckhaupt + |
+
+ Division of Surveillance, Hazard Evaluation, and Field Studies (DSHEFS), National Institute for Occupational Safety and Health (NIOSH) + |
+
|
+ Carissa Rocheleau + |
+
+ Division of Surveillance, Hazard Evaluation, and Field Studies (DSHEFS), National Institute for Occupational Safety and Health (NIOSH) + |
+
|
+ Claire Caruso + |
+
+ Division of Applied Research and Technology (DART)), National Institute for Occupational Safety and Health (NIOSH) + |
+
|
+ Nicole Edwards + |
+
+ Respiratory Health Division, National Institute for Occupational Safety and Health (NIOSH) + |
+
|
+ Deborah Hoyer + |
+
+ Office of the Director (OD), National Institute for Occupational Safety and Health (NIOSH) + |
+
|
+ E. Michael Goldcamp + |
+
+ DSR, NIOSH. Currently OD, NIOSH + |
+
+
Acknowledgements:
+Yvonne Boudreau, Western States Division (WSD), National Institute for Occupational Safety and Health (NIOSH)
+Susan Nowlin, Division of Surveillance, Hazard Evaluation, and Field Studies (DSHEFS), National Institute for Occupational Safety and Health (NIOSH)
+Anna Orlova, Public Health Data Standards Consortium (PHDSC). Currently Visiting Associate Professor, Division of Health Sciences Informatics, Johns Hopkins School of Medicine
++
This IG was produced by Mark Kramer using the Clinical Information Modeling and Profiling Language (CIMPL), a free, open source toolchain from MITRE Corporation..
diff --git a/spec/LandingPageOncocore.html b/spec/LandingPageOncocore.html new file mode 100644 index 00000000..ddcd0309 --- /dev/null +++ b/spec/LandingPageOncocore.html @@ -0,0 +1,30 @@ +This is the DRAFT VERSION 0.3 ALPHA of the Minimum Common Oncology Data Elements (mCODE) implementation guide.
+ +According to the National Cancer Institute, 38.5 percent of men and women will be diagnosed with cancer at some point during their lifetimes. In 2014, an estimated 14.7M people were living with cancer in the United States. While numbers for cancer and other major diseases are staggering in terms of human suffering, such large figures also provide a place to look for potential solutions. The ultimate goal is to establish data models, technologies, and methods that result in research-quality real-world EHR data for every patient that drives evidence-based and data-driven treatment and analytics for high-quality health outcomes. The intent is that this research-quality real-world data would allow the information gathered from all cancers patient to contribute substantially to improving care for all future cancer patients.
+ +Under the leadership of the American Society of Clinical Oncology (ASCO) and in partnership with CancerLinQ and MITRE, a committee of leading clinical experts in oncology is developing mCODE (minimal Common Oncology Data Elements). mCODE consists of a core set of structured data elements necessary to support clinical care and oncology research across all cancers.
+ +Disclaimers:
+TBD
+ ++ + +
Domain content was provided by the ASCO/CancerLinQ team with additional research from the MITRE Corporation. Help, guidance, and wisdom was generously provided by all members of the ASCO/CancerLinQ team, especially the Dr. Robert Miller and Dr. Wendy Rubenstein.
+This IG was authored by the MITRE Corporation using the Clinical Information Modeling and Profiling Language (CIMPL), a free, open source toolchain from MITRE Corporation.
+ + +TBD
++ +
- This is a preliminary version of the Skin and Wound FHIR Implementation Guide, based on the Clinical Information Modeling Initative (CIMI) class structure, and including CIMI logical models, FHIR profiles, value sets, and extensions.
-
-Lorem ipsum dolor sit amet, consectetur adipiscing elit. Sed non lacus tellus. Mauris in luctus ex. Donec nec leo mauris. Suspendisse nec velit ullamcorper, condimentum neque vel, consequat massa. Ut mattis fermentum facilisis. Etiam ut tortor tortor. Nam eget egestas dolor. Pellentesque dignissim purus mauris, id auctor purus iaculis sit amet. -
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+This a MITRE version of a Wound Assessment FHIR Implementation Guide, based on Standard Health Record (SHR) core classes.
+The use case under consideration is that repeated assessments of the same wound can occur at different times during the clinical course of the wound. These multiple assessments trace a relationship to the same wound by means of a common wound identifier.
+One of the key features of wound assessment is "nestedness", a hierarchical structure of containment with 1-to-many relationships at each level. One patient can have multiple wounds, each wound can have multiple tunnels, and each tunnel on each wound on each patient can have a measured length. This presents a modeling challenge.
+In this implementation, we take a hybrid approach, using components wherever possible, and sub-observations where necessary. Panel-type sub-observations are required where the panel observations themselves have sub-observations or components.
+The other key to our approach representing each wound by a condition. A wound is an identifiable entity located at a particular body site that maintains its identity over a period of time. As such, a wound has properties indicative of a condition, including onset time and abatement time. Explicitly representing the wound allows multiple observations about the wound to refer back to the same wound.
+ +Domain content was provided by Susan Matney (Intermountain Healthcare). Help, guidance, and wisdom was generously provided by all members of the CIMI Work Group especially the co-chairs, Dr. Stan Huff, Claude Nanjo, Galen Mulrooney, and Richard Esmond.
+This IG was authored by Dr. Mark Kramer using the Clinical Information Modeling and Profiling Language (CIMPL), a free, open source toolchain from MITRE Corporation.
\ No newline at end of file diff --git a/spec/brca.txt b/spec/brca.txt new file mode 100644 index 00000000..832f1613 --- /dev/null +++ b/spec/brca.txt @@ -0,0 +1,610 @@ +Grammar: DataElement 5.0 +Namespace: brca +Description: "Breast Cancer data elements." +Uses: shr.core, oncocore + +CodeSystem: LNC = http://loinc.org +CodeSystem: UCUM = http://unitsofmeasure.org +CodeSystem: HGNC = http://www.genenames.org +CodeSystem: CAP = https://sdt.cap.org +CodeSystem: OBSCAT = http://hl7.org/fhir/observation-category + + +Element: BreastSite +Based on: BodySite +Description: "A body site specific to the breast structure." + BodySiteCode from BreastSiteVS +1..1 Laterality +0..0 AnatomicalDirection +// TODO: causes mapping error +// DistanceFromLandmark.Quantity.Units is UCUM#cm + +EntryElement: BreastSpecimen +Based on: Specimen +Description: "Specimen resulting from biopsy or excision of breast and surrounding tissue." + Type from BreastSpecimenTypeVS + CollectionSite.BodySite is type BreastSite + CollectionMethod from BreastSpecimenCollectionMethodVS + PartOf value is type ref(BreastSpecimen) +0..1 ColdIschemiaTime + + Element: ColdIschemiaTime + Concept: LNC#44778-9 "Cold ischemic time {Organ}" + Description: "The time period between the chilling of a tissue or tissue sample and the time it is warmed." + Value: TimePeriod + + +EntryElement: BreastCancerCondition +Based on: CancerCondition +Concept: SCT#126926005 "Neoplasm of breast (disorder)" +Description: "Diagnosis of cancer originating in the tissues of the breast, and potentially spread to other organs of the body." + Code from BreastCancerDisorderVS + StageInformation.StageDetail value is type BreastTNMClinicalPrognosticStagePanel //or BreastTNMPathologicPrognosticStagePanel + Evidence.Manifestation should be from BreastCancerDetectionVS // can't change to 'could be' because us-core uses preferred binding + BodySite is type BreastSite + + +EntryElement: BreastCancerHistologicType +Based on: CancerHistologicType +Description: "Classification of breast cancer according to histopathologic subtypes, as determined by microscopic observation of breast tissue samples." + Code is LNC#44638-5 "Histologic type in Breast tumor" + DataValue from BreastCarcinomaHistologicTypeVS + SubjectOfInformation value is type ref(BreastCancerCondition) + + +EntryElement: BreastTNMClinicalPrognosticStagePanel +Based on: TNMClinicalPrognosticStagePanel +// Concept inherited from parent class, was not breast-specific in BrCa ballot either, was MTH#C2216702 "Malignant Neoplasm of Breast Staging" +Description: "A panel of breast cancer staging information that is performed prior to surgery, based on evidence such as physical examination, imaging, and/or biopsy. The panel should not include both a DCISNuclearGrade and a BreastCancerHistologicGrade, since the latter implies an invasive cancer." + Code is TBD#TBD // was MTH#C2216702 "Malignant Neoplasm of Breast Staging" //Not LNC#21908-9 since that is AJCC-specific and also not breast cancer specific. We do however, give the LOINC list of stage values as the preferred codes. + SubjectOfInformation value is type ref(BreastCancerCondition) +// PanelMembers.Observation.TNMClinicalPrimaryTumorClassification is type BreastTNMClinicalPrimaryTumorClassification +// PanelMembers.Observation.TNMClinicalRegionalNodesClassification is type BreastTNMClinicalRegionalNodesClassification +// PanelMembers.Observation.TNMClinicalDistantMetastasesClassification is type BreastTNMClinicalDistantMetastasesClassification + PanelMembers.Observation + includes 0..1 HER2ReceptorStatus + includes 0..1 EstrogenReceptorStatus + includes 0..1 ProgesteroneReceptorStatus + includes 0..1 DCISNuclearGrade + includes 0..1 BreastCancerHistologicGrade + + +EntryElement: BreastTNMClinicalPrimaryTumorClassification +Based on: TNMClinicalPrimaryTumorClassification +// Concept inherited from parent class, was not breast-specific in BrCa ballot either. +Description: "Classification based on the size and extent of the primary breast tumor, assessed prior to surgery, based on evidence such as physical examination, imaging, and/or biopsy." + SubjectOfInformation value is type ref(BreastCancerCondition) + PanelMembers.Observation + includes 0..1 TumorDimensions //TODO: need to distinguish tumor dimensions between clinical and pathologic, specify method? + + +EntryElement: BreastTNMClinicalRegionalNodesClassification +Based on: TNMClinicalRegionalNodesClassification +// Concept inherited from parent class, was not breast-specific in BrCa ballot either. +Description: "Classification of the presence or absence of metastases in regional lymph nodes for breast cancer, assessed using tests that are done before surgery." + SubjectOfInformation value is type ref(BreastCancerCondition) + PanelMembers.Observation + includes 0..* BreastClinicalLymphNodeInvolvement + + +EntryElement: BreastClinicalLymphNodeInvolvement +Based on: ComponentOnlyNonLaboratoryObservation +Concept: MTH#C0806692 "Lymph Node Involvement" +Description: "Clinical assessment of lymph nodes for presence of cancer cells in staging the N category in breast cancer." + BodySite is type BreastLymphNodeBodySite + Method from LymphNodeClinicalMethodVS if covered + Components.ObservationComponent + includes 0..1 LymphNodeMobility + includes 0..1 LymphNodeSize + + +EntryElement: BreastLymphNodeBodySite +Based on: BodySite +Description: "A body site specific to the breast lymph node structure." + BodySiteCode should be from BreastLymphNodeGroupVS if covered + + +Element: LymphNodeMobility +Based on: CodedObservationComponent +Concept: TBD#TBD //was MTH#C1112395 "Lymph node palpable", but that is a finding, not an observable +Description: "The degree of mobility of a lymph node or lymph node group upon palpation." + Code is TBD#TBD + DataValue from LymphNodeMobilityVS + +Element: LymphNodeSize +Based on: QuantitativeObservationComponent +Concept: SCT#364109001 "Size of lymph node (observable entity)" +Description: "Size of the lymph node or lymph node group which is being clinically assessed." + Code is SCT#364109001 "Size of lymph node (observable entity)" + DataValue.Quantity.Units is UCUM#mm + +// TODO: add in relationships to Met location and FindingMethod since both evaluate M category values. +EntryElement: BreastTNMClinicalDistantMetastasesClassification +Based on: TNMClinicalDistantMetastasesClassification +// Concept inherited from parent class, was not breast-specific in BrCa ballot either. +Description: "Classification of the presence or absense of metastases in remote anatomical locations relative to the breast, assessed using tests that are done before surgery." + SubjectOfInformation value is type ref(BreastCancerCondition) + + +EntryElement: BreastTNMPathologicPrognosticStagePanel +Based on: TNMPathologicPrognosticStagePanel +// Concept inherited from parent class, was not breast-specific in BrCa ballot either, was MTH#C2216702 "Malignant Neoplasm of Breast Staging" +Description: "A panel of breast cancer staging information that is performed prior to surgery, based on evidence such as physical examination, imaging, and/or biopsy. The panel includes biomarkers and histologic grade scales used specifically for breast cancer. The panel should not include both a DCISNuclearGrade and a BreastCancerHistologicGrade, since the latter implies an invasive cancer." + SubjectOfInformation value is type ref(BreastCancerCondition) +// PanelMembers.Observation.TNMPathologicPrimaryTumorClassification is type BreastTNMPathologicPrimaryTumorClassification +// PanelMembers.Observation.TNMPathologicRegionalNodesClassification is type BreastTNMPathologicRegionalNodesClassification +// PanelMembers.Observation.TNMPathologicDistantMetastasesClassification is type BreastTNMPathologicDistantMetastasesClassification + PanelMembers.Observation + includes 0..1 HER2ReceptorStatus + includes 0..1 EstrogenReceptorStatus + includes 0..1 ProgesteroneReceptorStatus + includes 0..1 DCISNuclearGrade + includes 0..1 BreastCancerHistologicGrade + + +EntryElement: BreastTNMPathologicPrimaryTumorClassification +Based on: TNMPathologicPrimaryTumorClassification +// Concept inherited from parent class, was not breast-specific in BrCa ballot. +Description: "Classification of the primary breast tumor, based on its size and extent, assessed through pathologic analysis of a tumor specimen." + SubjectOfInformation value is type ref(BreastCancerCondition) + PanelMembers.Observation + includes 0..1 TumorDimensions //TODO: need to distinguish tumor dimensions between clinical and pathologic, specify method? + +EntryElement: BreastTNMPathologicRegionalNodesClassification +Based on: TNMPathologicRegionalNodesClassification +// Concept inherited from parent class, was not breast-specific in BrCa ballot. +Description: "Classification of the presence or absence of metastases in regional lymph nodes for breast cancer, assessed through pathologic analysis of a specimen." + SubjectOfInformation value is type ref(BreastCancerCondition) + PanelMembers.Observation + includes 0..* BreastPathologicalLymphNodeInvolvement + + +EntryElement: BreastPathologicalLymphNodeInvolvement +Based on: LaboratoryObservation +Concept: SCT#399656008 "Status of tumor metastasis to regional lymph nodes (observable entity)" +Description: "Pathological assessment of lymph nodes for presence of cancer cells in staging the N category in cancers." + Code is SCT#399656008 "Status of tumor metastasis to regional lymph nodes (observable entity)" +0..0 DataValue +0..0 DataAbsentReason +0..0 Method +0..0 PanelMembers + Components.ObservationComponent + includes 0..1 BreastLymphNodeInvolvement + includes 0..1 LymphNodeSamplingMethod + includes 0..1 TotalNumberOfLymphNodesExamined + includes 0..1 NumberOfRegionalLymphNodes + includes 0..1 NumberOfSentinelLymphNodes + includes 0..1 NumberOfLymphNodesWithIsolatedTumorCells + includes 0..1 NumberOfLymphNodesWithMicrometastases + includes 0..1 NumberOfLymphNodesWithMacrometastases + includes 0..1 ExtraCapsularExtensionOfNodalTumorStatus + + + Element: BreastLymphNodeInvolvement + Based on: CodedObservationComponent + Description: "Identification of whether tumor cells have extended to the lymph nodes. Formerly known as BreastNodeInvolvementValues" + Code is SCT#399656008 "Status of tumor metastasis to regional lymph nodes (observable entity)" + DataValue from LymphNodeInvolvementVS + + Element: LymphNodeSamplingMethod + Based on: CodedObservationComponent + Description: "The procedure method used to obtain the specimen analyzed for the pathological lymph node involvement." + Code is SCT#118890000 "Procedure on lymph node (procedure)" + DataValue from LymphNodeSamplingMethodVS + + Element: TotalNumberOfLymphNodesExamined + Based on: QuantitativeObservationComponent + Description: "Total number of lymph nodes examined for the presence of cancer cells" + Code is SCT#444025001 "Number of lymph nodes examined (observable entity)" + DataValue value is type IntegerQuantity + + Element: NumberOfRegionalLymphNodes + Based on: QuantitativeObservationComponent + Description: "Number of regional lymph nodes examined for the presence of cancer cells" + Code is LNC#21894-1 "Regional lymph nodes examined [#] Specimen" + DataValue value is type IntegerQuantity + + Element: NumberOfSentinelLymphNodes + Based on: QuantitativeObservationComponent + Description: "Number of sentinel lymph nodes examined for the presence of cancer cells" + Code is LNC#85347-3 "Sentinel lymph nodes examined [#] in Cancer specimen by Light microscopy" + DataValue value is type IntegerQuantity + + Element: NumberOfLymphNodesWithIsolatedTumorCells + Based on: QuantitativeObservationComponent + Description: "Number of lymph nodes with isolated metatstatic tumor cells examined for the presence of cancer cells" + Code is LNC#85352-3 "Lymph nodes with isolated tumor cells [#] in Cancer specimen by Light microscopy" + DataValue value is type IntegerQuantity + + Element: NumberOfLymphNodesWithMicrometastases + Based on: QuantitativeObservationComponent + Description: "Number of lymph nodes with micrometastases examined" + Code is LNC#85344-0 "Lymph nodes with micrometastases [#] in Cancer specimen by Light microscopy" + DataValue value is type IntegerQuantity + + Element: NumberOfLymphNodesWithMacrometastases + Based on: QuantitativeObservationComponent + Description: "Number of lymph nodes with macrometastases examined" + Code is LNC#85343-2 "Lymph nodes with macrometastases [#] in Cancer specimen by Light microscopy" + DataValue value is type IntegerQuantity + + Element: ExtraCapsularExtensionOfNodalTumorStatus + Based on: CodedObservationComponent + Description: "Status for presence of extranodal extension of carcinoma where extranodal extension is the perforation of a cancer through the capsule of a lymph node into the tissue surrounding the node." + Code is LNC#85350-7 "Extranodal extension of carcinoma [Presence] in Cancer specimen by Light microscopy" + DataValue should be from http://loinc.org/vs/LL748-5 // mlt: LL748-5 missing one term from original VS (indeterminate) + + +// TODO: add in relationships to Met location and Method since both evaluate M category values. +EntryElement: BreastTNMPathologicDistantMetastasesClassification +Based on: TNMPathologicDistantMetastasesClassification +// Concept inherited from parent class, was not breast-specific in BrCa ballot. +Description: "Classification of the presence or absense of metastases in remote anatomical locations relative to the breast, assessed through pathologic analysis of a specimen." + SubjectOfInformation value is type ref(BreastCancerCondition) + +EntryElement: HER2ReceptorStatus +Based on: TumorMarkerObservation +Description: "HER2 receptor status. HER2 is a member of the human epidermal growth factor receptor family of proteins and is encoded by the ERBB2 oncogene. HER2 is overexpressed in 20-30% of breast tumors, and is associated with an aggressive clinical course and poor prognosis. HER2 status (positive=present or overexpressed; negative=absent) is a factor in determining prognosis and treatment options." + DataValue value is type CodeableConcept + DataValue from PositiveNegativeEquivocalIndeterminateVS + Code from HER2byIHCScoreVS + Specimen is type BreastSpecimen +0..0 Method // pre-coordinated in the Code +0..0 Components + PanelMembers.Observation + includes 0..* HER2byIHC + includes 0..* HER2byFISH + + +EntryElement: HER2byIHC +Based on: TumorMarkerObservation +Description: "HER2 presence in Breast cancer specimen by Immunohistochemistry (IHC). " + Code from HER2byIHCInterpretationTestsVS + DataValue value is type CodeableConcept + DataValue from HER2byIHCScoreVS + Interpretation from PositiveNegativeEquivocalIndeterminateVS +0..0 Method // pre-coordinated in the Code + Specimen is type BreastSpecimen + Components.ObservationComponent + includes 0..1 CompleteMembraneStainingPercent +0..0 PanelMembers + + Element: CompleteMembraneStainingPercent + Based on: QuantitativeObservationComponent + Description: "Percentage of cells with uniform intense complete membrane staining." + Code is LNC#85328-3 "Cells.HER2 uniform intense membrane staining/100 cells" + DataValue.Quantity.Units is UCUM#% + 0..0 ReferenceRange +// 0..0 Interpretation //This is zeroed out in the Sep 2018 BrCa IG spec. + +EntryElement: HER2byFISH +Based on: TumorMarkerObservation +Description: "HER2 receptor status as determined by single-probe or dual-probe Fluorescence In Situ Hybridization (FISH)." +0..0 DataValue +0..0 DataAbsentReason + Code from HER2byFISHInterpretationTestsVS + Method from HER2FISHMethodVS // single or double probe + Interpretation from PositiveNegativeEquivocalIndeterminateVS + Specimen is type BreastSpecimen + Components.ObservationComponent + includes 0..1 AverageHER2SignalsPerCell + includes 0..1 AverageCEP17SignalsPerCell + includes 0..1 HER2toCEP17Ratio +0..0 PanelMembers + + Element: AverageHER2SignalsPerCell + Based on: QuantitativeObservationComponent + Description: "Average number of HER2 signals per cell" + Code is LNC#74860-8 "HER2 signals/nucleus [Entitic number] in Tissue by FISH" + 0..0 ReferenceRange + + Element: AverageCEP17SignalsPerCell + Based on: QuantitativeObservationComponent + Description: "Average number CEP17 signals per cell (dual probe only)" + Code is LNC#74861-6 "CEP17 signals/nucleus [Entitic number] in Tissue by FISH" + 0..0 ReferenceRange + + Element: HER2toCEP17Ratio + Based on: QuantitativeObservationComponent + Description: "HER2 to CEP17 Ratio (dual probe only)" + Code is LNC#49683-6 "HER2/CEP17 [Ratio] in Tissue by FISH" + 0..0 ReferenceRange + + +EntryElement: EstrogenReceptorStatus +Based on: TumorMarkerObservation +Concept: LNC#16112-5 "Estrogen receptor [Interpretation] in Tissue" +Description: "Estrogen receptor alpha is the predominant estrogen receptor expressed in breast tissue and is overexpressed in around 50% of breast carcinomas. ER status (positive=present or overexpressed; negative=absent) is a factor in determining prognosis and treatment options. +The current approach is that positive/negative designation is a value, even though that value is (in fact) an interpretation of evidence (NuclearPositivity and AverageStainingIntensity)." + Code from EstrogenReceptorInterpretationTestsVS + DataValue from PositiveNegativeIndeterminateVS + Specimen is type BreastSpecimen + Components.ObservationComponent + includes 0..1 EstrogenReceptorNuclearPositivity + includes 0..1 EstrogenReceptorAverageStainingIntensity +0..0 PanelMembers + + + Element: EstrogenReceptorNuclearPositivity + Based on: ObservationComponent + Concept: LNC#14228-1 "Cells.estrogen receptor/100 cells in Tissue by Immune stain" // LOINC codes for nuclear positivity are specific to the receptor. TODO: Confirm this code is more appropriate than LNC#85329-1 "Cells.estrogen receptor/100 cells in Breast cancer specimen by Immune stain", which specifies the specimen as a breast specimen. + Description: "The percentage of cells that test (stain) positive for the presence of estrogen receptors. We are seeking feedback on whether nuclear positivity should be an exact percentage or a range of percentages. As currently defined, an exact nuclear positivity could be represented by a zero-width range, where the lower and upper bounds would be the same number." + Code is LNC#14228-1 "Cells.estrogen receptor/100 cells in Tissue by Immune stain" + DataValue value is type Range + 0..0 ReferenceRange + + Element: EstrogenReceptorAverageStainingIntensity + Concept: LNC#85310-1 "Estrogen receptor fluorescence intensity [Type] in Breast cancer specimen by Immune stain" //TODO: request LOINC codes that are not specimen-specific. Also, request answer list is specified in SNOMEDCT. + Based on: CodedObservationComponent + Description: "The degree or magnitude of staining across positively stained tumor cells on the entire tissue section relative to the intensity of positive controls run with the same batch." + Code is LNC#85310-1 "Estrogen receptor fluorescence intensity [Type] in Breast cancer specimen by Immune stain" // + DataValue from StainingIntensityVS + + +EntryElement: ProgesteroneReceptorStatus +Based on: TumorMarkerObservation +Concept: LNC#16113-3 "Progesterone receptor [Interpretation] in Tissue" +Description: "Progesterone receptor status is a factor in determining prognosis and treatment options. The value is the percentage of cells that test (stain) positive for the presence of a receptor. The interpretation of positive or negative (found in the interpretation property) is based on the staining percentage, and may take into account the staining intensity." + Code from ProgesteroneReceptorInterpretationTestsVS + DataValue from PositiveNegativeIndeterminateVS + Specimen is type BreastSpecimen + Components.ObservationComponent + includes 0..1 ProgesteroneReceptorNuclearPositivity + includes 0..1 ProgesteroneReceptorAverageStainingIntensity +0..0 PanelMembers + + Element: ProgesteroneReceptorNuclearPositivity + Based on: ObservationComponent + Description: "The percentage of cells that test (stain) positive for the presence of progesterone receptors. We are seeking feedback on whether nuclear positivity should be an exact percentage or a range of percentages. As currently defined, an exact nuclear positivity could be represented by a zero-width range, where the lower and upper bounds would be the same number. We are seeking feedback on whether nuclear positivity should be an exact percentage or a range of percentages. As currently defined, an exact nuclear positivity could be represented by a zero-width range, where the lower and upper bounds would be the same number." + Code is LNC#14230-7 "Cells.progesterone receptor/100 cells in Tissue by Immune stain" // LOINC codes for nuclear positivity are specific to the receptor. TODO: Confirm this code is more appropriate than LNC#85325-9 "Cells.progesterone receptor/100 cells in Breast cancer specimen by Immune stain", which specifies the specimen as a breast specimen. + DataValue value is type Range + 0..0 ReferenceRange + + Element: ProgesteroneReceptorAverageStainingIntensity + Based on: CodedObservationComponent + Description: "The degree or magnitude of staining across positively stained tumor cells on the entire tissue section relative to the intensity of positive controls run with the same batch." + Code is LNC#85331-7 "Progesterone receptor fluorescence intensity [Type] in Breast cancer specimen by Immune stain" //TODO: request LOINC codes that are not specimen-specific. Also, request answer list is specified in SNOMEDCT. + DataValue from StainingIntensityVS + + +EntryElement: DCISNuclearGrade +Concept: MTH#C18513 "Nuclear Grade" +Based on: SimpleCodedLaboratoryObservation +Description: "An evaluation of the size and shape of the nucleus in tumor cells and the percentage of tumor cells that are in the process of dividing or growing. Cancers with low nuclear grade grow and spread less quickly than cancers with high nuclear grade. In breast cancer, nuclear grade is typically evaluated for ductal carcinoma in situ (DCIS) only." + Code is MTH#C18513 "Nuclear Grade" + DataValue from NuclearGradeVS + Specimen is type BreastSpecimen +0..0 Device + + +EntryElement: BreastCancerHistologicGrade +Based on: CancerHistologicGrade +Description: "The Elston Grade/Nottingham Score, representative of the aggressive potential of the tumor. Well differentiated cells (Grade 1) look similar to normal cells and are usually slow growing, while poorly differentiated cells (Grade 3) look very different than normal and are fast-growing." + Code is LNC#44648-4 "Histologic grade [Score] in Breast cancer specimen Qualitative by Nottingham" + DataValue from http://loinc.org/vs/LL4561-8 + Specimen is type BreastSpecimen + Components.ObservationComponent + includes 0..1 TubuleFormationScore + includes 0..1 NuclearPleomorphismScore + includes 0..1 MitoticCountScore + + + Element: TubuleFormationScore + Based on: CodedObservationComponent + Description: "The degree of glandular differentiation or tubule formation in breast carcinoma is one component of the Nottingham histologic grade, which is a prognostic indicator for patients with breast carcinoma. Less aggressive cancers have more tubule formation." + Code is LNC#85321-8 "Glandular differentiation [Score] in Breast cancer specimen Qualitative by Nottingham" + DataValue from http://loinc.org/vs/LL4380-3 + + Element: NuclearPleomorphismScore + Based on: CodedObservationComponent + Description: "The degree of nuclear pleomorphism (variability of nuclei) in breast carcinoma is one component of the Nottingham histologic grade, which is a prognostic indicator for patients with breast carcinoma. Increasing degrees of pleomorphism are associated with increasingly aggressive cancers." + Code is LNC#44645-0 "Nuclear pleomorphism in Breast tumor Qualitative by Nottingham" + DataValue from http://loinc.org/vs/LL4382-9 + + Element: MitoticCountScore + Based on: CodedObservationComponent + Description: "The degree of mitotic activity in breast carcinoma is one component of the Nottingham histologic grade, which is a prognostic indicator for patients with breast carcinoma. Mitotic activity is assessed as the number of mitoses per 10 high power fields (HPF), with increasing mitotic activity being an indicator of more aggressive cancer. The specific scores assigned to the number of mitoses depends on the size of the HPF. For example, for a HPF size of 0.274 mm^2, less than 10 mitoses per 10 HPF gets a score of 1, 10-19 gets a score of 2, and greater than or equal to 20 gets a score of 3. When larger or smaller HPFs are used, the cutoffs for the number of mitoses corresponding to a specific score are adjusted according to published guidelines." + Code is LNC#85300-2 "Mitotic rate [Score] in Breast cancer specimen Qualitative by Nottingham" + DataValue from http://loinc.org/vs/LL4383-7 + + +EntryElement: OncotypeDxInvasiveRecurrenceScore +Based on: SimpleLaboratoryObservation +Concept: MTH#C1709318 "Oncotype DX Breast Cancer Assay" +Description: "The Oncotype DX test for invasive breast cancer examines the activity of 21 genes in a patient’s breast tumor tissue to provide personalized information for tailoring treatment based on the biology of their individual disease. The value from 0 to 100 indicates the estimated risk of recurrence, with the highest risk indicated by a score greater than 31. +No LOINC code currently exists for this test. We are seeking feedback on the value of separating OncotypeDx scores for DCIS and invasive breast carcinomas. Does it make more sense to report the OncotypeDx as a single score, regardless of the type of cancer?" + DataValue value is type IntegerQuantity + Code is MTH#C1709318 "Oncotype DX Breast Cancer Assay" + Interpretation from RecurrenceRiskScoreInterpretationVS + Specimen is type ref(BreastSpecimen) + + +EntryElement: OncotypeDxDCISRecurrenceScore +Based on: SimpleLaboratoryObservation +Description: "The Oncotype DX test for DCIS (Ductal Carcinoma in Situ) breast cancer. Risk scores range from 0 to 100 with the following interpretations: 0-38: Low-Risk, 39-54: Intermediate-Risk, 55+: High-Risk. +No LOINC code currently exists for this test. We are seeking feedback on the value of separating OncotypeDx scores for DCIS and invasive breast carcinomas. Does it make more sense to report the OncotypeDx as a single score, regardless of the type of cancer?" + DataValue value is type IntegerQuantity + Code is MTH#C3898101 + Interpretation from RecurrenceRiskScoreInterpretationVS + Specimen is type BreastSpecimen +0..0 Device + + +EntryElement: ProsignaRecurrenceScore +Based on: SimpleLaboratoryObservation +Description: "Breast cancer genomic signature assay for 10-year risk of distant recurrence score calculated by Prosigna. +The Prosigna Score is reported on a 0-100 scale (referred to as ROR Score or Risk of Recurrence Score in the literature), which is correlated with the probability of distant recurrence at ten years for post-menopausal women with hormone receptor positive, early stage breast cancer." + DataValue value is type IntegerQuantity + Code is LNC#76544-6 "Breast cancer 10-year risk of distant recurrence score Calculated by Prosigna" + Interpretation from RecurrenceRiskScoreInterpretationVS + Specimen is type BreastSpecimen +0..0 Device + + +EntryElement: MammaprintRecurrenceScore +Based on: SimpleLaboratoryObservation +Description: "Breast cancer genomic signature assay for 10-year risk of distant recurrence score calculated by Mammaprint. +In the United States, MammaPrint can only be used on cancers that are stage I or stage II, invasive, smaller than 5 centimeters, and estrogen-receptor-positive or -negative. Scores range from -1.0 to +1.0, with scores less than 0 indicating high risk, and scores greater than 0 indicating low risk. +The is currently no LOINC code for Mammaprint test." + DataValue value is type IntegerQuantity + Code is MTH#C2827401 "MammaPrint" + Interpretation from RecurrenceRiskScoreInterpretationVS + Specimen is type BreastSpecimen +0..0 Device + +/************* LEGACY BEGIN ************ + +EntryElement: BreastTumor +Based on: FindingSiteConditionPresenceStatement +Concept: SCT#395557000 "Tumor finding (finding)" +Description: "An abnormal mass of tissue that results when cells divide more than they should or do not die when they should. Tumors may be benign (not cancer), or malignant (cancer). Also called neoplasm. (source: NCI)" +1..1 TopicCode is SCT#395557000 "Tumor finding (finding)" +1..1 Category is OBSCAT#exam +0..1 FindingSiteConditionTopic.AnatomicalLocation is type BreastSite +0..0 FindingSiteConditionTopic.AlleviatingFactor +0..0 FindingSiteConditionTopic.ExacerbatingFactor + FindingSiteConditionTopic.FindingSiteIdentifier is type TumorIdentifier +0..0 ConditionPresenceContext.Severity + FindingSiteConditionTopic.FindingMethod should be from BreastCancerDetectionVS +0..0 ConditionPresenceContext.Stage // already covered under BreastCancerPrimaryTumorClassification + +********** LEGACY END ************/ + + +/* + + additional components from CAP form +includes 0..1 StainingControl +includes 0..1 PrimaryAntibody //from EstrogenAntibodyVS if covered +includes 0..1 AllredProportionScore +includes 0..1 AllredIntensityScore +includes 0..1 AllredTotalScore +includes 0..1 OtherReceptorScoringSystem + + + Element: Aneusomy + Based on: ObservationComponent + Concept: CAP#30478 + Description: "Aneusomy (as defined by vendor kit used)" + Value: CodeableConcept from YesNoVS + + Element: HeterogeneousSignals + Based on: ObservationComponent + Concept: CAP#30482 + Description: "Whether In Situ Hybridization signals were heterogeneous." + Value: CodeableConcept from YesNoVS + + Element: PercentageAmplified + Based on: ObservationComponent + Concept: CAP#31073 + Description: "Percentage of cells with amplified HER2 signals" + Value: Quantity with units UCUM#% + + Element: NuclearPositivity + Based on: ObservationComponent + Concept: TBD + Description: "The percentage of cells that test (stain) positive for the presence of a receptor." + Value: Range + + Element: PrimaryAntibody + Based on: ObservationComponent + Concept: CAP#31092 + Description: "" + Value: CodeableConcept + + Element: StainingControl + Based on: ObservationComponent + Concept: CAP#25895 + Description: "Whether control cells were present." + Value: CodeableConcept from StainingControlVS if covered + + Element: AllredProportionScore + Concept: CAP#31054 + Based on: ObservationComponent + Description: "Part of Allred scoring, based on the percentage of cells that stain for a receptor, on a scale of 0 to 5." + Value: IntegerQuantity + + Element: AllredIntensityScore + Concept: CAP#29749 + Based on: ObservationComponent + Description: "Part of the Allred scoring, based on the intensity of that staining, on a scale of 0 to 3." + Value: IntegerQuantity + + Element: AllredTotalScore + Concept: CAP#31056 + Based on: ObservationComponent + Description: "The total Allred score, the total of proportion and intensity scores, from 0 to 8." + Value: IntegerQuantity // unsignedInt - limit to max of 8 + + Element: OtherReceptorScoringSystem + Concept: CAP#31062 + Based on: ObservationComponent + Description: "A scoring system other than Allred." + + Element: Ki-67LabelingIndex + Based on: SimpleCodedObservation + Concept: MTH#C4049944 + Description: "Ki-67 is a protein phosphatase whose expression is strongly associated with cell proliferation and encoded by the MKI67 gene. The Ki67 labeling index is the fraction of Ki-67-positive cells to total cells in a tumor specimen and may be useful for determining prognosis with respect to survival and disease recurrence. The more positive cells there are, the more quickly they are dividing and forming new cells. ReferenceRange: Low <10, Intermediate 10-20, >20 High" + Value: Quantity with units UCUM#% + Code is LNC#29593-1 + Components.ObservationComponent + includes 0..1 PrimaryAntibody //from Ki67AntibodyVS if covered + + Element: S-PhaseFraction + Based on: SimpleCodedObservation + Concept: MTH#C0812425 + Description: "An expression of the number of mitoses found in a stated number of cells. The S-phase fraction number tells you what percentage of cells in the tissue sample are in the process of copying their genetic information (DNA). This S-phase, short for synthesis phase, happens just before a cell divides into two new cells. ReferenceRange: Low <6, Intermediate 6-10, >10 High." + Value: Quantity with units UCUM#% + Code is LNC#29593-1 + +EntryElement: GeneticVariant +Based on: Observation +Concept: MTH#C0678941 +Description: "Whether a subject carries a mutation in a particular gene." +Value: CodeableConcept from PositiveNegativeVS +// SubjectOfInformation.CodeableConcept from GeneIdentifierVS +0..0 ReferenceRange +//0..0 DeltaFlag +0..0 BodySite + Components.ObservationComponent +includes 0..1 Refseq + + Element: Refseq + Based on: ObservationComponent + Concept: TBD + Description: "The Reference Sequence (RefSeq) collection provides a comprehensive, integrated, non-redundant, well-annotated set of sequences, including genomic DNA, transcripts, and proteins. RefSeq sequences form a foundation for medical, functional, and diversity studies. They provide a stable reference for genome annotation, gene identification and characterization, mutation and polymorphism analysis (especially RefSeqGene records), expression studies, and comparative analyses." + Value: CodeableConcept from RefseqVS + +EntryElement: BreastCancerGeneticAnalysisObservation +Concept: TBD +Based on: Observation +Description: "The status of genes known or suspected to play a role in breast cancer risk, for example, the tumor suppressor genes, BRCA1 and BRCA2." + Observation.Code is TBD#TBD +0..0 Components + PanelMembers.Observation +includes 1..1 BRCA1Variant +includes 1..1 BRCA2Variant + + Element: BRCA1Variant + Concept: TBD + Based on: GeneticVariant + Description: "Whether the patient has a mutation in the BRCA1 gene." + Value: CodeableConcept from PositiveNegativeVS +// SubjectOfInformation.CodeableConcept is HGNC#BRCA1Gene + + + Element: BRCA2Variant + Concept: TBD + Based on: GeneticVariant + Description: "Whether the patient has a mutation in the BRCA2 gene." + Value: CodeableConcept from PositiveNegativeVS +// SubjectOfInformation.CodeableConcept is HGNC#BRCA2Gene + + +FHIR Genomics: +https://www.hl7.org/FHIR/2016Jan/obs-genetics-example3-bcr1%20and%20bcr2%20sequencing%20with%20FamilyHistory%20-1.json.html +https://www.hl7.org/FHIR/2016Jan/observation-genetics-cg-prf-1a.html +https://www.hl7.org/FHIR/2016Jan/observation-genetics.html +https://www.hl7.org/FHIR/2016Jan/obs-genetics-example2-germline.html +*/ + diff --git a/spec/shr_oncology_vs.txt b/spec/brca_vs.txt similarity index 63% rename from spec/shr_oncology_vs.txt rename to spec/brca_vs.txt index a20ac9b5..df45acf7 100644 --- a/spec/shr_oncology_vs.txt +++ b/spec/brca_vs.txt @@ -1,19 +1,20 @@ Grammar: ValueSet 5.0 -Namespace: shr.oncology +Namespace: brca CodeSystem: SCT = http://snomed.info/sct +CodeSystem: LNC = http://loinc.org ValueSet: BreastSiteVS -Description: "Topography of the breast. Codes are drawn from Snomed and correspond to ICD-O-3." -SCT#24142002 "Nipple structure (body structure) - corresponds to ICDO3#C50.0" -SCT#49058007 "Structure of central portion of breast (body structure) - corresponds to ICDO3#C50.1" -SCT#77831004 "Structure of upper inner quadrant of breast (body structure) - corresponds to ICDO3#C50.2" -SCT#19100000 "Structure of lower inner quadrant of breast (body structure) - corresponds to ICDO3#C50.3" -SCT#76365002 "Structure of upper outer quadrant of breast (body structure) - corresponds to ICDO3#C50.4" -SCT#33564002 "Structure of lower outer quadrant of breast (body structure) - corresponds to ICDO3#C50.5" -SCT#38412008 "Structure of axillary tail of breast (body structure) - corresponds to ICDO3#C50.6" -SCT#276825009 "Overlapping sites (qualifier value) - corresponds to ICDO3#C50.8" -SCT#76752008 "Breast structure (body structure) - corresponds to ICDO3#C50.9" // NOS +Description: "Topography of the breast. Codes are drawn from SNOMED CT and can be regarded as equivalent to ICD-O-3 topography codes." +SCT#24142002 "Nipple structure (body structure)" +SCT#49058007 "Structure of central portion of breast (body structure)" +SCT#77831004 "Structure of upper inner quadrant of breast (body structure)" +SCT#19100000 "Structure of lower inner quadrant of breast (body structure)" +SCT#76365002 "Structure of upper outer quadrant of breast (body structure)" +SCT#33564002 "Structure of lower outer quadrant of breast (body structure)" +SCT#38412008 "Structure of axillary tail of breast (body structure)" +SCT#276825009 "Overlapping sites (qualifier value)" +SCT#76752008 "Breast structure (body structure)" // NOS ValueSet: BreastSpecimenTypeVS Description: "The type of specimen obtained from the breast. Codes are drawn from Snomed CT where available. Local codes are used where Snomed codes are currently unavailable." @@ -32,71 +33,82 @@ SCT#48635004 "Fine needle biopsy (procedure)" SCT#172043006 "Simple mastectomy (procedure)" SCT#237372000 "Excisional biopsy of breast (procedure)" -// Can we add synonyms (both Snomed and ICD-O-3)? -ValueSet: BreastCancerTypeVS -Description: "Histologic types of breast cancer. Codes are drawn from Snomed. Correspondence to ICD-O-3 is specified. Local codes are used where Snomed codes are currently unavailable." -SCT#86049000 "Malignant neoplasm, primary (morphologic abnormality)" -SCT#68956006 "Carcinoma in situ (morphologic abnormality) - corresponds to ICDO3#8010 Carcinoma, NOS" -SCT#65692009 "Spindle cell carcinoma (morphologic abnormality)- corresponds to ICDO3#8032 Spindle cell carcinoma" -SCT#128631001 "Carcinoma with osteoclast-like giant cells (morphologic abnormality)- corresponds to ICDO3#8035 Carcinoma with osteoclast-like stromal giant cells" -SCT#74364000 "Small cell carcinoma (morphologic abnormality)- corresponds to ICDO3#8041 Neuroendocrine carcinoma, poorly differentiated (small cell carcinoma)" -SCT#59529006 "Squamous cell carcinoma in situ (morphologic abnormality)- corresponds to ICDO3#8070 Squamous cell carcinoma" -SCT#35917007 "Adenocarcinoma, no subtype (morphologic abnormality)- corresponds to ICDO3#8140 Adenocarcinoma, N" -SCT#11671000 "Adenoid cystic carcinoma (morphologic abnormality)- corresponds to ICDO3#8200 Adenoid cystic carcinoma" -SCT#30156004 "Cribriform carcinoma (morphologic abnormality)- corresponds to ICDO3#8201 Cribriform carcinoma" -SCT#19665009 "Tubular adenoma (morphologic abnormality)- corresponds to ICDO3#8211 Tubular carcinoma" -SCT#55937004 "Neuroendocrine carcinoma (morphologic abnormality)- corresponds to ICDO3#8246 Neuroendocrine tumor, well-differentiated" -SCT#128662002 "Adenocarcinoma with mixed subtypes (morphologic abnormality)- corresponds to ICDO3#8255 Adenocarcinoma with mixed subtypes" -SCT#89439007 "Oxyphilic adenoma (morphologic abnormality)- corresponds to ICDO3#8290 Oncocytic carcinoma" -SCT#3839000 "Lipid-rich carcinoma (morphologic abnormality)- corresponds to ICDO3#8314 Lipid-rich carcinoma" -SCT#74280008 "Glycogen-rich carcinoma (morphologic abnormality)- corresponds to ICDO3#8315 Glycogen-rich clear cell carcinoma" -SCT#36318001 "Apocrine adenoma (morphologic abnormality)- corresponds to ICDO3#8401 Apocrine adenocarcinoma" -SCT#78424008 "Sebaceous adenoma (morphologic abnormality)- corresponds to ICDO3#8410 Sebaceous carcinoma" -SCT#39892006 "Mucoepidermoid tumor (morphologic abnormality)- corresponds to ICDO3#8430 Mucoepidermoid carcinoma" -SCT#33170000 "Mucinous adenoma (morphologic abnormality)- corresponds to ICDO3#8480 Mucinous carcinoma" -SCT#86616005 "Intraductal carcinoma, noninfiltrating (morphologic abnormality)- corresponds to ICDO3#8500 Ductal carcinoma" -SCT#36425007 "Comedocarcinoma (morphologic abnormality)- corresponds to ICDO3#8501 Comedocarcinoma, NOS" -SCT#41919003 "Juvenile carcinoma of the breast (morphologic abnormality)- corresponds to ICDO3#8502 Secretory carcinoma" -SCT#30566004 "Noninfiltrating intraductal papillary adenocarcinoma (morphologic abnormality)- corresponds to ICDO3#8503 Intraductal papillary carcinoma" -SCT#47488001 "Intracystic papillary adenoma (morphologic abnormality)- corresponds to ICDO3#8504 Encapsulated papillary carcinoma" -SCT#128696009 "Intraductal micropapillary carcinoma (morphologic abnormality)- corresponds to ICDO3#8507 Invasive micropapillary carcinoma" -SCT#421980000 "Papillary carcinoma, solid (morphologic abnormality)- corresponds to ICDO3#8509 Solid papillary carcinoma" -SCT#32913002 "Medullary carcinoma (morphologic abnormality)- corresponds to ICDO3#8510 Medullary carcinoma" -SCT#128698005 "Atypical medullary carcinoma (morphologic abnormality)- corresponds to ICDO3#8513 Atypical medullary carcinoma" -SCT#58477004 "Infiltrating ductular carcinoma (morphologic abnormality)- corresponds to ICDO3#8520 Invasive lobular carcinoma" -SCT#35232005 "Infiltrating duct and lobular carcinoma (morphologic abnormality)- corresponds to ICDO3#8521 Infiltrating ductular carcinoma" -SCT#128700001 "Infiltrating duct mixed with other types of carcinoma (morphologic abnormality)- corresponds to ICDO3#8522 Infiltrating duct and lobular carcinoma" -SCT#128701002 "Infiltrating lobular mixed with other types of carcinoma (morphologic abnormality)- corresponds to ICDO3#8524 Infiltrating lobular mixed with other types of carcinoma" -SCT#128702009 "Polymorphous low grade adenocarcinoma (morphologic abnormality)- corresponds to ICDO3#8525 Polymorphous carcinoma" -SCT#32968003 "Inflammatory carcinoma (morphologic abnormality)- corresponds to ICDO3#8530 Inflammatory carcinoma" -SCT#2985005 "Paget's disease, mammary (morphologic abnormality)- corresponds to ICDO3#8540 Paget disease of the nipple" -SCT#82591005 "Paget's disease and infiltrating duct carcinoma of breast (morphologic abnormality)- corresponds to ICDO3#8541 Paget disease and infiltrating duct carcinoma of breast" -SCT#54666007 "Paget's disease and intraductal carcinoma of breast (morphologic abnormality)- corresponds to ICDO3#8543 Paget disease and intraductal carcinoma" -SCT#15176003 "Adenocarcinoma with squamous metaplasia (morphologic abnormality)- corresponds to ICDO3#8570 Low-grade adenosquamous carcinoma" -#8571 "Metaplastic carcinoma with mesenchymal differentiation- corresponds to ICDO3#8571 Metaplastic carcinoma with mesenchymal differentiation" -SCT#733875004 "Fibromatosis-like metaplastic carcinoma (morphologic abnormality)- corresponds to ICDO3#8572 Fibromatosis-like metaplastic carcinoma" -SCT#128704005 "Adenocarcinoma with neuroendocrine differentiation (morphologic abnormality)- corresponds to ICDO3#8574 Carcinoma with neuroendocrine differentiation" -SCT#128705006 "Metaplastic carcinoma (morphologic abnormality)- corresponds to ICDO3#8575 Metaplastic carcinoma" -SCT#69291002 "Myoepithelioma (morphologic abnormality)- corresponds to ICDO3#8982 Myoepithelial carcinoma" -SCT#128765009 "Adenomyoepithelioma (morphologic abnormality)- corresponds to ICDO3#8983 Adenomyoepithelioma with carcinoma" +ValueSet: BreastCancerDisorderVS +Description: "Classification of cancer by site, in this case, the breast." +Includes codes descending from SCT#254837009 "Malignant neoplasm of breast (disorder)" + +ValueSet: BreastCarcinomaHistologicTypeVS +// TODO: request missing SNOMEDCT terms to fully cover ICD-O-3. +Description: "Histologic types of breast carcinomas, including invasive carcinoma and ductal carcinoma in situ. Codes are drawn from SNOMED CT; local codes are used where SNOMED CT codes are unavailable. +The codes are intended to match the scope of breast carcinoma histologic types specified in ICD-O-3. Additional SNOMED CT codes may be appropriate to include in this value set. We are requesting feedback on the perceived need to request SNOMED CT codes to represent the histologic types currently represented by local codes." +SCT#82711006 "Infiltrating duct carcinoma (morphologic abnormality)" +SCT#16741004 "Pleomorphic carcinoma (morphologic abnormality)" +SCT#128631001 "Carcinoma with osteoclast-like giant cells (morphologic abnormality)" +SCT#89740008 "Lobular carcinoma (morphologic abnormality)" +SCT#4631006 "Tubular adenocarcinoma (morphologic abnormality)" +SCT#30156004 "Cribriform carcinoma (morphologic abnormality)" +SCT#72495009 "Mucinous adenocarcinoma (morphologic abnormality)" +SCT#32913002 "Medullary carcinoma (morphologic abnormality)" +SCT#128698005 "Atypical medullary carcinoma (morphologic abnormality)" +SCT#82711006 "Infiltrating duct carcinoma (morphologic abnormality)" +SCT#22694002 "Adenocarcinoma with apocrine metaplasia (morphologic abnormality)" +SCT#703578005 "Invasive micropapillary carcinoma of breast (morphologic abnormality)" +SCT#128705006 "Metaplastic carcinoma (morphologic abnormality)" +SCT#59367005 "Adenosquamous carcinoma (morphologic abnormality)" +SCT#15176003 "Adenocarcinoma with squamous metaplasia (morphologic abnormality)" +SCT#733875004 "Fibromatosis-like metaplastic carcinoma (morphologic abnormality)" +SCT#399739006 "Metaplastic squamous cell carcinoma (morphologic abnormality)" +SCT#65692009 "Spindle cell carcinoma (morphologic abnormality)" +SCT#128705006 "Metaplastic carcinoma (morphologic abnormality)" +SCT#128884000 "Malignant myoepithelioma (morphologic abnormality)" +SCT#703644009 "Adenomyoepithelioma with carcinoma (morphologic abnormality)" +SCT#11671000 "Adenoid cystic carcinoma (morphologic abnormality)" +SCT#55937004 "Neuroendocrine carcinoma (morphologic abnormality)" +SCT#719105002 "Small cell neuroendocrine carcinoma (morphologic abnormality)" +SCT#128704005 "Adenocarcinoma with neuroendocrine differentiation (morphologic abnormality(" +SCT#41919003 "Juvenile carcinoma of the breast (morphologic abnormality)" +SCT#64524002 "Intraductal papillary adenocarcinoma with invasion (morphologic abnormality)" +SCT#45410002 "Acinar cell carcinoma (morphologic abnormality)" +SCT#4079000 "Mucoepidermoid carcinoma (morphologic abnormality)" +SCT#57596004 "Oxyphilic adenocarcinoma (morphologic abnormality)" +SCT#3839000 "Lipid-rich carcinoma (morphologic abnormality)" +SCT#74280008 "Glycogen-rich carcinoma (morphologic abnormality)" +SCT#78424008 "Sebaceous adenocarcinoma (morphologic abnormality)" +SCT#399935008 "Ductal carcinoma in situ - category (morphologic abnormality)" +SCT#30566004 "Noninfiltrating intraductal papillary adenocarcinoma (morphologic abnormality)" +SCT#703545003 "Encapsulated papillary carcinoma (morphologic abnormality)" +SCT#703547006 "Encapsulated papillary carcinoma with invasion (morphologic abnormality)" +SCT#703546002 "Solid papillary carcinoma in situ (morphologic abnormality)" +SCT#703594003 "Solid papillary carcinoma with invasion (morphologic abnormality)" +SCT#32968003 "Inflammatory carcinoma (morphologic abnormality)" +SCT#2985005 "Paget's disease, mammary (morphologic abnormality)" +#metaplastic_chondroid "Metaplastic carcinoma with chondroid differentiation" +#metaplastic_osseous "Metaplastic carcinoma with osseous differentiation" +#metaplastic_mesenchymal "Metaplastic carcinoma with mesenchymal differentiation" +#metaplastic_mixed "Mixed metaplastic carcinoma" +#polymorphous_carcinoma "Polymorphous carcinoma" ValueSet: BreastCancerDetectionVS -Description: "Basis for cancer detection, from HL7 CDA® R2 Implementation Guide: Clinical Oncology Treatment Plan and Summary, Release 1 - US Realm Standard for Trial Use Release 3, October 2016, Volume 2 — Templates and Supporting Material." +Description: "The method through which breast cancer was detected." +SCT#113011001 "Palpation (procedure)" +SCT#32750006 "Inspection (procedure)" +SCT#71651007 "Mammography (procedure)" +SCT#82918005 "Positron emission tomography (procedure)" +SCT#16310003 "Diagnostic ultrasonography (procedure)" +SCT#113091000 "Magnetic resonance imaging (procedure)" +SCT#448764002 "Ultrasound elastography (procedure)" +SCT#725404004 "Molecular breast imaging (procedure)" +SCT#62434009 "Breast thermography (procedure)" +SCT#450566007 "Digital breast tomosynthesis (procedure)" + +/* These HL7 CDA IG codes speak to the context in which the cancer was detected, rather than the method. SCT#360156006 "Screening" SCT#160237006 "History/Symptoms" SCT#261087003 "Incidental" -//TO DO methods of observation, limit to direct visual observation (32750006), palpation (113011001), or imaging procedures (363679005) such as computed tomography (77477000), plain x-ray, MRI (113091000), ultrasonography, etc. - -ValueSet: MorphologyBehaviorVS -Description: "The morphologic behavior of the cancer. These are the suffix to the ICD-O-3 histologic type codes. Codes are presented as local codes because they are portions of the full code to be post-coordinated, and not full ICD-O-3 codes." -#0 "Benign" -#1 "Uncertain whether benign or malignant" -#2 "In situ" -#3 "Malignant, primary site" -#6 "Malignant, metastatic site" -#9 "Malignant, uncertain whether primary or metastatic site" +*/ +/* no longer used ValueSet: StagingMethodVS Description: "The methodology or standard used to assign the cancer's overall stage." #ajcc_v7 "AJCC Cancer Staging Manual 7th Edition" @@ -105,14 +117,9 @@ Description: "The methodology or standard used to assign the cancer's overall st #seer_ss77 "SEER Summary Stage 1977" #seer_ss00 "SEER Summary Stage 2000" #seer_ss18 "SEER Summary Stage 2018" +*/ -ValueSet: StageTimingPrefixVS -Description: "When staging was done, relative to treatment events (qualifier)." -#cli "Clinical stage: Staging performed prior to surgery, based on evidence such as physical examination, imaging, and/or biopsy." -#path "Pathologic stage: Staging performed based on examination of tissue samples removed during surgery, in addition to physical examination and imaging." -#postther_cli "Post-therapeutic (post-neoadjuvant) clinical staging based on clinical examination after the first treatment with systemic drugs or radiation, when no surgery has been performed." -#postther_path "Post-therapeutic (post-neoadjuvant) pathologic staging, based on tissue samples removed during surgery after the first treatment with systemic drugs or radiation." - +/* No longer used ValueSet: NottinghamCombinedGradeVS Description: "Combined score from the Nottingham grading system." SCT#369790002 "Nottingham Combined Grade I: 3-5 points (finding)" @@ -120,12 +127,42 @@ SCT#369791003 "Nottingham Combined Grade II: 6-7 points (finding)" SCT#369792005 "Nottingham Combined Grade III: 8-9 points (finding)" ValueSet: NottinghamNullVS -//MK 7/14/2018 Added one missing code for the normative list. -Description: "Data absent reasons (null values) for Nottingham Combined Grade scores. Removes non-applicable values from the ExceptionValueVS, and adds values that align with LOINC normative answer list LL4561-8" +Description: "Data absent reasons (null values) for Nottingham Combined Grade scores. Removes non-applicable values from the DataAbsentReasonVS, and adds values that align with LOINC normative answer list LL4561-8" LNC#LA27219-7 "Only microinvasion present (not graded)" LNC#LA27220-5 "No residual invasive carcinoma after presurgical (neoadjuvant) therapy" LNC#LA11884-6 "Indeterminate" LNC#LA27221-3 "Score cannot be determined" +*/ + +ValueSet: LymphNodeInvolvementVS +Description: "The pathological finding for lymph node involvement." +SCT#399374009 "Regional lymph node metastasis present (finding)" +SCT#399522007 "Regional lymph nodes cannot be assessed (finding)" +SCT#399647000 "No regional lymph node metastasis (finding)" + +ValueSet: LymphNodeSamplingMethodVS +Description: "The procedure method used to obtain the specimen analyzed for the pathological lymph node involvement." +SCT#396487001 "Sentinel lymph node biopsy (procedure)" +SCT#234262008 "Axillary lymph node dissection (procedure)" +SCT#9911007 "Core needle biopsy (procedure)" +SCT#48635004 "Fine needle biopsy (procedure)" + +ValueSet: BreastLymphNodeGroupVS +Description: "The breast regional lymph node locations" +SCT#245269009 "Axillary lymph node group (body structure)" +SCT#245282001 "Internal mammary lymph node group (body structure)" +SCT#245265003 "Supraclavicular lymph node group (body structure)" +SCT#279807001 "Infraclavicular lymph node group (body structure)" + +ValueSet: LymphNodeClinicalMethodVS +Description: "The method of lymph node sample collection for clinical LNI assessment." +SCT#363679005 "Physical examination procedure (procedure)" +SCT#363679005 "Imaging (procedure)" + +ValueSet: LymphNodeMobilityVS +Description: "Values expressing the degree of moveability of lymph node upon palpation." +SCT#261010008 "Fixed (qualifier)" +SCT#300824007 "Moveable (qualifier)" ValueSet: NuclearGradeVS Description: "The nuclear grade describes how closely the nuclei of cancer cells look like the nuclei of normal breast cells. In general, the higher the nuclear grade, the more abnormal the nuclei are and the more aggressive the tumor cells tend to be. The nuclear grade is a part of overall tumor grade. Local codes are used due to unavailability of suitable LOINC and Snomed codes." @@ -134,7 +171,9 @@ SCT#54102005 "G1 grade (finding) - well differentiated" SCT#1663004 "G2 grade (finding) - moderately differentiated" SCT#61026006 "G3 grade (finding) - pooly differentiated" SCT#258245003 "G4 grade (finding) - undifferentiated" +SCT#12619005 "GX grade (finding)" +/* No longer used ValueSet: TubuleFormationScoreVS // MK 7/14/2018 -- Since we identify the test by LOINC, and that test has a normative value set, the results should always be reported using the normative value set. Description: "The degree of glandular differentiation or tubule formation in breast carcinoma. Aligns with normative LOINC answer list LL4380-3. Less aggressive cancers have more tubule formation, with scores assigned as follows: @@ -177,7 +216,7 @@ ValueSet: MitoticCountScoreNullVS Description: "Data absent reasons (null values) for mitotic count. Aligns with LOINC normative answer list LL4383-7." LNC#LA27220-5 "No residual invasive carcinoma after presurgical (neoadjuvant) therapy" LNC#LA27221-3 "Score cannot be determined" - +*/ ValueSet: HER2FISHMethodVS // TODO: request LOINC codes (probably pre-coordinated with FISH) @@ -186,6 +225,16 @@ Description: "Value set containing In Situ Hybridization methods of determining SCT#257430009 "Double probe" SCT#257453005 "Single probe" +ValueSet: HER2byFISHInterpretationTestsVS +Description: "Laboratory observations holding the interpretation of FISH HER2 receptor tests (e.g. positive, negative, equivocal)" +LNC#31150-6 "HER2 [Presence] in Tissue by FISH" +LNC#85318-4 "HER2 [Presence] in Breast cancer specimen by FISH" + +ValueSet: HER2byIHCInterpretationTestsVS +Description: "Laboratory observations holding the interpretation of immunohistochemistry HER2 receptor tests (e.g. positive, negative, equivocal)." +LNC#18474-7 "HER2 Ag [Presence] in Tissue by Immune stain" +LNC#85319-2 "HER2 [Presence] in Breast cancer specimen by Immune stain" + ValueSet: HER2byIHCScoreVS Description: "Value set containing possible scores resulting from determining HER2 status by immunohistochemistry. Based on LNC#LL4396-9 answer list." LNC#LA6111-4 "0" @@ -193,9 +242,17 @@ LNC#LA11841-6 "1+" LNC#LA11842-4 "2+" LNC#LA11843-2 "3+" -ValueSet: HER2byIHCScoreNullVS -Description: "Null values permissible for HER2 status by immunohistochemistry. Based on LNC#LL4396-9 answer list." -LNC#LA11884-6 "Indeterminate" +ValueSet: EstrogenReceptorInterpretationTestsVS +Description: "Laboratory observations holding the interpretation of estrogen receptor status (e.g. positive, negative)." +LNC#16112-5 "Estrogen receptor [Interpretation] in Tissue" +LNC#40556-3 "Estrogen receptor Ag [Presence] in Tissue by Immune stain" +LNC#85337-4 "Estrogen receptor Ag [Presence] in Breast cancer specimen by Immune stain" + +ValueSet: ProgesteroneReceptorInterpretationTestsVS +Description: "Laboratory observations holding the interpretation of progesterone receptor status (e.g. positive, negative)." +LNC#16113-3 "Progesterone receptor [Interpretation] in TissueProgesterone receptor [Interpretation] in Tissue" +LNC#40557-1 "Progesterone receptor Ag [Presence] in Tissue by Immune stainProgesterone receptor Ag [Presence] in Tissue by Immune stain" +LNC#85339-0 "Progesterone receptor Ag [Presence] in Breast cancer specimen by Immune stain" ValueSet: RecurrenceRiskScoreInterpretationVS Description: "Interpretations of risk as high, intermediate, or low. Answer set taken from LOINC LL3198-0." @@ -211,8 +268,6 @@ SCT#450501000124104 "Light intensity (qualifier value)" SCT#4901000175103 "Moderate intensity (qualifier value)" SCT#450511000124101 "High intensity (qualifier value)" - - /* NOT USED CodeSystem: MTH = http://ncimeta.nci.nih.gov diff --git a/spec/cimi_adverse.txt b/spec/cimi_adverse.txt deleted file mode 100644 index 15b2bdf0..00000000 --- a/spec/cimi_adverse.txt +++ /dev/null @@ -1,76 +0,0 @@ -Grammar: DataElement 5.0 -Namespace: cimi.adverse -Description: "The CIMI Adverse domain contains definitions for describing adverse events and adverse reactions." -Uses: shr.core, shr.base, cimi.core, cimi.element, cimi.context, cimi.topic, cimi.statement, cimi.entity, shr.research, cimi.medication - -CodeSystem: MTH = http://ncimeta.nci.nih.gov - -Element: AdverseEventEntry -Based on: InformationEntry -Description: "An entry in the patient record documenting an untoward or unexpected finding observed during the course of an activity or an activity. Adverse events may capture either a workflow breach that may or may not result in harm but that must be documented for quality improvement purposes or an adverse finding whether or not it can be traceable to an actual workflow breach." - Signed.Attribution.EntityOrRole is type PatientOrPractitionerOrRelatedPerson // to facilitate mapping to FHIR, which only allows Patient, Practitioner, or RelatedPerson as recorder (note: CLI crashes if we write this as Signed.Value.EntityOrRole) -0..1 Type from MedDRAVS // no topic code -1..1 OccurrenceTime -1..1 Seriousness from SeriousnessVS // to be replaced with http://hl7.org/fhir/ValueSet/adverse-event-seriousness in FHIR 4 -//0..1 TBD "PatternOfEvent" // from STDM -0..1 Outcome from http://hl7.org/fhir/ValueSet/adverse-event-outcome -0..1 Details // aka description -0..* CausalAttribution -0..* ActionTaken -0..1 AssociatedStudy - - Element: Seriousness // aka seriousness - Concept: MTH#C2985911 - Description: "A coded value specifying the level of injury suffered by the subject for whom the event is reported, using the CTCAE coding system." - Value: CodeableConcept - - Element: CausalAttribution - Concept: MTH#C1510821 "Adverse Event Attribution to Product or ProcedurePerformed" - Description: "A possible cause of an observed adverse event, known or theorized. There can be more than one possible cause." - Value: CodeableConcept should be from http://hl7.org/fhir/ValueSet/substance-code or ref(Substance) or ref(Medication) or ref(MedicationUsedStatement) or ref(Device) //ref(ActionPerformedStatement) - 1..1 CauseCategory - 1..1 Certainty - 0..1 RouteIntoBody // aka exposure route - - Element: CauseCategory - Concept: TBD - Description: "Whether the adverse event is attributed to a treatment, course of the disease, unrelated to either, or unknown. " - Value: CodeableConcept from AttributionCategoryVS - - Element: ActionTaken - Concept: TBD - Description: "The action taken as a result of the adverse reaction. May include changing or discontinuing medication, reducing dose, etc." - 1..1 Details - 0..1 ref(ActionStatement) // such as MedicationChangeStatement - - Element: AssociatedStudy - Description: "The related clinical trial or other formal study." - Value: ref(Study) - - -Element: AdverseReactionTopic -Based on: AssertionTopic -Description: "An instance of a negative response to a substance." -0..* Manifestation -0..* CausalAttribution - - Element: Manifestation - Concept: MTH#C1280464 - Description: "A sign or symptom of an underlying condition." - Value: CodeableConcept from ManifestationVS - 0..1 Severity from http://hl7.org/fhir/ValueSet/reaction-event-severity - -//---------------- Instantiations -------------- - -EntryElement: AdverseReactionPresenceStatement -Based on: ClinicalStatement - StatementTopic is type AdverseReactionTopic - StatementContext is type PresenceContext -// AdverseReactionTopic.CausalAttribution value is type CodeableConcept // mapping to FHIR - - -EntryElement: ToxicEventEntry // In truth, this should be a filter on AdverseEventPresenceStatement, not a separate class -Based on: AdverseEventEntry -Concept: MTH#C0542243 -Description: "A grade 3 or 4 adverse reaction to medication, radiation treatment, or other therapy." - Seriousness from ToxicSeriousnessVS diff --git a/spec/cimi_adverse_map.txt b/spec/cimi_adverse_map.txt deleted file mode 100644 index 8dc60e5d..00000000 --- a/spec/cimi_adverse_map.txt +++ /dev/null @@ -1,19 +0,0 @@ -Grammar: Map 5.1 -Namespace: cimi.adverse -Target: FHIR_STU_3 - -AdverseEventEntry maps to AdverseEvent: - Signed.Value.EntityOrRole maps to recorder -// EntityOrRole is the name of the property; don't say Signed.Value.Role - Type maps to type - Details maps to description - PersonOfRecord maps to subject - AssociatedStudy maps to study - Seriousness maps to seriousness - OccurrenceTime maps to date - Outcome maps to outcome -// FHIR TODO: AdverseEvent.eventParticipant is underdefined (no role) - CausalAttribution maps to suspectEntity.instance - CausalAttribution.Certainty maps to suspectEntity.causalityAssessment - -//AdverseReactionStatement maps to ??? diff --git a/spec/cimi_allergy.txt b/spec/cimi_allergy.txt deleted file mode 100644 index b0411b12..00000000 --- a/spec/cimi_allergy.txt +++ /dev/null @@ -1,100 +0,0 @@ -Grammar: DataElement 5.0 -Namespace: cimi.allergy -Description: "The SHR Allergy domain contains definitions for statements dealing with substance-related risks, particularly, allergies and intolerances." -Uses: shr.core, shr.base, cimi.core, cimi.context, cimi.topic, cimi.statement, cimi.entity, cimi.element, cimi.adverse - -CodeSystem: SCT = http://snomed.info/sct -CodeSystem: CAT = http://hl7.org/fhir/allergy-intolerance-category - -Element: AdverseSensitivityTopic -Based on: AssertionTopic -Concept: TBD -Description: "A finding related to the presence or absence of an individual's risk or sensitivity to a substance or class of substances. A finding can be taken as tantamount to a representation of an allergic condition, allowing it to be tracked over time." -0..1 AllergenIrritant -0..* SubstanceCategory from http://hl7.org/fhir/ValueSet/allergy-intolerance-category -0..1 Type from http://hl7.org/fhir/ValueSet/allergy-intolerance-type - - Element: AllergenIrritant - Concept: TBD - Description:"A substance that causes an allergic reaction or irritation." - Value: CodeableConcept from http://hl7.org/fhir/us/core/ValueSet/us-core-substance - -Element: AdverseSensitivityPresenceContext -Based on: PresenceContext -Description: "Context for adverse sensitivities that are known or suspected to exist." -0..1 ClinicalStatus from http://hl7.org/fhir/ValueSet/allergy-clinical-status -1..1 VerificationStatus from http://hl7.org/fhir/ValueSet/allergy-verification-status -0..1 Criticality from http://hl7.org/fhir/ValueSet/allergy-intolerance-criticality -0..1 MostRecentOccurrenceTime -0..* ref(AdverseReactionPresenceStatement) - - Element: SubstanceCategory - Concept: TBD - Description: "Categorization of the risk substance as a food, drug, or environmental agent. For difficult-to-classify substances, one can leave this field empty or choose the most typical category." - Value: code - -// Element: VerificationStatus -// Concept: TBD -// Description: "Whether an assessment has been confirmed by testing or observation." -// Value: code - - Element: MostRecentOccurrenceTime - Concept: TBD - Description: "The time of the last or latest of a series of events." - Value: dateTime - - -//--------------- Instantiations ------------------- - -EntryElement: AdverseSensitivityToSubstanceStatement -Based on: ClinicalStatement -Concept: SCT#473010000 "Hypersensitivity condition (disorder)" // or SCT#420134006 "Propensity to adverse reactions (disorder)"? -Description: "A finding related to the presence or absence of an individual's risk or sensitivity to a substance or class of substances. A finding can be taken as tantamount to a representation of an allergic condition, allowing it to be tracked over time." -1..1 PersonOfRecord - SourceOfInformation value is type PatientOrPractitionerOrRelatedPerson - Signed.Attribution.EntityOrRole is type PatientOrPractitioner // to facilitate mapping to FHIR, which only allows Patient or Practitioner as recorder (note: CLI crashes if we write this as Signed.Value.EntityOrRole) - StatementTopic is type AdverseSensitivityTopic - StatementContext is type AdverseSensitivityPresenceContext -1..1 StatementTopic.AllergenIrritant // US Core requirement. See http://hl7.org/fhir/us/core/StructureDefinition-us-core-allergyintolerance.html - StatementTopic.TopicCode is SCT#473010000 "Hypersensitivity condition (disorder)" -// not needed AdverseSensitivityPresenceContext.AdverseReactionPresenceStatement.AdverseReactionTopic.CausalAttribution value is type CodeableConcept - - -EntryElement: NoAdverseSensitivityToSubstanceStatement -Based on: ClinicalStatement -Description: "Used to record that a particular substance or class of substances does not pose a known elevated risk to the subject." -1..1 PersonOfRecord - SourceOfInformation value is type PatientOrPractitionerOrRelatedPerson - Signed.Attribution.EntityOrRole is type PatientOrPractitioner - StatementTopic is type AdverseSensitivityTopic - AdverseSensitivityTopic.TopicCode is SCT#716186003 "No known allergy (situation)" - StatementContext is type AbsenceContext - StatementTopic.TopicCode from NoKnownAllergyVS - -EntryElement: NoKnownDrugAllergyStatement -Based on: NoAdverseSensitivityToSubstanceStatement - AdverseSensitivityTopic.TopicCode is SCT#409137002 "No known drug allergy (situation)" -0..0 AdverseSensitivityTopic.AllergenIrritant -0..0 AdverseSensitivityTopic.SubstanceCategory //is CAT#medication - -EntryElement: NoKnownFoodAllergyStatement -Based on: NoAdverseSensitivityToSubstanceStatement -Description: "Statement expressings no known allergies or hypersensitivity to any food substance." - AdverseSensitivityTopic.TopicCode is SCT#429625007 "No known food allergy (situation)" -0..0 AdverseSensitivityTopic.AllergenIrritant -0..0 AdverseSensitivityTopic.SubstanceCategory //is CAT#food - -EntryElement: NoKnownEvironmentalAllergyStatement -Based on: NoAdverseSensitivityToSubstanceStatement -Description: "Statement expressings no known allergies or hypersensitivity to environmental substances." - AdverseSensitivityTopic.TopicCode is SCT#428607008 "No known environmental allergy (situation)" -0..0 AdverseSensitivityTopic.AllergenIrritant -0..0 AdverseSensitivityTopic.SubstanceCategory //is CAT#environment - -EntryElement: NoKnownAllergyStatement -Based on: NoAdverseSensitivityToSubstanceStatement -Concept: MTH#C0262580 -Description: "Statement expressings no known allergies or hypersensitivity to any food, drug, biologic, or environmental substance." - AdverseSensitivityTopic.TopicCode is SCT#716186003 "No known allergy (situation)" -0..0 AdverseSensitivityTopic.AllergenIrritant -0..0 AdverseSensitivityTopic.SubstanceCategory \ No newline at end of file diff --git a/spec/cimi_allergy_map.txt b/spec/cimi_allergy_map.txt deleted file mode 100644 index 82e7ec92..00000000 --- a/spec/cimi_allergy_map.txt +++ /dev/null @@ -1,56 +0,0 @@ -Grammar: Map 5.1 -Namespace: cimi.allergy -Target: FHIR_STU_3 - - -AdverseSensitivityToSubstanceStatement maps to http://hl7.org/fhir/us/core/StructureDefinition/us-core-allergyintolerance: - PersonOfRecord maps to patient - SourceOfInformation.Value maps to asserter - Signed.Value.EntityOrRole maps to recorder - _Entry.CreationTime maps to assertedDate - AdverseSensitivityTopic.AllergenIrritant maps to code - AdverseSensitivityTopic.Type maps to type - AdverseSensitivityTopic.SubstanceCategory maps to category - AdverseSensitivityPresenceContext.VerificationStatus maps to verificationStatus - AdverseSensitivityPresenceContext.ClinicalStatus maps to clinicalStatus - AdverseSensitivityPresenceContext.Criticality maps to criticality - AdverseSensitivityPresenceContext.Onset maps to onset[x] - AdverseSensitivityPresenceContext.MostRecentOccurrenceTime maps to lastOccurrence - AdverseSensitivityPresenceContext.AdverseReactionPresenceStatement.AdverseReactionTopic.Manifestation.Severity maps to reaction.severity - AdverseSensitivityPresenceContext.AdverseReactionPresenceStatement.AdverseReactionTopic.CausalAttribution.RouteIntoBody maps to reaction.exposureRoute - AdverseSensitivityPresenceContext.AdverseReactionPresenceStatement.AdverseReactionTopic.CausalAttribution maps to reaction.substance - AdverseSensitivityPresenceContext.AdverseReactionPresenceStatement.AdverseReactionTopic.Manifestation.Value maps to reaction.manifestation - AdverseSensitivityPresenceContext.AdverseReactionPresenceStatement.AdverseReactionTopic.Details maps to reaction.description - AdverseSensitivityPresenceContext.AdverseReactionPresenceStatement.PresenceContext.Onset maps to reaction.onset - - -NoAdverseSensitivityToSubstanceStatement maps to http://hl7.org/fhir/us/core/StructureDefinition/us-core-allergyintolerance: - PersonOfRecord maps to patient - SourceOfInformation.Value maps to asserter - Signed.Value.EntityOrRole maps to recorder - _Entry.CreationTime maps to assertedDate - AdverseSensitivityTopic.TopicCode maps to code - constrain type to 0..0 - constrain category to 0..0 - constrain clinicalStatus to 0..0 - constrain criticality to 0..0 - constrain onset[x] to 0..0 - constrain lastOccurrence to 0..0 - constrain reaction to 0..0 - - -NoKnownAllergyStatement maps to http://hl7.org/fhir/us/core/StructureDefinition/us-core-allergyintolerance: -constrain clinicalStatus to 0..0 -constrain criticality to 0..0 - - -/* fix code to SCT#716186003 - -NoKnownDrugAllergyStatement: - fix code to SCT#409137002 - -NoKnownFoodAllergyStatement: - fix code to SCT#429625007 - -NoKnownEnvironmentalAllergyStatement: - fix code to SCT#428607008 */ diff --git a/spec/cimi_allergy_vs.txt b/spec/cimi_allergy_vs.txt deleted file mode 100644 index 6dd4451e..00000000 --- a/spec/cimi_allergy_vs.txt +++ /dev/null @@ -1,27 +0,0 @@ -Grammar: ValueSet 5.0 -Namespace: cimi.allergy - - -CodeSystem: SCT = http://snomed.info/sct -CodeSystem: RXN = http://www.nlm.nih.gov/research/umls/rxnorm -CodeSystem: AVS = http://hl7.org/fhir/allergy-verification-status - - -ValueSet: AllergyVerificationStatusVS -Description: "Whether the allergy has been verified or not. Intentionally a subset of the codes in FHIR, since refuted would be reflected by correcting the 'elevated risk' element, and records entered in error are not included in SHR." -AVS#confirmed "Confirmed" -AVS#unconfirmed "Unconfirmed" - -ValueSet: NoKnownAllergyVS -Description: "Codes that express no known allergies to food, environmtal agents, drugs, etc." -Includes codes descending from SCT#716186003 - -/* -ValueSet: FoodSubstanceVS -Includes codes descending from TBD#TBD - -ValueSet: DrugIngredientVS -Description: "Drug allergies involve ingredients or mixtures, not specific dose forms. The value set focuses on drug ingredients." -// Includes codes from RXN with TTY=IN // See https://www.nlm.nih.gov/research/umls/rxnorm/docs/2015/appendix5.html for explanation of RxNorm term types (TTY) -// Includes codes from RXN with TTY=MIN -*/ \ No newline at end of file diff --git a/spec/cimi_composition.txt b/spec/cimi_composition.txt deleted file mode 100644 index 1cd9c929..00000000 --- a/spec/cimi_composition.txt +++ /dev/null @@ -1,27 +0,0 @@ -Grammar: DataElement 5.0 -Namespace: cimi.composition -Description: "Documents, compositions, reports, and other structures involving multiple resources." -Uses: cimi.core, cimi.statement - -EntryElement: Composition -Based on: Independent -Description: "A composition represents a document such as a patient record, a knowledge artifact, or a catalog definition." -//1..1 Status from http://hl7.org/fhir/ValueSet/composition-status -//1..1 Type should be from http://hl7.org/fhir/ValueSet/doc-typecodes -//1..1 CreationTime -- from Entry -- maps to date -0..* Section - - Element: Section - Based on: Content - Description: "Represents a section containing entries in a composition." - //0..1 Title - 0..* ClinicalStatement - -// Element: EntryReference -// Value: ref(ClinicalStatment) - - - - - - diff --git a/spec/cimi_composition_map.txt b/spec/cimi_composition_map.txt deleted file mode 100644 index c2449339..00000000 --- a/spec/cimi_composition_map.txt +++ /dev/null @@ -1,14 +0,0 @@ -Grammar: Map 5.1 -Namespace: cimi.composition -Target: FHIR_STU_3 - -//Independent maps to Resource: - - - -Composition maps to Composition: - Section maps to section - Section.ClinicalStatement maps to section.entry (slice on = reference.resolve(); slice on type = profile; slice strategy = includes) - - - // (slice on = coding.code; slice strategy = includes) \ No newline at end of file diff --git a/spec/cimi_context.txt b/spec/cimi_context.txt deleted file mode 100644 index 84112103..00000000 --- a/spec/cimi_context.txt +++ /dev/null @@ -1,340 +0,0 @@ -Grammar: DataElement 5.0 -Namespace: cimi.context -Description: "The Context Package defines the high-level clinical statement context classes. Three types of contexts are currently defined in CIMI (1) Finding Contexts, (2) Action Contexts, and (3) Event Concepts. Finding contexts are used to specify whether a finding was observed to be present or absent. Action contexts are used to specify whether a clinical activity was performed, ordered, planned, or perhaps not performed. The Event context is experimental and has not yet been formally modeled." -Uses: shr.core, shr.base, cimi.core, cimi.element, cimi.topic, cimi.statement, cimi.entity, cimi.encounter, shr.entity - -CodeSystem: MTH = http://ncimeta.nci.nih.gov -// -Element: StatementContext -Based on: NonIndependent -Concept: TBD -Description: "Compositional and reusable grouping of clinical statement attributes that provides the context for the topic of a clinical statement. -The StatementContext class aligns with the SNOMED CT Situations with Explicit Context (SWEC) Concept Model. The StatementContext provides the expressivity required to specify that an act was performed or not performed or that a finding was asserted to be present or absent for the given subject of information. It also often holds provenance information relevant to the context of the clinical statement. It is important to note that by default the context applies to the conjunction of the attribute specified in the statement. For instance, if a clinical statement has a topic describing a rash on left arm and a context of 'absent', then the statement states that the subject of interest did not have a rash on the left arm but might have had one on the right arm." -1..1 ContextCode -0..1 Encounter // clinical statements are often associated with specific encounters - - Element: ContextCode - Concept: TBD - Description: "A code representing the ontological status of the statement, e.g., whether it exists, does not exist, is planned, etc. - Attribute aligns with the SNOMED CT Situation with Explicit Context (SWEC) Concept Model context attributes: 'Finding context (attribute)' (SCTID: 408729009) and 'Procedure context (attribute)' (SCTID: 408730004). The range allowed for this attribute shall be consistent with the SNOMED CT concept model specification for SWEC." - Value: CodeableConcept - -Element: ActionContext -Based on: StatementContext -Description: "The ontological status of the intervention, e.g., performed/not performed, requested/not requested." -0..* Reason - - Element: Reason - Concept: MTH#C0566251 - Description: "The justification for an action or non-action, conclusion, opinion, etc." - Value: string or CodeableConcept or ref(ClinicalStatement) - -Element: PerformedContext -Based on: ActionContext -Concept: TBD -Description: "ActionContext indicating actual performance or execution of a healthcare-related action, e.g., 3rd dose of Hepatitis B vaccine administered on Dec 4th 2012, appendectomy performed today." -1..1 OccurrenceTimeOrPeriod // when the action took place -0..* Participant -1..1 Status should be from http://hl7.org/fhir/ValueSet/event-status -0..1 Method -0..* RelatedRequest -//0..1 EnactsPlan -//0..1 FulfillsOrder -0..1 ref(Facility) -0..1 Outcome // e.g., AdverseEvent - - Element: Participant - Concept: MTH#C1550369 - Description: "An entity (usually a Practitioner, Patient, or Organization but potentially a device or other entity) that participates in a healthcare task or activity." - Value: ref(EntityOrRole) - 0..1 ParticipationType // role - 0..1 ParticipationPeriod - 0..1 OnBehalfOf - - Element: ParticipationType - Concept: MTH#C1553854 - Description: "The role played by the participant engaged in the action, for example, as the attending physician, surgical assistant, etc." - Value: CodeableConcept from FHIR/v3-ParticipationType - - Element: ParticipationPeriod - Concept: TBD - Description: "The point in time or span of time the participant is involved." - Value: TimePeriod - - Element: Method - Concept: TBD - Description: "The technique used to carry out an action, for example, the specific imaging technical or assessment vehicle." - Value: CodeableConcept // TODO: limit to a procedure code - - Element: RelatedRequest - Concept: TBD - Description: "The proposal, order, or plan that is partly or wholly fulfilled by the performance of this act." - Value: ref(ActionRequestedStatement) - - /* - Element: EnactsPlan - Concept: TBD - Description: "The plan that is partly or wholly enacted by the performance of this act." - Value: ref(ActionRequestedStatement) - - Element: FulfillsOrder - Concept: TBD - Description: "The order that is partly or wholly enacted by the performance of this act." - Value: ref() - */ - Element: Outcome - Concept: TBD - Description: "The result of performing an action or behavior, for example, an adverse reaction or new finding." - Value: CodeableConcept could be from http://hl7.org/fhir/ValueSet/procedure-outcome - 0..* ref(ClinicalStatement) - - -Element: NotPerformedContext -Based on: ActionContext -Concept: TBD -Description: "A record that a clinical act was not performed at a certain time or during a stated period of time, particularly when there might be an expectation of performing such an act, for example, if a vaccination is not given because of parental objection. Do not use this context if the act was initiated or started but aborted or cancelled." -0..1 RelatedRequest -1..1 NonOccurrenceTimeOrPeriod - - -Element: RequestedContext -Concept: MTH#C1705178 -Based on: ActionContext -Description: "An order for something to take place." -1..1 Status should be from http://hl7.org/fhir/ValueSet/request-status -1..1 RequestIntent -0..1 ExpectedPerformanceTime -0..1 ExpectedPerformerType -0..1 ExpectedPerformer -0..1 ExpectedMethod -0..1 PriorityRank should be from http://hl7.org/fhir/ValueSet/request-priority -0..1 PerformerInstructions -0..1 PatientInstructions -0..1 CommunicationMethod - - Element: RequestIntent - Concept: TBD - Description: "Indicates the level of authority/intentionality associated with the request and where the request fits into the workflow chain." - Value: code from http://hl7.org/fhir/ValueSet/request-intent - - Element: ExpectedPerformanceTime - Concept: TBD - Description: "When an action should be done. If the action is a series or recurs (e.g. daily blood sugar testing in the morning) then a Timing can be used to describe the periodicity." - Value: dateTime or date or TimePeriod or Timing - - Element: ExpectedPerformerType - Concept: TBD - Description: "What type of party should carry out the testing." - Value: CodeableConcept // what ValueSet?? - - Element: ExpectedPerformer - Concept: TBD - Description: "Who should carry out the tests. For example, the patient or caregiver." - Value: ref(Entity) or ref(Organization) - - Element: ExpectedMethod - Concept: TBD - Description: "The method that should be used to carry out the action." - Value: ref(Method) - - Element: PerformerInstructions - Concept: TBD - Description: "Information for the performer of the test, if needed." - Value: string - - Element: PatientInstructions - Concept: TBD - Description: "Information for the patient, such as, where to get the test, how to prepare for the test, etc." - Value: string - - Element: CommunicationMethod - Concept: TBD - Description: "This is the method the provider used to communicate. Examples include: Written, Telephoned, Verbal, Electronically Entered, Policy, Service Correction, Duplicate, etc. 'Code indicating the origin of the prescription.' - NCPDP Telecommunication (Field 419-DJ, Data Dictionary 201104). Possible values include: Written; Telephone; Electronic; Facsimile; Pharmacy; Not Known." - Value: CodeableConcept - -Element: RequestedAgainstContext -Concept: TBD -Based on: ActionContext -Description: "Represents a recommendation or order from a practitioner or clinical decision support system to NOT perform an act." - - -Element: FindingContext -Based on: StatementContext -Concept: SCT#410514004 -Description: "The base class for representing the ontological status of a finding, e.g., present, absent, goal, risk, expectation, etc. This class aligns with the SNOMED Situation with Explicit Context." - - -Element: AssertionContext -Based on: FindingContext -Concept: TBD -Description: "The parent class of contexts that can associate with AssertionTopic and its subclasses." - -Element: PresenceContext -Based on: AssertionContext -Concept: SCT#410515003 -Description: "PresenceContext indicates that the finding in question exists or is present to some level of certainty. -For example, if the finding involves a myocardial infarction, the presence context implies that cardiac arrest has (or may have) taken place. Note that the name Presence is used rather than Present to prevent confusion with the temporal meaning of present." - ContextCode from PresenceContextVS -1..1 VerificationStatus -0..1 Onset -0..1 Abatement -0..1 Certainty - - Element: VerificationStatus - Concept: TBD - Description: "Whether an assessment has been confirmed by testing or observation. - CIMI Alignment: This attribute corresponds to FindingContext.status, but has been defined to align with FHIR. In AllergyIntolerance, the type is code." - Value: CodeableConcept - - Element: Onset - Concept: LNC#85585-8 - Description: "The beginning or first appearance of a mental or physical disorder." - Value: dateTime or Age or TimePeriod or Range or string - - Element: Abatement - Concept: LNC#88878-4 - Description: "The end, remission or resolution." - Value: dateTime or Age or boolean or TimePeriod or Range or string - - Element: Certainty - Concept: TBD - Description: "The degree of confidence in a conclusion or assertion." - Value: CodeableConcept - -Element: ConditionPresenceContext -Based on: PresenceContext -Concept: TBD -Description: "The context for a condition that is known, suspected, or possibly present." -1..1 ClinicalStatus from http://hl7.org/fhir/ValueSet/condition-clinical -0..1 WhenClinicallyRecognized -0..1 Preexisting -0..1 Severity from http://hl7.org/fhir/ValueSet/condition-severity -0..1 Criticality from http://hl7.org/fhir/ValueSet/allergy-intolerance-criticality -0..1 Stage - - Element: ClinicalStatus - Concept: TBD - Description: "A flag indicating whether the condition is active or inactive, recurring, in remission, or resolved (as of the last update of the Condition)." - Value: code - - Element: WhenClinicallyRecognized - Concept: TBD - Description: "The time at which a condition or condition was first identified in a healthcare context." - Value: date - - Element: Preexisting - Concept: LNC#89251-3 "Condition present on admission" - Description: "If the problem or condition existed before the current episode of care." - Value: CodeableConcept from YesNoUnknownVS - - Element: Severity - Concept: MTH#C0392364 - Description: "Degree of harshness or extent of a symptom, disorder, or condition." - Value: CodeableConcept - - Element: Criticality - Concept: MTH#C3858539 "Criticality" - Description: "The potential clinical harm associated with a condition. When the worst case result is assessed to have a life-threatening or organ system threatening potential, it is considered to be of high criticality." - Value: code - - Element: Stage - Concept: MTH#C0699749 - Description: "The relative advancement in the course of a disease. The value is the summary stage or stage group. StageDetail optionally contains the full staging information." - Value: CodeableConcept - 0..1 StageDetail - - Element: StageDetail - Concept: TBD - Description: "The full staging information" - Value: ref(Observation) - - Element: RecordedContext - Based on: FindingContext - Concept: TBD - Description: "Context for recording a finding, used to indicate an evaluation has been made." - ContextCode is SCT#424975005 "Record Entity" - 0..1 Interpretation - 1..1 FindingStatus - 0..1 RelevantTime // ClinicallyRelevantTime isn't a good name when it comes to employment and other life history events - - Element: Interpretation - Concept: MTH#C0420833 - Description: "A clinical interpretation of a finding (applies to both assertions and observation)." - Value: CodeableConcept from http://hl7.org/fhir/ValueSet/observation-interpretation if covered - - Element: FindingStatus - Concept: TBD - Description: "Indicates whether the finding is preliminary, amended, final, etc." - Value: code from http://hl7.org/fhir/ValueSet/observation-status - - Element: RelevantTime - Concept: TBD - Description: "The time or time period that the finding addresses. - The clinically relevant time is not necessarily when the information is gathered or when a test is carried out, but for example, when a specimen was collected, or the time period referred to by the question. Use a TimePeriod for a measurement or specimen collection continued over a significant period of time (e.g. 24 hour Urine Sodium)." - Value: dateTime or TimePeriod - - Element: ObservationContext - Based on: RecordedContext - Concept: TBD - Description: "Context for recording an evaluation result, used to indicate an evaluation has been made." - 0..1 ResultValue - 0..1 ExceptionValue from ExceptionValueVS if covered - 0..1 DeltaFlag - 0..1 Issued - 0..* Observer - - Element: ResultValue - Concept: TBD - Description: "The finding itself, such as the blood pressure value recorded." - Value: (Quantity or CodeableConcept or string or boolean or Range or Ratio or time or dateTime or TimePeriod) - - Element: ExceptionValue - Concept: TBD - Description: "Reason that a value associated with a test or other finding is missing." - Value: CodeableConcept - - Element: DeltaFlag - Concept: MTH#C1705241 - Description: "Indicator of significant change (delta) from the last or previous measurement." - Value: CodeableConcept from DeltaFlagVS - - Element: Issued - Description: "The date and time this observation was made available to providers, typically after the results have been reviewed and verified." - Value: instant - - Element: Observer - Description: "The person or organization who observed or informed the reporter about the characteristic, potentially the clinician, the patient, or a related person." - Value: ref(Practitioner) or ref(Organization) or ref(Patient) or ref(RelatedPerson) - - Element: AbsenceContext - Based on: AssertionContext - Concept: TBD - Description: "Indicates the finding in question is either known absent (ruled out), not suspected, or unknown." - ContextCode from AbsenceContextVS - - Element: AtRiskContext - Based on: FindingContext - Concept: SCT#410519009 - Description: "At risk indicates the finding should be interpreted as a future possibility or expectation." - ContextCode from AtRiskContextVS - - Element: ExpectationContext - Based on: FindingContext - Concept: SCT#410517006 - Description: "A context indicating the finding is an expectation, prognosis, or likely outcome." - ContextCode from ExpectationContextVS - - Element: GoalContext - Based on: FindingContext - Concept: SCT#410518001 - Description: "A hypothetical or future finding that represents an objective or goal." - ContextCode from GoalContextVS - -/* TBD -Element: DefinitionalContext -Based on: StatementContext -Concept: MTH#C1704788 -Description: "An indicator that the item is a description of a thing, not a thing that actually exists. For example, a group of people between ages 30 and 40 with Type II diabetes can be defined, without existing as a set of particular people." -Value: boolean -*/ - \ No newline at end of file diff --git a/spec/cimi_context_vs.txt b/spec/cimi_context_vs.txt deleted file mode 100644 index a1f17440..00000000 --- a/spec/cimi_context_vs.txt +++ /dev/null @@ -1,86 +0,0 @@ -Grammar: ValueSet 5.0 -Namespace: cimi.context - -CodeSystem: SCT = http://snomed.info/sct -CodeSystem: MTH = http://ncimeta.nci.nih.gov - -ValueSet: ExceptionValueVS -Description: "Reasons that a value associated with a test or other finding is missing. Includes all codes from http://hl7.org/fhir/ValueSet/data-absent-reason version 3.3.0 and additional codes covering other missing value circumstances." -#unknown "Unknown: The value is not known." -#asked-unknown "Asked But Unknown: The source human does not know the value." -#temp-unknown "Temporarily Unknown: There is reason to expect (from the workflow) that the value may become known." -#not-asked "Not Asked: The workflow didn't lead to this value being known." -#asked-declined "Asked But Declined: The source was asked but declined to answer." -#masked "Masked: The information is not available due to security, privacy or related reasons." -#not-applicable "Not Applicable: There is no proper value for this element (e.g. last menstrual period for a male)" -#unsupported "Unsupported: The source system wasn't capable of supporting this element." -#as-text "As Text: The content of the data is represented in the resource narrative." -#error "Error: Some system or workflow process error means that the information is not available." -#not-a-number "Not a Number (NaN): The numeric value is undefined or unrepresentable due to a floating point processing error." -#negative-infinity "Negative Infinity (NINF): The numeric value is excessively low and unrepresentable due to a floating point processing error." -#positive-infinity "Positive Infinity (PINF): The numeric value is excessively high and unrepresentable due to a floating point processing error." -#not-performed "Not Performed: The value is not available because the observation procedure (test, etc.) was not performed." -#not-permitted "Not Permitted: The value is not permitted in this context (e.g. due to profiles, or the base data types)" -// The following values are extensions to the FHIR values, applicable to lab tests -#indeterminate-value "The value could not be determined or established with accuracy or certainty." -#no-further-explanation "The reason the information is not present is not known." -#null-answer "The answer is appears missing because the correct answer is null or empty; e.g., a question that asks for a list of the names of siblings applied to an only child." -#specimen-unavailable "Missing due to a problem collecting, identifying, or locating the specimen, including patient refusal or unable to provide specimen" -#specimen-inadequate "Missing due to a problem with the specimen, e.g. inadequate specimen, contamination, clotting, improper tube type, improper storage, too small, etc." -#instrument-malfunction "Missing due to instrument malfunction." - - -ValueSet: PresenceContextVS -Description: "A code describing whether the finding in question is present, possible, suspected, etc." -//SCT#36692007 "Known" -//SCT#410605003 "Confirmed present" -//SCT#410591008 "Definitely present" -SCT#410515003 "Known present" -SCT#410590009 "Known possible" -SCT#410592001 "Probably present" -SCT#415684004 "Suspected" -SCT#410593006 "Probably not present" -SCT#261665006 "Unknown" - -ValueSet: AbsenceContextVS -Description: "A code describing whether the finding is question is absent, unknown, or not suspected." -SCT#410516002 "Known absent" -SCT#410594000 "Definitely not present" -SCT#410593006 "Probably not present" -SCT#428263003 "NOT suspected" -// No known?? - -ValueSet: AtRiskContextVS -Description: "A code describing the sense in which the subject has risk of a hypothetical (future) finding. At present, this value set contains only one code, but it is presented as a value set to allow for more nuanced meanings in the future." -SCT#410519009 "At risk" - -ValueSet: ExpectationContextVS -Description: "A code describing the sense in which a finding is expected." -SCT#410517006 "Expected" -SCT#410596003 "Likely outcome" -SCT#410595004 "Prognosis" -SCT#71033007 "Impending" - -ValueSet: GoalContextVS -Description: "A code describing the sense in which a finding is a goal or objective." -SCT#703039001 "Health objective" -SCT#410518001 "Goal" - - -ValueSet: DeltaFlagVS -Concept: MTH#C1705241 -Description: "Indicators for degree of change (delta) from the last or previous measurement." -Includes codes descending from SCT#263703002 "Changed status (qualifier value)" -// Also see LOINC #89253-9 Trend ... has values improved, deteriorated, stablized, resolved - -/* -ValueSet: DeltaFlagVS -Description: "Change patterns and trends, including resolved." -Includes codes descending from SCT#385634002 "Change patterns (qualifier value)" -//SCT#58158008 "Stable (qualifier value)" -//SCT#385633008 "Improving (qualifier value)" -//SCT#230993007 "Worsening (qualifier value)" -//SCT#260369004 "Increasing (qualifier value)" -//SCT#260371004 "Decreasing (qualifier value)" -SCT#723506003 "Resolved (qualifier value)" -*/ \ No newline at end of file diff --git a/spec/cimi_core.txt b/spec/cimi_core.txt deleted file mode 100644 index 4ef327b3..00000000 --- a/spec/cimi_core.txt +++ /dev/null @@ -1,91 +0,0 @@ -Grammar: DataElement 5.0 -Namespace: cimi.core -Description: "The namespace containing definitions for basic classes in CIMI." -Uses: shr.core, cimi.element, cimi.entity - -CodeSystem: MTH = http://ncimeta.nci.nih.gov - -Element: Locatable -Description: "Abstract top level class in the CIMI hierarchy. The Locatable class reflects CIMI's implementation using Archetype Description Language (ADL). Its attributes (archetype_node_id, name, and archetype_details) are necessary to serialize CIMI definitions in ADL, but have no clinical relevance. To avoid complicating the profiles with irrelevant extensions, the attributes of Locatable have been omitted." - -Element: Independent -Based on: Locatable -Description: "Base class for classes in CIMI that include enough context to stand alone. Analogous to FHIR's DomainResource." - -Element: NonIndependent // aka data element -Based on: Locatable -Description: "Parent for classes in CIMI that do not have enough context to stand alone. These reusable building blocks/data elements can be used to create classes by composition." - -Element: DataType -Based on: NonIndependent -Description: "Serves as a common ancestor of all CIMI types which represent the core granularity of the model." - -Element: Content -Based on: Independent -Description: "Abstract ancestor of all concrete content types. A unit of content that makes up a composition - e.g., a clinical statement in a patient record, a simple or composite action is a knowledge document, a catalog entry in a catalog." - -Element: InformationEntry -Based on: Content -Concept: MTH#C1705654 -Description: "An entry in a patient record or in a report, generally used for the documentation of clinical information about a subject of information such as a patient or a relative of the patient, asserted by a particular source, recorded, and potentially verified." -0..1 PersonOfRecord -0..1 SubjectIfNotPersonOfRecord -0..1 SourceOfInformation // should this be 0..*? -//0..* Annotation -//0..1 RecordStatus -0..1 Recorded -0..1 Signed // Author -//0..* Cosigned -//0..* Verified - - Element: PersonOfRecord - Concept: TBD - Description: "The person this entry belongs to." - Value: ref(Patient) - - Element: SubjectIfNotPersonOfRecord - Concept: MTH#C0449416 - Description: "The person or entity that provided the information in the entry, e.g. the subject (patient), medical professional, family member, device or software program, as distinct from who recorded the entry." - Value: 0..1 ref(EntityOrRole) //string or ref(Patient) or ref(Group) or ref(Device) or ref(RelatedPerson) or ref(Organization) - 0..1 RelationshipToPersonOfRecord - - Element: SourceOfInformation - Concept: MTH#C0449416 - Description: "The person or entity that provided the information in the entry, e.g. the subject (patient), medical professional, family member, device or software program, as distinct from who recorded the entry." - Value: ref(EntityOrRole) //string or ref(Patient) or ref(Group) or ref(Device) or ref(RelatedPerson) or ref(Organization) - 0..1 RelationshipToPersonOfRecord - - Element: RelationshipToPersonOfRecord - Concept: MTH#C0015608 - Description: "The relationship of the SubjectIfNotPersonOfRecord to the subject of record." - Value: CodeableConcept from http://hl7.org/fhir/ValueSet/relatedperson-relationshiptype if covered - - Element: RecordStatus - Description: "Concept indicating the state of this record, e.g., 'entered in error'." - Value: CodeableConcept - - Element: Recorded - Description: "The person who entered the order on behalf of another individual for example in the case of a verbal or a telephone order." - Value: Attribution - - Element: Signed - Description: "Provenance information specific to the signing of the clinical statement." - Value: Attribution - - Element: Cosigned - Description: "Provenance information specific to the cosigning of the clinical statement." - Value: Attribution - - Element: Verified - Description: "Provenance information specific to the verification process associated with this statement (e.g., verifier, when verified, etc.)" - Value: Attribution - - Element: Attribution - Description: "Information ascribing the record to a particular contributor or responsible person." - 1..1 EntityOrRole - 0..1 RecordedOn - 0..1 Signature - - Element: RecordedOn - Description: "The time of the attribution action." - Value: instant diff --git a/spec/cimi_element.txt b/spec/cimi_element.txt deleted file mode 100644 index f764efce..00000000 --- a/spec/cimi_element.txt +++ /dev/null @@ -1,153 +0,0 @@ -Grammar: DataElement 5.0 -Namespace: cimi.element -Description: "The Element Package defines reusable data elements that are used across multiple packages." -Uses: shr.core, shr.base, cimi.core, cimi.entity - - -Element: Annotation -Description: "An added or follow-up note, often after the fact, that contains metadata about who made the statement and when." -Value: string // change to language-text -1..1 Author -1..1 OccurrenceTime - - Element: Author - Concept: TBD - Description: "The person or organization who created the entry and is responsible for (and may certify) the content." - //Value: string or ref(EntityOrRole) - Value: string or ref(Patient) or ref(Group) or ref(Device) or ref(RelatedPerson) or ref(Organization) - - -Element: Signature -Description: "A digital Signature - XML DigSig, JWT, Graphical image of signature, etc." -1..* SignatureType from http://hl7.org/fhir/ValueSet/signature-type if covered -1..1 CreationTime -1..1 Signatory -0..1 OnBehalfOf -0..1 ContentType -0..1 BinaryData - - Element: SignatureType - Concept: MTH#C0332307 - Description: "Type of signature" - Value: Coding - - Element: Signatory - Concept: TBD - Description: "The party signing." - Value: uri or ref(Entity) - - Element: OnBehalfOf - Concept: TBD - Description: "The party represented by the actual participant." - Value: uri or ref(Organization) - - -Element: RouteIntoBody -Concept: MTH#C0013153 -Description: "The way a substance enters an organism after contact, particularly, the route of drug administration." -Value: CodeableConcept from http://hl7.org/fhir/ValueSet/route-codes - -Element: AnatomicalLocation -Concept: LNC#72369-2 // Body site identification panel -Description: "A location or structure in the body, including tissues, regions, cavities, and spaces; for example, right elbow, or left ventricle of the heart." -Value: CodeableConcept from AnatomicalLocationVS -0..1 Laterality -0..1 AnatomicalDirection - - - Element: Laterality - Concept: MTH#C0925205 "Anatomical laterality" - Description: "Anatomical location or specimen further detailing the side(s) of interest." - Value: CodeableConcept from http://hl7.org/fhir/ValueSet/bodysite-laterality - - Element: AnatomicalDirection - Concept: NCI#C99074 - Description: "Anatomical location or specimen further detailing directionality." - Value: CodeableConcept from AnatomicalDirectionVS - -Element: Identifier -Concept: MTH#C0600091 -Description: "A unique string that identifies a specific person or thing." -Value: string // or id or code or CodeableConcept? -0..1 Purpose from http://hl7.org/fhir/ValueSet/identifier-use -0..1 Type from http://hl7.org/fhir/ValueSet/identifier-type if covered -0..1 CodeSystem -0..1 EffectiveTimePeriod -0..1 Issuer - - - Element: Issuer - Concept: TBD - Description: "An organization who issues a qualification, identifier, or license." - Value: ref(Organization) - -Element: PartOf -Description: "The larger entity that this is a portion of. For example, an organization might be part of a larger organization, or an encounter with a hospitalist might be part of a larger hospitalization encounter." -Value: ref(Independent) - - -Element: Status -Concept: MTH#C0449438 -Description: "The current standing or state." -Value: code or Coding or CodeableConcept - -Element: TermMapping -Description: "Represents an alternative (mapped) Concept associated with a source concept (i.e., CodedText.concept or the textual value of the CodedText when no equivalent concept has been defined), and the relative match of the mapped Concept with respect to the source Concept. Mappings may be used to add classification terms (e.g. adding ICD classifiers to SNOMED descriptive terms), for computational convenience, or to provide equivalents in other terminologies (e.g. across nursing vocabularies)." -Value: Coding -1..1 Match -0..1 Purpose - - Element: Match - Description: "The relative match of the mapped concept to the original (target) concept. Examples include broader (i.e., the mapped term is more general than the original), equivalent, narrower (e.g. mapped concept is 'atypical diabetes mellitus' and the original term is 'diabetes mellitus'), or unknown." - Value: Coding - -Element: Name -Description: "Abstract supertype for the name of an entity." -0..1 NameAsText -0..* Purpose -0..1 EffectiveTimePeriod - - Element: NameAsText - Description: "The name as plain unstructured or semi-structured text." - Value: string // TODO: should be PlainText - -Element: PersonName -Based on: Name -Concept: MTH#C1547383 -Description: "A name used by a human being, written as it would be typically expressed. May include a breakdown of the various elements of the name (family name, given name, etc.)." -0..1 PreferredFlag -0..* Prefix -0..* GivenName -0..* MiddleName -0..* FamilyName -0..* Suffix -0..1 Purpose from http://hl7.org/fhir/ValueSet/name-use - - Element: PreferredFlag - Description: "Code indicating the preference associated with the use of this name." - Value: CodeableConcept - - Element: Prefix - Concept: MTH#C3476361 - Description: "Contains a set of honorific terms that typically appear before a person's name, for example Mr., Mrs., Dr., etc." - Value: string // punting on value set - there is little value in standardizing this element - - Element: GivenName - Concept: LNC#45392-8, SCT#408677003 - Description: "The person's given name - e.g., John" - Value: string - - Element: MiddleName - Concept: LNC#45392-8, SCT#408677003 - Description: "The person's middle name." - Value: string - - Element: FamilyName - Concept: LNC#45394-4 - Description: "The portion of a person's name that reflects the genealogy of the person. In western cultures, this is the 'last' name. In eastern cultures, the family name appears before the person's given name(s). In some cultures (e.g. Eritrea) the family name of a son is the first name of his father. (Source: HL7 V3)." - Value: string - - Element: Suffix - Concept: LNC#45395-1, SCT#715196001 - Description: "Part of the name that is acquired as a title due to academic, legal, employment or nobility status, etc. and that appears at the end of the name." - Value: string diff --git a/spec/cimi_element_map.txt b/spec/cimi_element_map.txt deleted file mode 100644 index 938b1136..00000000 --- a/spec/cimi_element_map.txt +++ /dev/null @@ -1,30 +0,0 @@ -Grammar: Map 5.1 -Namespace: cimi.element -Target: FHIR_STU_3 - - -AnatomicalLocation maps to BodySite: - Value maps to code - Laterality maps to qualifier (slice on = coding.code) - AnatomicalDirection maps to qualifier - -Annotation maps to Annotation: - Value maps to text - Author maps to author[x] - OccurrenceTime maps to time - -Identifier maps to Identifier: - Value maps to value - Purpose maps to use - Type maps to type - CodeSystem maps to system - EffectiveTimePeriod maps to period - Issuer maps to assigner - -Signature maps to Signature: - SignatureType maps to type - CreationTime maps to when - Signatory maps to who[x] - OnBehalfOf maps to onBehalfOf[x] - ContentType maps to contentType - BinaryData maps to blob \ No newline at end of file diff --git a/spec/cimi_element_vs.txt b/spec/cimi_element_vs.txt deleted file mode 100644 index bf9c7379..00000000 --- a/spec/cimi_element_vs.txt +++ /dev/null @@ -1,46 +0,0 @@ -Grammar: ValueSet 5.0 -Namespace: cimi.element - -CodeSystem: MTH = http://ncimeta.nci.nih.gov -CodeSystem: NCI = https://evs.nci.nih.gov/ftp1/CDISC/SDTM/ -CodeSystem: SCT = http://snomed.info/sct - -ValueSet: AnatomicalLocationVS -Concept: MTH#C1545955 -Description: "Codes that describe normal and pathologic anatomic systems, regions, cavities, and spaces." -Includes codes descending from SCT#123037004 "Body Structure" - -ValueSet: AnatomicalDirectionVS -Concept: NCI#C99074 -Description: "Anatomical location or specimen further detailing directionality. Codes are from NCI" -#C25231 "ANTERIOR Denoting the front portion of the body or a structure." -#C25423 "APICAL Relating to or located at the apex." -#C90067 "BASAL Relating to or located at the lowest portion of a structure." -#C73851 "CAUDAL Toward the tail in a body." -#C25445 "CENTRAL A point or area that is approximately central within some larger region or structure." -#C37936 "CRANIAL Toward the head in a body." -#C25240 "DEEP Extending relatively far inward." -#C25237 "DISTAL Situated farthest from a point of reference." -#C45874 "DORSAL Pertaining to the back or upper surface of the body." -#C90376 "DORSOLATERAL Toward the back and side of a body." -#C90386 "FORE Of or involving the front of a main body." -#C90393 "HIND Of or involving the back of a main body." -#C25353 "INFERIOR Pertaining to a point below a given reference point." -#C37980 "INNER Inside or closer to the inside of the body or object." -#C73705 "INTERMEDIATE Located between two points or extremes." -#C25309 "LOWER The bottom one of two." -#C25232 "MEDIAL Toward the middle or in a limb toward the median plane." -#C81170 "MIDLINE A medial line, especially the medial line or medial plane of the body (or some part of the body)." -#C27958 "NASAL Of, or related to, or in the direction of the nose." -#C38166 "OUTER Being on or toward the outside of the body or object." -#C25233 "PERIPHERAL On or near an edge or constituting an outer boundary;the outer area." -#C25622 "POSTERIOR Denoting the back portion of the body or a structure." -#C94393 "ROSTRAL Toward the muzzle in the head." -#C25239 "SUPERFICIAL Of or pertaining to the exterior surface." -#C25235 "SUPERIOR Pertaining to a point above a given reference point." -#C25245 "SURFACE The extended two-dimensional outer layer or area of a three-dimensional object." -#C117754 "TEMPORAL Of, or related to, anatomic sites that are located in the cranium, brain, and eye." -#C90069 "TIP The pointed end of a structure." -#C25355 "UPPER The top one of two." -#C45875 "VENTRAL Pertaining to the front or lower surface of the body." -#C98798 "VENTROLATERAL Of or pertaining to the front and side of a main body." diff --git a/spec/cimi_encounter.txt b/spec/cimi_encounter.txt deleted file mode 100644 index 935784e4..00000000 --- a/spec/cimi_encounter.txt +++ /dev/null @@ -1,183 +0,0 @@ -Grammar: DataElement 5.0 -Namespace: cimi.encounter -Description: "The Encounter domain contains definitions that capture interactions between the person of record and healthcare providers, including inpatient, ambulatory care, and telecare." -Uses: shr.core, shr.base, cimi.core, cimi.element, cimi.context, cimi.topic, cimi.statement, cimi.entity - - -Element: Encounter -Based on: InformationEntry -Concept: TBD -Description: "A description of an interaction between a patient and healthcare provider(s) for the purpose of providing healthcare service(s) or assessing the health status of a patient." -0..1 EncounterClass -0..* EncounterType -0..1 TimePeriod -1..1 Status from http://hl7.org/fhir/ValueSet/encounter-status -0..1 PartOf value is type ref(Encounter) -0..* Diagnosis -// SHR Extension -0..1 ref(ClinicalNote) - - Element: PatientOrGroup - Based on: SubjectIfNotPersonOfRecord - Description: "A subject of information that is constrained to be either a patient or a group." - Value: ref(Patient) or ref(Group) - - Element: EncounterClass - Description: "Concepts representing classification of patient encounter such as ambulatory (outpatient), inpatient, emergency, home health or others due to local variations." - Value: CodeableConcept - - Element: EncounterType - Description: "Specific type of encounter (e.g. e-mail consultation, surgical day-care, skilled nursing, rehabilitation)." - Value: CodeableConcept from http://hl7.org/fhir/ValueSet/v3-ActEncounterCode if covered - - Element: Diagnosis - Description: "A diagnosis, which is a disease or injury determined to be present through evaluation of patient history, examination, and/or review of laboratory data." - Value: code - 0..1 PriorityRank - 0..1 Type should be from http://hl7.org/fhir/ValueSet/diagnosis-role - - -Element: DetailedEncounter -Based on: Encounter -Concept: TBD -Description: "A detailed description of an interaction between a patient and healthcare provider(s) for the purpose of providing healthcare service(s) or assessing the health status of a patient." -/* -0..1 AccountId -0..1 AccountStatus -0..* AlternateVisitId -0..1 AmbulatoryStatus -0..1 ChargePriceIndicator -0..1 ChiefComplaint -0..1 EncounterBillingType -0..1 FinancialClass -0..1 HospitalService -0..1 IsEmploymentRelated -0..1 ModeOfArrival -0..1 PatientType -0..1 PreviousServiceDate -0..1 PublicityCode -0..* ReasonForVisit should be from http://hl7.org/fhir/ValueSet/encounter-reason -0..1 ReferralSource -0..1 ServicingFacility -0..* SpecialArrangements -0..* SpecialCourtesy -0..* TriageNotes -0..1 AssignedPatientLocation -0..1 PendingLocation -0..1 ServiceDeliveryLocation -0..1 TemporaryLocation -0..* PriorTemporaryLocation -0..1 Origin -0..1 ServiceProvider -0..1 ConfidentialityCode -0..1 Duration - -// SHR Extensions -0..1 TreatmentCooperation -0..1 PaymentSource -0..1 TBD "HealthConcern" -0..* TBD "PertinentFindings" -0..* TBD "Diagnosis" -0..1 TBD "FullClinicalNote" -1..1 TBD "ClinicalSummary" -1..* TBD "TreatmentServiceRendered" -0..1 TBD "CompletionStatus" - - Element: ReferralDate - Concept: MTH#C2735614 - Description: "The date when the provider received a referral for service. A referral includes an oral, written, faxed or electronic request for services made by the client or on the client's behalf." - Value: dateTime - - Element: ReferralSourceType - Concept: TBD - Description: "The type of person or entity that instigated the encounter." - Value: CodeableConcept from ReferralSourceTypeVS - - Element: TreatmentCooperation - Concept: TBD - Description: "Whether the patient is undergoing treatment voluntarily, or under a legal order." - Value: CodeableConcept from TreatmentCooperationVS - - Element: TreatmentServiceRendered - Concept: TBD - Description: "" - Value: CodeableConcept from TreatmentServiceVS - 1..1 TBD "UnitsOfService" - - Element: PaymentSource - Concept: MTH#C0680269 - Description: "The source of payment for the current encounter." - Value: TBD "PaymentSourceVS" - - Element: EpisodeOfCareCompletion - Concept: TBD - Description: "Denotes how and why an episode of care ended." - Value: CodeableConcept from EpisodeOfCareCompletionVS -*/ - - -/* - -Element: EncounterRequestedContext -Based on: RequestedContext -Description: "Context for encounter requests." - Status from http://hl7.org/fhir/ValueSet/request-status - PriorityRank from http://hl7.org/fhir/ValueSet/request-priority - -Element: EncounterPerformedContext -Based on: PerformedContext -Description: "Context for encounters performed." - Status from http://hl7.org/fhir/ValueSet/encounter-status - OccurrenceTimeOrPeriod is type OccurrencePeriod - Reason should be from http://hl7.org/fhir/ValueSet/encounter-reason -// RelatedRequest value is type ref(EncounterRequested) -// RelatedPlan is type EncounterPlanned - Participant.Entity is type PractitionerOrRelatedPerson -0..* ServiceGiven -0..1 ServiceProvider - - - Element: ServiceProvider - Concept: TBD - Description: "The organization that provided the services rendered during this encounter." - Value: ref(Organization) - - Element: ServiceGiven - Concept: TBD - Description: "Indicates a medical service provided." - Value: CodeableConcept // TODO: Link to ICD-10 value set -*/ - - - -/* -EntryElement: Hospitalization -Based on: - DateTime TimePeriod - Location Reference - Organization Reference - AdmitSource Enum? - Transferred Boolean - Attending Physician-Admission Practitioner - Admitting Condition/Complaint/Diagnosis (-es) Reference(s) - Attending Physician-Discharge Practitioner - Discharge Diagnosis (-es) Reference(s) - Discharge Services Multi Enum - Discharge or Transfer Destination ? - Discharge Summary Document - -EntryElement: EmergencyEncounter -Based on: DetailedEncounter - DateTime TimePeriod - Location Reference - Organization Reference - AdmitSource - Transferred Boolean - Attending Physician-Admission Provider - Admitting Finding/Complaint/Diagnosis (-es) Reference(s) - Attending Physician-Discharge Provider - Discharge Diagnosis (-es) Reference(s) - Discharge Services Multi Enum - Discharge or Transfer Destination ? - Discharge Summary Document - */ \ No newline at end of file diff --git a/spec/cimi_encounter_map.txt b/spec/cimi_encounter_map.txt deleted file mode 100644 index 50abad33..00000000 --- a/spec/cimi_encounter_map.txt +++ /dev/null @@ -1,43 +0,0 @@ -Grammar: Map 5.1 -Namespace: cimi.encounter -Target: FHIR_STU_3 - - -Encounter maps to Encounter: - PersonOfRecord maps to subject - EncounterType maps to type -// ServiceProvider maps to serviceProvider - Status maps to status - TimePeriod maps to period -// Participant maps to participant -// Participant.Entity maps to participant.individual -// constrain participant.type to 0..1 -// Participant.ParticipationType maps to participant.type -// Participant.ParticipationPeriod maps to participant.period -// PerformedContext.RelatedRequest.Value maps to incomingReferral -// constrain location to 0..1 -// Facility maps to location.location -// Reason maps to reason -// what maps to apppointment? RelatedPromise? -// TBD "HealthConcern" maps to indication - -/* -EncounterRequested maps to ReferralRequest: - Signed.EntityOrRole maps to requester.agent - PersonOfRecord maps to subject - ReferralDate maps to authoredOn -//ReferralSourceType - TopicCode maps to type -//TreatmentCooperation -//PaymentSource - EncounterRequestedContext.Status maps to status -//RequestedContext.RequestIntent - EncounterRequestedContext.ExpectedPerformanceTime maps to occurrence[x] - EncounterRequestedContext.ExpectedPerformerType maps to specialty -//RequestedContext.ExpectedPerformer -//RequestedContext.ExpectedMethod - EncounterRequestedContext.PriorityRank maps to priority -//RequestedContext.PerformerInstructions -//RequestedContext.PatientInstructions -//RequestedContext.CommunicationMethod -*/ \ No newline at end of file diff --git a/spec/cimi_entity_map.txt b/spec/cimi_entity_map.txt deleted file mode 100644 index 454135b4..00000000 --- a/spec/cimi_entity_map.txt +++ /dev/null @@ -1,140 +0,0 @@ -Grammar: Map 5.1 -Namespace: cimi.entity -Target: FHIR_STU_3 - - -Patient maps to http://hl7.org/fhir/us/core/StructureDefinition/us-core-patient: - Person.ActiveFlag maps to active - Person.HumanName maps to name - Person.AdministrativeGender maps to gender - Person.Headshot maps to photo - Person.Address maps to address - Person.ContactPoint maps to telecom - Person.LanguageUsed maps to communication - Person.DateOfBirth maps to birthDate - PlaceOfBirth maps to http://hl7.org/fhir/StructureDefinition/birthPlace - MultipleBirth maps to multipleBirth[x].boolean - MultipleBirth.MultipleBirthOrder maps to multipleBirth[x].integer - BirthSex maps to http://hl7.org/fhir/us/core/StructureDefinition/us-core-birthsex - Race maps to http://hl7.org/fhir/us/core/StructureDefinition/us-core-race - Ethnicity maps to http://hl7.org/fhir/us/core/StructureDefinition/us-core-ethnicity - MaritalStatus maps to maritalStatus - MothersMaidenName maps to http://hl7.org/fhir/StructureDefinition/patient-mothersMaidenName - MedicalInterpreterNeeded maps to http://hl7.org/fhir/StructureDefinition/patient-interpreterRequired - Deceased maps to deceased[x].boolean - Deceased.DateOfDeath maps to deceased[x].dateTime - -Practitioner maps to http://hl7.org/fhir/us/core/StructureDefinition/us-core-practitioner: - Person.ActiveFlag maps to active - Person.HumanName maps to name - Person.AdministrativeGender maps to gender - Person.Headshot maps to photo - Person.Address maps to address - Person.ContactPoint maps to telecom - Person.LanguageUsed maps to communication - NationalProviderIdentifier maps to identifier - Qualification maps to qualification - Qualification.Type maps to qualification.code - Qualification.EffectiveTimePeriod maps to qualification.period - Qualification.Issuer maps to qualification.issuer - -RelatedPerson maps to RelatedPerson: - Person.ActiveFlag maps to active - Person.HumanName maps to name - Person.DateOfBirth maps to birthDate - Person.AdministrativeGender maps to gender - Person.Address maps to address - Person.Headshot maps to photo - Person.ContactPoint maps to telecom - RelationshipToPersonOfRecord maps to relationship - EffectiveTimePeriod maps to period - -Organization maps to http://hl7.org/fhir/us/core/StructureDefinition/us-core-organization: - OrganizationName maps to name - OrganizationAlias maps to alias // I wish FHIR allowed multiple names, but it doesn't - Type maps to type - OrganizationIdentifier maps to identifier - Address maps to address - ContactPoint maps to telecom - ActiveFlag maps to active - PartOf maps to partOf - ContactPoint maps to contact - -Group maps to Group: - ActiveFlag maps to active - Type maps to type - Actual maps to actual - constrain code to 0..0 - Title maps to name - GroupCharacteristic maps to characteristic.value[x] - GroupCharacteristic.GroupCharacteristicCode maps to characteristic.code - GroupCharacteristic.ExcludeFlag maps to characteristic.exclude - GroupCharacteristic.TimePeriod maps to characteristic.period - Member.Value maps to member.entity - Member.ParticipationPeriod maps to member.period - Member.ActiveFlag maps to member.inactive // TODO this is an inverse TF mapping - Count maps to quantity - -Facility maps to http://hl7.org/fhir/us/core/StructureDefinition/us-core-location: - FacilityName maps to name - Location[Address] maps to address - Location[Geoposition].Latitude maps to position.latitude - Location[Geoposition].Longitude maps to position.longitude - Location[Geoposition].Altitude maps to position.altitude - // Location[GeopoliticalLocation] maps to address // Can't do this since address is 0..1 and already mapped above - ContactPoint maps to telecom - ManagingOrganization maps to managingOrganization - Type maps to type - -Substance maps to Substance: - Type maps to code - Ingredient maps to ingredient - Ingredient.IngredientAmount maps to ingredient.quantity - Ingredient.Value maps to ingredient.substance[x] - -Medication maps to http://hl7.org/fhir/us/core/StructureDefinition/us-core-medication: - Type maps to code - DoseForm maps to form - MedicationIngredient.Value maps to ingredient.item[x] - MedicationIngredient.IngredientAmount maps to ingredient.amount - MedicationIngredient.IsActiveIngredient maps to ingredient.isActive - Brand maps to isBrand - OverTheCounter maps to isOverTheCounter - Manufacturer maps to manufacturer - constrain package.batch to 0..1 - LotNumber maps to package.batch.lotNumber - ExpirationDate maps to package.batch.expirationDate - Package maps to package.container - -Specimen maps to Specimen: - AccessionIdentifier maps to accessionIdentifier - SpecimenStatus maps to status - Type maps to type - CollectionSource maps to subject - SourceSpecimen maps to parent - ReceivedTime maps to receivedTime -// SpecimenCollectionPerformed.AmountOrSize maps to collection.quantity -// SpecimenCollectionPerformed.BodySite maps to collection.bodySite -// SpecimenCollectionPerformed.ProcedurePerformedContext.OccurrenceTimeOrPeriod maps to collection.collected[x] -// SpecimenCollectionPerformed.ProcedurePerformedContext.Participant.Entity maps to collection.collector -// SpecimenCollectionPerformed.ProcedurePerformedContext.Method maps to collection.method -// SpecimenCollectionPerformed.ProcedurePerformedContext.RelatedRequest.Value maps to request - SpecimenContainer.Identifier maps to container.identifier - SpecimenContainer.Details maps to container.description - SpecimenContainer.Type maps to container.type - SpecimenContainer.Capacity maps to container.capacity - SpecimenContainer.SpecimenQuantity maps to container.specimenQuantity - SpecimenContainer.Additive maps to container.additive[x] - -Device maps to http://hl7.org/fhir/us/core/StructureDefinition/us-core-device: - Type maps to type - DeviceUdi maps to udi.carrierHRF - VendorModelNumber maps to model - ManufacturerName maps to manufacturer - ManufactureDate maps to manufactureDate - ExpirationDate maps to expirationDate - Version maps to version - Url maps to url - - - \ No newline at end of file diff --git a/spec/cimi_medication.txt b/spec/cimi_medication.txt deleted file mode 100644 index bbf05480..00000000 --- a/spec/cimi_medication.txt +++ /dev/null @@ -1,192 +0,0 @@ -Grammar: DataElement 5.0 -Namespace: cimi.medication -Description: "The CIMI Medication domain contains definitions related to medications taken, or not taken, by the person of record, both currently and in the past." -Uses: shr.core, shr.base, cimi.core, cimi.element, cimi.context, cimi.topic, cimi.statement, cimi.entity, cimi.encounter - -/* Taking out for now since the Planned context has not been defined -EntryElement: MedicationRegimen // Definitional -Concept: MTH#C0237125 -Description: "Defines a specific application of over-the-counter and prescribed/recommended medications and infusions to meet guidelines for therapeutic action, safety, and schedule." -1..* MedicationUsePlanned -*/ - -Element: MedicationTopic -Based on: ActionTopic -Concept: TBD -Description: "Base class for actions involving medications, independent of context." -1..1 Medication -0..1 Dosage - - Element: Dosage - Concept: MTH#C0178602 - Description: "The dosage of the medication, prescribed or taken." - 1..1 DoseAmount - 1..1 TimingOfDoses - 1..1 AsNeededIndicator - 0..1 DoseInstructionsText - 0..* AdditionalDoseInstruction from http://hl7.org/fhir/ValueSet/additional-instruction-codes - 0..1 RouteIntoBody - 0..1 AdministrationMethod from http://hl7.org/fhir/ValueSet/administration-method-codes - 0..1 AdministrationBodySite - 0..1 MaximumDosePerTimePeriod - - Element: DoseAmount - Concept: TBD - Description: "The amount of medication taken per dose, as a quantity or range." - Value: SimpleQuantity or Range - - Element: TimingOfDoses - Concept: TBD - Description: "When doses of medication should be administered." - Value: Timing - - Element: AsNeededIndicator - Concept: MTH#C1883728 - Description: "Indicates the pre-condition under which the drug or intervention should be used." - Value: boolean or CodeableConcept could be from http://hl7.org/fhir/ValueSet/medication-as-needed-reason - - Element: DoseInstructionsText - Concept: TBD - Description: "The directions (signetur) on the drug prescription or dispensing record." - Value: string - - Element: AdditionalDoseInstruction - Concept: MTH#C1644714 - Description: "Supplemental instructions - e.g. 'with meals'." - Value: CodeableConcept - - Element: AdministrationMethod - Concept: MTH#C1547585 - Description: "Technique for administering medication." - Value: CodeableConcept - - Element: AdministrationBodySite - Concept: MTH#C0229986 - Description: "The anatomic site at which medical intervention is applied." - Value: AnatomicalLocation - - Element: MaximumDosePerTimePeriod - Concept: TBD - Description: "The maximum amount of a medication to be taken in a given period of time (e.g., no more than x in any 24-hour period)" - Value: Ratio - -EntryElement: MedicationDispenseTopic -Concept: TBD -Based on: MedicationTopic -Description: "The action of ordering and deliving a medication to the party responsible for administering the medication." -0..1 NumberOfRefillsAllowed -0..1 QuantityPerDispense -0..1 SupplyDuration - - Element: NumberOfRefillsAllowed - Concept: TBD - Description: "The maximum number of times the dispense can be repeated. For medication dispense, this integer does NOT include the original order dispense. This means that if an order indicates dispense 30 tablets plus 3 repeats, then the order can be dispensed a total of 4 times and the patient can receive a total of 120 tablets." - Value: positiveInt // should be unsignedInt, but that causes a mapping error in FHIR 3.0 - - Element: QuantityPerDispense - Concept: TBD - Description: "The amount that is to be dispensed for one fill." - Value: SimpleQuantity - - Element: SupplyDuration - Concept: TBD - Description: "Identifies the period time over which the supplied product is expected to be used, or the length of time the dispense is expected to last." - Value: Duration - - -Element: MedicationUseTopic -Based on: MedicationTopic -Concept: TBD -Description: "A course or dose of medication for a patient, independent of context of being recommended, used, or not used. Medication use can be reported, directly observed, or inferred from clinical events associated with orders, prescriptions written, pharmacy dispensings, procedural administrations, and other patient-reported information." - - -Element: MedicationChangeTopic -Based on: ActionTopic -1..1 Type from MedicationChangeTypeVS //"Whether the change is a dose change, switch to a new medication, or discontinuation." -0..* MedicationBeforeChange //might be more than one -0..* MedicationAfterChange - - Element: MedicationBeforeChange - Concept: TBD - Description: "The medication taken, prior to the change." - Value: ref(MedicationDispenseRequestedStatement) or ref(MedicationUsedStatement) - - Element: MedicationAfterChange - Concept: TBD - Description: "The medication taken, prior to the change." - Value: ref(MedicationDispenseRequestedStatement) or ref(MedicationUsedStatement) - - -EntryElement: MedicationUsedStatement -Based on: ActionPerformedStatement -Concept: TBD -Description: "A record of the use of a medication." - SourceOfInformation value is type AnyPersonOrOrganization - StatementTopic is type MedicationUseTopic -0..1 MedicationUseTopic.Category should be from http://hl7.org/fhir/ValueSet/medication-statement-category - StatementContext is type PerformedContext - PerformedContext.Status from http://hl7.org/fhir/ValueSet/medication-statement-status -0..0 PerformedContext.Method // because of Dosage.Method - -EntryElement: MedicationAdherenceStatement // This could be attached to MedicationUsed directly as an extension, but modeling as an observation avoids creating an extension -Based on: SimpleCodedNonLaboratoryObservation -Concept: MTH#C2364172 -Description: "The degree (frequency) that the stated treatment plan, prescription, or protocol was followed. A statement of the ability and cooperation of the patient in taking medicine or supplement as recommended or prescribed. This includes correct timing, dosage, and frequency." - ObservationContext.ResultValue from QualitativeFrequencyVS - ObservationTopic.TopicCode is MTH#C2364172 - ObservationTopic.Focus value is type ref(EntityOrRole) - ObservationTopic.Focus.EntityOrRole is type ref(Medication) -0..* MedicationNonAdherenceReason - - Element: MedicationNonAdherenceReason - Description: "Reason that patient did not adhere to a medication regimen." - Value: CodeableConcept from MedicationNonAdherenceReasonVS - - -EntryElement: MedicationNotUsedStatement -Based on: ActionNotPerformedStatement -Concept: TBD -Description: "A record of a medication NOT used. Although usually not required, a medication not used is sometimes reported when deviating from normal expectation or care plan." - SourceOfInformation value is type AnyPersonOrOrganization - StatementTopic is type MedicationUseTopic -0..1 MedicationUseTopic.Category should be from http://hl7.org/fhir/ValueSet/medication-statement-category -0..0 MedicationUseTopic.Dosage - NotPerformedContext.Reason from MedicationNotUsedReasonVS - - -EntryElement: MedicationDispenseRequestedStatement -Based on: ActionRequestedStatement -Concept: TBD -Description: "An order for a medication to be dispensed and instructions for use." - StatementTopic is type MedicationDispenseTopic - RequestedContext.Status from http://hl7.org/fhir/ValueSet/medication-request-status - RequestedContext.PriorityRank from http://hl7.org/fhir/ValueSet/medication-request-priority - -EntryElement: MedicationNotPrescribedStatement -Based on: ActionRequestedAgainstStatement -Concept: TBD -Description: "A record of a medication NOT being prescribed. Recorded only when deviating from the normal expectation, care plan, or standard of care." - StatementTopic is type MedicationDispenseTopic - RequestedAgainstContext.Reason from MedicationNotUsedReasonVS - -Element: MedicationDispensedStatement -Based on: ActionPerformedStatement -Concept: TBD -Description: "Indicates that a medication product has been dispensed for a named person/patient. This includes a description of the medication product (supply) provided and the instructions for administering the medication. The medication dispense is the result of a pharmacy system responding to a medication order." - StatementTopic is type MedicationDispenseTopic - -Element: MedicationNotDispensedStatement -Based on: ActionNotPerformedStatement -Concept: TBD -Description: "Indicates that a medication product has NOT been dispensed for a named person/patient. This may be a result of the timing out of an order or detection of pharmacist of duplicate prescription or other reason." - StatementTopic is type MedicationDispenseTopic - -EntryElement: MedicationChangeStatement -Based on: ActionPerformedStatement -Concept: MTH#C0554834 -Description: "Description of a modification or change of a medication or dosage." - StatementTopic is type MedicationChangeTopic - PerformedContext.Reason from MedicationChangeReasonVS // why was the medication changed? - - - diff --git a/spec/cimi_medication_map.txt b/spec/cimi_medication_map.txt deleted file mode 100644 index f7b2ec64..00000000 --- a/spec/cimi_medication_map.txt +++ /dev/null @@ -1,55 +0,0 @@ -Grammar: Map 5.1 -Namespace: cimi.medication -Target: FHIR_STU_3 - -Dosage maps to Dosage: - DoseAmount maps to dose[x] - TimingOfDoses maps to timing - AsNeededIndicator maps to asNeeded[x] - DoseInstructionsText maps to text - AdditionalDoseInstruction maps to additionalInstruction - RouteIntoBody maps to route - AdministrationMethod maps to method - AdministrationBodySite.Value maps to site - MaximumDosePerTimePeriod maps to maxDosePerPeriod - -MedicationUsedStatement maps to http://hl7.org/fhir/us/core/StructureDefinition/us-core-medicationstatement: - SourceOfInformation.Value maps to informationSource - _Entry.CreationTime maps to dateAsserted // date asserted and date recorded may not be the same - constrain reasonNotTaken to 0..0 - constrain dosage to 0..1 - MedicationUseTopic.Dosage maps to dosage - MedicationUseTopic.Medication maps to medication[x] - MedicationUseTopic.Category maps to category - fix taken to #y - PerformedContext.Reason maps to reasonCode - PerformedContext.OccurrenceTimeOrPeriod maps to effective[x] - PerformedContext.Status maps to status - -MedicationNotUsedStatement maps to http://hl7.org/fhir/us/core/StructureDefinition/us-core-medicationstatement: - SourceOfInformation.Value maps to informationSource - _Entry.CreationTime maps to dateAsserted - MedicationUseTopic.Medication maps to medication[x] - MedicationUseTopic.Category maps to category - fix taken to #n - constrain dosage to 0..0 - NotPerformedContext.Reason maps to reasonNotTaken - NotPerformedContext.NonOccurrenceTimeOrPeriod maps to effective[x] - -MedicationDispenseRequestedStatement maps to http://hl7.org/fhir/us/core/StructureDefinition/us-core-medicationrequest: - MedicationDispenseTopic.Medication maps to medication[x] - MedicationDispenseTopic.NumberOfRefillsAllowed maps to dispenseRequest.numberOfRepeatsAllowed - MedicationDispenseTopic.QuantityPerDispense maps to dispenseRequest.quantity - MedicationDispenseTopic.SupplyDuration maps to dispenseRequest.expectedSupplyDuration - constrain dosageInstruction to 0..1 - MedicationDispenseTopic.Dosage maps to dosageInstruction - RequestedContext.Reason maps to reasonCode - RequestedContext.Status maps to status - RequestedContext.ExpectedPerformanceTime maps to dispenseRequest.validityPeriod - RequestedContext.PriorityRank maps to priority - RequestedContext.PerformerInstructions maps to note.text - RequestedContext.ExpectedPerformer[Organization] maps to dispenseRequest.performer - constrain note to 0..1 - - - \ No newline at end of file diff --git a/spec/cimi_procedure.txt b/spec/cimi_procedure.txt deleted file mode 100644 index e684ebe4..00000000 --- a/spec/cimi_procedure.txt +++ /dev/null @@ -1,237 +0,0 @@ -Grammar: DataElement 5.0 -Namespace: cimi.procedure -Description: "The CIMI procedure domain contains contexts, topics, and statements related to procedures." -Uses: shr.core, shr.base, cimi.core, cimi.element, cimi.context, cimi.topic, cimi.statement, cimi.entity - -CodeSystem: OBSCAT = http://hl7.org/fhir/observation-category - -Element: ProcedureTopic -Based on: ActionTopic -Concept: TBD -Description: "Description of a healthcare procedure, independent of action context. This can be a physical intervention like an operation, or less invasive like counseling or hypnotherapy." -1..1 TopicCode from http://hl7.org/fhir/us/core/ValueSet/us-core-procedure-code if covered -0..* AnatomicalLocation -0..1 PartOf value is type ref(ProcedurePerformedStatement) -0..1 Category // this is a constraint on the cardinality of Action.Category -0..* Annotation -0..1 Reason -0..1 Method -0..* Precondition -0..* InputFinding -0..* Indication -0..* ref(Device) -0..1 Location - - Element: InputFinding - Description: "Patient findings expected for the performance of the specified procedure. For instance, an x-ray of a fracture prior to a surgical procedure for a bone fracture." - Value: ref(FindingStatement) - - Element: Indication - Description: "Conditions or situations where the procedure is recommended. In the Performed context, the actual indication should be reported." - Value: CodeableConcept - - -//---------- Specialized Types of Procedure Topics ---------------- - -Element: ImagingProcedureTopic -Based on: ProcedureTopic -Concept: TBD -Description: "Experimental class for an imaging procedure. This class is still incomplete at this time." -0..* ImagingSubstance - - Element: ImagingSubstance - Concept: TBD - Description: "Substance used for this imaging procedure such as a contrast agent." - Value: CodeableConcept - -Element: LaboratoryProcedureTopic -Based on: ProcedureTopic -Concept: MTH#C0456984 -Description: "A procedure performed on a collected specimen such as a blood panel or a biopsy." -1..1 TopicCode from http://hl7.org/fhir/ValueSet/observation-codes - Category is OBSCAT#laboratory -0..1 ref(Specimen) -//0..1 ref(Device) // constraint from 0..* - - -Element: SurgicalProcedureTopic -Based on: ProcedureTopic -Concept: TBD -Description: "A surgical action, independent of action context." -0..* DirectSite -0..* DirectSiteCode -0..* IndirectSite -0..* IndirectSiteCode -0..* SurgicalApproach -0..* Access -0..* UsingDevice -0..* UsingDeviceCode -0..* UsingAccessDevice -0..* UsingAccessDeviceCode -0..* IndirectDevice -0..* IndirectDeviceCode - - Element: DirectSite - Description: "The site where the procedure is performed." - Value: AnatomicalLocation - - Element: DirectSiteCode - Description: "The site where the procedure is performed." - Value: CodeableConcept - - Element: IndirectSite - Description: "The indirect site for this procedure." - Value: AnatomicalLocation - - Element: IndirectSiteCode - Description: "The indirect site for this procedure." - Value: CodeableConcept - - Element: SurgicalApproach - Description: "The technique used to reach the site of the procedure. Approaches may be through the skin or mucous membrane, through an orifice or external." - Value: CodeableConcept - - Element: Access - Description: "The route used to access the site of a procedure. It is used to distinguish open, closed, and percutaneous procedures." - Value: CodeableConcept - - Element: UsingDevice - Description: "The device used to perform the procedure." - Value: Device - - Element: UsingDeviceCode - Description: "The device used to perform the procedure." - Value: CodeableConcept - - Element: UsingAccessDevice - Description: "The access device used to perform the procedure." - Value: Device - - Element: UsingAccessDeviceCode - Description: "The access device used to perform the procedure." - Value: CodeableConcept - - Element: IndirectDevice - Description: "An indirect device used for this procedure." - Value: Device - - Element: IndirectDeviceCode - Description: "An indirect device used for this procedure." - Value: CodeableConcept - -Element: SpecimenCollectionTopic -Based on: ProcedureTopic -Description: "Base class for actions related to the collection of a specimen, independent of context." -0..* AmountOrSize - - Element: AmountOrSize - Description: "The quantity of specimen collected" - Value: SimpleQuantity - -// Specialized Contexts for Procedures - -Element: ProcedurePerformedContext -Based on: PerformedContext -Description: "The performed context with constraints applicable to procedures." - Participant.OnBehalfOf value is type ref(Organization) - Status must be from http://hl7.org/fhir/ValueSet/event-status -// Participant.EntityOrRole is type ref(Practitioner) - Participant is type FHIRProcedureParticipant - RelatedRequest value is type ref(ProcedureRequestedStatement) -0..* OutputFinding // in CIMI, this is part of ProcedureTopic, but the definition hinges on performance, so it belongs here, not there. - - Element: FHIRProcedureParticipant - Based on: Participant - Description: "Constraints participants to classes that are accepted by FHIR as actors in procedures." - Value: ref(Practitioner) or ref(Organization) or ref(Patient) or ref(RelatedPerson) or ref(Device) -// inherited attributes: -// 0..1 ParticipationType // role -// 0..1 ParticipationPeriod -// 0..1 OnBehalfOf - - - Element: OutputFinding - Description: "Patient findings documented during the performance of the procedure." - Value: ref(FindingStatement) - -Element: ProcedureNotPerformedContext -Based on: NotPerformedContext -Description: "The not performed context with constraints applicable to procedures, namely, the request must be a procedure request." - RelatedRequest value is type ref(ProcedureRequestedStatement) - -Element: ProcedureRequestedContext -Based on: RequestedContext -Description: "The requested context with additional constraints applicable to procedures." - PriorityRank must be from http://hl7.org/fhir/ValueSet/request-priority // required - Status must be from http://hl7.org/fhir/ValueSet/request-status - -// Statements derived from Procedure Topics and Contexts - -EntryElement: ProcedurePerformedStatement -Based on: ActionPerformedStatement -1..1 PersonOfRecord - StatementTopic is type ProcedureTopic - StatementContext is type ProcedurePerformedContext - -EntryElement: ProcedureNotPerformedStatement -Based on: ActionNotPerformedStatement -1..1 PersonOfRecord - StatementTopic is type ProcedureTopic - StatementContext is type ProcedureNotPerformedContext -0..1 ProcedureNotPerformedContext.Reason // limit to 0..1 to match FHIR Procedure.notDoneReason - -EntryElement: ProcedureRequestedStatement -Based on: ActionRequestedStatement -1..1 PersonOfRecord - StatementTopic is type ProcedureTopic - StatementContext is type ProcedureRequestedContext - -EntryElement: ProcedureRequestedAgainstStatement -Based on: ActionRequestedAgainstStatement -1..1 PersonOfRecord - StatementTopic is type ProcedureTopic - StatementContext is type RequestedAgainstContext - -EntryElement: SpecimenCollectionPerformedStatement -Based on: ProcedurePerformedStatement - StatementTopic is type SpecimenCollectionTopic -0..1 AnatomicalLocation // FHIR limits Specimen.collection.bodySite to 0..1 - -EntryElement: SpecimenCollectionRequestedStatement -Based on: ProcedureRequestedStatement - StatementTopic is type SpecimenCollectionTopic - -EntryElement: ImagingProcedurePerformedStatement -Based on: ProcedurePerformedStatement - StatementTopic is type ImagingProcedureTopic - -EntryElement: ImagingProcedureRequestedStatement -Based on: ProcedureRequestedStatement - StatementTopic is type ImagingProcedureTopic - -EntryElement: SurgicalProcedurePerformedStatement -Based on: ProcedurePerformedStatement - StatementTopic is type SurgicalProcedureTopic - -EntryElement: SurgicalProcedureRequestedStatement -Based on: ProcedureRequestedStatement - StatementTopic is type SurgicalProcedureTopic - -EntryElement: SurgicalProcedureNotPerformedStatement -Based on: ProcedureNotPerformedStatement - StatementTopic is type SurgicalProcedureTopic - -EntryElement: SurgicalProcedureRequestedAgainstStatement -Based on: ProcedureRequestedAgainstStatement - StatementTopic is type SurgicalProcedureTopic - -EntryElement: LaboratoryProcedurePerformedStatement -Based on: ProcedurePerformedStatement - StatementTopic is type LaboratoryProcedureTopic - -EntryElement: LaboratoryProcedureRequestedStatement -Based on: ProcedureRequestedStatement - StatementTopic is type LaboratoryProcedureTopic - - - diff --git a/spec/cimi_procedure_map.txt b/spec/cimi_procedure_map.txt deleted file mode 100644 index cebe7611..00000000 --- a/spec/cimi_procedure_map.txt +++ /dev/null @@ -1,83 +0,0 @@ -Grammar: Map 5.1 -Namespace: cimi.procedure -Target: FHIR_STU_3 - - -ProcedurePerformedStatement maps to http://hl7.org/fhir/us/core/StructureDefinition/us-core-procedure: - ProcedureTopic.TopicCode maps to code - PersonOfRecord maps to subject - ProcedureTopic.Category maps to category - constrain notDone to 0..0 - constrain notDoneReason to 0..0 - ProcedureTopic.AnatomicalLocation maps to bodySite - ProcedureTopic.PartOf maps to partOf - ProcedureTopic.Annotation maps to note - ProcedurePerformedContext.Encounter maps to context - ProcedurePerformedContext.Reason maps to reasonCode - ProcedurePerformedContext.OccurrenceTimeOrPeriod maps to performed[x] - ProcedurePerformedContext.FHIRProcedureParticipant maps to performer - ProcedurePerformedContext.FHIRProcedureParticipant.Value maps to performer.actor - ProcedurePerformedContext.FHIRProcedureParticipant.ParticipationType maps to performer.role - ProcedurePerformedContext.FHIRProcedureParticipant.OnBehalfOf maps to performer.onBehalfOf - ProcedurePerformedContext.Status maps to status -// TODO The following statement is failing it might be a bug -// ProcedurePerformedContext.Method maps to http://hl7.org/fhir/StructureDefinition/procedure-method - ProcedurePerformedContext.RelatedRequest.Value maps to basedOn -// ProcedurePerformedContext.RelatedPlan maps to definition - ProcedurePerformedContext.Outcome maps to outcome - ProcedurePerformedContext.Facility maps to location - - -ProcedureNotPerformedStatement maps to http://hl7.org/fhir/us/core/StructureDefinition/us-core-procedure: - ProcedureTopic.TopicCode maps to code - PersonOfRecord maps to subject - ProcedureTopic.Category maps to category -// TODO the following is causing a crash -// fix notDone to true - NotPerformedContext.Reason maps to notDoneReason - ProcedureTopic.AnatomicalLocation maps to bodySite - ProcedureTopic.PartOf maps to partOf - ProcedureTopic.Annotation maps to note - constrain performed[x] to 0..0 - constrain performer to 0..0 - fix status to http://hl7.org/fhir/event-status#suspended // FHIR is lacking a not-done status (see Gforge issue #14256) -// NotPerformedContext.Encounter maps to context - NotPerformedContext.RelatedRequest.Value maps to basedOn -// NotPerformedContext.RelatedPlan maps to definition - constrain outcome to 0..0 - constrain location to 0..0 - -SurgicalProcedurePerformedStatement maps to http://hl7.org/fhir/us/core/StructureDefinition/us-core-procedure: - SurgicalProcedureTopic.DirectSite maps to http://hl7.org/fhir/StructureDefinition/procedure-targetBodySite - SurgicalProcedureTopic.IndirectSite maps to http://hl7.org/fhir/StructureDefinition/procedure-approachBodySite - SurgicalProcedureTopic.SurgicalApproach maps to http://hl7.org/fhir/StructureDefinition/procedure-approachBodySite - - -ProcedureRequestedStatement maps to ProcedureRequest: - _Entry.CreationTime maps to authoredOn - Signed.Value.EntityOrRole maps to requester - ProcedureTopic.TopicCode maps to code - ProcedureTopic.Category maps to category - constrain doNotPerform to 0..0 - PersonOfRecord maps to subject - ProcedureTopic.AnatomicalLocation maps to bodySite - ProcedureRequestedContext.Encounter maps to context - ProcedureRequestedContext.Reason maps to reasonCode - ProcedureRequestedContext.Status maps to status - ProcedureRequestedContext.RequestIntent maps to intent - ProcedureRequestedContext.ExpectedPerformanceTime maps to occurrence[x] - ProcedureRequestedContext.ExpectedPerformerType maps to performerType - ProcedureRequestedContext.ExpectedPerformer maps to performer - ProcedureRequestedContext.PriorityRank maps to priority - -ProcedureRequestedAgainstStatement maps to ProcedureRequest: - fix doNotPerform to true - fix intent to http://hl7.org/fhir/request-intent#proposal - _Entry.CreationTime maps to authoredOn - Signed.Value.EntityOrRole maps to requester - ProcedureTopic.TopicCode maps to code - ProcedureTopic.Category maps to category - PersonOfRecord maps to subject - ProcedureTopic.AnatomicalLocation maps to bodySite -// RequestedAgainstContext.Encounter maps to context - RequestedAgainstContext.Reason maps to reasonCode diff --git a/spec/cimi_statement.txt b/spec/cimi_statement.txt deleted file mode 100644 index 444db458..00000000 --- a/spec/cimi_statement.txt +++ /dev/null @@ -1,234 +0,0 @@ -Grammar: DataElement 5.0 -Namespace: cimi.statement -Description: "The namespace containing cimi-derived classes representing complete clinical statements. In this specification, these classes derive from the StatementTopic class hierarchy, not ClinicalStatement, which is a significant departure from CIMI. This simplifies the resulting logical models." -Uses: shr.core, cimi.core, cimi.element, cimi.topic, cimi.context, cimi.entity - - -CodeSystem: SCT = http://snomed.info/sct -CodeSystem: MTH = http://ncimeta.nci.nih.gov -CodeSystem: NCI = https://evs.nci.nih.gov/ftp1/CDISC/SDTM/ -CodeSystem: OBSCAT = http://hl7.org/fhir/observation-category - - -Element: ClinicalStatement -Based on: InformationEntry -Concept: TBD -Description: "A special type of information entry consisting of a topic and a context. -The ClinicalStatement class provides the core pattern for more specific clinical statement classes, such as a statement that a finding has been found in a patient or that a procedure has been proposed by a clinical decision support system. The ClinicalStatement pattern defines the core attributes common to most clinical statements and specifies a composition pattern that encourage model component reuse and better alignment with the SNOMED CT Concept Model. A clinical statement is composed of the StatementTopic class (grouping of attributes for capturing information about a procedure or a clinical finding) and the StatementContext class (grouping of attributes providing the context for the statement topic such as whether a procedure was performed, requested, not performed or whether a finding is suspected present or absent in the patient). At the archetype level, the topic and context components are coordinated to form the clinical statement. For instance, the composition of the ProcedureTopic with the NotPerformed context indicates that the given procedure was not performed." -1..1 StatementTopic -1..1 StatementContext - -//---------- Actions -------------- - -Abstract Element: ActionStatement -Based on: ClinicalStatement -Description: "Abstract class representing any type of action, independent of context." - StatementTopic is type ActionTopic - -Abstract Element: ActionPerformedStatement -Based on: ActionStatement -Description: "Abstract class representing performance of any type of action." - StatementContext is type PerformedContext - -Abstract Element: ActionRequestedStatement -Based on: ActionStatement -Description: "Abstract class representing a request for any type of action." - StatementContext is type RequestedContext - -Abstract Element: ActionNotPerformedStatement -Based on: ActionStatement -Description: "Abstract class representing non-performance of any type of action." - StatementContext is type NotPerformedContext - -Abstract Element: ActionRequestedAgainstStatement -Based on: ActionStatement -Description: "Abstract class representing a request to not perform any type of action." - StatementContext is type RequestedAgainstContext - -//-------------Findings------------ - -Abstract Element: FindingStatement -Based on: ClinicalStatement -Description: "Any clinical statement representing a finding." - StatementTopic is type FindingTopic -1..1 PersonOfRecord -/* -[Entry]ShrId -[Entry]EntryId -[Entry]PersonOfRecord -[Entry]Version -[Entry]EntryType -[Entry]CreationTime -[Entry]LastUpdated -[Entry]Narrative -[Entry]Language -[Entry]SecurityLabel -[Entry]Tag -[Entry]DerivedFrom -[InformationEntry]SubjectIfNotPersonOfRecord -[InformationEntry]SourceOfInformation -[InformationEntry]Annotation -[InformationEntry]RecordStatus -[InformationEntry]Recorded (who-when) -[InformationEntry]Signed (who-when) -[InformationEntry]Cosigned (who-when) -[InformationEntry]Verified (who-when) -FindingTopic.FindingMethod -FindingTopic.Details -*/ - -EntryElement: Observation // TODO: be consistent, or stop using the word "Statement" in class names -Based on: FindingStatement -Concept: TBD -Description: "Represents the result of evaluations (measurements, tests, or questions) that have been performed. -Observation has a value representing the result (answer), or an ExceptionValue indicating why the value is not present. The subject of a finding can be the entire patient, or an entity such as a location body structure, intervention, or condition. Things observed about the subject can include social and behavioral factors, subjective and objective observations, and assessments." - StatementTopic is type ObservationTopic - StatementContext is type ObservationContext - SourceOfInformation value is type AnyPersonOrOrganization // mapped to performer (who made the observation) -/* - Here's a list of all the attributes of Observation. - To keep things straight, always consider the constraints on each element in this order: - // ClinicalStatement - SubjectIfNotPersonOfRecord - SourceOfInformation - Annotation - RecordStatus - Recorded - Signed // aka Author - Cosigned - Verified - // Topic - ObservationTopic.TopicCode - ObservationTopic.FindingMethod - ObservationTopic.Details - ObservationTopic.Category from http://hl7.org/fhir/ValueSet/observation-category if covered - ObservationTopic.AnatomicalLocation // TODO: Change from element to code to align with FHIR?? - ObservationTopic.Focus - ObservationTopic.ref(Device) - ObservationTopic.ref(Specimen) - ObservationTopic.Precondition - ObservationTopic.ReferenceRange - ObservationTopic.EvaluationComponent - ObservationTopic.PanelMembers - ObservationTopic.EvaluationComponent.Value - ObservationTopic.EvaluationComponent.ExceptionValue - ObservationTopic.EvaluationComponent.Interpretation - ObservationTopic.EvaluationComponent.ReferenceRange - // Context - ObservationContext.ContextCode is SCT#424975005 "Record Entity" - ObservationContext.Interpretation - ObservationContext.FindingStatus - ObservationContext.RelevantTime - ObservationContext.Encounter - ObservationContext.ResultValue - ObservationContext.ExceptionValue - ObservationContext.DeltaFlag -*/ - -// Non-Laboratory Results - -EntryElement: NonLaboratoryObservation -Based on: Observation -Description: "An observation not based on a specimen." -0..0 ObservationTopic.Specimen - -EntryElement: SimpleNonLaboratoryObservation -Based on: NonLaboratoryObservation -Description: "An observation having no components or panel members" -0..0 ObservationTopic.EvaluationComponent -0..0 ObservationTopic.PanelMembers - -EntryElement: CodedNonLaboratoryObservation -Based on: NonLaboratoryObservation -Concept: TBD -Description: "The result of evaluations (measurements, tests, or questions) whose answer is expressed as a code." - ObservationContext.ResultValue value is type CodeableConcept -0..0 ObservationTopic.ReferenceRange - -EntryElement: SimpleCodedNonLaboratoryObservation -Based on: CodedNonLaboratoryObservation -Description: "An observation whose result is a code, and also having no components or panel members" -0..0 ObservationTopic.EvaluationComponent -0..0 ObservationTopic.PanelMembers - -EntryElement: ComponentOnlyNonLaboratoryObservation -Based on: NonLaboratoryObservation -Description: "An observation with components, but without a result value or panel members." -0..0 ObservationContext.ResultValue -0..0 ObservationContext.ExceptionValue -0..0 ObservationTopic.PanelMembers -0..0 ObservationTopic.ReferenceRange - -EntryElement: PanelOnlyNonLaboratoryObservation -Based on: NonLaboratoryObservation -Description: "An observation with panel members, but without a result value or components." -0..0 ObservationContext.ResultValue -0..0 ObservationContext.ExceptionValue -0..0 ObservationTopic.ReferenceRange -0..0 ObservationTopic.EvaluationComponent -1..1 ObservationTopic.PanelMembers - -// Laboratory Measurements and Results - -EntryElement: LaboratoryObservation -Based on: Observation -Description: "A coded finding based on a specimen collected from a patient." - ObservationTopic is type LaboratoryObservationTopic - - -EntryElement: CodedLaboratoryObservation -Based on: LaboratoryObservation -Description: "A coded finding from a laboratory test." - ObservationContext.ResultValue value is type CodeableConcept -0..0 LaboratoryObservationTopic.ReferenceRange - -EntryElement: SimpleLaboratoryObservation -Based on: LaboratoryObservation -Description: "A coded finding from a laboratory test without further panel members or components." -0..0 LaboratoryObservationTopic.EvaluationComponent -0..0 LaboratoryObservationTopic.PanelMembers - -EntryElement: SimpleCodedLaboratoryObservation -Based on: CodedLaboratoryObservation -Description: "A coded finding from a laboratory test without further panel members or components." -0..0 LaboratoryObservationTopic.EvaluationComponent -0..0 LaboratoryObservationTopic.PanelMembers - -//---------- Assertions ------------- - -Abstract Element: AssertionStatement -Based on: FindingStatement -Description: "A clinical statement that asserts presence or absence." - -Abstract Element: AssertionPresenceStatement // AssertPresence -Based on: AssertionStatement -Description: "Statement that a finding is present." - StatementContext is type PresenceContext - -Abstract Element: AssertionAbsenceStatement // AssertAbsence -Based on: AssertionStatement -Description: "Statement that a finding is absent." - StatementContext is type AbsenceContext - -EntryElement: ConditionPresenceStatement -Based on: AssertionPresenceStatement -Concept: TBD -Description: "A condition that is or may be present in a subject. 'Condition' is interpreted broadly and could be a disorder, abnormality, problem, injury, complaint, functionality, illness, disease, ailment, sickness, affliction, upset, difficulty, disorder, symptom, worry, or trouble." - SourceOfInformation value is type PatientOrPractitionerOrRelatedPerson - StatementTopic is type ConditionTopic - StatementContext is type ConditionPresenceContext - SubjectIfNotPersonOfRecord value is type ref(Patient) -0..0 SubjectIfNotPersonOfRecord.RelationshipToPersonOfRecord // could be self - -EntryElement: ConditionAbsenceStatement -Based on: AssertionAbsenceStatement -Concept: MTH#C0277541 "no disease present" -Description: "A finding that a condition is or was not present in the subject at a certain time, not necessarily the time the information is gathered." - StatementTopic is type ConditionTopic - -EntryElement: ClinicalNote -Based on: FindingStatement -Concept: MTH#C0747978 "Progress Note" -Description: "An entry concerning a patient where the result is a narrative text. Can be related to a specific Focus, such as a condition; and evidence and interpretation from FindingTopic." - StatementContext is type RecordedContext -1..1 StatementTopic.Details // TODO: change to "description" to synch with CIMI \ No newline at end of file diff --git a/spec/cimi_statement_map.txt b/spec/cimi_statement_map.txt deleted file mode 100644 index bc6882ef..00000000 --- a/spec/cimi_statement_map.txt +++ /dev/null @@ -1,70 +0,0 @@ -Grammar: Map 5.1 -Namespace: cimi.statement -Target: FHIR_STU_3 - -ClinicalStatement maps to DomainResource: - - -Observation maps to http://hl7.org/fhir/us/core/StructureDefinition/us-core-observationresults: - PersonOfRecord maps to subject - SubjectIfNotPersonOfRecord.RelationshipToPersonOfRecord maps to http://hl7.org/fhir/StructureDefinition/observation-focal-subject // CodeableConcept -// SourceOfInformation.Value maps to performer // Why doesn't this work??? -// Annotation maps to extension -// RecordStatus maps to extension -// Cosigned maps to extension -// Verified maps to extension - ObservationTopic.TopicCode maps to code - ObservationTopic.FindingMethod maps to method - ObservationTopic.Details maps to comment -// ObservationTopic.Media maps to extension - ObservationTopic.Category maps to category - ObservationTopic.AnatomicalLocation maps to bodySite - ObservationTopic.Device maps to device - ObservationTopic.Specimen maps to specimen -// ObservationTopic.Precondition maps to extension - ObservationTopic.ReferenceRange maps to referenceRange - ObservationTopic.ReferenceRange.Range.LowerBound maps to referenceRange.low - ObservationTopic.ReferenceRange.Range.UpperBound maps to referenceRange.high - ObservationTopic.ReferenceRange.Type maps to referenceRange.type - ObservationTopic.ReferenceRange.ApplicableSubpopulation maps to referenceRange.appliesTo - ObservationTopic.ReferenceRange.ApplicableAgeRange maps to referenceRange.age - ObservationTopic.EvaluationComponent maps to component (slice on = coding.code; slice strategy = includes) - ObservationTopic.EvaluationComponent._Concept maps to component.code - ObservationTopic.EvaluationComponent.Value maps to component.value[x] - ObservationTopic.EvaluationComponent.ExceptionValue maps to component.dataAbsentReason - ObservationTopic.EvaluationComponent.Interpretation maps to component.interpretation - ObservationTopic.EvaluationComponent.ReferenceRange maps to component.referenceRange - fix related.type to #has-member - ObservationTopic.PanelMembers.Observation maps to related.target (slice at = related; slice on = target.reference.resolve(); slice on type = profile; slice strategy = includes) -// ObservationContext.ContextCode maps to nothing // drop - ObservationContext.ResultValue maps to value[x] - ObservationContext.ExceptionValue maps to dataAbsentReason - ObservationContext.Interpretation maps to interpretation - ObservationContext.Issued maps to issued - ObservationContext.FindingStatus maps to status - ObservationContext.RelevantTime maps to effective[x] - ObservationContext.Encounter maps to context - ObservationContext.DeltaFlag maps to http://hl7.org/fhir/StructureDefinition/observation-delta - -ConditionPresenceStatement maps to http://hl7.org/fhir/us/core/StructureDefinition/us-core-condition: -// _Entry.CreationTime maps to assertedDate // why doesn't this work? - PersonOfRecord maps to subject -// SourceOfInformation.Value maps to asserter // why doesn't this work? - ConditionTopic.Category maps to category - ConditionTopic.TopicCode maps to code - constrain bodySite to 0..0 - ConditionTopic.AnatomicalLocation maps to http://hl7.org/fhir/StructureDefinition/condition-targetBodySite - ConditionPresenceContext.Encounter maps to context - ConditionPresenceContext.ClinicalStatus maps to clinicalStatus - ConditionPresenceContext.VerificationStatus maps to verificationStatus - ConditionPresenceContext.Onset maps to onset[x] - ConditionPresenceContext.Abatement maps to abatement[x] - ConditionPresenceContext.Severity maps to severity - ConditionPresenceContext.Stage maps to stage - ConditionPresenceContext.Stage.CodeableConcept maps to stage.summary - ConditionPresenceContext.Stage.StageDetail maps to stage.assessment - - -ConditionAbsenceStatement maps to Basic: -// There is no mechanism in FHIR (not Condition, not Observation) to say "Patient does not have Condition X" - diff --git a/spec/cimi_statement_vs.txt b/spec/cimi_statement_vs.txt deleted file mode 100644 index 4ff7c5fb..00000000 --- a/spec/cimi_statement_vs.txt +++ /dev/null @@ -1,18 +0,0 @@ -Grammar: ValueSet 5.0 -Namespace: cimi.statement - -CodeSystem: SCT = http://snomed.info/sct - -ValueSet: DiagnosticServiceVS -Description: "The type of laboratory service used in producing a laboratory result. Note -- we may want to include additional descendants of SCT#224891009 (Healthcare services)" -SCT#310078000 "Microbiology service (qualifier) -- Laboratory concerned with cultures, to look for suspected pathogens." -SCT#706900000 "Parasitology service (qualifier) -- Laboratory responsible for examining parasites, feces samples may be examined for evidence of intestinal parasites such as tapeworms or hookworms and others." -SCT#708185002 "Virology service (qualifier) -- Laboratory concerned with identification of viruses in specimens such as blood, urine, and cerebrospinal fluid." -SCT#708196005 "Hematology service (qualifier) -- Laboratory that works with whole blood to do full blood counts, and blood films as well as many other specialised tests." -SCT#310076001 "Biochemistry service (qualifier) -- Laboratory that usually receives serum or plasma and tests the serum for chemicals present in blood." -SCT#708191000 "Toxicology service (qualifier) -- Laboratory that mainly tests for pharmaceutical and recreational drugs. Urine and blood samples are submitted to this lab." -SCT#708190004 "Immunology service (qualifier) -- Immunology/Serology laboratory uses the concept of antigen-antibody interaction as a diagnostic tool. Compatibility of transplanted organs is also determined." -//#urinalysis "Laboratory tests urine for many analytes. Some health care providers have a urinalysis laboratory, while others don't." -SCT#310074003 "Pathology service (qualifier)-- Surgical, cytopathology, or histopathology laboratory. Surgical pathology examines organs, limbs, tumors, fetuses, and other tissues biopsied in surgery such as breast mastectomies." -SCT#310048009 "Genetics service (procedure) - note: should be in the Snomed (qualifier) hierarchy - Laboratory that mainly performs DNA analysis." -SCT#708178001 "Cytogenetics service (qualifier) -- Laboratory that uses blood and other cells to get a karyotype. This can be helpful in prenatal diagnosis (e.g. Down's syndrome) as well as in cancer (some cancers have abnormal chromosomes)." \ No newline at end of file diff --git a/spec/cimi_topic.txt b/spec/cimi_topic.txt deleted file mode 100644 index c9aafd2b..00000000 --- a/spec/cimi_topic.txt +++ /dev/null @@ -1,140 +0,0 @@ -Grammar: DataElement 5.0 -Namespace: cimi.topic -Description: "The Topic Core package contains the top-level specializations of the Statement Topic class, namely, the FindingTopic, ActionTopic (ProcedureTopic), and EventTopic classes." -Uses: shr.core, shr.base, cimi.core, cimi.context, cimi.element, cimi.entity, cimi.statement - -Element: StatementTopic -Based on: NonIndependent -Concept: TBD -Description: "Compositional and reusable grouping of clinical statement attributes that make up the clinical focus of a statement. - -StatementTopic class attributes are aligned with SNOMED CT Concept Model attributes when such an overlap exists. Note that this class does not include contextual attributes such as the nature of the action (ordered, proposed, planned, etc...), the nature of the patient state being described (e.g., present, suspected present, absent), and the attribution of this information (the who, when, where, how, why of the information recorded)." -1..1 TopicCode - - Element: TopicCode - Concept: TBD - Description: "The concept representing the finding or action that is the topic of the statement. - - For action topics, the TopicCode represents the action being described. For findings, the TopicCode represents the 'question' or property being investigated. For evaluation result findings, the TopicCode contains a concept for an observable entity, such as systolic blood pressure. For assertion findings, the TopicCode contains a code representing the condition, allergy, or other item being asserted. In all cases, the TopicCode describes the topic independent of the context of the action or the finding." - Value: CodeableConcept - -Abstract Element: ActionTopic -Based on: StatementTopic -Description: "An entry related to an action or intervention, whether potential or actual, past or future. An intervention is an action addressing a undesired health state, behavior, risk, or goal." -0..1 Category - - -Element: FindingTopic -Based on: StatementTopic -Concept: TBD -Description: "Base class - independent of context - for all kinds of determinations: questions/answers, conditions, observations, allergies, and other findings. -The subject of a finding can be the entire patient, or an entity such as a location body structure, intervention, or condition. Things observed about the subject can include social and behavioral factors, subjective and objective observations, and assessments." -0..1 FindingMethod -0..1 Details -0..* Media - - Element: FindingMethod - Concept: TBD - Description: "The technique used to create the finding, for example, the specific imaging technical, lab test code, or assessment vehicle." - Value: CodeableConcept should be from FindingMethodVS - -Element: ObservationTopic -// All attributes of observation are defined at this level. Any subclass uses subtractive methods to define relevant attributes -Based on: FindingTopic -Concept: MTH#C1554188 -Description: "The base class, independent of context for evaluations (measurements, tests, or questions). The subject of a finding can be the entire patient, or an entity such as a location body structure, intervention, or condition. Things observed about the subject can include social and behavioral factors, subjective and objective observations, and assessments." -1..* Category from http://hl7.org/fhir/ValueSet/observation-category if covered -0..1 AnatomicalLocation // TODO: Change from element to code to align with FHIR?? -0..1 Focus -0..1 ref(Device) -0..1 ref(Specimen) -0..* Precondition -0..* ReferenceRange // applies to a quantitative measurement only -0..* EvaluationComponent -0..1 PanelMembers - - - Element: Focus - Description: "The aspect or attribute of the subject of information that the finding relates to, other than an anatomical location. For example, the finding could deal with a condition, a behavior, a wound, or tumor. These are entities that are implied by clinical statements (see cimi.entity.MaterializedAssertion)" - Value: CodeableConcept or Identifier or ref(EntityOrRole) - - Element: EvaluationComponent - Description: "A simplified, non-separable evaluation consisting of a finding code (represented by the Concept), value (or exception value), reference range, and interpretation. The subject of the evaluation component is the same as in the parent evaluation." - Value: (Quantity or CodeableConcept or string or Range or Ratio or Media or time or dateTime or TimePeriod or IntegerQuantity) - 0..1 TopicCode - 0..1 ExceptionValue from ExceptionValueVS if covered - 0..1 Interpretation - 0..* ReferenceRange - - Element: CodedEvaluationComponent - Based on: EvaluationComponent - Description: "An evaluation component whose value is a code (concept)." - Value: CodeableConcept - 0..0 ReferenceRange - - Element: PanelMembers - Concept: TBD - Description: "PanelMembers represent the elements of a group of a related but independent evaluations. - Examples are the measurements that compose a complete blood count (CBC), or the elements of a pathology report. Each member is an independent evaluation, but the grouping reflects a composite lab order, shared specimen, or a single report author. Typically the Category and Reason are not given for individual findings that are part of the panel, but rather given at the level of the panel itself." - 0..* ref(Observation) - - Element: Precondition - Concept: TBD - Description: "A description of the conditions or context of an observation, for example, under sedation, fasting or post-exercise. Body position and body site are also qualifiers, but handled separately. A qualifier cannot modify the measurement type; for example, a fasting blood sugar is still a blood sugar. " - Value: CodeableConcept or ref(Observation) - - Element: ReferenceRange - Concept: MTH#C0883335 - Description: "The usual or acceptable range for a test result." - Value: Range // TODO: align this with FHIR - 0..1 Type from http://hl7.org/fhir/ValueSet/referencerange-meaning if covered - 0..1 ApplicableSubpopulation - 0..1 ApplicableAgeRange - - Element: ApplicableSubpopulation - Concept: MTH#C0039309 "Target Population" - Description: "Codes to indicate the target population this reference range applies to. For example, a reference range may be based on the normal population or a particular sex or race." - Value: CodeableConcept from http://hl7.org/fhir/ValueSet/referencerange-appliesto if covered - - Element: ApplicableAgeRange - Concept: TBD - Description: "The age at which this reference range is applicable. This is a neonatal age (e.g. number of weeks at term) if the meaning says so." // FHIR: how exactly does one indicate a neonatal or prenatal age? - Value: Range - -Element: LaboratoryObservationTopic -Based on: ObservationTopic -Description: "The topic composition for laboratory observations. A specimen is required, anatomical location is excluded (since the specimen indicates the collection body site). Also includes a diagnostic service (indicating the type of laboratory), not present in general observations." -1..1 ref(Specimen) -0..0 AnatomicalLocation // AnatomicalLocation is where the Specimen was collected - Category is OBSCAT#laboratory -0..* DiagnosticService - - Element: DiagnosticService - Concept: TBD - Description: "The service completing the observations, e.g. biochemistry, microbiology, blood bank, etc." - Value: CodeableConcept from DiagnosticServiceVS if covered - - -Element: AssertionTopic -Based on: FindingTopic -Description: "The base topic for conditions, allergies, adverse events, etc. These are things that are asserted to exist or not. The Value is interpreted in the context of the class; for an AdverseSensitivityToSubstance, the value is the substance, for a Condition, the Value represents the type of condition found." - -Element: ConditionTopic -Based on: AssertionTopic -Description: "A condition, independent of context. 'Condition' is interpreted broadly to include disorder, abnormality, problem, injury, complaint, functionality, concern, illness, disease, ailment, sickness, affliction, upset, difficulty, disorder, symptom, worry, or trouble, independent of context. -CIMI deviation: AnatomicalLocation is included here, rather than being a property of FindingSiteAssertionTopic, since it is a common property of conditions. Severity, diseasePhase, periodicity, and other properites of an actual observed condition belong in ConditionPresenceContext. " - TopicCode from http://hl7.org/fhir/us/core/ValueSet/us-core-problem if covered -1..* Category from ConditionCategoryVS -0..* AnatomicalLocation -0..* ConditionCause - - Element: ConditionCause - Description: "The cause of the condition. This includes such causes as disease vectors and endogenous states (e.g., macular degeneration due to diabetes), substances, medications, micro-organisms, and forces associated with the occurrence of a Condition from temporal or causative perspectives" - Value: CodeableConcept or ref(Entity) or ref(ClinicalStatement) - // probably other attributes needed, such as likelihood or type of cause - - - - - - diff --git a/spec/cimi_topic_vs.txt b/spec/cimi_topic_vs.txt deleted file mode 100644 index 2014be2c..00000000 --- a/spec/cimi_topic_vs.txt +++ /dev/null @@ -1,17 +0,0 @@ -Grammar: ValueSet 5.0 -Namespace: shr.core - -CodeSystem: MTH = http://ncimeta.nci.nih.gov -CodeSystem: LNC = http://loinc.org - - -ValueSet: ConditionCategoryVS -#disease "A disorder of structure or function in a human, animal, or plant, especially one that produces specific signs or symptoms or that affects a specific location and is not simply a direct result of physical injury." -#functional_impairment "A disability experienced by the subject." -#structural_abnormality "An abnormality of physiologic structure." -#concern "Something the subject is worried about, which may or may not have yet been manifested. The object of the concern does not have to be a medical disorder." -#symptom "A sign or manifestation of a deeper cause, of known or unknown etiology, e.g. pain or ringing in the ears." -#adverse_reaction "An adverse reaction to an intervention." - -ValueSet: FindingMethodVS -Includes codes from LNC \ No newline at end of file diff --git a/spec/config.json b/spec/config.json index 08c4891c..1bf0bb6a 100644 --- a/spec/config.json +++ b/spec/config.json @@ -1,20 +1,36 @@ { - "projectName": "Example Project", - "projectShorthand": "EXAMPLE", - "projectURL": "http://example.com", - "fhirURL": "http://example.com/fhir", - "implementationGuide": { - "indexContent": "exampleIndexContent.html" + "projectName": "Standard Health Record", + "projectShorthand": "SHR", + "projectURL": "http://hl7.org/fhir/us/projectURL/", + "fhirURL": "http://hl7.org/fhir/us/shr/DSTU2/", + "entryTypeURL": "http://hl7.org/fhir/us/entryTypeURL/spec", + "fhirTarget": "FHIR_DSTU_2", + "implementationGuide": + { + "npmName": "hl7.fhir.us.shr", + "version": "0.1.0", + "includeLogicalModels": true, + "includeModelDoc": true, + "indexContent": "LandingPageShr.html", + "historyLink": "http://hl7.org/fhir/us/shr/history.html", + "primarySelectionStrategy": + { + "strategy": "entry" + } }, - "publisher": "Example Publisher", + "filterStrategy": + { + "filter": false + }, + "publisher": "The MITRE Corporation: Standard Health Record Collaborative", "contact": [ { "telecom": [ { "system": "url", - "value": "http://example.com" + "value": "http://standardhealthrecord.org" } ] } ] -} +} \ No newline at end of file diff --git a/spec/dme.txt b/spec/dme.txt new file mode 100644 index 00000000..b4d66422 --- /dev/null +++ b/spec/dme.txt @@ -0,0 +1,35 @@ +Grammar: DataElement 5.0 +Namespace: dme +Description: "Classes pertaining to ordering durable medical devices." +Uses: shr.core + +CodeSystem: PUB = http://hl7.org/fhir/publication-status + +EntryElement: DTR-Questionnaire +Based on: Questionnaire +Description: "Document templates and rules." +Status is PUB#active +0..0 IsExperimental +1..* ContactDetail +1..1 LastUpdated +1..* QuestionnaireItem +1..1 QuestionnaireItem.Question +1..* PayerLibrary + QuestionnaireItem is type DTR-QuestionnaireItem + + + Element: PayerLibrary + Description: "Computable rules and queries to determine if a patient meets requirements for desired service." + Value: ref(Library) + + EntryElement: Library + + Element: DTR-QuestionnaireItem + Based on: QuestionnaireItem + Description: "Includes extensions" + 1..1 CalculatedValue + + Element: CalculatedValue + Description: "output value" + Value: string + diff --git a/spec/dme_map_stu3.txt b/spec/dme_map_stu3.txt new file mode 100644 index 00000000..62e7ff28 --- /dev/null +++ b/spec/dme_map_stu3.txt @@ -0,0 +1,14 @@ +Grammar: Map 5.1 +Namespace: dme +Target: FHIR_STU_3 + +Library maps to Library: + +//CalculatedValue maps to http://hl7.org/fhir/StructureDefinition/cqif-calculatedValue: + +DTR-Questionnaire maps to http://hl7.org/fhir/StructureDefinition/cqif-questionnaire: + PayerLibrary maps to http://hl7.org/fhir/StructureDefinition/cqif-library +// DTR-QuestionnaireItem.CalculatedValue maps to item.cqif-calculatedValue +// DTR-QuestionnaireItem.CalculatedValue maps to http://hl7.org/fhir/StructureDefinition/cqif-calculatedValue + + diff --git a/spec/exampleIndexContent.html b/spec/exampleIndexContent.html deleted file mode 100644 index 0eca1a97..00000000 --- a/spec/exampleIndexContent.html +++ /dev/null @@ -1 +0,0 @@ -This is a Example Project FHIR implementation guide.
\ No newline at end of file diff --git a/spec/ig-breast-config.json b/spec/ig-breast-config.json index 09cf24fc..734e4a0c 100644 --- a/spec/ig-breast-config.json +++ b/spec/ig-breast-config.json @@ -1,32 +1,38 @@ { - "projectName": "Standard Health Record", - "projectShorthand": "SHR", - "projectURL": "http://standardhealthrecord.org", - "fhirURL": "http://standardhealthrecord.org/fhir", - "entryTypeURL": "http://standardhealthrecord.org/spec/", - "implementationGuide": + "projectName": "HL7 FHIR Implementation Guide: Breast Cancer Data, Release 1 - US Realm (Draft for Comment 2)", + "projectShorthand": "BC", + "projectURL": "http://hl7.org/fhir/us/projectURL/", + "fhirURL": "http://hl7.org/fhir/us/shr/", + "entryTypeURL": "http://hl7.org/fhir/us/entryTypeURL/spec", + "fhirTarget": "FHIR_STU_3", + "implementationGuide": { + "npmName": "hl7.fhir.us.breastcancer", + "version": "0.2.0", "includeLogicalModels": true, "includeModelDoc": true, - "indexContent": "LandingPageBreastCancer.html", - "primarySelectionStrategy": + "indexContent": "LandingPageBreastCancer.html", + "historyLink": "http://hl7.org/fhir/us/breastcancer/history.html", + "primarySelectionStrategy": { - "strategy": "entry" + "strategy": "namespace", + "primary": ["oncology"], + "hideSupporting": true } - }, + }, "filterStrategy": { "filter": true, "strategy": "namespace", - "target": ["shr.oncology"] + "target": ["oncology"] }, - "publisher": "The MITRE Corporation: Standard Health Record Collaborative", + "publisher": "The HL7 Cancer Interoperability Group sponsored by Clinical Interoperability Council Work Group (CIC)", "contact": [ { "telecom": [ { "system": "url", - "value": "http://standardhealthrecord.org" + "value": "http://www.hl7.org/Special/committees/cic/index.cfm" } ] } diff --git a/spec/ig-cimi-config.json b/spec/ig-cimi-config.json deleted file mode 100644 index 1bcfedee..00000000 --- a/spec/ig-cimi-config.json +++ /dev/null @@ -1,34 +0,0 @@ -{ - "projectName": "Clinical Information Modeling Initiative", - "projectShorthand": "CIMI", - "projectURL": "http://hl7.org/cimi", - "fhirURL": "http://hl7.org/cimi/fhir", - "entryTypeURL": "http://hl7.org/cimi/spec/", - "implementationGuide": - { - "includeLogicalModels": true, - "includeModelDoc": true, - "indexContent": "LandingPageCimi.html", - "primarySelectionStrategy": - { - "strategy": "entry" - } - }, - "filterStrategy": - { - "filter": true, - "strategy": "namespace", - "target": ["cimi.context", "cimi.core", "cimi.element", "cimi.encounter", "cimi.entity", "cimi.statement", "cimi.topic"] - }, - "publisher": "The Clinical Information Modeling Initiative (CIMI)", - "contact": [ - { - "telecom": [ - { - "system": "url", - "value": "http://hl7.org/cimi" - } - ] - } - ] -} \ No newline at end of file diff --git a/spec/ig-dme-config.json b/spec/ig-dme-config.json new file mode 100644 index 00000000..fd45c07e --- /dev/null +++ b/spec/ig-dme-config.json @@ -0,0 +1,40 @@ +{ + "projectName": "HL7 FHIR Profile: Durable Medical Device, Release 0.1.0", + "projectShorthand": "DME", + "projectURL": "http://hl7.org/fhir/us/dme/", + "fhirURL": "http://hl7.org/fhir/us/shr/", + "entryTypeURL": "http://hl7.org/fhir/us/entryTypeURL/spec", + "fhirTarget": "FHIR_STU_3", + "implementationGuide": + { + "npmName": "hl7.fhir.us.dme", + "version": "0.1.0", + "includeLogicalModels": false, + "includeModelDoc": false, + "indexContent": "LandingPageExample.html", + "historyLink": "http://hl7.org/fhir/us/dme/history.html", + "primarySelectionStrategy": + { + "strategy": "namespace", + "primary": ["dme"], + "hideSupporting": true + } + }, + "filterStrategy": + { + "filter": true, + "strategy": "namespace", + "target": ["dme"] + }, + "publisher": "HL7", + "contact": [ + { + "telecom": [ + { + "system": "url", + "value": "http://standardhealthrecord.org" + } + ] + } + ] +} \ No newline at end of file diff --git a/spec/ig-odh-config.json b/spec/ig-odh-config.json index a6583598..db101a22 100644 --- a/spec/ig-odh-config.json +++ b/spec/ig-odh-config.json @@ -1,25 +1,30 @@ { - "projectName": "Standard Health Record", - "projectShorthand": "SHR", - "projectURL": "http://standardhealthrecord.org", - "fhirURL": "http://standardhealthrecord.org/fhir", - "entryTypeURL": "http://standardhealthrecord.org/spec/", - "implementationGuide": + "projectName": "HL7 FHIR Profile: Occupational Data for Health (ODH), Release 1 (Standard for Trial Use)", + "projectShorthand": "ODH", + "projectURL": "http://hl7.org/fhir/us/odh/", + "fhirURL": "http://hl7.org/fhir/us/shr/", + "entryTypeURL": "http://hl7.org/fhir/us/entryTypeURL/spec", + "fhirTarget": "FHIR_STU_3", + "implementationGuide": { + "npmName": "hl7.fhir.us.odh", + "version": "1.0.0", "includeLogicalModels": true, "includeModelDoc": false, - "indexContent": "LandingPageOccupation.html", - "primarySelectionStrategy": + "indexContent": "LandingPageOccupation.html", + "historyLink": "http://hl7.org/fhir/us/odh/history.html", + "primarySelectionStrategy": { "strategy": "namespace", - "primary": ["shr.occupation"] + "primary": ["odh"], + "hideSupporting": true } - }, + }, "filterStrategy": { "filter": true, "strategy": "namespace", - "target": ["shr.occupation"] + "target": ["odh"] }, "publisher": "HL7", "contact": [ diff --git a/spec/ig-oncocore-config.json b/spec/ig-oncocore-config.json new file mode 100644 index 00000000..b8883c4c --- /dev/null +++ b/spec/ig-oncocore-config.json @@ -0,0 +1,39 @@ +{ + "projectName": "HL7 FHIR Implementation Guide: minimal Common Oncology Data Elements (mCODE), Release 0.7 - US Realm (Draft for Comment 1)", + "projectShorthand": "oncocore", + "projectURL": "http://hl7.org/fhir/us/projectURL/", + "fhirURL": "http://hl7.org/fhir/us/shr/", + "entryTypeURL": "http://hl7.org/fhir/us/entryTypeURL/spec/", + "fhirTarget": "FHIR_DSTU_2", + "implementationGuide": + { + "npmName": "oncocore", + "version": "0.7.0", + "includeLogicalModels": false, + "includeModelDoc": true, + "indexContent": "IndexFolder_Oncocore", + "primarySelectionStrategy": + { + "strategy": "hybrid", + "primary": ["oncocore"], + "hideSupporting": true + } + }, + "filterStrategy": + { + "filter": true, + "strategy": "hybrid", + "target": ["oncocore", "shr.base.Entry"] + }, + "publisher": "The MITRE Corporation", + "contact": [ + { + "telecom": [ + { + "system": "url", + "value": "http://www.hl7.org/Special/committees/cic/index.cfm" + } + ] + } + ] +} diff --git a/spec/ig-shr-all-config.json b/spec/ig-shr-all-config.json new file mode 100644 index 00000000..ec43f85e --- /dev/null +++ b/spec/ig-shr-all-config.json @@ -0,0 +1,36 @@ +{ + "projectName": "HL7 FHIR Implementation Guide: Standard Health Record, Release 0.5", + "projectShorthand": "shr", + "projectURL": "http://hl7.org/fhir/us/shr/", + "fhirURL": "http://hl7.org/fhir/us/shr/", + "entryTypeURL": "http://hl7.org/fhir/us/shr/", + "fhirTarget": "FHIR_STU_3", + "filterStrategy": + { + "filter": false + }, + "implementationGuide": + { + "npmName": "shr", + "version": "0.5.0", + "includeLogicalModels": true, + "includeModelDoc": true, + "indexContent": "LandingPageShr.html", + "primarySelectionStrategy": + { + "strategy": "entry", + "hideSupporting": true + } + }, + "publisher": "The MITRE Corporation", + "contact": [ + { + "telecom": [ + { + "system": "url", + "value": "http://www.standardhealthrecord.org" + } + ] + } + ] +} diff --git a/spec/ig-shr-config.json b/spec/ig-shr-config.json deleted file mode 100644 index d998a826..00000000 --- a/spec/ig-shr-config.json +++ /dev/null @@ -1,28 +0,0 @@ -{ - "projectName": "Standard Health Record", - "projectShorthand": "SHR", - "projectURL": "http://standardhealthrecord.org", - "fhirURL": "http://standardhealthrecord.org/fhir", - "entryTypeURL": "http://standardhealthrecord.org/spec/", - "implementationGuide": - { - "includeLogicalModels": true, - "includeModelDoc": true, - "indexContent": "LandingPageShr.html", - "primarySelectionStrategy": - { - "strategy": "entry" - } - }, - "publisher": "The MITRE Corporation: Standard Health Record Collaborative", - "contact": [ - { - "telecom": [ - { - "system": "url", - "value": "http://standardhealthrecord.org" - } - ] - } - ] -} \ No newline at end of file diff --git a/spec/ig-shrcore-config.json b/spec/ig-shrcore-config.json new file mode 100644 index 00000000..1fbe0301 --- /dev/null +++ b/spec/ig-shrcore-config.json @@ -0,0 +1,39 @@ +{ + "projectName": "HL7 FHIR Implementation Guide: SHR Core, Release 0.5 - US Realm (Draft for Comment 1)", + "projectShorthand": "shrcore", + "projectURL": "http://hl7.org/fhir/us/shrcore/", + "fhirURL": "http://hl7.org/fhir/us/shr/", + "entryTypeURL": "http://hl7.org/fhir/us/shrcore/spec/", + "fhirTarget": "FHIR_STU_3", + "filterStrategy": + { + "filter": true, + "strategy": "namespace", + "target": ["shr.core"] + }, + "implementationGuide": + { + "npmName": "shr", + "version": "0.5.0", + "includeLogicalModels": true, + "includeModelDoc": true, + "indexContent": "LandingPageShr.html", + "primarySelectionStrategy": + { + "strategy": "namespace", + "primary": ["shr.core"], + "hideSupporting": true + } + }, + "publisher": "The MITRE Corporation", + "contact": [ + { + "telecom": [ + { + "system": "url", + "value": "http://www.standardhealthrecord.org" + } + ] + } + ] +} diff --git a/spec/ig-wound-config.json b/spec/ig-wound-config.json index 312bf446..df566a2f 100644 --- a/spec/ig-wound-config.json +++ b/spec/ig-wound-config.json @@ -1,24 +1,57 @@ { - "projectName": "Skin and Wound", + "projectName": "HL7 FHIR Profile: Skin and Wound Assessment, Release 1 (For Comment)", "projectShorthand": "SW", - "projectURL": "http://standardhealthrecord.org", - "fhirURL": "http://standardhealthrecord.org/fhir", - "entryTypeURL": "http://standardhealthrecord.org/spec/", - "implementationGuide": + "projectURL": "http://hl7.org/fhir/us/projectURL/", + "fhirURL": "http://hl7.org/fhir/us/shr/", + "entryTypeURL": "http://hl7.org/fhir/us/entryTypeURL/spec", + "fhirTarget": "FHIR_STU_3", + "provinenceInfo": { + "leadAuthor": { + "name":"Mark Kramer", + "organization": "The MITRE Corporation", + "email": "mkramer@mitre.org" + }, + "otherAuthors": [ + { + "name": "Rute Martins Baptista", + "email": "rbatiste@mitre.org" + }, + { + "name": "Abhijay Bhatnagar", + "email": "abhatnagar@mitre.org" + }, + { + "name": "Chris Moesel", + "email": "cmoesel@mitre.org" + }, + { + "name": "May Terry", + "email": "mokeefe@mitre.org" + } + ], + "license": "Creative Commons CC-BYThis is a Standard Health Record FHIR implementation guide.
\ No newline at end of file diff --git a/spec/shr_action.txt b/spec/shr_action.txt new file mode 100644 index 00000000..197b7aec --- /dev/null +++ b/spec/shr_action.txt @@ -0,0 +1,115 @@ +Grammar: DataElement 5.0 +Namespace: shr.core + +//---------- Actions -------------- + +Abstract Element: ActionStatement +Based on: ClinicalStatement +Description: "Abstract class representing any type of action or event." +0..* ReasonCode +0..* ReasonReference +1..1 SubjectOfRecord + StatusOrActive is type Status + + Element: ReasonCode + Concept: MTH#C0566251 + Description: "The justification, as a code. + Reason is a string or CodeableConcept in DSTU2 but in later versions only a CodeableConcept, so we are not going to support a string." + Value: CodeableConcept + + Element: ReasonReference + Description: "The justification, as reference to a condition or observation." + Value: ref(Condition) or ref(Observation) + +Abstract Element: ActionPerformed +Based on: ActionStatement +Description: "Abstract class representing an event occurrence or performance of any type of action." +1..1 OccurrenceTimeOrPeriod +0..* Participation +1..1 Status // change to required... should be from http://hl7.org/fhir/ValueSet/event-status DSTU 2 change (conflict in required data sets) +0..1 Method +0..1 RelatedRequest + + Element: Participation + Concept: TBD + Description: "Record of someone or something involvement in an activity or event." + 0..1 Participant + 0..1 ParticipationType // role + 0..1 ParticipationPeriod + 0..1 OnBehalfOf + + Element: ParticipationType + Concept: MTH#C1553854 + Description: "The role played by the participant engaged in the action, for example, as the attending physician, surgical assistant, etc." + Value: CodeableConcept could be from http://hl7.org/fhir/ValueSet/performer-role + + Element: ParticipationPeriod + Concept: TBD + Description: "The point in time or span of time the participant is involved." + Value: TimePeriod + + + Element: Method + Concept: TBD + Description: "The technique used to carry out an action, for example, the specific imaging technical or assessment vehicle." + Value: CodeableConcept // TODO: limit to a procedure code + + Element: RelatedRequest + Concept: TBD + Description: "The proposal, order, or plan that is partly or wholly fulfilled by the performance of this act." + Value: ref(ActionRequested) + + /* + Element: EnactsPlan + Concept: TBD + Description: "The plan that is partly or wholly enacted by the performance of this act." + Value: ref(ActionRequested) +*/ + + Element: Outcome + Concept: TBD + Description: "The result of performing an action or behavior, for example, an adverse reaction or new finding." + Value: CodeableConcept could be from http://hl7.org/fhir/ValueSet/procedure-outcome + + +Abstract Element: ActionRequested +Based on: ActionStatement +Description: "Abstract class representing a request for any type of action to be performed." +0..1 Type // type of request +0..1 Author +1..1 RequestIntent +1..1 Status // should be from http://hl7.org/fhir/ValueSet/request-status + // DSTU2 change (conflicting required value sets in MedicationRequest between argo and us-core) +0..1 ExpectedPerformanceTime +0..1 ExpectedPerformerType +0..1 Recipient +0..1 PriorityCode //should be from http://hl7.org/fhir/ValueSet/request-priority // DSTU2 change (conflicting value sets) +0..* Annotation +0..1 CommunicationMethod +0..0 InformationSource +0..0 Recorder + + Element: RequestIntent + Description: "Indicates the level of authority/intentionality associated with the request and where the request fits into the workflow chain." + Value: CodeableConcept should be from http://hl7.org/fhir/ValueSet/request-intent + + Element: ExpectedPerformanceTime + Concept: TBD + Description: "When an action should be done. If the action is a series or recurs (e.g. daily blood sugar testing in the morning) then a Timing can be used to describe the periodicity." + Value: dateTime or TimePeriod or Timing + + Element: ExpectedPerformerType + Concept: TBD + Description: "What type of party should carry out the testing." + Value: CodeableConcept // what ValueSet?? + + Element: Recipient + Concept: TBD + Description: "Who this request is being addressed to." + Value: ref(EntityOrRole) + + Element: CommunicationMethod + Concept: TBD + Description: "This is the method the provider used to communicate. Examples include: Written, Telephoned, Verbal, Electronically Entered, Policy, Service Correction, Duplicate, etc. 'Code indicating the origin of the prescription.' - NCPDP Telecommunication (Field 419-DJ, Data Dictionary 201104). Possible values include: Written; Telephone; Electronic; Facsimile; Pharmacy; Not Known." + + Value: CodeableConcept diff --git a/spec/shr_adverse.txt b/spec/shr_adverse.txt new file mode 100644 index 00000000..717290c9 --- /dev/null +++ b/spec/shr_adverse.txt @@ -0,0 +1,86 @@ +Grammar: DataElement 5.0 +Namespace: shr.core + +CodeSystem: MTH = http://ncimeta.nci.nih.gov + + +Element: AdverseEvent +Based on: ClinicalStatement +Description: "A record of an untoward or unexpected event in a patient under treatment, and which does not necessarily have to have a causal relationship with that treatment. Adverse events may capture either a workflow breach that may or may not result in harm, but must be documented for quality improvement purposes, or an adverse finding whether or not it can be traceable to an actual workflow breach." +0..1 Identifier + Recorder value is type PatientOrPractitionerOrRelatedPerson +1..1 SubjectOfRecord value is type PatientOrResearchSubjectOrMedicationOrDevice +1..1 OccurrenceTime +0..1 Type from MedDRAVS +1..1 Seriousness from SeriousnessVS // to be replaced with http://hl7.org/fhir/ValueSet/adverse-event-seriousness in FHIR 4 +//0..1 TBD "PatternOfEvent" // from STDM +0..1 Outcome from http://hl7.org/fhir/ValueSet/adverse-event-outcome +0..1 CommentOrDescription +0..* AdverseEventCondition +0..* CausalAttribution +0..* ActionTaken +0..1 AssociatedStudy + + + Element: Seriousness + Concept: MTH#C2985911 + Description: "A coded value specifying the level of injury suffered by the subject for whom the event is reported, using the CTCAE coding system." + Value: CodeableConcept + + Element: AdverseEventCondition + Concept: MTH#C1280464 + Description: "The condition, sign or symptom triggering the adverse event report." + 1..1 ref(Condition) + + Element: CausalAttribution + Concept: MTH#C1510821 "Adverse Event Attribution to Product or Procedure" + Description: "A possible cause of an observed adverse event, known or theorized. There can be more than one possible cause." + 1..1 PossibleCause + 1..1 CauseCategory + 1..1 Certainty + 0..1 RouteIntoBody // aka exposure route + + Element: PossibleCause + Concept: TBD + Description: "The possible cause of the adverse event." + Value: CodeableConcept should be from http://hl7.org/fhir/ValueSet/substance-code or ref(Substance) or ref(Medication) or ref(MedicationAdministration) or ref(MedicationStatement) or ref(Device) // or ref(ProcedurePerformed) or ref(Immunization) (in FHIR R4) + + Element: CauseCategory + Concept: TBD + Description: "Whether the adverse event is attributed to a treatment, course of the disease, unrelated to either, or unknown. " + Value: CodeableConcept from AttributionCategoryVS + + Element: Certainty + Concept: TBD + Description: "The degree of confidence in a conclusion or assertion." + Value: CodeableConcept + + Element: ActionTaken + Concept: TBD + Description: "The action taken as a result of the adverse reaction. May include changing or discontinuing medication, reducing dose, etc." + 1..1 CommentOrDescription + 0..1 ref(ActionStatement) // such as MedicationChangeStatement + + Element: AssociatedStudy + Description: "The related clinical trial or other formal study." + Value: ref(ResearchStudy) + +// Adverse drug reactions are a subset of adverse events, and are specifically associated with an exposure to a medication. +EntryElement: AdverseDrugReaction +Based on: AdverseEvent +Description: "A noxious and unintended response to a medicinal product. To be considered an ADR, a causal relationship must be at least suspected by the medical practitioner. The principal difference between an adverse drug reaction (ADR) an adverse event (AE) and is that a causal relationship is suspected for the ADR, but is not required for the AE. Adverse drug reactions are therefore a subset of adverse event reports." +1..* CausalAttribution + CausalAttribution.PossibleCause is type PossibleDrugCause + + Element: PossibleDrugCause + Based on: PossibleCause + Concept: TBD + Description: "Drug suspected as possible cause of the adverse event." + Value: ref(Medication) or ref(MedicationAdministration) or ref(MedicationStatement) + +// In truth, this should be a filter on AdverseDrugReaction, not a separate class +EntryElement: ToxicAdverseDrugReaction +Based on: AdverseDrugReaction +Concept: MTH#C0542243 +Description: "A grade 3 or 4 adverse reaction to medication." + Seriousness from ToxicSeriousnessVS diff --git a/spec/shr_adverse_map_dstu2.txt b/spec/shr_adverse_map_dstu2.txt new file mode 100644 index 00000000..6629d5ce --- /dev/null +++ b/spec/shr_adverse_map_dstu2.txt @@ -0,0 +1,7 @@ +Grammar: Map 5.1 +Namespace: shr.core +Target: FHIR_STU_2 + +AdverseEvent maps to Basic: + + diff --git a/spec/shr_adverse_map_stu3.txt b/spec/shr_adverse_map_stu3.txt new file mode 100644 index 00000000..fb1ffee9 --- /dev/null +++ b/spec/shr_adverse_map_stu3.txt @@ -0,0 +1,20 @@ +Grammar: Map 5.1 +Namespace: shr.core +Target: FHIR_STU_3 + +AdverseEvent maps to AdverseEvent: + Identifier maps to identifier + Recorder maps to recorder + Type maps to extension + CommentOrDescription maps to description + SubjectOfRecord maps to subject + AssociatedStudy maps to study + Seriousness maps to seriousness + OccurrenceTime maps to date + Outcome maps to outcome +// FHIR TODO: AdverseEvent.eventParticipant is underdefined (no role) + CausalAttribution.PossibleCause maps to suspectEntity.instance + CausalAttribution.Certainty maps to suspectEntity.causalityAssessment + +AdverseDrugReaction maps to AdverseEvent: + constrain suspectEntity to 1..* \ No newline at end of file diff --git a/spec/cimi_adverse_vs.txt b/spec/shr_adverse_vs.txt similarity index 68% rename from spec/cimi_adverse_vs.txt rename to spec/shr_adverse_vs.txt index 71b04022..88508a22 100644 --- a/spec/cimi_adverse_vs.txt +++ b/spec/shr_adverse_vs.txt @@ -1,5 +1,5 @@ Grammar: ValueSet 5.0 -Namespace: cimi.adverse +Namespace: shr.core CodeSystem: MDR = http://www.meddra.org CodeSystem: MTH = http://ncimeta.nci.nih.gov @@ -10,12 +10,18 @@ Includes codes from MDR ValueSet: SeriousnessVS Description: "Grade of adverse event." +SCT#255604002 "Mild (qualifier value)" +SCT#6736007 "Moderate (severity modifier) (qualifier value)" +SCT#24484000 "Severe (severity modifier) (qualifier value)" +SCT#442452003 "Life threatening severity (qualifier value)" +SCT#399166001 "Fatal (qualifier value)" +/* MTH#C1513302 "Mild Adverse Event. Transient or mild discomfort, no limitaion in activity; no medical intervention or therapy required" MTH#C1513374 "Moderate Adverse Event. Daily activity is affected moderately; some assistance might be needed; no or minimal medical intervention/therapy required." MTH#C1519275 "Severe Adverse Event. Daily activity is markedly reduced; some assistance usually required; medical intervention/therapy required, hospitalization or hospice care possible." MTH#C1517874 "Potentially Life-Threatening Adverse Event. Extreme limitation to daily activity, significant assistance required; significant medical intervention/therapy, hospitalization or hospice care very likely." MTH#C1559081 "Fatal Adverse Event. Adverse event associated with death" - +*/ ValueSet: AttributionCategoryVS Description: "Whether the adverse event is attributed to a treatment, course of the disease, medical error, unrelated to either, or unknown. " @@ -28,9 +34,9 @@ Description: "Whether the adverse event is attributed to a treatment, course of ValueSet: ToxicSeriousnessVS Description: "Grade of adverse event at severe or higher grade." -MTH#C1519275 "Severe Adverse Event. Daily activity is markedly reduced; some assistance usually required; medical intervention/therapy required, hospitalization or hospice care possible." -MTH#C1517874 "Potentially Life-Threatening Adverse Event. Extreme limitation to daily activity, significant assistance required; significant medical intervention/therapy, hospitalization or hospice care very likely." -MTH#C1559081 "Fatal Adverse Event. Adverse event associated with death" +SCT#24484000 "Severe (severity modifier) (qualifier value)" //"Severe Adverse Event. Daily activity is markedly reduced; some assistance usually required; medical intervention/therapy required, hospitalization or hospice care possible." +SCT#442452003 "Life threatening severity (qualifier value)" // "Potentially Life-Threatening Adverse Event. Extreme limitation to daily activity, significant assistance required; significant medical intervention/therapy, hospitalization or hospice care very likely." +SCT#399166001 "Fatal (qualifier value)" // "Fatal Adverse Event. Adverse event associated with death." ValueSet: ManifestationVS Description: "An observable sign or symptom of an underlying physical or psychological cause." diff --git a/spec/shr_allergy.txt b/spec/shr_allergy.txt new file mode 100644 index 00000000..553320db --- /dev/null +++ b/spec/shr_allergy.txt @@ -0,0 +1,60 @@ +Grammar: DataElement 5.0 +Namespace: shr.core + +CodeSystem: SCT = http://snomed.info/sct +CodeSystem: CAT = http://hl7.org/fhir/allergy-intolerance-category + + +EntryElement: AllergyIntolerance +Based on: ConditionOrObservation +Concept: SCT#473010000 "Hypersensitivity condition (disorder)" +// or SCT#420134006 "Propensity to adverse reactions (disorder)"? +Description: "A finding related to the presence of an individual's risk or sensitivity to a substance or class of substances. Per US Core specification, the result includes SNOMED codes representing 'No known allergy'. In AllergyIntolerance, the reactions are included in-line, rather than referencing to conditions (in contrast to AdverseEvent)." + InformationSource value is type PatientOrPractitionerOrRelatedPerson + Recorder value is type PatientOrPractitioner // FHIR only allows Patient or Practitioner as recorder +1..1 SubjectOfRecord value is type ref(Patient) +1..1 Status // from http://hl7.org/fhir/ValueSet/allergy-verification-status + // Conflict between V2 and V3 -- Cannot override value set constraint from http://hl7.org/fhir/ValueSet/allergy-intolerance-status to http://hl7.org/fhir/ValueSet/allergy-verification-status +0..1 ClinicalStatus from http://hl7.org/fhir/ValueSet/allergy-clinical-status +1..1 Code // from http://hl7.org/fhir/us/core/ValueSet-us-core-substance.html if covered // DSTU 2 change different required value sets +0..1 SubstanceCategory // DSTU 2 change (restrict upper cardinality to 1) +0..1 Onset +0..1 Type from http://hl7.org/fhir/ValueSet/allergy-intolerance-type +0..1 Criticality +0..1 MostRecentOccurrenceTime +0..* AllergyIntoleranceReaction + + Element: SubstanceCategory + Concept: TBD + Description: "Categorization of the risk substance as a food, drug, or environmental agent. For difficult-to-classify substances, one can leave this field empty or choose the most typical category." + Value: CodeableConcept from http://hl7.org/fhir/ValueSet/allergy-intolerance-category // change to code? + + Element: MostRecentOccurrenceTime + Description: "The time of the last or latest of a series of events." + Value: dateTime + + Element: AllergyIntoleranceReaction + Description: "Observed reaction event associated with the allergy or intolerance, expressed as a condition." + 0..1 SubstanceCode + 1..* Manifestation could be from http://hl7.org/fhir/ValueSet/clinical-findings + 0..1 BeginDateTime // from core + 0..1 Severity from http://hl7.org/fhir/ValueSet/reaction-event-severity + 0..1 RouteIntoBody + 0..1 CommentOrDescription + + Element: SubstanceCode + Concept: TBD + Description: "The substance triggering a particular allergy or intolerance reaction event. The substance may be the same as the substance cited in the AllergyIntolerance, but should be a specific substance rather than a class of substances, if known. For example, if the allergy intolerance DataValue substance is 'shellfish' the substance code for the reaction might be 'oyster'." + Value: CodeableConcept from http://hl7.org/fhir/us/core/ValueSet-us-core-substance.html if covered + + + + +/* Probably the most consistent way to define the absence (no known) allergy is to use an absence assertion, but this is not the way US Core has decided to go. Comments here are for reference only. + +// DataValue from NoKnownAllergyVS +// DataValue is SCT#716186003 "No known allergy (situation)" +// DataValue is SCT#428607008 "No known environmental allergy (situation)" +// DataValue is SCT#429625007 "No known food allergy (situation)" +// DataValue is SCT#409137002 "No known drug allergy (situation)" +*/ \ No newline at end of file diff --git a/spec/shr_allergy_map_dstu2.txt b/spec/shr_allergy_map_dstu2.txt new file mode 100644 index 00000000..87365145 --- /dev/null +++ b/spec/shr_allergy_map_dstu2.txt @@ -0,0 +1,43 @@ +Grammar: Map 5.1 +Namespace: shr.core +Target: FHIR_DSTU_2 + + +AllergyIntolerance maps to http://fhir.org/guides/argonaut/StructureDefinition/argo-allergyintolerance: + Identifier maps to identifier + SubjectOfRecord maps to patient + InformationSource maps to reporter + Recorder maps to recorder + StatementDateTime maps to recordedDate + Code maps to substance + Type maps to type + SubstanceCategory maps to category + Status maps to status + Criticality maps to criticality + // DSTU 2 change (onset only dateTime, not a choice [x]) + Onset maps to onset + // DSTU 2 change (attribute name spelling error was corrected in STU 3) + MostRecentOccurrenceTime maps to lastOccurence + AllergyIntoleranceReaction.SubstanceCode maps to reaction.substance + AllergyIntoleranceReaction.Manifestation maps to reaction.manifestation + AllergyIntoleranceReaction.BeginDateTime maps to reaction.onset + AllergyIntoleranceReaction.Severity maps to reaction.severity + AllergyIntoleranceReaction.RouteIntoBody maps to reaction.exposureRoute + AllergyIntoleranceReaction.CommentOrDescription maps to reaction.description + +/* + + +NoKnownAllergy maps to http://fhir.org/guides/argonaut/StructureDefinition/argo-allergyintolerance: +constrain clinicalStatus to 0..0 +constrain criticality to 0..0 + fix code to SCT#716186003 + +NoKnownDrugAllergyStatement: + fix code to SCT#409137002 + +NoKnownFoodAllergyStatement: + fix code to SCT#429625007 + +NoKnownEnvironmentalAllergyStatement: + fix code to SCT#428607008 */ diff --git a/spec/shr_allergy_map_stu3.txt b/spec/shr_allergy_map_stu3.txt new file mode 100644 index 00000000..41d92e84 --- /dev/null +++ b/spec/shr_allergy_map_stu3.txt @@ -0,0 +1,24 @@ +Grammar: Map 5.1 +Namespace: shr.core +Target: FHIR_STU_3 + +AllergyIntolerance maps to http://hl7.org/fhir/us/core/StructureDefinition/us-core-allergyintolerance: + Identifier maps to identifier + SubjectOfRecord maps to patient + InformationSource maps to asserter + Recorder maps to recorder + StatementDateTime maps to assertedDate + Code maps to code + Type maps to type + SubstanceCategory maps to category + Status maps to verificationStatus + ClinicalStatus maps to clinicalStatus + Criticality maps to criticality + Onset maps to onset[x] + MostRecentOccurrenceTime maps to lastOccurrence + AllergyIntoleranceReaction.SubstanceCode maps to reaction.substance + AllergyIntoleranceReaction.Manifestation maps to reaction.manifestation + AllergyIntoleranceReaction.BeginDateTime maps to reaction.onset + AllergyIntoleranceReaction.Severity maps to reaction.severity + AllergyIntoleranceReaction.RouteIntoBody maps to reaction.exposureRoute + AllergyIntoleranceReaction.CommentOrDescription maps to reaction.description diff --git a/spec/shr_allergy_vs.txt b/spec/shr_allergy_vs.txt new file mode 100644 index 00000000..169dafe0 --- /dev/null +++ b/spec/shr_allergy_vs.txt @@ -0,0 +1,13 @@ +Grammar: ValueSet 5.0 +Namespace: shr.core + + +CodeSystem: SCT = http://snomed.info/sct +CodeSystem: RXN = http://www.nlm.nih.gov/research/umls/rxnorm +CodeSystem: AVS = http://hl7.org/fhir/allergy-verification-status + + +ValueSet: AllergyVerificationStatusVS +Description: "Whether the allergy has been verified or not. Intentionally a subset of the codes in FHIR, since refuted would be reflected by correcting the 'elevated risk' element, and records entered in error are not included in SHR." +AVS#confirmed "Confirmed" +AVS#unconfirmed "Unconfirmed" diff --git a/spec/shr_assessment.txt b/spec/shr_assessment.txt new file mode 100644 index 00000000..402a9d8d --- /dev/null +++ b/spec/shr_assessment.txt @@ -0,0 +1,34 @@ +Grammar: DataElement 5.0 +Namespace: shr.core + + +EntryElement: ECOGPerformanceStatus +Based on: SimpleNonLaboratoryObservation +Description: "The Eastern Cooperative Oncology Group (ECOG) performance status grade or score, which indicates a patient’s level of daily functioning and physical ability. Source: LOINC" + Code is LNC#89247-1 "ECOG Performance Status score" + DataValue value is type IntegerQuantity + Interpretation from http://loinc.org/vs/LL529-9 +//0..0 ReferenceRange // set to 0 to 5 +0..0 SubjectOfInformation +0..0 BodySite +0..0 Device + + + +// MK: This is not cancer-specific. Probably belongs in another namespace, but not sure where. +EntryElement: KarnofskyPerformanceStatus +Based on: SimpleNonLaboratoryObservation +Description: "The Karnofsky Performance Status (KPS) is a tool used to measure a patient's functional status. It can be used to compare the effectiveness of different therapies and to help assess the prognosis of certain patients, such as those with certain cancers. The KPS score ranges from 0 to 100. Higher scores are associated with better functional status, with 100 representing no symptoms or evidence of disease, and 0 representing death [PMID: 23870327] . This panel contains LOINC terms to report the KPS score [LOINC: 89243-0] and its interpretation [LOINC: 89245-5]." + Code is LNC#89243-0 "Karnofsky Performance Status panel" + DataValue value is type IntegerQuantity + Interpretation from http://loinc.org/vs/LL4986-7 // normative answer list +0..0 SubjectOfInformation // always the patient +0..0 BodySite // not body-site specific +0..0 Device // does not require a device +// ReferenceRange.Range.LowerBound.Quantity.Number is 0.0 + ReferenceRange.Range.LowerBound.Quantity.Units is UCUM#1 +// ReferenceRange.Range.UpperBound.Quantity.Number is 5.0 + ReferenceRange.Range.UpperBound.Quantity.Units is UCUM#1 +0..0 ReferenceRange.ApplicableSubpopulation +0..0 ReferenceRange.ApplicableAgeRange + diff --git a/spec/shr_base.txt b/spec/shr_base.txt deleted file mode 100644 index da2fd301..00000000 --- a/spec/shr_base.txt +++ /dev/null @@ -1,78 +0,0 @@ -Grammar: DataElement 5.0 -Namespace: shr.base -Description: "Contains the SHR Entry definition -- the metadata added to any independent item in the SHR." -Uses: shr.core, cimi.entity, cimi.statement - -CodeSystem: MTH = http://ncimeta.nci.nih.gov - -Element: Entry -Concept: MTH#C1705654 -Description: "Metadata attributes that apply to any item represented in the standard health record. An Entry may not belong exclusively to a single person's health record, but could represent an entity that surfaces in multiple records, such as organizations or practitioners. If the entry belongs to a single person's record, then the identity of the person of record must be recorded." -0..1 ShrId -1..1 EntryId -0..1 Version -1..1 EntryType -1..1 CreationTime -1..1 LastUpdated -0..1 Narrative -0..1 Language -0..* SecurityLabel -0..* Tag -0..* DerivedFrom - Version value is type id - - Element: ShrId - Concept: TBD - Description: "A unique, persistent, permanent identifier for the overall health record belonging to the PersonOfRecord." - Value: id - - Element: EntryId - Concept: MTH#C0600091 - Description: "A persistent, permanent identifier for an entry in a health record, unique within the scope of the health record." - Value: id - - Element: EntryType // Would EntryClass be clearer? - Concept: TBD - Description: "SHR data element identifier, as a URI." - Value: uri - - Element: LastUpdated - Concept: TBD - Description: "The most recent date the entry was changed." - Value: instant - - Element: Narrative - Concept: TBD - Description: "A human-readable narrative, potentially including images, that contains a summary of the resource, and may be used to represent the content of the resource to a human." - Value: xhtml - 1..1 NarrativeQualifier - - Element: NarrativeQualifier - Concept: TBD - Description: "Additional information on how the narrative was generated, and the scope of information contained." - Value: code from http://hl7.org/fhir/ValueSet/narrative-status - - Element: SecurityLabel - Concept: TBD - Description: "A code that connects the entry to a security policy. Security labels can be updated when the resource changes, or whenever the security sub-system chooses to." - Value: Coding - - Element: Tag - Concept: TBD - Description: "A code used to relate entries to categories or workflows. Applications are not required to consider the tags when interpreting the meaning of an entry." - Value: Coding - - Element: DerivedFrom - Concept: TBD - Description: "Indicates the source of information in the case the Entry has been created by logical extension or modification of one or more source entries." - Value: ref(ClinicalStatement) - - -/* - Element: HealthRecordId - Concept: MTH#C1549718 - Description: "A unique, persistent, permanent identifier for a health record." - Value: id -*/ - - diff --git a/spec/shr_base_map.txt b/spec/shr_base_map.txt deleted file mode 100644 index 99589c2a..00000000 --- a/spec/shr_base_map.txt +++ /dev/null @@ -1,20 +0,0 @@ -Grammar: Map 5.1 -Namespace: shr.base -Target: FHIR_STU_3 - - -Entry maps to DomainResource: - EntryId maps to id - constrain meta to 1..1 - Version maps to meta.versionId - EntryType maps to meta.profile - LastUpdated maps to meta.lastUpdated - Language maps to language - Narrative maps to text - SecurityLabel maps to meta.security - Tag maps to meta.tag - - -Narrative maps to Narrative: - Value maps to div - NarrativeQualifier maps to status diff --git a/spec/shr_condition.txt b/spec/shr_condition.txt deleted file mode 100644 index 038254fb..00000000 --- a/spec/shr_condition.txt +++ /dev/null @@ -1,62 +0,0 @@ -Grammar: DataElement 5.0 -Namespace: shr.condition -Description: "The SHR Condition domain contains additional definitions used to capture assessments, diagnoses, and judgments related to problems reported or experienced by a subject." -Uses: shr.core, shr.base, cimi.core, cimi.element, cimi.context, cimi.topic, cimi.statement, cimi.entity - -CodeSystem: SCT = http://snomed.info/sct -CodeSystem: MTH = http://ncimeta.nci.nih.gov - -// -Abstract Element: BodyStructureTopic -Based on: ConditionTopic -Concept: MTH#C1268086 -Description: "Presence (or absence) of a distinct anatomical or pathological morphological feature or organizational pattern, acquired or innate. Examples include tissue types, tumors, and wounds." -0..1 Identifier -0..1 Morphology -1..* AnatomicalLocation - - Element: Morphology - Concept: TBD - Description: "The kind of structure being represented. This can define both normal and abnormal morphologies." - Value: CodeableConcept - - -EntryElement: BodyStructurePresenceStatement -Based on: ConditionPresenceStatement -Concept: TBD -Description: "Presence of a distinct anatomical or pathological morphological feature or organizational pattern, acquired or innate. Examples include tissue types, tumors, and wounds. Body structures are continuants that allow observations of the same body structure to be related to be tracked over time." - StatementTopic is type BodyStructureTopic - - -EntryElement: BodyStructureAbsenceStatement // AssertionOfAbsenceStatement? -Based on: ConditionAbsenceStatement -Concept: TBD -Description: "Absence of a distinct anatomical or pathological morphological feature or organizational pattern, acquired or innate. Examples include tissue types, tumors, and wounds. Body structures are continuants that allow observations of the same body structure to be related to be tracked over time." - StatementTopic is type BodyStructureTopic - -EntryElement: DiseaseProgression -Based on: Observation -Concept: MTH#C0421176 "Progression" -Description: "A finding related to the current trend of a particular existing disease. This concept is most often used for chronic and incurable diseases where the status and trendline of the disease is an important determinant of therapy and prognosis. The specific disorder being evaluated must be cited in the Focus_Reference or Focus_CodeableConcept as a reference to a Condition." - ObservationContext.ResultValue value is type CodeableConcept - ObservationContext.ResultValue from ProgressionVS - ObservationTopic.TopicCode is MTH#C0421176 "Progression" -0..* ProgressionEvidence -// "ProgressionEvidence" is somewhat related to FindingMethod, which represents the test or procedure used to generate the result; it is typically a LOINC code (0..1) - ObservationTopic.Focus.CodeableConcept from http://hl7.org/fhir/us/core/ValueSet/us-core-problem if covered -0..0 ObservationTopic.Specimen -0..0 ObservationTopic.EvaluationComponent -0..0 ObservationTopic.Precondition -0..0 ObservationTopic.ReferenceRange // applies to a quantitative measurement only - - Element: ProgressionEvidence - Description: "The type of evidence considered in determining disease progression." - Value: CodeableConcept from ProgressionEvidenceVS - - - - -// - - - \ No newline at end of file diff --git a/spec/shr_condition_vs.txt b/spec/shr_condition_vs.txt deleted file mode 100644 index d49a63e4..00000000 --- a/spec/shr_condition_vs.txt +++ /dev/null @@ -1,42 +0,0 @@ -Grammar: ValueSet 5.0 -Namespace: shr.condition - -CodeSystem: SCT = http://snomed.info/sct -CodeSystem: MTH = http://ncimeta.nci.nih.gov - - -ValueSet: ProgressionVS -MTH#C0677874 "Complete response or remission; no measurable or observable evidence of cancer." -MTH#C0015250 "Complete resection/excision of cancerous tumor" -MTH#C1272745 "Improving, responding to treatment" -MTH#C0205360 "Stable, neither improving nor worsening" -MTH#C1546960 "Worsening, disease progressing" -MTH#C3858734 "Insufficient evidence" - -ValueSet: ProgressionEvidenceVS -MTH#C0011923 "Progression determined based on imaging" -MTH#C0030664 "Progression determined based on pathology" -MTH#C1457887 "Progression determined based on physical signs or symptoms" -MTH#C0031809 "Progression determined based on physical examination" -MTH#C0005516 "Progression determined based on biomarkers" - - - -/* Save for later -ValueSet: AssessmentTypeVS -Description: "A code describing the type of assessment activity, e.g. diagnosis, prognosis, disease progression, healing, toxicity, treatment efficacy." -MTH#C0033325 "Prognosis - a prediction of the probable outcome of a disease based on a individual's condition and the usual course of the disease as seen in similar situations" -MTH#C0011900 "Diagnosis - The determination of the nature and/or extent of a disease or condition, or the distinguishing of one disease or condition from another. The assessment may be made through physical examination, laboratory tests, or the likes. Computerized programs may be used to enhance the decision-making process." -MTH#C0421176 "Assessment of disease progression" -MTH#C2004454 "Assessment of recovery process, from surgery, therapy, or similar treatment." -MTH#C0879626 "Assessment of adverse effects of a treatment." -MTH#C0087113 "Assessment of the effectiveness of a treatment." -MTH#C4040556 "Assessment of risk for a disease." - - -ValueSet: EvidenceQualityVS -#compelling_evidence "Compelling evidence; indicates that assessments are based on high-quality information from multiple sources. High quality evidence does not imply that the assessment is a fact or certainty." -#suggestive_evidence "Suggestive evidence; indicates that assessments are based on credible and plausible information, but not of sufficient quality or corroborated sufficiently to warrant a higher level of confidence." -#weak_evidence "Weak evidence, its credibility and/or plausibility is uncertain, fragmented or poorly corroborated to make solid judgments." -MTH#C0332125 "No evidence" -*/ \ No newline at end of file diff --git a/spec/shr_core.txt b/spec/shr_datatype.txt similarity index 66% rename from spec/shr_core.txt rename to spec/shr_datatype.txt index 3eb4652d..68df7abd 100644 --- a/spec/shr_core.txt +++ b/spec/shr_datatype.txt @@ -1,7 +1,6 @@ Grammar: DataElement 5.0 Namespace: shr.core Description: "The SHR Core domain contains definitions for a variety of general-purpose elements that are used widely in SHR. These include definitions for coding, expressions of time, quantities, addresses, names, and more." -Uses: cimi.element, cimi.topic Path: FHIR = http://hl7.org/fhir/ValueSet // CodeSystem: CC = http://www.nationsonline.org/oneworld/country_code_list @@ -12,20 +11,29 @@ CodeSystem: NCI = https://evs.nci.nih.gov/ftp1/CDISC/SDTM/ CodeSystem: UCUM = http://unitsofmeasure.org -//------------ Complex Types aligned to FHIR --------------- +//------------ Data Types aligned to FHIR --------------- + +Element: Text +Description: "A simple string." +Value: string Element: Quantity Description: "A quantity with units, whose value may be bounded from above or below, as defined in FHIR" -Value: decimal +0..1 Number 0..1 Comparator 0..1 Units + Element: Number + Description: "A decimal value." + Value: decimal + Element: Comparator - Value: code from http://hl7.org/fhir/ValueSet/quantity-comparator + Description: "A code indicated if the value represents an upper or lower bound" + Value: CodeableConcept from http://hl7.org/fhir/ValueSet/quantity-comparator Element: Units Concept: TBD - Description: "Code for the unit of measure of the quantity." + Description: "The unit of measure of the quantity." Value: Coding should be from AllUnitsVS Element: SimpleQuantity @@ -36,108 +44,51 @@ Description: "A quantity where the comparator is not used, as defined in FHIR" Element: IntegerQuantity Based on: Quantity Description: "A Quantity that is an integer." - Units.Coding is UCUM#1 + Units is UCUM#1 Element: Age Based on: Quantity Concept: MTH#C0001779 Description: "How long someone has been alive, or something has existed." - Units with Coding from http://hl7.org/fhir/ValueSet/units-of-time + Units from http://hl7.org/fhir/ValueSet/units-of-time Element: Distance Based on: Quantity Concept: MTH#C0012751 Description: "The measure of space separating two objects or points." - Units with Coding from UnitsOfLengthVS + Units from UnitsOfLengthVS Element: Duration Based on: SimpleQuantity Concept: MTH#C0449238 Description: "The length of time that something continues." - Units with Coding from TimeUnitOfMeasureVS + Units from TimeUnitOfMeasureVS Element: Money Based on: Quantity Concept: TBD Description: "Representation of an amount of currency or monetary value." - Units with Coding from CurrencyVS - - -//------------- Complex data types in FHIR 3.0 --------------- - -Element: Media -Based on: EmbeddedContent -Concept: TBD -Description: "A file that contains audio, video, image, or similar content." -0..1 BinaryData -0..1 ContentType -0..1 Language -0..1 ResourceLocation -0..1 ResourceSize -0..1 Hash -0..1 Title -0..1 CreationTime - - Element: BinaryData - Concept: TBD - Description: "The data itself." - Value: base64Binary - - Element: ContentType - Concept: TBD - Description: "Mime type of the content, with charset etc." - Value: code - - Element: Language - Concept: MTH#C0023008 - Description: "A human language, spoken or written." - Value: CodeableConcept from http://hl7.org/fhir/ValueSet/languages if covered - - Element: ResourceLocation - Concept: TBD - Description: "URI where data can be found." - Value: uri - - Element: ResourceSize - Concept: TBD - Description: "Number of bytes of content in the resource (if url provided)" - Value: unsignedInt - - Element: Hash - Concept: TBD - Description: "A hash code of the data (sha-1, base64ed)" - Value: base64Binary - - Element: CreationTime - Concept: MTH#C3669169 - Description: "The point in time when the information was recorded in the system of record." - Value: dateTime // we can map to instant from dateTime - - Element: PhotographicImage - Based on: Media - Concept: LNC#72170-4 -// ContentType from ImageMimeTypeVS - - -//---- Coding departs from CIMI to align with FHIR + Units from CurrencyVS Element: Coding Concept: MTH#C0805701 Description: "Coding of a concept, drawn from a controlled vocabulary. Includes the vocabulary and version, if applicable. May include a display text, and a descriptor expressing the intended interpretation of the code." -Value: 0..1 code // changed to 0..1 so SHR won't generate a profile. +0..1 CodeValue 0..1 CodeSystem 0..1 CodeSystemVersion 0..1 DisplayText -//0..* CodingQualifier + Element: CodeValue + Description: "A coded value, or expression, in syntax defined by the system" + Value: code + /* TODO: Suggest changing FHIR's Coding.userSelected to Coding.qualifier Element: CodingQualifier Concept: TBD Description: "A description of the purpose or origin of the code that assists in understanding the code." - Value: code from CodingQualifierVS + Value: CodeableConcept from CodingQualifierVS */ - Element: CodeSystem Concept: TBD Description: "A formal terminology system." @@ -154,6 +105,9 @@ Description: "A set of codes drawn from different coding systems, representing t 0..* Coding 0..1 DisplayText +Element: Code +Description: "The main type identifier for a lab, procedure, condition, etc., usually drawn from a controlled vocabulary." +Value: CodeableConcept Element: Range Concept: TBD @@ -175,8 +129,8 @@ Description: "An interval defined by a quantitative upper and/or lower bound. On Element: Ratio Concept: MTH#C0456603 Description: "A unit of measurement for the quotient of the amount of one entity to another." -1..1 Numerator -1..1 Denominator +0..1 Numerator +0..1 Denominator Element: Numerator Concept: MTH#C2825219 @@ -191,8 +145,8 @@ Description: "A unit of measurement for the quotient of the amount of one entity Element: ContactPoint Concept: MTH#C2986441 Description: "An electronic means of contacting an organization or individual." -1..1 TelecomNumberOrAddress -1..1 Type from http://hl7.org/fhir/ValueSet/contact-point-system +0..1 TelecomNumberOrAddress +0..1 Type from http://hl7.org/fhir/ValueSet/contact-point-system 0..1 Purpose from http://hl7.org/fhir/ValueSet/contact-point-use 0..1 PriorityRank 0..1 EffectiveTimePeriod @@ -204,12 +158,20 @@ Description: "An electronic means of contacting an organization or individual." Element: Type Concept: MTH#C0332307 - Description: "The most specific code (lowest level term) describing the kind or sort of thing being represented." + Description: "A code describing the item at a greater level of detail." Value: CodeableConcept Element: Purpose - Description: "Why the item is used." - Value: Coding + Description: "What it should be used for." + Value: CodeableConcept + + Element: PriorityRank + Description: "The priority of the procedure, as a number (1 being the highest priority)" + Value: positiveInt + + Element: PriorityRankUnsignedInt + Description: "The priority of the procedure, as a number (1 being the highest priority)" + Value: unsignedInt Element: ContactDetail @@ -218,30 +180,19 @@ Description: "Describes an individual and how to reach them." 0..1 HumanName 0..* ContactPoint - -/* TODO: Additional MetaData Types: see http://hl7.org/fhir/metadatatypes.html -Contributor -DataRequirement -ParameterDefinition -RelatedArtifact -TriggerDefinition -UseageContext -*/ - - Element: TimePeriod Concept: MTH#C1948053 Description: "A period of time defined by a start and end time, date, or year. If the start element is missing, the start of the period is not known. If the end element is missing, it means that the period is ongoing, or the start may be in the past, and the end date in the future, which means that period is expected/planned to end at the specified time. The end value includes any matching date/time. For example, the period 2011-05-23 to 2011-05-27 includes all the times from the start of the 23rd May through to the end of the 27th of May." -0..1 TimePeriodStart -0..1 TimePeriodEnd // lack of end time indicates the period was continuing at the time the entry was created +0..1 BeginDateTime +0..1 EndDateTime // lack of end time indicates the period was continuing at the time the entry was created - Element: TimePeriodStart // synonym "EffectiveDate" + Element: BeginDateTime // synonym "EffectiveDate" Concept: MTH#C1301880 Description: "The time at which something is to take effect, start, or did start. Boundary is considered inclusive." Value: dateTime // TODO: would like to have date or dateTime but that wouldn't be FHIR-compatible - Element: TimePeriodEnd + Element: EndDateTime Concept: MTH#C1522314 Description: "The time at which something is to end or did end. Boundary is considered inclusive." Value: dateTime // TODO: would like to have date or dateTime but that wouldn't be FHIR-compatible @@ -286,7 +237,7 @@ Timing offers a choice of multiple OccurrenceTime (used is used to specify speci Element: DayOfWeek Concept: TBD Description: "A day of the week that the pattern should take place." - Value: code from http://hl7.org/fhir/ValueSet/days-of-week + Value: CodeableConcept from http://hl7.org/fhir/ValueSet/days-of-week Element: TimeOfDay Concept: TBD @@ -297,7 +248,7 @@ Timing offers a choice of multiple OccurrenceTime (used is used to specify speci Element: DailyLifeEvent Concept: TBD Description: "A quotidian landmark, such as rising, mealtime, or bedtime, when an event should take place." - Value: code from http://hl7.org/fhir/ValueSet/event-timing + Value: CodeableConcept from http://hl7.org/fhir/ValueSet/event-timing Element: LifeEventOffset Concept: TBD @@ -329,11 +280,10 @@ Timing offers a choice of multiple OccurrenceTime (used is used to specify speci Value: positiveInt - Element: SampledData Concept: TBD Description: "Data that comes from a series of measurements taken by a device, which may have upper and lower limits. The data type also supports more than one dimension in the data." -Value: string +1..1 DataAsString 1..1 Origin 1..1 MillisecondsBetweenSamples 0..1 CorrectionFactor @@ -341,8 +291,12 @@ Value: string 0..1 UpperLimit 1..1 Dimensions + Element: DataAsString + Description: "Data represented as a text sting." + Value: string + Element: Origin - Description: "The base quantity that a measured value of zero represents. In addition, this provides the units of the entire measurement series." + Description: "The shr.base quantity that a measured value of zero represents. In addition, this provides the units of the entire measurement series." Value: SimpleQuantity Element: MillisecondsBetweenSamples @@ -358,10 +312,10 @@ Value: string Description: "The lower limit of detection of the measured points. This is needed if any of the data points have the value 'L' (lower than detection limit)." Value: decimal - Element: UpperLimit - Concept: TBD + Element: UpperLimit + Concept: TBD Description: "The upper limit of detection of the measured points. This is needed if any of the data points have the value 'U' (higher than detection limit)." - Value: decimal + Value: decimal Element: Dimensions Concept: TBD @@ -374,12 +328,12 @@ Description: "An address expressed using postal conventions (as opposed to GP 0..1 Purpose from http://hl7.org/fhir/ValueSet/address-use 0..1 Type from http://hl7.org/fhir/ValueSet/address-type 0..1 DisplayText -0..2 AddressLine +0..* AddressLine 0..1 City 0..1 District 0..1 State 0..1 PostalCode -1..1 Country +0..1 Country 0..1 EffectiveTimePeriod Element: AddressLine @@ -388,19 +342,16 @@ Description: "An address expressed using postal conventions (as opposed to GP Value: string Element: City - Based on: GeopoliticalLocation Concept: MTH#C1555315 Description: "The name of a municipality, city, town, village or other community or delivery center. (Source: HL7 FHIR)." Value: string Element: District - Based on: GeopoliticalLocation Concept: MTH#C0079170 Description: "The name of the administrative area at a level below that of a state but above that of a city or town. In the US, a county. Outside the US, a district or the equivalent. (Source: HL7 FHIR)." Value: string Element: State - Based on: GeopoliticalLocation Concept: MTH#C1552743 Description: "Sub-unit of a country with limited sovereignty in a federally organized country. A code may be used if codes are in common use (i.e. US 2 letter state codes). (Source: HL7 FHIR)." Value: string @@ -411,12 +362,10 @@ Description: "An address expressed using postal conventions (as opposed to GP Value: string Element: Country - Based on: GeopoliticalLocation Concept: MTH#C0454664 Description: "Country - a nation as commonly understood or generally accepted, expressed in ISO 3166 Alpha-2 (2-letter) codes." Value: string - //------------ Complex Data Types not in FHIR ---------------- Element: Count @@ -424,34 +373,10 @@ Concept: MTH#C0750480 Description: "The number of items (0 or more), as an integer." Value: unsignedInt -Element: PlainText -Concept: TBD -Description: "A text written in a human language." -Value: string -0..1 Language - -Element: EmbeddedContent -Concept: TBD -Description: "Abstract class defining the common metadata of all types of encapsulated data, such as images." - -Element: ParsableContent -Based on: EmbeddedContent -Concept: TBD -Description: "A string that follows a formal syntax and can be analyzed and broken into meaningful parts." +Element: CommentOrDescription +Concept: MTH#C0947611 +Description: "A text note containing additional details, explanation, description, comment, or summarization." Value: string -1..1 Formalism - - Element: Formalism - Concept: TBD - Description: "The system of formal syntax or interpretation associated with parsable content." - Value: CodeableConcept - -/* No can do! Can't restrict "value is type" to a primitive -Element: UnsignedIntegerRange -Description: "A range of non-negative integers. One of the two bounds must be present, and the lower bound must be less than or equal to the upper bound." -0..1 LowerBound value is type unsignedInt -0..1 UpperBound value is type unsignedInt -*/ Element: DurationRange Based on: Range @@ -470,62 +395,44 @@ Description: "A quantity that represents a statistic, e.g. maximum, minimum, mea Description: "The type of statistic that is represented by the value." Value: CodeableConcept from StatisticTypeVS -Element: PriorityRank +Element: PriorityCode Concept: MTH#C0549179 -Description: "An indication of the importance of an action." +Description: "An indication of the importance of an action relative to other actions." Value: positiveInt or CodeableConcept Element: Percentage Based on: SimpleQuantity Concept: MTH#C0439165 Description: "A percentage value where 100.0 represents 100%." - Units.Coding is UCUM#% - - -Element: Likelihood -Concept: MTH#C0033204 -Description: "A measure of the expectation of the occurrence of a particular event, as a percentage." -Value: positiveInt // 0-100 do not allow zero, since this will create an implicit modifier + Units is UCUM#% Element: QualitativeLikelihood Concept: TBD Description: "A qualitative (subjective) likelihood." Value: CodeableConcept from QualitativeLikelihoodVS +/* NOT suitable data types Element: Length -Based on: Quantity Concept: MTH#C1444754 Description: "The measurement or linear extent of something from end to end; the greatest dimensions of a body." - Units with Coding from UnitsOfLengthVS +Value: Quantity with Coding from UnitsOfLengthVS Element: Depth -Based on: EvaluationComponent Concept: SCT#131197000 "Depth (qualifier value)" Description: "The extent downward or inward; the perpendicular measurement from the surface downward to determine deepness." Value: Quantity with units UCUM#cm Element: Area -Based on: EvaluationComponent Concept: SCT#42798000 "Area (qualifier value)" Description: "The extent of a 2-dimensional surface enclosed within a boundary." Value: Quantity with units UCUM#cm2 -Element: ClockDirection -Based on: CodedEvaluationComponent -Concept: LNC#72294-2 -Description: "A direction indicated by an angle relative to 12 o'clock." -Value: CodeableConcept from ClockDirectionVS - - -/* Element: Volume -Based on: ??? Concept: MTH#C0449468 Description: "The amount of three dimensional space occupied by an object or the capacity of a space or container." Value: Quantity with units UCUM#TBD Element: Circumference -Based on: ??? Concept: MTH#C0332520 Description: "The length of such a boundary line of a figure, area, or object." */ @@ -547,20 +454,17 @@ Concept: MTH#C0027362 Description: "Subgroups of populations based on age." Value: CodeableConcept from AgeGroupVS +// TODO: this may be an observation - there are different methods (at least 10 LOINC codes) for estimating gestational age. Element: GestationalAge Concept: MTH#C0017504 Based on: Age Description: "The age of the embryo or fetus. This may be assessed by medical history, physical examination, early immunologic pregnancy tests, radiography, ultrasonography, and amniotic fluid analysis." + Element: GestationalTimePeriod Concept: TBD Description: "A time relative to a pregnancy or childbirth event." -Value: CodeableConcept from TBD "GestationalTimePeriodVS" // e.g., entire pregnancy, trimester, prior to conception, neonatal period, etc. - -Element: GestationalTemporalContext -Concept: TBD -Description: "A named gestational time period, or a gestational age." -Value: GestationalAge or GestationalTimePeriod +Value: CodeableConcept from GestationalTimePeriodVS // e.g., entire pregnancy, trimester, pre-conception, neonatal period, etc. //-------------- Duration and Frequency ----------------- @@ -571,13 +475,12 @@ Concept: TBD Description: "The duration of an event, described semi-quantitatively." Value: CodeableConcept from SemiquantitativeDurationVS - Element: Frequency // TODO: should be a ratio, but the problem is that ratio uses Quantity in numerator and denominator Based on: Ratio Concept: MTH#C0376249 Description: "How many occurrences of an event per unit of time." Numerator.Quantity with units UCUM#1 - Denominator.Quantity.Units with Coding from http://hl7.org/fhir/ValueSet/units-of-time + Denominator.Quantity.Units from http://hl7.org/fhir/ValueSet/units-of-time Element: SemiquantFrequency Concept: TBD @@ -630,12 +533,7 @@ Description: "The length of time in which something happens." Value: Duration -//--------------- Locations and Addresses ----------------- - -Element: GeopoliticalLocation -Concept: MTH#C0017446 -Description: "The countries of the world and major geopolitical subregions, such as US states." - +//--------------- Positions and Addresses ----------------- Element: Geoposition Concept: TBD @@ -666,10 +564,7 @@ Description: "Description of the place or type of surroundings where something i Value: CodeableConcept from SettingVS -//------------ US Address Profile ----------- - Element: UnitedStatesAddress -Concept: TBD // more specific concept than Address Based on: Address Description: "An address for a place in the USA, conforming to US mail postal conventions. (Source: HL7 FHIR)." 1..1 State is type UnitedStatesState @@ -681,11 +576,10 @@ Description: "An address for a place in the USA, conforming to US mail postal Description: "A state or territory in the USA expressed by 2-letter US Postal code." //Value: string from http://pe.usps.com/text/pub28/28apb.htm // expressed as string to conform with definition of State - Element: HumanName Based on: PersonName Concept: MTH#C1547383 -Description: "The CIMI person name, constrained to map correctly to FHIR." +Description: "The person name, constrained to map correctly to FHIR." 0..0 MiddleName 0..1 FamilyName Purpose from http://hl7.org/fhir/ValueSet/name-use @@ -695,29 +589,235 @@ Concept: MTH#C1262869 Description: "The position or physical attitude of the body." Value: CodeableConcept from BodyPositionVS -Element: Details -Concept: MTH#C0947611 -Description: "A text note containing additional details, explanation, description, comment, or summarization. Details can discuss, support, explain changes to, or dispute information." -Value: string // change to language-text - Element: DisplayText Concept: MTH#C1548311 Description: "A string meant for reading by a person, for example, accompanying a code." Value: string -Element: Version +Element: VersionString Concept: MTH#C0333052 -Description: "A number or code associated with the product that identifies a particular release iteration." -Value: string or id - +Description: "A string associated with the product that identifies a particular release iteration." +Value: string Element: Title Concept: TBD Description: "A distinguishing word or group of words naming an item." Value: string -Element: Category +Element: EmbeddedContent +Concept: TBD +Description: "Abstract class defining the common metadata of all types of encapsulated data, such as images." + +Element: ParsableContent +Based on: EmbeddedContent +Concept: TBD +Description: "A string that follows a formal syntax and can be analyzed and broken into meaningful parts." +1..1 Text +1..1 Formalism + + Element: Formalism + Concept: TBD + Description: "The system of formal syntax or interpretation associated with parsable content." + Value: CodeableConcept + +Element: Attachment +Based on: EmbeddedContent Concept: TBD -Description: "A class or division of people or things having particular shared characteristics" +Description: "A file that contains audio, video, image, or similar content." +0..1 BinaryData +0..1 ContentType //http://hl7.org/fhir/ValueSet/mimetypes in R4, http://www.rfc-editor.org/bcp/bcp13.txt in DSTU2 and STU3 +0..1 Language +0..1 ResourceLocation +0..1 ResourceSize +0..1 Hash +0..1 Title +0..1 CreationDateTime + + Element: BinaryData + Concept: TBD + Description: "The data itself." + Value: base64Binary + + Element: ContentType + Concept: TBD + Description: "The mime type of the content, with charset etc." + Value: CodeableConcept + + Element: ResourceLocation + Concept: TBD + Description: "URI where data can be found." + Value: uri + + Element: ResourceSize + Concept: TBD + Description: "Number of bytes of content in the resource (if url provided)" + Value: unsignedInt + + Element: Hash + Concept: TBD + Description: "A hash code of the data (sha-1, base64ed)" + Value: base64Binary + + Element: CreationDateTime + Concept: MTH#C3669169 + Description: "The point in time when the item was created." + Value: dateTime // we can map to instant from dateTime + +Element: PhotographicImage +Based on: Attachment +Concept: LNC#72170-4 "Photographic image [Attachment]" +Description: "An attachment of a photographic type. The mime type should be either bmp, gif, jpeg, png, svg, or tiff." + // ContentType from ImageMimeTypeVS if covered + +Element: Annotation +Description: "An added or follow-up note, often after the fact, that contains metadata about who made the statement and when." +1..1 Text +1..1 Author value is type PatientOrPractitionerOrRelatedPerson +0..1 OccurrenceTime + +Element: Signature +Description: "A digital Signature - XML DigSig, JWT, Graphical image of signature, etc." +1..* SignatureType from http://hl7.org/fhir/ValueSet/signature-type if covered +1..1 CreationDateTime +1..1 Signatory +0..1 OnBehalfOf +1..1 ContentType +1..1 BinaryData // DSTU 2 change (required attribute in DSTU 2) + + Element: SignatureType + Concept: MTH#C0332307 + Description: "Type of signature" + Value: CodeableConcept + + Element: Signatory + Concept: TBD + Description: "The party signing." + Value: uri or ref(Entity) + + Element: OnBehalfOf + Concept: TBD + Description: "The party represented by the actual participant." + Value: uri or ref(Organization) + +Element: RouteIntoBody +Concept: MTH#C0013153 +Description: "The way a substance enters an organism after contact, particularly, the route of drug administration." +Value: CodeableConcept from http://hl7.org/fhir/ValueSet/route-codes + +Element: BodySite +Concept: SCT#758637006 "Anatomical location (property) (qualifier value)" +Description: "A location or structure in the body, including tissues, regions, cavities, and spaces; for example, right elbow, or left ventricle of the heart. +SHR creates a BodySite structure that includes not only a code, but optional laterality, direction, clock direction, and distance. If included, the distance is measured from the location specified by the code, laterality, and direction." +1..1 BodySiteCode +0..1 Laterality +0..1 DistanceFromLandmark +0..1 AnatomicalDirection +0..1 ClockDirection +0..1 CommentOrDescription +0..* Attachment + + Element: BodySiteCode + Concept: TBD + Description: "Code for the anatomical location or landmark, without laterality, direction, or other modifiers needed to completely specify the body site." + Value: CodeableConcept should be from BodySiteVS + + Element: Laterality + Concept: MTH#C0925205 "Anatomical laterality" + Description: "Anatomical location or specimen further detailing the side(s) of interest." + Value: CodeableConcept from http://hl7.org/fhir/ValueSet/bodysite-laterality + + Element: AnatomicalDirection + Concept: NCI#C99074 + Description: "Anatomical location or specimen further detailing directionality." + Value: CodeableConcept from AnatomicalDirectionVS + + Element: ClockDirection + Concept: LNC#72294-2 + Description: "A direction indicated by an angle relative to 12 o'clock." + Value: CodeableConcept from ClockDirectionVS + + Element: DistanceFromLandmark + Concept: TBD + Description: "How far the anatomical location of interest is from the given landmark" + Value: Quantity + Quantity.Units.Coding from UnitsOfLengthVS + +Element: Identifier +Concept: MTH#C0600091 +Description: "Business identifier or external id for this resource." +0..1 IdentifierString // cardinality aligns with FHIR STU3 +0..1 Purpose from http://hl7.org/fhir/ValueSet/identifier-use +0..1 Type from http://hl7.org/fhir/ValueSet/identifier-type if covered +0..1 CodeSystem +0..1 EffectiveTimePeriod +//0..1 Issuer -- commented out to prevent generating a profile on identifier caused by having profile on Organization (which is unavoidable in DSTU 2, because US Core changes some cardinalities to 1..) + + Element: IdentifierString + Description: "An id for the item expresse as a string." + Value: string + + Element: Issuer + Description: "An organization who issues a qualification, identifier, or license." + Value: ref(Organization) + +/* +Element: TermMapping +Description: "Represents an alternative (mapped) Concept associated with a source concept (i.e., CodedText.concept or the textual value of the CodedText when no equivalent concept has been defined), and the relative match of the mapped Concept with respect to the source Concept. Mappings may be used to add classification terms (e.g. adding ICD classifiers to SNOMED descriptive terms), for computational convenience, or to provide equivalents in other terminologies (e.g. across nursing vocabularies)." Value: CodeableConcept +1..1 Match +0..1 Purpose + Element: Match + Description: "The relative match of the mapped concept to the original (target) concept. Examples include broader (i.e., the mapped term is more general than the original), equivalent, narrower (e.g. mapped concept is 'atypical diabetes mellitus' and the original term is 'diabetes mellitus'), or unknown." + Value: CodeableConcept +*/ + +Element: Name +Description: "Abstract supertype for the name of an entity." +0..1 NameAsText +0..* Purpose +0..1 EffectiveTimePeriod + + Element: NameAsText + Description: "The name as plain unstructured or semi-structured text." + Value: string // TODO: should be PlainText + +Element: PersonName +Based on: Name +Concept: MTH#C1547383 +Description: "A name used by a human being, written as it would be typically expressed. May include a breakdown of the various elements of the name (family name, given name, etc.)." +0..* Prefix +0..* GivenName +0..* MiddleName +0..* FamilyName +0..* Suffix +0..1 Purpose from http://hl7.org/fhir/ValueSet/name-use + + Element: Prefix + Description: "A string that should precede the item; for example, an honorific before a person's name, or a question number before a question." + Value: string // punting on value set - there is little value in standardizing this element + + Element: GivenName + Concept: LNC#45392-8, SCT#408677003 + Description: "The person's given name - e.g., John" + Value: string + + Element: MiddleName + Concept: LNC#45392-8, SCT#408677003 + Description: "The person's middle name." + Value: string + + Element: FamilyName + Concept: LNC#45394-4 + Description: "The portion of a person's name that reflects the genealogy of the person. In western cultures, this is the 'last' name. In eastern cultures, the family name appears before the person's given name(s). In some cultures (e.g. Eritrea) the family name of a son is the first name of his father. (Source: HL7 V3)." + Value: string + + Element: Suffix + Concept: LNC#45395-1, SCT#715196001 + Description: "Part of the name that is acquired as a title due to academic, legal, employment or nobility status, etc. and that appears at the end of the name." + Value: string + +Element: Category +Concept: TBD +Description: "The type, kind, or class of this item." +Value: CodeableConcept diff --git a/spec/shr_datatype_map_dstu2.txt b/spec/shr_datatype_map_dstu2.txt new file mode 100644 index 00000000..516254cc --- /dev/null +++ b/spec/shr_datatype_map_dstu2.txt @@ -0,0 +1,134 @@ +Grammar: Map 5.1 +Namespace: shr.core +Target: FHIR_DSTU_2 + + +// Code types map direction to FHIR +Coding maps to Coding: + CodeValue maps to code + CodeSystem maps to system + CodeSystemVersion maps to version + DisplayText maps to display + +CodeableConcept maps to CodeableConcept: + Coding maps to coding + DisplayText maps to text + +Quantity maps to Quantity: + Number maps to value + Units.Coding.CodeValue maps to code + Units.Coding.CodeSystem maps to system + Units.Coding.DisplayText maps to unit + Comparator maps to comparator + +// The following are profiles on Quantity; no additional attributes are defined in SHR +SimpleQuantity maps to SimpleQuantity: +Age maps to Age: +IntegerQuantity maps to Count: +Distance maps to Distance: +Duration maps to Duration: +Money maps to Money: + +Address maps to Address: + Purpose maps to use + Type maps to type + DisplayText maps to text + AddressLine maps to line + City maps to city + District maps to district + State maps to state + PostalCode maps to postalCode + Country maps to country + EffectiveTimePeriod maps to period + +HumanName maps to HumanName: + NameAsText maps to text + Prefix maps to prefix + GivenName maps to given + FamilyName maps to family + Suffix maps to suffix + Purpose maps to use + EffectiveTimePeriod maps to period + +TimePeriod maps to Period: + BeginDateTime maps to start + EndDateTime maps to end + +ContactPoint maps to ContactPoint: + TelecomNumberOrAddress maps to value + Type maps to system + Purpose maps to use + PriorityRank maps to rank + EffectiveTimePeriod maps to period + +/* dstu 2 change (no suitable target) +ContactDetail maps to ContactDetail: + HumanName.NameAsText maps to name + ContactPoint maps to telecom +*/ + +Range maps to Range: + LowerBound maps to low + UpperBound maps to high + +Ratio maps to Ratio: + Numerator maps to numerator + Denominator maps to denominator + +Timing maps to Timing: + OccurrenceTime maps to event + TimingCode maps to code + EventDuration.DurationRange.LowerBound.SimpleQuantity.Number maps to repeat.duration + EventDuration.DurationRange.UpperBound.SimpleQuantity.Number maps to repeat.durationMax + EventDuration.DurationRange.LowerBound.SimpleQuantity.Units.Coding.CodeValue maps to repeat.durationUnits // dstu 2 change (attribute name) + RecurrencePattern.RecurrenceInterval.Duration.Number maps to repeat.period + // dstu 2 change (attribute name) + RecurrencePattern.RecurrenceInterval.Duration.Units.Coding.CodeValue maps to repeat.periodUnits + constrain repeat.periodMax to 0..0 // TODO: why? +// RecurrencePattern.DayOfWeek maps to repeat.dayOfWeek // dstu 2 change (no such attribute) +// RecurrencePattern.TimeOfDay maps to repeat.timeOfDay // dstu 2 change (no such attribute) + RecurrencePattern.DailyLifeEvent maps to repeat.when +// RecurrencePattern.LifeEventOffset maps to repeat.offset // dstu 2 change (no such attribute) + RecurrencePattern.CountPerInterval.MinCount maps to repeat.frequency + RecurrencePattern.CountPerInterval.MaxCount maps to repeat.frequencyMax + +SampledData maps to SampledData: + DataAsString maps to data + Origin maps to origin + MillisecondsBetweenSamples maps to period + CorrectionFactor maps to factor + LowerLimit maps to lowerLimit + UpperLimit maps to upperLimit + Dimensions maps to dimensions + +Attachment maps to Attachment: + BinaryData maps to data + ContentType maps to contentType + Language maps to language + ResourceLocation maps to url + ResourceSize maps to size + Hash maps to hash + Title maps to title + CreationDateTime maps to creation + +Annotation maps to Annotation: + Text maps to text + Author maps to author[x] + OccurrenceTime maps to time + +Identifier maps to Identifier: + IdentifierString maps to value + Purpose maps to use + Type maps to type + CodeSystem maps to system + EffectiveTimePeriod maps to period +// Issuer maps to assigner MK - this causes a profile on Identifier because Organization is also profiled + +Signature maps to Signature: + SignatureType maps to type + CreationDateTime maps to when + Signatory maps to who[x] +// dstu 2 change (no such attribute) +// OnBehalfOf maps to onBehalfOf[x] + ContentType maps to contentType + BinaryData maps to blob \ No newline at end of file diff --git a/spec/shr_core_map.txt b/spec/shr_datatype_map_stu3.txt similarity index 57% rename from spec/shr_core_map.txt rename to spec/shr_datatype_map_stu3.txt index 875e52d2..9c993a22 100644 --- a/spec/shr_core_map.txt +++ b/spec/shr_datatype_map_stu3.txt @@ -3,9 +3,9 @@ Namespace: shr.core Target: FHIR_STU_3 -// Code types map direction to FHIR +// CodeValue types map direction to FHIR Coding maps to Coding: - Value maps to code + CodeValue maps to code CodeSystem maps to system CodeSystemVersion maps to version DisplayText maps to display @@ -15,8 +15,8 @@ CodeableConcept maps to CodeableConcept: DisplayText maps to text Quantity maps to Quantity: - Value maps to value - Units.Coding.code maps to code + Number maps to value + Units.Coding.CodeValue maps to code Units.Coding.CodeSystem maps to system Units.Coding.DisplayText maps to unit Comparator maps to comparator @@ -51,16 +51,9 @@ HumanName maps to HumanName: Purpose maps to use EffectiveTimePeriod maps to period - TimePeriod maps to Period: - TimePeriodStart maps to start - TimePeriodEnd maps to end - -Geoposition maps to http://hl7.org/fhir/us/core/StructureDefinition/us-core-location: - constrain position to 1..1 - Latitude maps to position.latitude - Longitude maps to position.longitude - Altitude maps to position.altitude + BeginDateTime maps to start + EndDateTime maps to end ContactPoint maps to ContactPoint: TelecomNumberOrAddress maps to value @@ -84,12 +77,12 @@ Ratio maps to Ratio: Timing maps to Timing: OccurrenceTime maps to event TimingCode maps to code - EventDuration.Value.LowerBound maps to repeat.duration - EventDuration.Value.UpperBound maps to repeat.durationMax - EventDuration.Value.LowerBound.Value.Units.Value.Value maps to repeat.durationUnit - RecurrencePattern.RecurrenceInterval.Value maps to repeat.period + EventDuration.DurationRange.LowerBound.SimpleQuantity.Number maps to repeat.duration + EventDuration.DurationRange.UpperBound.SimpleQuantity.Number maps to repeat.durationMax + EventDuration.DurationRange.LowerBound.SimpleQuantity.Units.Coding.CodeValue maps to repeat.durationUnit + RecurrencePattern.RecurrenceInterval.Duration.Number maps to repeat.period + RecurrencePattern.RecurrenceInterval.Duration.Units.Coding.CodeValue maps to repeat.periodUnit constrain repeat.periodMax to 0..0 - RecurrencePattern.RecurrenceInterval.Value.Units.Value.Value maps to repeat.periodUnit RecurrencePattern.DayOfWeek maps to repeat.dayOfWeek RecurrencePattern.TimeOfDay maps to repeat.timeOfDay RecurrencePattern.DailyLifeEvent maps to repeat.when @@ -97,7 +90,16 @@ Timing maps to Timing: RecurrencePattern.CountPerInterval.MinCount maps to repeat.frequency RecurrencePattern.CountPerInterval.MaxCount maps to repeat.frequencyMax -Media maps to Attachment: +SampledData maps to SampledData: + DataAsString maps to data + Origin maps to origin + MillisecondsBetweenSamples maps to period + CorrectionFactor maps to factor + LowerLimit maps to lowerLimit + UpperLimit maps to upperLimit + Dimensions maps to dimensions + +Attachment maps to Attachment: BinaryData maps to data ContentType maps to contentType Language maps to language @@ -105,18 +107,36 @@ Media maps to Attachment: ResourceSize maps to size Hash maps to hash Title maps to title - CreationTime maps to creation + CreationDateTime maps to creation + // Note that BodySite does not have a patient, whereas FHIR BodySite (BodyStructure in r4) does. From FHIR 3.5 documentation: "The BodyStructure resource is not ... intended for describing the type of anatomical location but rather a specific body site on a specific patient." +/* +BodySite maps to BodySite: + BodySiteCode maps to code + Laterality maps to qualifier (slice on = coding.code) + AnatomicalDirection maps to qualifier + CommentOrDescription maps to description + Attachment maps to image + DistanceFromLandmark maps to extension +*/ + +Annotation maps to Annotation: + Text maps to text + Author maps to author[x] + OccurrenceTime maps to time -SampledData maps to SampledData: - Value maps to data - Origin maps to origin - MillisecondsBetweenSamples maps to period - CorrectionFactor maps to factor - LowerLimit maps to lowerLimit - UpperLimit maps to upperLimit - Dimensions maps to dimensions - +Identifier maps to Identifier: + IdentifierString maps to value + Purpose maps to use + Type maps to type + CodeSystem maps to system + EffectiveTimePeriod maps to period +// Issuer maps to assigner MK - this causes a profile on Identifier because Organization is also profiled - - \ No newline at end of file +Signature maps to Signature: + SignatureType maps to type + CreationDateTime maps to when + Signatory maps to who[x] + OnBehalfOf maps to onBehalfOf[x] + ContentType maps to contentType + BinaryData maps to blob \ No newline at end of file diff --git a/spec/shr_core_vs.txt b/spec/shr_datatype_vs.txt similarity index 61% rename from spec/shr_core_vs.txt rename to spec/shr_datatype_vs.txt index 74066178..3418ced9 100644 --- a/spec/shr_core_vs.txt +++ b/spec/shr_datatype_vs.txt @@ -10,6 +10,7 @@ CodeSystem: SCT = http://snomed.info/sct CodeSystem: CURRENCY = urn:iso:std:iso:4217 ValueSet: AllUnitsVS +Description: "Includes all codes from UCUM and monetary units from ISO." Includes codes from UCUM Includes codes from CURRENCY @@ -17,6 +18,7 @@ ValueSet: CurrencyVS Description: "Value set containing ISO 4217 currency codes." Includes codes from CURRENCY +/* Not currently used, but worth preserving ValueSet: CodingQualifierVS #preferred_code "The preferred, standardized code for interoperability purposes. There should be only one coding in a CodeableConcept with this tag." #source_code "The code found in the information source for this entry, e.g., the raw, original, or first encoding." @@ -25,6 +27,7 @@ ValueSet: CodingQualifierVS #category_code "Indicates the code is a less specific term or a categorization of the source or standard code, i.e., a hypernym. For example, a code for 'vital sign' in the context of a body weight measurement would be a category code. Category codes can be useful for search and query purposes." #coded_expression "The code is an expression in an expression language defined by the CodeSystem" #default_code "The code was supplied by the system by default, because no specific coded value was available." +*/ ValueSet: ClockDirectionVS Description: "The relative direction of an object described using the analogy of a 12-hour clock to describe angles and directions. One imagines a clock face lying either upright or flat in front of oneself, and identifies the twelve hour markings with the directions in which they point." @@ -75,16 +78,29 @@ UCUM#in-us "Inch" UCUM#mi_us "Mile" ValueSet: AgeGroupVS +Description: "Descriptions of life periods such as " MTH#C0935562 "Neonatal period (~0-1 mo)" MTH#C0231330 "Infancy (~0-12 mo)" +MTH#C0682053 "Toddler (~1-2)" MTH#C0599196 "Early childhood (~2-5)" -MTH#C0001578 "Teenage (~13-17)" +MTH#C0231335 "Childhood (~6-10)" +MTH#C0001578 "Teenage or Adolescent (~10-18)" MTH#C0680085 "Early Adulthood (~18-35)" MTH#C0205847 "Middle Aged (~36-64)" MTH#C0001792 "Elderly (~65-79)" MTH#C1999167 "Old Age (~80+)" +ValueSet: GestationalTimePeriodVS // e.g., entire pregnancy, trimester, pre-conception, neonatal period, etc. +Description: "Time periods of pregnancy" +MTH#C0032979 "Pregnancy Trimester, First" +MTH#C0032980 "Pregnancy Trimester, Second" +MTH#C0032981 "Pregnancy Trimester, Third" +MTH#C0747967 "PRIOR TO CONCEPTION" +MTH#C0585037 "Entire pregnancy time period" +MTH#C1839947 "Birth-newborn period" + ValueSet: QualitativeDateTimeVS +Description: "Qualitative and approximate descriptions of time, relative to the present time." #past "A time or time period in the indefinite past" #many_years_ago "Many years ago" #several_years_ago "Several years ago" @@ -107,6 +123,7 @@ ValueSet: QualitativeDateTimeVS #future "A time or time period in the indefinite future" ValueSet: SemiquantitativeDurationVS +Description: "Qualitative and approximate descriptions of durations, on human scale of days, weeks, months or years." #many_years "Many years" #several_years "Several years" #one_year "About a year" @@ -118,6 +135,7 @@ ValueSet: SemiquantitativeDurationVS #seconds "Several seconds but less than a minute" ValueSet: SemiquantitativeFrequencyVS +Description: "Semi-quanitative but approximate descriptions of frequency of an event, on human scale of minutes, hours, days, weeks, months, etc." #never "Never" #less_than_yearly "Less than yearly" #yearly "Yearly" @@ -133,7 +151,7 @@ ValueSet: SemiquantitativeFrequencyVS #continuously "Continuously" ValueSet: QualitativeFrequencyVS -Description: "Code set indicating the frequency of an event in qualitative terms." +Description: "Value set indicating the frequency of an event in qualitative terms." #always "Virtually always or every time" #usually "Frequently or often" #sometimes "Occasionally or sometimes" @@ -141,31 +159,32 @@ Description: "Code set indicating the frequency of an event in qualitative ter #never "Never" ValueSet: YesNoVS -Description: "Code set indicating yes or no." -#yes "Yes, or true" -#no "No, or false" +Description: "Value set indicating yes or no (values drawn from Snomed CT)." +SCT#373066001 "Yes (qualifier value)" +SCT#373067005 "No (qualifier value)" ValueSet: YesNoUnknownVS -Description: "Code set indicating yes, no, or unknown." -#yes "Yes, or true" -#no "No, or false" -#unknown "Unknown" +Description: "A value set containing yes, no, and unknown." +SCT#373066001 "Yes (qualifier value)" +SCT#373067005 "No (qualifier value)" +SCT#261665006 "Unknown (qualifier value)" ValueSet: QualitativeValueScaleVS +Description: "Terms that describe a level, such as a level of physical activity, in qualitative terms, e.g., high, medium, low." #very_high "Very high" #high "High" -#moderate "Moderate/Intermediate or Borderline" +#medium "Medium" #low "Low" #very_low "Very low" ValueSet: QualitativeLikelihoodVS Description: "The likelihood of an event or state, expressed qualitatively. Qualitative likelihoods are associated with judgments and assessments. Values are based on US Intelligence Community's standard language used to describe judgements of likelihood." -#definitely "With certainty or near-complete certainty, an event that definitely has or almost certainly will happen" -#very_likely "Very likely, highly probable, e.g., an event with more than 80% but less than 100% likelihood" -#likely "Likely or probable, e.g., an event with 60% to 80% likelihood" -#even_chance "Roughly equal chance or even odds of happening, between 40% and 60% probability" -#unlikely "Not likely or improbable, e.g., an event with 20% to 40% likelihood" -#very_unlikely "Very unlikely, highly improbable, e.g., an event with less than 20% but non-zero likelihood" +MTH#C3899394 "Definitely; with certainty or near-complete certainty, an event that definitely has or almost certainly will happen" +MTH#C3840799 "Very likely, highly probable, e.g., an event with more than 80% but less than 100% likelihood" +MTH#C0750492 "Probably, e.g., an event with 60% to 80% likelihood" +MTH#C3842586 "Fifty percent; Roughly equal chance or even odds of happening, between 40% and 60% probability" +MTH#C0750558 "Unlikely or improbable, e.g., an event with 20% to 40% likelihood" +MTH#C3841878 "Very unlikely, highly improbable, e.g., an event with less than 20% but non-zero likelihood" // Do not include "definitely not" because that could creates an implicit modifier ValueSet: ThreePriorityVS @@ -237,13 +256,6 @@ Description: "A simple performance grading scale. Also useful for grading qualit #fair "Fair" #poor "Poor" -ValueSet: DiseaseFindingVS -Includes codes descending from SCT#64572001 - -ValueSet: ClinicalFindingAbsentVS -Includes codes descending from SCT#373572006 - - ValueSet: ImageMimeTypeVS Concept: TBD Description: "Mime types that apply to photographic images." @@ -259,22 +271,101 @@ Description: "Value set containing the values positive and negative. VSAC valu SCT#10828004 "Positive" SCT#260385009 "Negative" +ValueSet: PositiveNegativeIndeterminateVS +Description: "Value set containing the values positive, negative and indeterminate. Equivalent to values in LOINC answer list LL2038-9/LL759-2" +SCT#10828004 "Positive (qualifier value)" +SCT#260385009 "Negative (qualifier value)" +SCT#82334004 "Indeterminate (qualifier value)" + ValueSet: PositiveNegativeEquivocalVS Description: "Interpretation of a test result as positive, negative or equivocal. Equivalent values to LOINC LL2009-0." SCT#10828004 "Positive (qualifier value)" //LA6576-8 SCT#260385009 "Negative (qualifier value)" //LA6577-6 SCT#42425007 "Equivocal (qualifier value)" //LA11885-3 +ValueSet: PositiveNegativeEquivocalIndeterminateVS +Description: "Interpretation of a test result as positive, negative, equivocal, or indeterminate." +SCT#10828004 "Positive (qualifier value)" +SCT#260385009 "Negative (qualifier value)" +SCT#42425007 "Equivocal (qualifier value)" +SCT#82334004 "Indeterminate (qualifier value)" ValueSet: PresentAbsentVS Description: "Whether a feature or condition is present or absent." SCT#52101004 "Present (qualifier value)" SCT#2667000 "Absent (qualifier value)" -// ValueSet: ManifestationChangeVS (much better, better, about the same, worse, much worse, etc) +ValueSet: LanguageQualifierVS +Description: "A code indicating whether the language is preferred, secondary, or practiced in an unconventional or limited way." +#preferred_spoken "Preferred language" +#secondary_spoken "Secondary language" +#apraxia "Difficulty speaking due to motor disorder" +#aphasia "Difficulty in speaking, listening, reading, and writing" +#signs "Uses sign language" +#braille "Reads using braille" +#lipreads "Uses lipreading (speechreading)" +#aac "Uses augmentative and alternative communication" + + +/* not used +ValueSet: TelephoneTypeVS +#mobile "Mobile phone (assumed text capable)" +#land "Landline telephone" + +ValueSet: AddressUseVS +Description: "How an address is used by the subject, for example, as a dwelling or as a mailing address." +#primary_residence "The address at which a person dwells most frequently or maintains as his or her official premises." +#secondary_residence "An address at which a person dwells on a secondary basis, for example, during vacation periods, when residing with other parent or relative, at boarding school, etc." +#temporary_dwelling "An address temporarily used as a dwelling" +#former_address "Address (residence, postal, or work address) that is no longer in use" +#mailing_address "Address is a postal address, such as a PO box" +#work_address "Address of place of business where the subject is employed" + +*/ + + +ValueSet: BodySiteVS +Concept: MTH#C1545955 +Description: "Codes that describe normal and pathologic anatomic systems, regions, cavities, and spaces." +Includes codes descending from SCT#123037004 "Body Structure" + +ValueSet: AnatomicalDirectionVS +Concept: NCI#C99074 +Description: "Anatomical location or specimen further detailing directionality. Codes are from NCI" +NCI#C25231 "ANTERIOR Denoting the front portion of the body or a structure." +NCI#C25423 "APICAL Relating to or located at the apex." +NCI#C90067 "BASAL Relating to or located at the lowest portion of a structure." +NCI#C73851 "CAUDAL Toward the tail in a body." +NCI#C25445 "CENTRAL A point or area that is approximately central within some larger region or structure." +NCI#C37936 "CRANIAL Toward the head in a body." +NCI#C25240 "DEEP Extending relatively far inward." +NCI#C25237 "DISTAL Situated farthest from a point of reference." +NCI#C45874 "DORSAL Pertaining to the back or upper surface of the body." +NCI#C90376 "DORSOLATERAL Toward the back and side of a body." +NCI#C90386 "FORE Of or involving the front of a main body." +NCI#C90393 "HIND Of or involving the back of a main body." +NCI#C25353 "INFERIOR Pertaining to a point below a given reference point." +NCI#C37980 "INNER Inside or closer to the inside of the body or object." +NCI#C73705 "INTERMEDIATE Located between two points or extremes." +NCI#C25309 "LOWER The bottom one of two." +NCI#C25232 "MEDIAL Toward the middle or in a limb toward the median plane." +NCI#C81170 "MIDLINE A medial line, especially the medial line or medial plane of the body (or some part of the body)." +NCI#C27958 "NASAL Of, or related to, or in the direction of the nose." +NCI#C38166 "OUTER Being on or toward the outside of the body or object." +NCI#C25233 "PERIPHERAL On or near an edge or constituting an outer boundary;the outer area." +NCI#C25622 "POSTERIOR Denoting the back portion of the body or a structure." +NCI#C94393 "ROSTRAL Toward the muzzle in the head." +NCI#C25239 "SUPERFICIAL Of or pertaining to the exterior surface." +NCI#C25235 "SUPERIOR Pertaining to a point above a given reference point." +NCI#C25245 "SURFACE The extended two-dimensional outer layer or area of a three-dimensional object." +NCI#C117754 "TEMPORAL Of, or related to, anatomic sites that are located in the cranium, brain, and eye." +NCI#C90069 "TIP The pointed end of a structure." +NCI#C25355 "UPPER The top one of two." +NCI#C45875 "VENTRAL Pertaining to the front or lower surface of the body." +NCI#C98798 "VENTROLATERAL Of or pertaining to the front and side of a main body." /*------------- -NCI Code: C99073 LAT, Codelist extensible: Yes +NCI Value: C99073 LAT, Codelist extensible: Yes C13332 BILATERAL Affecting both sides of the body, or a pair of organs. Bilateral C25307 CONTRALATERAL Having to do with the opposite side of the body, in relation to a pre-existing reference point. C25308 IPSILATERAL Having to do with the same side of the body, in relation to a pre-existing reference point. diff --git a/spec/shr_deprecated.txt b/spec/shr_deprecated.txt new file mode 100644 index 00000000..a533b5c3 --- /dev/null +++ b/spec/shr_deprecated.txt @@ -0,0 +1,24 @@ +Grammar: DataElement 5.0 +Namespace: shr.base +Description: "Contains only the SHR Entry definition which is deprecated." + +// NOTE: Entry will eventually be deprecated, as its fields are really a part +// of the implementation, not part of the model. Once the CIMPL tooling +// makes these implicit, Entry and its field elements will go away. +Element: Entry +Description: "Obsolete. Use DomainResource" +0..1 ShrId +0..1 EntryId +0..1 EntryType + + Element: ShrId + Description: "A unique, persistent, permanent identifier for the overall health record belonging to the Patient." + Value: id + + Element: EntryId + Description: "A persistent, permanent identifier for an entry in a health record, unique within the scope of the health record." + Value: id + + Element: EntryType // Would EntryClass be clearer? + Description: "The class of the item, as a URI." + Value: uri \ No newline at end of file diff --git a/spec/shr_encounter.txt b/spec/shr_encounter.txt new file mode 100644 index 00000000..70dfce87 --- /dev/null +++ b/spec/shr_encounter.txt @@ -0,0 +1,238 @@ +Grammar: DataElement 5.0 +Namespace: shr.core + +Abstract Element: EncounterOrEpisode +Based on: DomainResource +Description: "Abstract element representing a group of services delivered to a patient." + StatusOrActive is type Status +1..1 Status +0..* StatusHistory +0..1 TimePeriod +0..* EncounterDiagnosis +1..1 SubjectOfRecord value is type ref(Patient) // EpisodeOfCare restricted in v2 (otherwise could be Patient or Group) +0..* Type +0..1 ref(Organization) +//0..* ref(Account) +0..* ref(ReferralRequest) + +Element: CareContext +Description: "The encounter or episode of care" +Value: ref(Encounter) or ref(EpisodeOfCare) + + +EntryElement: Encounter +Based on: EncounterOrEpisode +Description: "A description of an interaction between a patient and healthcare provider(s) for the purpose of providing healthcare service(s) or assessing the health status of a patient." +// Required value sets for Status are incompatible between DSTU 2 and STU3 +// from http://hl7.org/fhir/ValueSet/encounter-status in STU3 +// from http://hl7.org/fhir/ValueSet/encounter-state in DSTU2 +// StatusHistory.Status from // incompatible VS, see above +0..1 EncounterClass +0..* ClassHistory + Type from http://hl7.org/fhir/ValueSet/v3-ActEncounterCode if covered +0..1 PriorityCode could be from http://hl7.org/fhir/ValueSet/v3-ActPriority +0..* ref(EpisodeOfCare) +0..* Participation + Participation.Participant value is type PractitionerOrRelatedPerson + Participation.ParticipationType from http://hl7.org/fhir/ValueSet/encounter-participant-type if covered +0..1 ref(Appointment) +0..1 Duration +0..* ReasonCode should be from http://hl7.org/fhir/ValueSet/encounter-reason +//0..1 Hospitalization +0..* EncounterLocation +0..1 PartOf value is type ref(Encounter) + + Element: StatusHistory + Description: "List of past encounter statuses" + 1..1 Status + 1..1 TimePeriod + + Element: EncounterClass + Description: "Concepts representing classification of patient encounter such as ambulatory (outpatient), inpatient, emergency, home health or others due to local variations." + Value: CodeableConcept from http://hl7.org/fhir/ValueSet/v3-ActEncounterCode + + Element: ClassHistory + Description: "List of past encounter statuses" + 1..1 EncounterClass + 1..1 TimePeriod + + Element: EncounterDiagnosis + Description: "A diagnosis, which is a disease or injury determined to be present through evaluation of patient history, examination, and/or review of laboratory data. This element is not a stand-alone representation of the condition that was diagnosed, but is meant to be used as an sub-structure in a resource, such as Encounter." + 0..1 DiagnosisCode + 1..1 ref(Condition) + 0..1 PriorityRank + 0..1 Type should be from http://hl7.org/fhir/ValueSet/diagnosis-role + + Element: DiagnosisCode + Description: "Codes for a diagnosis." + Value: CodeableConcept + + Element: EncounterLocation + Description: "Locations where the patient has been." + 1..1 ref(Location) + 0..1 Status from http://hl7.org/fhir/ValueSet/encounter-location-status + 0..1 TimePeriod + + +EntryElement: EpisodeOfCare +Based on: EncounterOrEpisode +Description: "An association between a patient and an organization / healthcare provider(s) during which time encounters may occur. The managing organization assumes a level of responsibility for the patient during this time." + Status from http://hl7.org/fhir/ValueSet/episode-of-care-status + StatusHistory.Status from http://hl7.org/fhir/ValueSet/episode-of-care-status + Type could be from http://hl7.org/fhir/ValueSet/episodeofcare-type +0..1 CareManager +//0..* ref(CareTeam) + + Element: CareManager + Description: "Care manager/care co-ordinator for the patient" + Value: ref(Practitioner) + + + +EntryElement: ReferralRequest +Based on: ActionRequested +Description: "Used to record and send details about a request for referral service or transfer of a patient to the care of another provider or provider organization." + Author value is type PersonOrOrganizationOrDevice + SubjectOfRecord value is type PatientOrGroup +0..* Replaces + Replaces value is type ref(ReferralRequest) + Recipient value is type PractitionerOrOrganization +1..1 Status from http://hl7.org/fhir/ValueSet/request-status + RequestIntent from http://hl7.org/fhir/ValueSet/request-intent + Type could be from http://hl7.org/fhir/ValueSet/referral-type + PriorityCode from http://hl7.org/fhir/ValueSet/request-priority +0..* ServiceType +0..1 CommentOrDescription +0..* RelatedInformation + + + Element: ServiceType + Description: "A service requested or to be performed during this appointment" + Value: CodeableConcept could be from http://hl7.org/fhir/ValueSet/service-type + + Element: Replaces + Description: "Request(s) replaced by this request" + Value: ref(ActionRequested) + + Element: RelatedInformation + Description: "Additional information to support referral or transfer of care request" + Value: ref(DomainResource) + + +EntryElement: Appointment +Based on: DomainResource +Description: "A booking of a healthcare event among patient(s), practitioner(s), related person(s) and/or device(s) for a specific date/time." +1..1 StatusOrActive is type Status + Status from http://hl7.org/fhir/ValueSet/appointmentstatus +0..1 ServiceCategory +0..* ServiceType +0..* Specialty +0..1 Type should be from http://hl7.org/fhir/ValueSet/v2-0276 +0..* ReasonCode +0..* ReasonReference +0..* Indication +0..1 PriorityRankUnsignedInt +0..1 CommentOrDescription +0..* RelatedInformation +0..* ref(ReferralRequest) +1..* AppointmentParticipation +0..1 TimePeriod +0..* ExpectedPerformanceTime +0..1 StatementDateTime + + Element: ServiceCategory + Description: "A broad categorization of the service (ordered, planned, or performed)." + Value: CodeableConcept could be from http://hl7.org/fhir/ValueSet/service-category + + Element: Specialty + Description: "The specialty of a practitioner who (should, will, or did) perform a service." + Value: CodeableConcept should be from http://hl7.org/fhir/ValueSet/c80-practice-codes + + Element: Indication + Description: "Conditions or situations where the procedure is recommended. In the Performed context, the actual indication should be reported." + Value: ref(Condition) or ref(Procedure) + + Element: AppointmentParticipation + Description: "Participants involved in appointment" + 1..* ParticipationType from http://hl7.org/fhir/ValueSet/encounter-participant-type if covered + 0..1 Participant value is type PersonOrDeviceOrLocation // HealthcareService not implemented yet + 0..1 Need from http://hl7.org/fhir/ValueSet/participantrequired + 1..1 Status from http://hl7.org/fhir/ValueSet/participationstatus + + Element: Need + Description: "A code expressing the degree or type of need for the person or item." + Value: CodeableConcept + + +/* CIMI attributes for possible future use + +0..1 AccountId +0..1 AccountStatus +0..* AlternateVisitId +0..1 AmbulatoryStatus +0..1 ChargePriceIndicator +0..1 ChiefComplaint +0..1 EncounterBillingType +0..1 FinancialClass +0..1 HospitalService +0..1 IsEmploymentRelated +0..1 ModeOfArrival +0..1 PatientType +0..1 PreviousServiceDate +0..1 PublicityCode +0..* ReasonForVisit should be from http://hl7.org/fhir/ValueSet/encounter-reason +0..1 ReferralSource +0..1 ServicingFacility +0..* SpecialArrangements +0..* SpecialCourtesy +0..* TriageNotes +0..1 AssignedPatientLocation +0..1 PendingLocation +0..1 ServiceDeliveryLocation +0..1 TemporaryLocation +0..* PriorTemporaryLocation +0..1 Origin +0..1 ServiceProvider +0..1 ConfidentialityCode +0..1 Duration +0..1 TreatmentCooperation +0..1 PaymentSource +0..1 TBD "HealthConcern" +0..* TBD "PertinentFindings" +0..1 TBD "FullClinicalNote" +1..1 TBD "ClinicalSummary" +1..* TBD "TreatmentServiceRendered" +0..1 TBD "CompletionStatus" + + Element: ReferralDate + Concept: MTH#C2735614 + Description: "The date when the provider received a referral for service. A referral includes an oral, written, faxed or electronic request for services made by the client or on the client's behalf." + Value: dateTime + + Element: ReferralSourceType + Concept: TBD + Description: "The type of person or entity that instigated the encounter." + Value: CodeableConcept from ReferralSourceTypeVS + + Element: TreatmentCooperation + Concept: TBD + Description: "Whether the patient is undergoing treatment voluntarily, or under a legal order." + Value: CodeableConcept from TreatmentCooperationVS + + Element: TreatmentServiceRendered + Concept: TBD + Description: "" + Value: CodeableConcept from TreatmentServiceVS + 1..1 TBD "UnitsOfService" + + Element: PaymentSource + Concept: MTH#C0680269 + Description: "The source of payment for the current encounter." + Value: TBD "PaymentSourceVS" + + Element: EpisodeOfCareCompletion + Concept: TBD + Description: "Denotes how and why an episode of care ended." + Value: CodeableConcept from EpisodeOfCareCompletionVS + +*/ diff --git a/spec/shr_encounter_map_dstu2.txt b/spec/shr_encounter_map_dstu2.txt new file mode 100644 index 00000000..30b86f94 --- /dev/null +++ b/spec/shr_encounter_map_dstu2.txt @@ -0,0 +1,16 @@ +Grammar: Map 5.1 +Namespace: shr.core +Target: FHIR_DSTU_2 + + +Encounter maps to Encounter: + + +EpisodeOfCare maps to EpisodeOfCare: + + +ReferralRequest maps to ReferralRequest: + + +Appointment maps to Appointment: + diff --git a/spec/shr_encounter_map_stu3.txt b/spec/shr_encounter_map_stu3.txt new file mode 100644 index 00000000..4fbab7a4 --- /dev/null +++ b/spec/shr_encounter_map_stu3.txt @@ -0,0 +1,116 @@ +Grammar: Map 5.1 +Namespace: shr.core +Target: FHIR_STU_3 + +Encounter maps to Encounter: + Identifier maps to identifier + Status maps to status + StatusHistory maps to statusHistory + StatusHistory.Status maps to statusHistory.status + StatusHistory.TimePeriod maps to statusHistory.period + EncounterClass maps to class + ClassHistory maps to classHistory + ClassHistory.EncounterClass maps to classHistory.class + ClassHistory.TimePeriod maps to classHistory.period + Type maps to type + PriorityCode maps to priority + SubjectOfRecord maps to subject + EpisodeOfCare maps to episodeOfCare + ReferralRequest maps to incomingReferral + Participation maps to participant + Participation.ParticipationType maps to participant.type + Participation.ParticipationPeriod maps to participant.period + Participation.Participant maps to participant.individual + Appointment maps to appointment + TimePeriod maps to period + Duration maps to length + ReasonCode maps to reason + EncounterDiagnosis maps to diagnosis + EncounterDiagnosis.DiagnosisCode maps to diagnosis.extension + EncounterDiagnosis.Condition maps to diagnosis.condition + EncounterDiagnosis.Type maps to diagnosis.role + EncounterDiagnosis.PriorityRank maps to diagnosis.rank +// Account maps to account +// haven't touched hospitalization yet + EncounterLocation maps to location + EncounterLocation.Location maps to location.location + EncounterLocation.Status maps to location.status + EncounterLocation.TimePeriod maps to location.period + Organization maps to serviceProvider + PartOf maps to partOf + +EpisodeOfCare maps to EpisodeOfCare: + Identifier maps to identifier + Status maps to status + StatusHistory maps to statusHistory + StatusHistory.Status maps to statusHistory.status + StatusHistory.TimePeriod maps to statusHistory.period + Type maps to type + EncounterDiagnosis maps to diagnosis + EncounterDiagnosis.DiagnosisCode maps to diagnosis.extension + EncounterDiagnosis.Condition maps to diagnosis.condition + EncounterDiagnosis.Type maps to diagnosis.role + EncounterDiagnosis.PriorityRank maps to diagnosis.rank + SubjectOfRecord maps to patient + Organization maps to managingOrganization + TimePeriod maps to period + ReferralRequest maps to referralRequest + CareManager maps to careManager +// Account maps to account + +ReferralRequest maps to ReferralRequest: + Identifier maps to identifier + // maps to defintion + // maps to basedOn + Replaces maps to replaces + // maps to groupIdentifier + Status maps to status + RequestIntent maps to intent + Type maps to type + PriorityCode maps to priority + ServiceType maps to serviceRequested + SubjectOfRecord maps to subject + CareContext maps to context + ExpectedPerformanceTime maps to occurrence[x] + StatementDateTime maps to authoredOn + Author maps to requester.agent + // maps to requester.onHalfOf + ExpectedPerformerType maps to specialty + Recipient maps to recipient + ReasonCode maps to reasonCode + ReasonReference maps to reasonReference + CommentOrDescription maps to description + RelatedInformation maps to supportingInfo + Annotation maps to note + // maps to relevantHistory + +Appointment maps to Appointment: + Identifier maps to identifier + Status maps to status + ServiceCategory maps to serviceCategory + ServiceType maps to serviceType + Specialty maps to specialty + Type maps to appointmentType + ReasonCode maps to reason + ReasonReference maps to extension + Indication maps to indication + PriorityRankUnsignedInt maps to priority + CommentOrDescription maps to description + RelatedInformation maps to supportingInformation + TimePeriod.BeginDateTime maps to start + TimePeriod.EndDateTime maps to end + //maps to minutesDuration + //maps to slot + StatementDateTime maps to created + //maps to comment + ReferralRequest maps to incomingReferral + AppointmentParticipation maps to participant + AppointmentParticipation.ParticipationType maps to participant.type + AppointmentParticipation.Participant maps to participant.actor + AppointmentParticipation.Need maps to participant.required + AppointmentParticipation.Status maps to participant.status + ExpectedPerformanceTime maps to requestedPeriod + + + + diff --git a/spec/cimi_encounter_vs.txt b/spec/shr_encounter_vs.txt similarity index 64% rename from spec/cimi_encounter_vs.txt rename to spec/shr_encounter_vs.txt index aab31d93..2160ee42 100644 --- a/spec/cimi_encounter_vs.txt +++ b/spec/shr_encounter_vs.txt @@ -1,33 +1,17 @@ Grammar: ValueSet 5.0 -Namespace: cimi.encounter +Namespace: shr.core +/* NOT USED -ValueSet: EpisodeOfCareCompletionVS -#completed "Treatment was completed." -#eligibility "Insurance eligibility changed." -#declined "Declined further treatment." -#lost_contact "Client fell out of contact." -#incarcerated "Client was detained/incarcerated." -#moved "Client moved out of the area." -#transferred "Care was tranferred to the care of another provider." -#failed "Client was unable to complete the course of treatment." -#noncompliance "Client did not comply with the course of treatment." -#death "Client died." +// Currently unused as it violates FHIR's extensible binding on Encounter.class. Ideally we would extend the FHIR VS and add the tele_* codes as level 2 codes under 'VR', but apparently this is not possible + ValueSet: EncounterClassVS + #inpatient "In-facility or hospital setting encounter" + #ambulatory "Ambulatory encounter in office or facility setting" + #home_visit "Encounter in patient's home or location of residence" + #tele_video "Non-face to face contact via synchronous audio and video connection" + #tele_audio "Non-face to face contact via telephone or audio-only connection" + #tele_asynch "Non-face to face contact via text messaging or similar non-simultaneous mode" -ValueSet: EncounterUrgencyVS -SCT#4525004 "Emergency, Crisis, or Urgent Care" -SCT#14736009 "Routine care" - -// Currently unused as it violates FHIR's extensible binding on Encounter.class. Ideally -// we would extend the FHIR VS and add the tele_* codes as level 2 codes under 'VR', but -// apparently this is not possible -// ValueSet: EncounterClassVS -// #inpatient "In-facility or hospital setting encounter" -// #ambulatory "Ambulatory encounter in office or facility setting" -// #home_visit "Encounter in patient's home or location of residence" -// #tele_video "Non-face to face contact via synchronous audio and video connection" -// #tele_audio "Non-face to face contact via telephone or audio-only connection" -// #tele_asynch "Non-face to face contact via text messaging or similar non-simultaneous mode" ValueSet: ReferralSourceTypeVS #self "Self, or personal associated, such as family or friend" @@ -40,6 +24,7 @@ ValueSet: ReferralSourceTypeVS #hp "Health Plan" #employer "Employer" + ValueSet: TreatmentCooperationVS #voluntary "Voluntary cooperation" #ordered_criminal "Criminal court ordered treatment" @@ -51,3 +36,17 @@ ValueSet: ReasonEncounterDidNotHappenVS #lost_touch "Lost touch with patient" #withdrew "Patient withdrew from trial" #hospitalized "Patient was hospitalized" + +ValueSet: EpisodeOfCareCompletionVS +#completed "Treatment was completed." +#eligibility "Insurance eligibility changed." +#declined "Declined further treatment." +#lost_contact "Client fell out of contact." +#incarcerated "Client was detained/incarcerated." +#moved "Client moved out of the area." +#transferred "Care was tranferred to the care of another provider." +#failed "Client was unable to complete the course of treatment." +#noncompliance "Client did not comply with the course of treatment." +#death "Client died." + +*/ \ No newline at end of file diff --git a/spec/cimi_entity.txt b/spec/shr_entity.txt similarity index 60% rename from spec/cimi_entity.txt rename to spec/shr_entity.txt index 65dbbf99..804a4bfe 100644 --- a/spec/cimi_entity.txt +++ b/spec/shr_entity.txt @@ -1,14 +1,9 @@ Grammar: DataElement 5.0 -Namespace: cimi.entity -Description: "The namespace containing definitions for basic classes in CIMI." -Uses: shr.core, cimi.core, cimi.context, cimi.element, cimi.statement - +Namespace: shr.core Abstract Element: EntityOrRole -Based on: Independent -Description: "Parent class entity and role." -//Identifier - +Based on: DomainResource +Description: "Abstract parent class for both Entity and Role." Abstract Element: Role Based on: EntityOrRole @@ -18,131 +13,41 @@ Abstract Element: Entity Based on: EntityOrRole Concept: TBD Description: "Root class for entities such as people, organizations, and devices that have a separately identifiable existence." +0..1 PartOf + + Element: PartOf + Description: "The larger entity that the asserted item is a portion of. For example, an organization part of a larger organization, or an encounter with a hospitalist might be part of a larger hospitalization encounter." + Value: ref(DomainResource) EntryElement: Patient Based on: Role Concept: MTH#C1299487 -Description: "A person in the role of a patient, including extended demographic information about the subject of this health record." -1..1 ref(Person) -0..1 PlaceOfBirth -0..1 MultipleBirth -0..1 BirthSex -0..1 Race -0..1 Ethnicity -0..1 MaritalStatus -0..1 MothersMaidenName -0..1 FathersName -0..1 SocialSecurityNumber -0..1 DriversLicenseNumber -0..* PassportNumber -0..1 MedicalInterpreterNeeded -0..1 Deceased - - Element: PlaceOfBirth - Concept: MTH#C0032040 - Description: "The location of a birth event. There may be multiple entries, but a person has only one place of birth." - Value: GeopoliticalLocation - - Element: MultipleBirth - Concept: MTH#C0026753 - Description: "Indication if the person was part of a multiple birth event." - Value: boolean - 0..1 MultipleBirthOrder - - Element: MultipleBirthOrder - Concept: LNC#73771-8 - Description: "Order of birth of the person in multiple birth event (if part of multiple birth)." - Value: integer - // should be positiveInt, but it is an integer in FHIR (no issue yet logged) - - Element: BirthSex - Concept: MTH#C4086849 - Description: "Administrative sex assigned at birth and recorded on birth certificate." - Value: CodeableConcept from http://hl7.org/fhir/us/core/ValueSet/us-core-birthsex - - Element: Race - Concept: MTH#C0034510 - Description: "Subjective association of a person with a named category of humans sharing common history, traits, place of family origin, nationality, tribe, or other inherited background." - Value: CodeableConcept from http://hl7.org/fhir/us/core/ValueSet/omb-ethnicity - 0..* RaceDetail +Description: "A person in the role of a patient. Sometimes, the patient is not the subject of information in a clinical statement where the Patient is the SubjectOfRecord. - Element: RaceDetail - Concept: TBD - Description: "Additional description of race or heritage." - Value: CodeableConcept from http://hl7.org/fhir/us/core/ValueSet/detailed-race or CodeableConcept from http://hl7.org/fhir/us/core/ValueSet/omb-ethnicity - - Element: Ethnicity - Concept: MTH#C0015031 - Description: "Indicator of Hispanic or Latino origin." - Value: CodeableConcept from http://hl7.org/fhir/us/core/ValueSet/omb-ethnicity - 0..* EthnicityDetail +SHR follows Argonaut and makes the value set binding on marital status required. SHR also adds optional extensions on communication ability to more fully characterize language skills. +MaritalStatus has a required binding in Argonaut, but an extensible binding in US-Core. To be feasible under both DSTU2 Argonaut and STU3 US-Core, the required binding strength is adopted." +1..* Identifier +1..1 Person +0..1 StatusOrActive is type Active - Element: EthnicityDetail - Concept: TBD - Description: "Additional description of ethnicity." - Value: CodeableConcept from http://hl7.org/fhir/us/core/ValueSet/omb-ethnicity or CodeableConcept from http://hl7.org/fhir/us/core/ValueSet/detailed-ethnicity - - - Element: MaritalStatus - Concept: MTH#C0024819 - Description: "The most recent marital status of a person." - Value: CodeableConcept from FHIR/marital-status - - Element: MothersMaidenName - Concept: MTH#C0806887 - Description: "The name of the mother as it was or likely to have been recorded on the birth certificate of the subject. This is most likely the name prior to marriage of the mother (aka the maiden name)." - Value: HumanName - - Element: FathersName - Concept: TBD - Description: "The name of the father as it was or likely to have been recorded on the birth certificate of the subject; most likely the name of the father at the time of birth of the subject." - Value: HumanName - - Element: SocialSecurityNumber - Concept: MTH#C1301821 - Description: "A US social security number (SSN)." - Value: string // note that missing value reasons include "none" - meaning the subject does not have a SSN - - Element: DriversLicenseNumber + Element: AccessTime Concept: TBD - Description: "Identifying information from a drivers license." - Value: string - 0..1 StateOfIssue - 0..1 EffectiveTimePeriod - - Element: StateOfIssue - Concept: TBD - Description: "A state or country acting as an assuing authority for a document." - Value: State - - Element: PassportNumber - Concept: MTH#C1549737 - Description: "Credential indicating citizenship." - Value: string - 1..1 CountryOfIssue - 0..1 EffectiveTimePeriod - - Element: CountryOfIssue - Concept: TBD - Description: "A country acting as an assuing authority for a document." - Value: Country - - - Element: MedicalInterpreterNeeded - Concept: MTH#C1442531 - Description: "Whether the subject requires an interpreter to communicate with an English-speaking provider." - Value: CodeableConcept from YesNoUnknownVS - 1..1 Language + Description: "Point in time when data was accessed." + Value: dateTime EntryElement: Practitioner Based on: Role Concept: MTH#C2220264 -Description: "A person who practices a healing art." -1..1 ref(Person) +Description: "A person who practices a healing art. +HumanName is limited to one required value by US-Core. Gender is required by US-Core." +1..1 Person +0..1 StatusOrActive is type Active 1..1 Person.HumanName // only one (limitation imposed by us-core) // 0..* Affiliation // handled by ProviderRelationship in FHIR -1..1 NationalProviderIdentifier +1..* Identifier + Identifier +includes 1..1 NationalProviderIdentifier 0..* Qualification Element: Affiliation @@ -153,12 +58,13 @@ Description: "A person who practices a healing art." Element: NationalProviderIdentifier Based on: Identifier Concept: MTH#C1549728 - Description: "A unique 10 digit number to allow US healthcare providers to identify themselves in a standard way throughout the healthcare industry." + Description: "NPI: a unique 10 digit number to allow US healthcare providers to identify themselves in a standard way throughout the healthcare industry." Element: Qualification Concept: MTH#C0037778 Description: "A right to practice medicine obtained by training and certification." - 1..1 Type from http://hl7.org/fhir/ValueSet/c80-practice-codes + 0..* Identifier + 1..1 Type could be from http://hl7.org/fhir/ValueSet/v2-2.7-0360 0..1 EffectiveTimePeriod 0..1 Issuer // or http://www.wpc-edi.com/reference/codelists/healthcare/health-care-provider-taxonomy-code-set/ @@ -167,41 +73,27 @@ Description: "A person who practices a healing art." EntryElement: RelatedPerson Based on: Role Description: "A person in a role defined in relationship to a patient" -0..1 ref(Person) -0..1 RelationshipToPersonOfRecord +0..1 Person +0..1 StatusOrActive is type Active +0..1 RelationshipToPatient 0..1 EffectiveTimePeriod +1..1 Person.HumanName // DSTU 2 change (max cardinality of 1 imposed by DSTU 2) -Element: PatientOrPractitioner -Based on: EntityOrRole -Description: "A choice of Patient or Practitioner. Needed for mapping to FHIR." -Value: ref(Patient) or ref(Practitioner) - -Element: PatientOrPractitionerOrRelatedPerson -Based on: EntityOrRole -Description: "A choice of Patient, Practitioner and RelatedPerson. Needed for mapping to FHIR, for example, mapping AdverseEvent.Signed to FHIR AdverseEvent." -Value: ref(Patient) or ref(Practitioner) or ref(RelatedPerson) - -Element: PractitionerOrRelatedPerson -Based on: EntityOrRole -Description: "A choice of Practitioner and RelatedPerson. Needed for mapping to FHIR, for example, mapping EncounterPerformed.Participant to FHIR Encounter.participant.individual" -Value: ref(Practitioner) or ref(RelatedPerson) - -Element: AnyPersonOrOrganization -Based on: EntityOrRole -Description: "Needed for mapping to FHIR, for example, mapping to FHIR MedicationStatement.informationSource." -Value: ref(Patient) or ref(Practitioner) or ref(RelatedPerson) //or ref(Organization) - + Element: RelationshipToPatient + Concept: MTH#C0015608 + Description: "The relationship to the person of record." + Value: CodeableConcept from http://hl7.org/fhir/ValueSet/relatedperson-relationshiptype // DSTU 2 change -- change from extensible to required since this value set is required in DSTU 2 EntryElement: Group -Based on: EntityOrRole +Based on: Entity Concept: MTH#C0441833 Description: "A set of entities (personnel, material, or places) to be considered together. May be a pool of like-type resources, a team, or combination of personnel, material and places." -0..1 ActiveFlag +0..1 StatusOrActive is type Active 1..1 Type from http://hl7.org/fhir/ValueSet/group-type 0..1 Title // name 1..1 Actual 0..* GroupCharacteristic -0..* Member +0..* MemberParticipation 0..1 Count Element: Actual @@ -210,44 +102,80 @@ Description: "A set of entities (personnel, material, or places) to be considere Element: GroupCharacteristic Concept: MTH#C0599755 - Description: "An inclusion or exclusion criterion as part of defining a cohort. If the criterion is an unary, then TopicCode must be SCT#385432009 (not applicable)" - Value: boolean or Quantity or Range - 1..1 GroupCharacteristicCode + Description: "An inclusion or exclusion criterion as part of defining a cohort." + 1..1 Code + 0..1 GroupCharacteristicValue 1..1 ExcludeFlag 0..1 TimePeriod - - Element: GroupCharacteristicCode - Description: "A code describing the characteristic present, absent, or having a value in this group." - Value: CodeableConcept + + Element: GroupCharacteristicValue + Description: "The value or range of the characteristic." + Value: boolean or Quantity or Range Element: ExcludeFlag Concept: MTH#C0680251 Description: "If true, exclude the subjects that match the criterion." Value: boolean - Element: Member + Element: MemberParticipation Concept: MTH#C0682343 "Member of Target Group" Description: "A person or entity in a group." - Value: ref(Patient) or ref(Practitioner) or ref(Device) or ref(Medication) or ref(Substance) + 1..1 Member 0..1 ParticipationPeriod - 1..1 ActiveFlag + 1..1 InactiveFlag + + Element: Member + Concept: TBD + Description: "A person or entity in a group." + Value: ref(Patient) or ref(Practitioner) or ref(Device) or ref(Medication) or ref(Substance) + + Element: InactiveFlag + Concept: TBD + Description: "Indicates if the member is inactive in the context of the group." + Value: boolean + -EntryElement: Facility +EntryElement: Location Based on: Entity Concept: MTH#C1547538 Description: "Services and space and equipment provided for a particular purpose; a building or place that provides a particular service or is used for a particular industry. Could be a clinical site, community site, or a mobile facility." -1..1 FacilityName -1..1 Type from http://hl7.org/fhir/ValueSet/v3-ServiceDeliveryLocationRoleType -1..1 Location +0..1 StatusOrActive is type Status + Status from http://hl7.org/fhir/ValueSet/location-status +0..1 OperationalStatus +1..1 LocationName +0..* Alias +0..1 CommentOrDescription +0..1 Mode from http://hl7.org/fhir/ValueSet/location-mode +1..1 Type from http://hl7.org/fhir/ValueSet/v3-ServiceDeliveryLocationRoleType if covered +0..* ContactPoint +0..1 Address +0..1 PhysicalType +0..1 Geoposition 0..1 MobileFacility -0..1 ContactPoint -1..1 ManagingOrganization +1..1 ref(ManagingOrganization) + PartOf value is type Location + + Element: OperationalStatus + Description: "The operational status covers operation values most relevant to beds (but can also apply to rooms/units/chairs/etc. such as an isolation unit/dialysis chair). This typically covers concepts such as contamination, housekeeping, and other activities like maintenance." + Value: CodeableConcept should be from http://terminology.hl7.org/ValueSet/v2-0116 + + Element: Alias + Description: "A list of alternate names the subject is or was known as." + Value: string - Element: FacilityName + Element: Mode + Description: "Indicates whether a resource instance represents a specific item or a class of items." + Value: CodeableConcept + + Element: LocationName Concept: MTH#C3261404 Description: "The DBA (doing business as) or most commonly-used name for a facility." Value: string + Element: PhysicalType + Description: "Physical form of the location, e.g. building, room, vehicle, road." + Value: CodeableConcept could be from http://hl7.org/fhir/ValueSet/location-physical-type + Element: MobileFacility Concept: MTH#C0231435 Description: "A facility that moves from place to place, such as Meals-On-Wheels." @@ -255,27 +183,34 @@ Description: "Services and space and equipment provided for a particular purpose Element: ManagingOrganization Concept: MTH#C0677351 - Description: "The organization that manages the operation of an activity, facility, or service provision." + Description: "The organization that manages an activity, facility, document, or service provision." Value: ref(Organization) - EntryElement: Substance Based on: Entity Concept: MTH#C0439861 Description: "Any matter of defined composition that has discrete existence, whose origin may be biological, mineral or chemical." -1..1 Type should be from http://hl7.org/fhir/ValueSet/substance-code +1..1 Type could be from http://hl7.org/fhir/ValueSet/substance-code 0..* Category from http://hl7.org/fhir/ValueSet/substance-category if covered -0..1 ActiveFlagAsaCodeableConcept from http://hl7.org/fhir/ValueSet/substance-status -0..1 Details + StatusOrActive is type Status +0..1 Status from http://hl7.org/fhir/ValueSet/substance-status +0..1 CommentOrDescription 0..* Ingredient +0..0 PartOf Element: Ingredient Concept: MTH#C3176062 Description: "Specifies an material component in a non-medication substance." - Value: CodeableConcept or ref(Substance) + 1..1 SubstanceOrCode 1..1 IngredientAmount - + 0..1 IsActiveIngredient + + Element: SubstanceOrCode + Concept: TBD + Description: "A code or substance reference identifying the ingredient." + Value: CodeableConcept or ref(Substance) or ref(Medication) + Element: IsActiveIngredient Concept: TBD Description: "True if the ingredient is an active ingredient in the medication." @@ -289,16 +224,22 @@ Description: "Any matter of defined composition that has discrete existence, who EntryElement: Medication Based on: Entity Concept: MTH#C0013227 -Description: "A type of prescription drug or over-the-counter drug that is used to prevent, treat, or relieve symptoms of a disease or abnormal condition, but excluding vaccines." +Description: "A type of prescription drug or over-the-counter drug that is used to prevent, treat, or relieve symptoms of a disease or abnormal condition, but excluding vaccines. +In FHIR DSTU2 and STU3, Medication lacks the identifer attribute, which is included in SHR as an extension. +DSTU2 lacks the status attribute, which is required by US-Core. +Batch is 0..1 in FHIR R4, and accordingly is restricted here." + StatusOrActive is type Status + Status from http://hl7.org/fhir/ValueSet/medication-status 1..1 Type from http://hl7.org/fhir/us/core/ValueSet/us-core-medication-codes if covered 0..1 DoseForm 0..1 Brand 0..1 OverTheCounter -0..* MedicationIngredient +0..* Ingredient 0..1 Manufacturer 0..1 LotNumber 0..1 ExpirationDate 0..1 Package could be from http://hl7.org/fhir/ValueSet/medication-package-form +0..0 PartOf Element: DoseForm Concept: MTH#C0013058 @@ -308,9 +249,14 @@ Description: "A type of prescription drug or over-the-counter drug that is used Element: Brand Concept: TBD Description: "If the product is branded, and if so, the brand name of a product." - Value: boolean + 1..1 IsBrand 0..1 BrandName + Element: IsBrand + Concept: TBD + Description: "If the product is branded." + Value: boolean + Element: BrandName Concept: TBD Description: "The marketing name for a brand name product" @@ -321,18 +267,6 @@ Description: "A type of prescription drug or over-the-counter drug that is used Description: "True if the medication is available to consumers without a prescription." Value: boolean - Element: MedicationIngredient - Concept: MTH#C3176062 - Description: "Specifies an material component in a medication." - Value: CodeableConcept or ref(Substance) or ref(Medication) - 1..1 IngredientAmount - 1..1 IsActiveIngredient - - Element: IsActiveIngredient - Concept: TBD - Description: "True if the ingredient is an active ingredient in the medication." - Value: boolean // forced to use boolean by FHIR mapping - Element: Manufacturer Concept: MTH#C1114744 Description: "The organization producing the product or test." @@ -353,23 +287,141 @@ Description: "A type of prescription drug or over-the-counter drug that is used Description: "The kind of container the medication comes in." Value: CodeableConcept - - -EntryElement: Person -Based on: Entity +Element: Person Concept: MTH#C0027361 -Description: "A person relevant to the health or social situation of the subject (including the person of record him or herself)." +Description: "A person relevant to the health or social situation of the subject (including the subject him- or herself)." 1..* HumanName -0..1 AnonymizedFlag -0..1 FictionalPersonFlag +//0..1 AnonymizedFlag +//0..1 FictionalPersonFlag 0..1 DateOfBirth 1..1 AdministrativeGender 0..* Address -0..1 Headshot +0..* PhotographicImage 0..* ContactPoint -0..* LanguageUsed -0..1 ActiveFlag -0..* ref(ExternalHealthRecord) +0..* Communication +0..1 MaritalStatus +0..1 MultipleBirth +0..1 BirthSex +0..1 Race +0..1 Ethnicity +0..1 Deceased +//0..1 PlaceOfBirth +//0..1 MothersMaidenName +//0..1 FathersName +//0..1 SocialSecurityNumber +//0..1 DriversLicenseNumber +//0..* PassportNumber + + + Element: PlaceOfBirth + Concept: MTH#C0032040 + Description: "The location of a birth event. There may be multiple entries, but a person has only one place of birth." + Value: Address + + Element: MultipleBirth + Description: "If the person was part of a multiple birth event, and if so in which order." + Value: boolean or integer + + Element: BirthSex + Concept: MTH#C4086849 + Description: "Administrative sex assigned at birth and recorded on birth certificate." + Value: CodeableConcept from http://hl7.org/fhir/us/core/ValueSet/us-core-birthsex + + Element: Race + Concept: MTH#C0034510 + Description: "Subjective association of a person with a named category of humans sharing common history, traits, place of family origin, nationality, tribe, or other inherited background." + 0..1 RaceCode + 0..* RaceDetail + + Element: RaceCode + Concept: TBD + Description: "A code for the person's race" + Value: CodeableConcept from http://hl7.org/fhir/us/core/ValueSet/omb-race + + Element: RaceDetail + Concept: TBD + Description: "Additional description of race or heritage." + Value: CodeableConcept from http://hl7.org/fhir/us/core/ValueSet/detailed-race + + Element: Ethnicity + Concept: MTH#C0015031 + Description: "Indicator of Hispanic or Latino origin." + 1..1 EthnicityCode + 0..* EthnicityDetail + + Element: EthnicityCode + Concept: TBD + Description: "A code for the person's ethnicity" + Value: CodeableConcept from http://hl7.org/fhir/us/core/ValueSet/omb-ethnicity + + Element: EthnicityDetail + Concept: TBD + Description: "Additional description of ethnicity." + Value: CodeableConcept from http://hl7.org/fhir/us/core/ValueSet/detailed-ethnicity + + Element: MothersMaidenName + Concept: MTH#C0806887 + Description: "The name of the mother as it was or likely to have been recorded on the birth certificate of the subject. This is most likely the name prior to marriage of the mother (aka the maiden name)." + Value: HumanName + + Element: FathersName + Concept: TBD + Description: "The name of the father as it was or likely to have been recorded on the birth certificate of the subject; most likely the name of the father at the time of birth of the subject." + Value: HumanName + + Element: SocialSecurityNumber + Concept: MTH#C1301821 + Description: "A US social security number (SSN)." + Value: string // note that missing value reasons include "none" - meaning the subject does not have a SSN + + Element: DriversLicenseInformation + Concept: TBD + Description: "Identifying information from a drivers license." + 0..1 DriversLicenseNumber + 0..1 StateOfIssue + 0..1 EffectiveTimePeriod + + Element: DriversLicenseNumber + Description: "The drivers license number." + Value: string + + Element: StateOfIssue + Concept: TBD + Description: "A state or country acting as an assuing authority for a document." + Value: State + + Element: PassportInformation + Concept: MTH#C1549737 + Description: "Credential indicating citizenship." + 1..1 PassportNumber + 1..1 CountryOfIssue + 0..1 EffectiveTimePeriod + + Element: PassportNumber + Description: "The passport number." + Value: string + + Element: CountryOfIssue + Concept: TBD + Description: "A country acting as an assuing authority for a document." + Value: Country + + + Element: MedicalInterpreter + Concept: MTH#C1442531 + Description: "Whether the subject requires an interpreter to communicate with an English-speaking provider." + 1..1 MedicalInterpreterNeeded + 1..1 Language + + Element: MedicalInterpreterNeeded + Concept: MTH#C1442531 + Description: "Whether the subject requires an interpreter to communicate with an English-speaking provider." + Value: CodeableConcept from YesNoUnknownVS + + Element: MaritalStatus + Concept: MTH#C0024819 + Description: "The most recent marital status of a person." + Value: CodeableConcept from http://hl7.org/fhir/ValueSet/marital-status // if covered // DSTU 2 change -- MaritalStatus has a required binding in Argonaut Element: AnonymizedFlag Concept: MTH#C3858751 @@ -389,21 +441,21 @@ Description: "A person relevant to the health or social situation of the subject Element: AdministrativeGender Concept: MTH#C1550327 Description: "A gender classification used for administrative purposes. Administrative gender is not necessarily the same as a biological description or a gender identity. This attribute does not include terms related to clinical gender." - Value: code from http://hl7.org/fhir/ValueSet/administrative-gender - - Element: Headshot - Concept: TBD - Description: "A photograph showing a person's face." - Value: Media + Value: CodeableConcept from http://hl7.org/fhir/ValueSet/administrative-gender - Element: LanguageUsed // needs to be aligned with CCDA 2.1 + Element: Communication // needs to be aligned with CCDA 2.1 Concept: TBD Description: "Language used for communication by a human, either the subject of record, parent, or other involved person." - Value: Language + 1..1 Language // do not specify value set because argo R2 is different than US-Core in STU3 + 0..1 Preferred 0..1 SpokenLanguageProficiency 0..1 WrittenLanguageProficiency 0..* LanguageQualifier + Element: Preferred + Description: "Indicates preference." + Value: boolean + Element: SpokenLanguageProficiency Concept: MTH#C0678997 Description: "Accuracy and fluency in spoken communication in a language." @@ -418,58 +470,31 @@ Description: "A person relevant to the health or social situation of the subject Description: "Additional information about a person's use of language." Value: CodeableConcept from LanguageQualifierVS - Element: ActiveFlag - Concept: TBD - Description: "If the ActiveFlag is false, it indicates the record or item is no longer to be used and should generally be hidden for the user in the UI." - Value: boolean - Element: Deceased Concept: MTH#C0011065 - Description: "An indication that the person is no longer living, given by a date, time of death, or a boolean value which, when true, indicates the person is deceased." - Value: boolean - 0..1 DateOfDeath - 0..1 AgeAtDeath - - Element: DateOfDeath - Concept: MTH#C1148348 - Description: "The calendar date of subject's death." - Value: dateTime + Description: "An indication that the person is no longer living, given by a date of death, or boolean value. The latter, when true, indicates the person is deceased." + Value: boolean or dateTime +/* Element: AgeAtDeath Concept: MTH#C1546180 Description: "The age, age range, or age group when the cessation of life happens." Value: Age or Range - - Element: ActiveFlagAsaCodeableConcept - Concept: TBD - Description: "If the ActiveFlag is false, it indicates the record or item is no longer to be used and should generally be hidden for the user in the UI." - Value: CodeableConcept - - Element: ExternalHealthRecord - Based on: Entity - Concept: TBD - Description: "A health record other than the current health record; may have been used to help populate the current record." - 1..1 Identifier - 1..1 AccessTime - - Element: AccessTime - Concept: TBD - Description: "Point in time when data was accessed." - Value: dateTime - +*/ EntryElement: Organization Based on: Entity Concept: MTH#C1561598 -Description: "A social or legal structure formed by human beings." +Description: "A social or legal structure formed by human beings. + +Organization type is restricted to 0..1 in FHIR DSTU2, similarly restricted here." +// Required attributes come from STU 3 mapping to us-core-organization 1..1 OrganizationName -0..* OrganizationAlias -1..* OrganizationIdentifier -1..1 Type from http://hl7.org/fhir/ValueSet/organization-type -1..* OrganizationIdentifier +1..* Identifier // cardinality constraint +0..1 Type could be from http://hl7.org/fhir/ValueSet/organization-type 1..* Address 1..* ContactPoint -1..1 ActiveFlag +1..1 StatusOrActive is type Active 0..1 PartOf value is type ref(Organization) Element: OrganizationName @@ -477,33 +502,22 @@ Description: "A social or legal structure formed by human beings." Description: "The name of the organization." Value: string - Element: OrganizationAlias - Concept: TBD - Description: "A list of alternate names that the organization is known as, or was known as in the past." - Value: string - - Element: OrganizationIdentifier - Based on: Identifier - Concept: TBD - Description: "An identifier of the organization. An NPI preferred, tax id is allowed, and a local id is allowed in addition to ‘authoritative’ identifier" - - -Element: Location -Based on: Entity -Concept: MTH#C0450429 -Description: "A position, site, or point in space where something can be found." -Value: Address or Geoposition or GeopoliticalLocation - -Element: Device +EntryElement: Device Based on: Entity -Description: "A specific durable physical device used in diagnosis or treatment. The value is the coding for a type of device, for example, a CPAP machine. The same device might be used on multiple patients." -1..1 Type from DeviceVS // currently (4/2018) called 'key' in CIMI -0..* DeviceUdi +Description: "A specific durable physical device used in diagnosis or treatment. The value is the coding for a type of device, for example, a CPAP machine. The same device might be used on multiple patients. +Device status cannot be reconciled between Argonaut and US-Core, each having different required value sets. +Device type has extensible mappings to different value sets in Argonaut and US-Core, however both value sets have identical SNOMED content (descendants of 49062001 (Device). We adopt the US-Core value set, which is allowable because the binding is extensible." + StatusOrActive is type Status + //Status + // from http://hl7.org/fhir/ValueSet/devicestatus in V2 argo + // from http://hl7.org/fhir/ValueSet/device-status in V3 us-core +1..1 Type from http://hl7.org/fhir/ValueSet/device-kind +1..1 DeviceUdi // DSTU 2 change -- Argonaut requires 1..1 Udi (see http://build.fhir.org/ig/Healthedata1/Argo-DSTU2/StructureDefinition-argo-device.html) 0..1 VendorModelNumber // called 'model' in CIMI 0..1 ManufacturerName // string, not ref(Organization) - only because of mapping to FHIR 0..1 ManufactureDate 0..1 ExpirationDate -0..1 Version +0..1 VersionString 0..1 Url Element: DeviceUdi @@ -518,7 +532,7 @@ Description: "A specific durable physical device used in diagnosis or treatment. Element: ManufacturerName Concept: TBD - Description: "The name of the company who produce the device." + Description: "The name of the company who produced the item." Value: string Element: ManufactureDate @@ -531,19 +545,21 @@ Description: "A specific durable physical device used in diagnosis or treatment. Description: "A unique URL on which the device may be contacted directly." Value: uri -Element: Specimen +EntryElement: Specimen Based on: Entity Description: "A specimen is a substance, physical object, or collection of objects, that the laboratory considers a single discrete, uniquely identified unit that is the subject of one or more steps in the laboratory workflow. A specimen may include multiple physical pieces as long as they are considered a single unit within the laboratory workflow. A specimen results from one to many specimen collection procedures, and may be contained in multiple specimen containers. Specimen may have one or more processing activities." 0..1 AccessionIdentifier -0..1 SpecimenStatus from http://hl7.org/fhir/ValueSet/specimen-status + StatusOrActive is type Status +0..1 Status from http://hl7.org/fhir/ValueSet/specimen-status 1..1 Type from http://hl7.org/fhir/ValueSet/v2-0487 0..1 CollectionSource 0..1 CollectionTime 0..1 CollectionMethod 0..1 CollectionSite -0..1 SourceSpecimen +0..1 AmountOrSize + PartOf value is type ref(Specimen) 0..1 ReceivedTime -0..* ref(SpecimenContainer) +0..* SpecimenContainer 0..* SpecimenTreatment 0..* HandlingRisk 0..* SpecialHandling @@ -566,22 +582,13 @@ Description: "A specimen is a substance, physical object, or collection of objec Element: CollectionSite Concept: TBD Description: "The body site where specimen was collected" - Value: AnatomicalLocation + Value: BodySite + Element: AccessionIdentifier Based on: Identifier Concept: TBD Description: "Identifier assigned by the lab" - Element: SpecimenStatus - Concept: MTH#C0449438 - Description: "State of the specimen, such as obtained, processed, used." - Value: CodeableConcept - - Element: SourceSpecimen - Concept: TBD - Description: "Identifier for the source specimen from which this specimen was derived." - Value: ref(Specimen) - Element: HandlingRisk Concept: TBD Description: "Cautions on the handling of this specimen." @@ -592,20 +599,20 @@ Description: "A specimen is a substance, physical object, or collection of objec Description: "Information about the proper handling of the specimen." Value: CodeableConcept - EntryElement: SpecimenTreatment -// Based on: ProcedurePerformed + Element: SpecimenTreatment Concept: TBD - Description: "Treatment performed on the specimen." + Description: "Additives added to the specimen." 0..* Additive - -EntryElement: SpecimenContainer -Based on: Entity -Concept: TBD -Description: "Direct container of specimen (tube/slide, etc.)" + Element: AmountOrSize + Description: "The quantity of specimen collected" + Value: SimpleQuantity + +Element: SpecimenContainer +Description: "Direct container of specimen (slide, etc.)" +0..* Identifier 0..1 Type //"Kind of container holding the specimen - e.g. a vial or well." -0..1 Identifier -0..1 Details +0..1 CommentOrDescription 0..1 Capacity 0..1 SpecimenQuantity 0..* Additive @@ -615,31 +622,65 @@ Description: "Direct container of specimen (tube/slide, etc.)" // BALLOT: In SpecimenContainer, SpecimenQuantity (datatype Quantity) describes the amount of specimen. SpecimenCollectionAction breaks out amount of specimen in a number of individual attributes: amount, volume, dimension, and size. Which is the best way to do this? Shouldn't we be consistent about how we refer to the size or amount of a specimen? Element: Capacity - Concept: TBD Description: "Container volume or size." Value: SimpleQuantity Element: SpecimenQuantity - Concept: TBD Description: "Quantity of specimen within container." Value: SimpleQuantity Element: Additive - Concept: TBD Description: "Additive associated with container." Value: CodeableConcept or ref(Substance) Element: SequenceNumber - Concept: TBD Description: "The sequence number for this specimen in a collection of specimens." Value: CodeableConcept // BALLOT: Why is SpecimenContainer.SequenceNumber a CodeableConcept? It should be an integer or a string. I don't think the sequence number will ever be coded, and CodeableConcept datatype is specifically designed for code mapping. -Element: MaterializedAssertion -Based on: Entity -Description: "A thing whose existence is implied by an assertion of presence. For example, a wound presence assertion implies there is a physical wound that exists. Observation of a tumor implies there is a tumor that exists. Assertion of a condition in a patient implies there is one more countable instance (case) of that condition in the world. The MaterializedAssertion allows one to refer to the implied entity as an actual entity. In other words, MaterializedAssertion represents the reification of a clinical statement. -CIMI Alignment: not part of CIMI." -Value: ref(ConditionPresenceStatement) - - +EntryElement: Media +Based on: Entity +Description: "A photo, video, or audio recording acquired or used in healthcare. The actual content may be inline or provided by direct reference." +0..* RelatedRequest value is type ref(ProcedureRequest) +1..1 Type from http://hl7.org/fhir/ValueSet/digital-media-type +0..1 Subtype +0..1 View +0..1 SubjectOfRecord value is type PatientOrPractitionerOrGroupOrDeviceOrSpecimen +0..1 CareContext +0..1 RelevantTime // like observation +0..1 ref(Practitioner) +0..* ReasonCode could be from http://hl7.org/fhir/ValueSet/procedure-reason +0..1 BodySite +0..1 ref(Device) +0..1 PixelHeight +0..1 PixelWidth +0..1 Frames +0..1 NumberOfSecondsDuration // this is not how duration should be captured. See Duration +1..1 Attachment +0..* Annotation + + + Element: Subtype + Description: "A further refinement of type." + Value: CodeableConcept + + Element: View + Description: "The name of the imaging view e.g. Lateral or Antero-posterior (AP)." + Value: CodeableConcept could be from http://hl7.org/fhir/ValueSet/media-view + + Element: PixelHeight + Description: "Height of the image in pixels (photo/video)" + Value: positiveInt + + Element: PixelWidth + Description: "Width of the image in pixels (photo/video)" + Value: positiveInt + + Element: Frames + Description: "Number of frames if > 1 (photo)" + Value: positiveInt + + Element: NumberOfSecondsDuration + Description: "Length in seconds (rounded to nearest whole second)" + Value: unsignedInt diff --git a/spec/shr_entity_map_dstu2.txt b/spec/shr_entity_map_dstu2.txt new file mode 100644 index 00000000..828b9336 --- /dev/null +++ b/spec/shr_entity_map_dstu2.txt @@ -0,0 +1,174 @@ +Grammar: Map 5.1 +Namespace: shr.core +Target: FHIR_DSTU_2 + +Patient maps to http://fhir.org/guides/argonaut/StructureDefinition/argo-patient: // dstu 2 change (different mapping target) + Identifier maps to identifier + Active maps to active + Person.HumanName maps to name + Person.AdministrativeGender maps to gender + Person.PhotographicImage maps to photo + Person.Address maps to address + Person.ContactPoint maps to telecom + Person.Communication.Language maps to communication.language + Person.Communication.Preferred maps to communication.preferred +// Person.Communication.SpokenLanguageProficiency maps to communication.extension +// Person.Communication.WrittenLanguageProficiency maps to communication.extension +// Person.Communication.LanguageQualifier maps to communication.extension + Person.DateOfBirth maps to birthDate + Person.MaritalStatus maps to maritalStatus + Person.MultipleBirth maps to multipleBirth[x] + Person.BirthSex maps to http://fhir.org/guides/argonaut/StructureDefinition/argo-birthsex + Person.Race maps to http://fhir.org/guides/argonaut/StructureDefinition/argo-race + Person.Ethnicity maps to http://fhir.org/guides/argonaut/StructureDefinition/argo-ethnicity +// MothersMaidenName maps to http://hl7.org/fhir/StructureDefinition/patient-mothersMaidenName +// MedicalInterpreterNeeded maps to http://hl7.org/fhir/StructureDefinition/patient-interpreterRequired +// PlaceOfBirth maps to http://hl7.org/fhir/StructureDefinition/birthPlace + Person.Deceased maps to deceased[x] + +Practitioner maps to Practitioner: // dstu 2 change (different mapping target) + Identifier maps to identifier + Active maps to active + Person.HumanName maps to name + Person.AdministrativeGender maps to gender + Person.PhotographicImage maps to photo + Person.Address maps to address + Person.ContactPoint maps to telecom + Person.Communication.Language maps to communication + Qualification maps to qualification + Qualification.Identifier maps to qualification.identifier + Qualification.Type maps to qualification.code + Qualification.EffectiveTimePeriod maps to qualification.period + Qualification.Issuer maps to qualification.issuer + +RelatedPerson maps to RelatedPerson: + Identifier maps to identifier + Active maps to extension + Person.HumanName maps to name + Person.DateOfBirth maps to birthDate + Person.AdministrativeGender maps to gender + Person.Address maps to address + Person.PhotographicImage maps to photo + Person.ContactPoint maps to telecom + RelationshipToPatient maps to relationship + EffectiveTimePeriod maps to period + +Organization maps to Organization: + Identifier maps to identifier + Active maps to active + Type maps to type + OrganizationName maps to name + Address maps to address + ContactPoint maps to telecom + PartOf maps to partOf + +Group maps to Group: + Identifier maps to identifier + Active maps to extension + Type maps to type + Actual maps to actual + constrain code to 0..0 // why? + Title maps to name + GroupCharacteristic.GroupCharacteristicValue maps to characteristic.value[x] + GroupCharacteristic.Code maps to characteristic.code + GroupCharacteristic.ExcludeFlag maps to characteristic.exclude + GroupCharacteristic.TimePeriod maps to characteristic.period + MemberParticipation.Member maps to member.entity + MemberParticipation.ParticipationPeriod maps to member.period + MemberParticipation.InactiveFlag maps to member.inactive + Count maps to quantity + +Location maps to Location: + Identifier maps to identifier + Status maps to status + OperationalStatus maps to extension + LocationName maps to name + Alias maps to extension + CommentOrDescription maps to description + Mode maps to mode + Type maps to type + ContactPoint maps to telecom + Address maps to address + PhysicalType maps to physicalType + Geoposition.Latitude maps to position.latitude + Geoposition.Longitude maps to position.longitude + Geoposition.Altitude maps to position.altitude + ManagingOrganization maps to managingOrganization + MobileFacility maps to extension + PartOf maps to partOf + +Substance maps to Substance: + Identifier maps to identifier + Status maps to extension + Type maps to code + Category maps to category + CommentOrDescription maps to description + Ingredient maps to ingredient + Ingredient.IngredientAmount maps to ingredient.quantity + Ingredient.SubstanceOrCode[Substance] maps to ingredient.substance + +Medication maps to http://fhir.org/guides/argonaut/StructureDefinition/argo-medication: + Identifier maps to extension + Status maps to extension + Type maps to code + // dstu 2 change (different attribute) + DoseForm maps to product.form + // dstu 2 change (different attribute) + Ingredient.SubstanceOrCode maps to product.ingredient.item + // dstu 2 change (different attribute) + Ingredient.IngredientAmount maps to product.ingredient.amount + // dstu 2 change (no such attribute) + // Ingredient.IsActiveIngredient maps to ingredient.isActive + Brand.IsBrand maps to isBrand + // dstu 2 change (no such attribute) + // OverTheCounter maps to isOverTheCounter + Manufacturer maps to manufacturer + // dstu 2 change (different attribute) + constrain product.batch to 0..1 + // dstu 2 change (different attribute) + LotNumber maps to product.batch.lotNumber + // dstu 2 change (different attribute) + ExpirationDate maps to product.batch.expirationDate + Package maps to package.container + +Specimen maps to Specimen: + Identifier maps to identifier + Status maps to status + Type maps to type + AccessionIdentifier maps to accessionIdentifier + CollectionSource maps to subject + PartOf maps to parent + ReceivedTime maps to receivedTime + AmountOrSize maps to collection.quantity + CollectionSite.BodySite.BodySiteCode maps to collection.bodySite + CollectionSite.BodySite.Laterality maps to collection.bodySite.extension + CollectionSite.BodySite.AnatomicalDirection maps to collection.bodySite.extension + CollectionSite.BodySite.ClockDirection maps to collection.bodySite.extension + CollectionSite.BodySite.CommentOrDescription maps to collection.bodySite.extension + CollectionSite.BodySite.Attachment maps to collection.bodySite.extension + CollectionSite.BodySite.DistanceFromLandmark maps to collection.bodySite.extension + + + CollectionTime maps to collection.collected[x] +// SpecimenCollection.Participation.Participant maps to collection.collector + CollectionMethod maps to collection.method + SpecimenContainer.Identifier maps to container.identifier + SpecimenContainer.CommentOrDescription maps to container.description + SpecimenContainer.Type maps to container.type + SpecimenContainer.Capacity maps to container.capacity + SpecimenContainer.SpecimenQuantity maps to container.specimenQuantity + SpecimenContainer.Additive maps to container.additive[x] + +Device maps to http://fhir.org/guides/argonaut/StructureDefinition/argo-device: + Identifier maps to identifier + Status maps to status + Type maps to type + // dstu 2 change (different attribute) + DeviceUdi maps to udi + VendorModelNumber maps to model + ManufacturerName maps to manufacturer + ManufactureDate maps to manufactureDate + // dstu 2 change (different attribute) + ExpirationDate maps to expiry + VersionString maps to version + Url maps to url diff --git a/spec/shr_entity_map_stu3.txt b/spec/shr_entity_map_stu3.txt new file mode 100644 index 00000000..10270744 --- /dev/null +++ b/spec/shr_entity_map_stu3.txt @@ -0,0 +1,190 @@ +Grammar: Map 5.1 +Namespace: shr.core +Target: FHIR_STU_3 + +Patient maps to http://hl7.org/fhir/us/core/StructureDefinition/us-core-patient: + Identifier maps to identifier + Active maps to active + Person.HumanName maps to name + Person.AdministrativeGender maps to gender + Person.PhotographicImage maps to photo + Person.Address maps to address + Person.ContactPoint maps to telecom + Person.Communication.Language maps to communication.language + Person.Communication.Preferred maps to communication.preferred + Person.Communication.SpokenLanguageProficiency maps to communication.extension + Person.Communication.WrittenLanguageProficiency maps to communication.extension + Person.Communication.LanguageQualifier maps to communication.extension + Person.DateOfBirth maps to birthDate + Person.MaritalStatus maps to maritalStatus +// PlaceOfBirth maps to http://hl7.org/fhir/StructureDefinition/birthPlace + Person.MultipleBirth maps to multipleBirth[x] + Person.BirthSex maps to http://hl7.org/fhir/us/core/StructureDefinition/us-core-birthsex + Person.Race maps to http://hl7.org/fhir/us/core/StructureDefinition/us-core-race + Person.Ethnicity maps to http://hl7.org/fhir/us/core/StructureDefinition/us-core-ethnicity +// MothersMaidenName maps to http://hl7.org/fhir/StructureDefinition/patient-mothersMaidenName +// MedicalInterpreterNeeded maps to http://hl7.org/fhir/StructureDefinition/patient-interpreterRequired + Person.Deceased maps to deceased[x] + +Practitioner maps to http://hl7.org/fhir/us/core/StructureDefinition/us-core-practitioner: + Identifier maps to identifier + Active maps to active + Person.HumanName maps to name + Person.AdministrativeGender maps to gender + Person.PhotographicImage maps to photo + Person.Address maps to address + Person.ContactPoint maps to telecom + Person.Communication.Language maps to communication + Qualification maps to qualification + Qualification.Identifier maps to qualification.identifier + Qualification.Type maps to qualification.code + Qualification.EffectiveTimePeriod maps to qualification.period + Qualification.Issuer maps to qualification.issuer + +RelatedPerson maps to RelatedPerson: + Identifier maps to identifier + Active maps to active + Person.HumanName maps to name + Person.DateOfBirth maps to birthDate + Person.AdministrativeGender maps to gender + Person.Address maps to address + Person.PhotographicImage maps to photo + Person.ContactPoint maps to telecom + RelationshipToPatient maps to relationship + EffectiveTimePeriod maps to period + +Organization maps to http://hl7.org/fhir/us/core/StructureDefinition/us-core-organization: + Identifier maps to identifier + Active maps to active + OrganizationName maps to name + Type maps to type + Address maps to address + ContactPoint maps to telecom + PartOf maps to partOf + +Group maps to Group: + Identifier maps to identifier + Active maps to active + Type maps to type + Actual maps to actual + constrain code to 0..0 + Title maps to name + GroupCharacteristic.GroupCharacteristicValue maps to characteristic.value[x] + GroupCharacteristic.Code maps to characteristic.code + GroupCharacteristic.ExcludeFlag maps to characteristic.exclude + GroupCharacteristic.TimePeriod maps to characteristic.period + MemberParticipation.Member maps to member.entity + MemberParticipation.ParticipationPeriod maps to member.period + MemberParticipation.InactiveFlag maps to member.inactive + Count maps to quantity + +Location maps to http://hl7.org/fhir/us/core/StructureDefinition/us-core-location: + Identifier maps to identifier + Status maps to status + OperationalStatus maps to operationalStatus + LocationName maps to name + Alias maps to alias + CommentOrDescription maps to description + Mode maps to mode + Type maps to type + ContactPoint maps to telecom + Address maps to address + PhysicalType maps to physicalType + Geoposition.Latitude maps to position.latitude + Geoposition.Longitude maps to position.longitude + Geoposition.Altitude maps to position.altitude + ManagingOrganization maps to managingOrganization + MobileFacility maps to extension + PartOf maps to partOf + +Substance maps to Substance: + Identifier maps to identifier + Type maps to code + Status maps to status + Category maps to category + CommentOrDescription maps to description + Ingredient maps to ingredient + Ingredient.IngredientAmount maps to ingredient.quantity + Ingredient.SubstanceOrCode maps to ingredient.substance[x] + +Medication maps to http://hl7.org/fhir/us/core/StructureDefinition/us-core-medication: + Identifier maps to extension + Type maps to code + Status maps to status + DoseForm maps to form + Ingredient.SubstanceOrCode maps to ingredient.item[x] + Ingredient.IngredientAmount maps to ingredient.amount + Ingredient.IsActiveIngredient maps to ingredient.isActive + Brand.IsBrand maps to isBrand + OverTheCounter maps to isOverTheCounter + Manufacturer maps to manufacturer + constrain package.batch to 0..1 + LotNumber maps to package.batch.lotNumber + ExpirationDate maps to package.batch.expirationDate + Package maps to package.container + +Specimen maps to Specimen: + Identifier maps to identifier + Type maps to type + AccessionIdentifier maps to accessionIdentifier + Status maps to status + CollectionSource maps to subject + PartOf maps to parent + ReceivedTime maps to receivedTime + AmountOrSize maps to collection.quantity + CollectionSite.BodySite.BodySiteCode maps to collection.bodySite + CollectionSite.BodySite.Laterality maps to collection.bodySite.extension + CollectionSite.BodySite.AnatomicalDirection maps to collection.bodySite.extension + CollectionSite.BodySite.ClockDirection maps to collection.bodySite.extension + CollectionSite.BodySite.CommentOrDescription maps to collection.bodySite.extension + CollectionSite.BodySite.Attachment maps to collection.bodySite.extension + CollectionSite.BodySite.DistanceFromLandmark maps to collection.bodySite.extension + CollectionTime maps to collection.collected[x] +// SpecimenCollection.Participation.Participant maps to collection.collector + CollectionMethod maps to collection.method +// SpecimenCollection.RelatedRequest.Value maps to request + SpecimenContainer.Identifier maps to container.identifier + SpecimenContainer.CommentOrDescription maps to container.description + SpecimenContainer.Type maps to container.type + SpecimenContainer.Capacity maps to container.capacity + SpecimenContainer.SpecimenQuantity maps to container.specimenQuantity + SpecimenContainer.Additive maps to container.additive[x] + +Device maps to http://hl7.org/fhir/us/core/StructureDefinition/us-core-device: + Identifier maps to identifier + Type maps to type + Status maps to status + constrain udi to 1..1 + DeviceUdi maps to udi.carrierHRF + VendorModelNumber maps to model + ManufacturerName maps to manufacturer + ManufactureDate maps to manufactureDate + ExpirationDate maps to expirationDate + VersionString maps to version + Url maps to url + +Media maps to Media: + Identifier maps to identifier + RelatedRequest maps to basedOn + Type maps to type + Subtype maps to subtype + View maps to view + SubjectOfRecord maps to subject + CareContext maps to context + RelevantTime maps to occurrence[x] + Practitioner maps to operator + ReasonCode maps to reasonCode + BodySite.BodySiteCode maps to bodySite + BodySite.Laterality maps to bodySite.extension + BodySite.AnatomicalDirection maps to bodySite.extension + BodySite.ClockDirection maps to bodySite.extension + BodySite.CommentOrDescription maps to bodySite.extension + BodySite.Attachment maps to bodySite.extension + BodySite.DistanceFromLandmark maps to bodySite.extension + Device maps to device + PixelHeight maps to height + PixelWidth maps to width + Frames maps to frames + NumberOfSecondsDuration maps to duration + Attachment maps to content + Annotation maps to note diff --git a/spec/cimi_entity_vs.txt b/spec/shr_entity_vs.txt similarity index 71% rename from spec/cimi_entity_vs.txt rename to spec/shr_entity_vs.txt index 025de500..9e5bb480 100644 --- a/spec/cimi_entity_vs.txt +++ b/spec/shr_entity_vs.txt @@ -1,14 +1,7 @@ Grammar: ValueSet 5.0 -Namespace: cimi.entity +Namespace: shr.core -CodeSystem: MTH = http://ncimeta.nci.nih.gov -CodeSystem: NCI = https://evs.nci.nih.gov/ftp1/CDISC/SDTM/ -CodeSystem: SCT = http://snomed.info/sct - - -ValueSet: DeviceVS -Description: "Codes describing medical devices." -Includes codes descending from SCT#49062001 +/* not used ValueSet: HealthcareRoleVS //Includes codes from http://hl7.org/fhir/ValueSet/c80-practice-codes @@ -28,19 +21,6 @@ MTH#C0871042 "Parole officer" MTH#C0042799 "Visting nurse" MTH#C1552023 "Emergency contact" - -ValueSet: LanguageQualifierVS -Description: "A code indicating whether the language is preferred, secondary, or practiced in an unconventional or limited way." -#preferred_spoken "Preferred language" -#secondary_spoken "Secondary language" -#apraxia "Difficulty speaking due to motor disorder" -#aphasia "Difficulty in speaking, listening, reading, and writing" -#signs "Uses sign language" -#braille "Reads using braille" -#lipreads "Uses lipreading (speechreading)" -#aac "Uses augmentative and alternative communication" - - ValueSet: TelecomQualifierVS #primary "Primary (preferred) method of contact" #secondary "Secondary method of contact" @@ -54,8 +34,6 @@ ValueSet: TelecomQualifierVS #shared "A shared telecom address, e.g., facility telephone or family email" #direct "An encrypted DIRECT email address" #portal "Portal-based secure messaging address" - -/* not used ValueSet: TelephoneTypeVS #mobile "Mobile phone (assumed text capable)" #land "Landline telephone" diff --git a/spec/shr_environment.txt b/spec/shr_environment.txt new file mode 100644 index 00000000..d3c6f5a3 --- /dev/null +++ b/spec/shr_environment.txt @@ -0,0 +1,266 @@ +Grammar: DataElement 5.0 +Namespace: environment +Description: "The SHR Environment domain contains definitions related to surroundings experienced by the person of record, including both the physical and sociological environments." +Uses: shr.core + +CodeSystem: CURRENCY = urn:iso:std:iso:4217 + +EntryElement: HouseholdIncome +Based on: SocialHistoryObservation +Description: "The amount of earnings made by a family unit in one year, estimated or self-reported." + Code is SCT#224168007 "Household income (observable entity)" + DataValue value is type Range +// TODO: Ask Chris why this isn't working +// DataValue.Range.LowerBound.Quantity.Units is CURRENCY#USD +// DataValue.Range.UpperBound.Quantity.Units is CURRENCY#USD + +EntryElement: IncomeSource +Based on: SocialHistoryObservation +Description: "Where the household income comes from." + Code is MTH#C0557162 + DataValue from IncomeSourceVS + +EntryElement: NonCashBenefit +Based on: SocialHistoryObservation +Description: "Where the household income comes from." + Code is MTH#C0557162 + DataValue from IncomeSourceVS + +EntryElement: FinancialStability +Based on: SocialHistoryObservation +Description: "Whether the subject regards his or her source of income as dependable." + Code is MTH#C1820459 + DataValue from ResourceStabilityVS + +EntryElement: IncomeAdequacy +Based on: NonLaboratoryObservation +Description: "Whether the subject regards their income as sufficient to meet the needs of the subject and his/her dependents." + Code is MTH#C1820459 + DataValue from IncomeAdequacyVS + Components.ObservationComponent +includes 0..1 TroubleAffordingFood +includes 0..1 TroubleAffordingHousing +includes 0..1 TroubleAffordingUtilities +includes 0..1 TroubleAffordingTransportation +includes 0..1 TroubleAffordingMedication +includes 0..1 TroubleAffordingDentalCare +includes 0..1 TroubleAffordingChildCare + + Element: TroubleAffordingFood + Based on: CodedObservationComponent + Description: "How often does the subject have trouble affording food?" + Code is TBD#TBD + DataValue from QualitativeFrequencyVS + + Element: TroubleAffordingHousing + Based on: CodedObservationComponent + Description: "How often does the subject have trouble affording housing?" + Code is TBD#TBD + DataValue from QualitativeFrequencyVS + + Element: TroubleAffordingUtilities + Based on: CodedObservationComponent + Description: "How often does the subject have trouble affording utilities?" + Code is TBD#TBD + DataValue from QualitativeFrequencyVS + + Element: TroubleAffordingTransportation + Based on: CodedObservationComponent + Description: "How often does the subject have trouble affording transportation?" + Code is TBD#TBD + DataValue from QualitativeFrequencyVS + + Element: TroubleAffordingMedication + Based on: CodedObservationComponent + Description: "How often does the subject have trouble affording medications?" + Code is TBD#TBD + DataValue from QualitativeFrequencyVS + + Element: TroubleAffordingDentalCare + Based on: CodedObservationComponent + Description: "How often does the subject have trouble affording dental care?" + Code is TBD#TBD + DataValue from QualitativeFrequencyVS + + Element: TroubleAffordingChildCare + Based on: CodedObservationComponent + Description: "How often does the subject have trouble affording child care?" + Code is TBD#TBD + DataValue from QualitativeFrequencyVS + +EntryElement: HouseholdSize +Based on: CodedSocialHistoryObservation +Description: "The number of people living together with mutual financial dependency. Besides the subject, the household size may include spouse or partner, dependent children including adopted and foster children, dependent parents, dependent siblings and other relatives, but not roommates, ex-spouses, non-dependent children, and unborn children. If the subject lives alone, the household size is 1." + Code is MTH#C0000768 + DataValue.Quantity.Units is UCUM#1 + +EntryElement: Coinhabitant +Based on: CodedSocialHistoryObservation // Related person? +Description: "A person living with the subject." + Code is SCT#224085006 "Family details / household composition (observable entity)" + DataValue from http://hl7.org/fhir/ValueSet/relatedperson-relationshiptype + +EntryElement: NumberOfDependents +Based on: QuantitativeNonLaboratoryObservation +Description: "The number of dependents supported by the subject." + Code is MTH#C0557509 + DataValue.Quantity.Units is UCUM#1 + +EntryElement: TransportationAvailability +Based on: CodedSocialHistoryObservation +Description: "Whether the subject has reliable transportation to bring him or her to medical appointments and to get medications." + Code is TBD#TBD + DataValue from QualitativeFrequencyVS + +EntryElement: HousingSecurity +Based on: CodedSocialHistoryObservation +Description: "Whether the subject is at-risk of losing their housing or in a stable housing situation." + Code is TBD#TBD + DataValue from ResourceStabilityVS + +EntryElement: PhysicalSafety +Based on: SocialHistoryObservation +Description: "How often the subject feels physically safe in the subject's home environment." + Code is TBD#TBD + DataValue from QualitativeFrequencyVS + +EntryElement: EmotionalSafety +Based on: CodedSocialHistoryObservation +Description: "Whether the subject feels physically safe in the subject's home environment." + Code is TBD#TBD + DataValue from QualitativeFrequencyVS + +EntryElement: DomesticViolence +Based on: CodedSocialHistoryObservation +Description: "Whether the subject experiences domestic violence." + Code is MTH#C0206073 + DataValue from QualitativeFrequencyVS + +EntryElement: HomeEnvironmentRisk +Based on: CodedSocialHistoryObservation +Description: "A risk experienced in the home environment." + Code is TBD#TBD + DataValue from HomeEnvironmentRiskVS + +EntryElement: EducationalAttainment +Based on: CodedSocialHistoryObservation +Description: "Educational attainment or level of education of individuals." + Code is LNC#63504-5 + DataValue from http://loinc.org/vs/LL1069-5 + +EntryElement: ForeignCountryOfTravelTwoYears +Based on: CodedSocialHistoryObservation +Description: "A travel history of the countries that the patient has visited within the last two-years, particularly when a health risk is involved." + Code is LNC#82764-2 "Country of travel outside the U.S. [Location] 2 years" + DataValue from https://phinvads.cdc.gov/vads/ViewValueSet.action?oid=2.16.840.1.114222.4.11.828 + +//------------- Exposures --------------------- + + +EntryElement: UnprescribedExposure +Based on: NonLaboratoryObservation +Description: "Record of an exposure to a risk agent, whether intentional, environmental, or accidental. Non-prescribed substances include recreational marijuana, disease vector, mutagens, excessive heat or cold, blood products, farm animals or pets, recreational drugs, second hand smoke, sexually-transmitted diseases, suspect foods, toxins, pathogens, noise, radiation, pollutants, and prenatal exposures to teratogens, etc. The exposure time period is given in the RelevantTime." + Code is SCT#418715001 "Exposure to potentially harmful entity (event)" +0..1 SubstanceOrAgent + DataValue could be from YesNoUnknownVS + Components.ObservationComponent +includes 0..* ExposureMode +includes 0..* ExposureAmount +includes 0..* ExposureReason +includes 0..* ExposureRoute + + Element: SubstanceOrAgent + Description: "The agent (substance, environment, disease vector) the patient may or may not have been exposed to." + Value: CodeableConcept + + Element: ExposureMode + Based on: CodedObservationComponent + Description: "Where the substance originated, e.g., animal to human, environmental, etc." + Code is SCT#409496000 "Mode of transmission" + DataValue from ExposureModeVS if covered + + Element: ExposureAmount + Based on: ObservationComponent + Description: "The amount of substance used or exposed to in a given period of time (e.g., 10 cigarettes per day). Can also be used to record total lifetime exposure (e.g., 80 REMS/lifetime)." + Code is SCT#118555000 "Substance Amount" + // Data value can be a code or a quantity, even a text + DataValue value is type Ratio + + Element: ExposureReason + Based on: CodedObservationComponent + Description: "Why the exposure occurred." + Code is TBD#TBD + DataValue from ExposureReasonVS + + // Redundant with RouteIntoBody, but that isn't an ObservationComponent + Element: ExposureRoute + Based on: CodedObservationComponent + Description: "The way a substance enters an organism after contact, particularly, the route of drug administration." + Code is MTH#C0013153 "Drug Administration Routes" + DataValue should be from http://hl7.org/fhir/ValueSet/route-codes + +EntryElement: AnimalExposure +Based on: UnprescribedExposure +Description: "The type of animals or pets the subject is exposed to." + Code is MTH#C0238646 "Animal Exposure" + SubstanceOrAgent from CommonAnimalVS if covered // TODO: and if not, use SNOMED... + +EntryElement: PrenatalExposure +Based on: UnprescribedExposure +Description: "Fetal contact with a dangerous substance via the mother." + Code is MTH#C0871747 "fetal exposure" + SubstanceOrAgent from TeratogenVS if covered +0..1 GestationalTimePeriod // brings the temporal context into the picture + +EntryElement: SubstanceUse +Based on: UnprescribedExposure +Description: "Assertion concerning the past or current use of a substance (alcohol, recreational drugs, illegal drugs, or abuse of prescription medication) that could negatively impact the subject's health." + Code is MTH#C0237123 "Alcohol or Other Drug Use" + SubstanceOrAgent should be from SubstanceOfAbuseVS + +EntryElement: IntravenousDrugUse +Based on: SubstanceUse +Description: "Records whether the subject injects recreational drugs. To record no intravenous drug use, the data value should be " + Code is MTH#C0699778 "intravenous drug use" + Components.ObservationComponent.ExposureRoute.DataValue.CodeableConcept is MTH#C1522726 "Intravenous route" + Components.ObservationComponent.ExposureMode.DataValue.CodeableConcept is MTH#C0021494 "Intravenous Injection" + +EntryElement: NicotineExposure +Based on: SubstanceUse +Description: "The subject's current or past use of nicotine." + Code is MTH#C0240502 "Nicotine exposure" + SubstanceOrAgent is SCT#68540007 "Nicotine (substance)" + Components.ObservationComponent.ExposureRoute.DataValue from TBD "NicotineRouteVS" + Components.ObservationComponent.ExposureMode.DataValue from TBD "NicotineExposureModeVS" // e.g. smoked, second hand smoke, vaped, chewed + +EntryElement: TobaccoSmokingStatusNHIS +Based on: NicotineExposure +Description: "Records the extent of the subject's use of tobacco." + Code is LNC#72166-2 "Tobacco smoking status NHIS" +1..1 DataValue value is type CodeableConcept + DataValue from http://hl7.org/fhir/us/core/ValueSet/us-core-observation-ccdasmokingstatus if covered +1..1 SubjectOfRecord value is type PatientOnly +1..1 StatementDateTime + + +EntryElement: AlcoholUse +Based on: SubstanceUse +Description: "The subject's current or past use of alcohol." + Code is MTH#C0552479 "Alcohol use history" + SubstanceOrAgent is SCT#419442005 "Ethyl Alcohol (substance)" + Method from AlcoholUseScreeningToolVS if covered + DataValue value is type Ratio // could be coded, also + +Element: AlcoholBingeEpisodes +Based on: SubstanceUse +Description: "Alcohol binge episodes per month (define as 6 or more Units if female, or 8 or more if male)." + Code is LNC#11286-2 "Alcohol binge episodes per month - Reported" + SubstanceOrAgent is SCT#419442005 "Ethyl Alcohol (substance)" + DataValue value is type Ratio + + +/* TO DO +EntryElement: Depression +EntryElement: Anxiety +EntryElement: JusticeInvolvement +*/ \ No newline at end of file diff --git a/spec/shr_environment_map_dstu2.txt b/spec/shr_environment_map_dstu2.txt new file mode 100644 index 00000000..93bcd152 --- /dev/null +++ b/spec/shr_environment_map_dstu2.txt @@ -0,0 +1,6 @@ +Grammar: Map 5.1 +Namespace: environment +Target: FHIR_STU_2 + +TobaccoSmokingStatusNHIS maps to http://hl7.org/fhir/us/core/StructureDefinition/us-core-smokingstatus: + DataValue maps to valueCodeableConcept \ No newline at end of file diff --git a/spec/shr_environment_map_stu3.txt b/spec/shr_environment_map_stu3.txt new file mode 100644 index 00000000..61c13a81 --- /dev/null +++ b/spec/shr_environment_map_stu3.txt @@ -0,0 +1,6 @@ +Grammar: Map 5.1 +Namespace: environment +Target: FHIR_STU_3 + +TobaccoSmokingStatusNHIS maps to http://hl7.org/fhir/us/core/StructureDefinition/us-core-smokingstatus: + DataValue maps to valueCodeableConcept \ No newline at end of file diff --git a/spec/shr_environment_vs.txt b/spec/shr_environment_vs.txt new file mode 100644 index 00000000..7dd231fb --- /dev/null +++ b/spec/shr_environment_vs.txt @@ -0,0 +1,194 @@ +Grammar: ValueSet 5.0 +Namespace: environment + +ValueSet: ResourceStabilityVS +Description: "Terms that describe the possibility of losing access to a resource." +#stable "Not at risk or minimal risk of losing the resource (or a significant portion of the income)" +#at_risk "Some risk of losing the resource (or a significant portion of the resource)" +#imminent_risk "Imminent risk of loss of the resource (or a significant portion of the resource)" +#recent_loss "Recent loss of the resource (or a significant portion of the resource)" + +ValueSet: IncomeAdequacyVS +Description: "Aligns with LOINC normative answer list LL4200-3, Rating of financial resources." +LNC#LA26877-3 "Financially secure, resources adequate, no identified problems" +LNC#LA26878-1 "Financially secure, some resource challenges" +LNC#LA26879-9 "Financially insecure, some resource challenges" +LNC#LA26880-7 "Financially insecure, very few resources, immediate challenges" + + +ValueSet: IncomeSourceVS +Description: "The origin of income." +#earned "Earned Income (i.e., employment income)" +#unemployment "Unemployment Insurance" +#ssi "Supplemental Security Income (SSI)" +#ssdi "Social Security Disability Income (SSDI)" +#disability_va "Veteran’s disability payment" +#disability_private "Private disability insurance" +#disability_workers "Worker’s compensation" +#tanf "Temporary Assistance for Needy Families (TANF) or similar local program" +#ga "General Assistance (GA) or similar local program" +#ss "Retirement income from Social Security" +#savings "Savings" +#pension_va "Veteran’s pension" +#child_support "Child support" +#alimony "Alimony or other spousal support" + +ValueSet: NonCashBenefitVS +Description: "A social support grant in non-monetary form." +#snap "Supplemental Nutrition Assistance Program (SNAP) (Previously known as Food Stamps)" +#medicaid "MEDICAID health insurance program or local equivalent" +#schip "State Children’s Health Insurance Program or local equivalent" +#wic "Special Supplemental Nutrition Program for Women, Infants, and Children (WIC)" +#vams "Veteran’s Administration (VA) Medical Services" +#tanf "Temporary Assistance for Needy Families (TANF) or similar local program" +#tanf_transport "Temporary Assistance for Needy Families (TANF) transportation services" +#tanf_other "Temporary Assistance for Needy Families (TANF) other services" +#section8 "Section 8, public housing, or other ongoing rental assistance" +#temp_rental "Temporary Rental Assistance" + +ValueSet: ExposureModeVS +Description: "How an exposure occurred; mode of transmission of pathogen or contaminant." +Includes codes descending from SCT#414753003 "Mode of transmission values (qualifier value)" + +ValueSet: ExposureReasonVS +Description: "The reason that an exposure occurred." +#voluntary "The subject voluntarily subjects him or herself to the exposure, for example, smoking or using a drug recreationally." +#self_prescribed "The subject voluntarily takes a non-prescription substance to address health issues or for prevention, e.g. herbal remedy for depression." +#domestic "Involuntary exposure in a domestic setting., e.g., exposure to second-hand smoke." +#occupational "Involuntary exposure in a workplace setting." +#accidental "Involuntary exposure as a result of an accident." +#addiction "The subject is addicted to the substance." + +ValueSet: CommonAnimalVS +Description: "Common animals that humans can be exposed to." +SCT#448771007 "Domestic dog" +SCT#448771007 "Domestic cat" +SCT#387972009 "Bird" +SCT#90580008 "Fish" +SCT#107241004 "Reptile" +SCT#388077003 "Rodent" +SCT#54121002 "Monkey" +MTH#C0162318 "Farm animal" +SCT#47290002 "Chicken" + +ValueSet: HomeEnvironmentRiskVS +#guns "Guns in household" +#more_guns "Guns in neighborhood" +#smoke_detectors "No Smoke Detectors" +#radiation "Radon or other radiation source" +#swimming_pool "Swimming Pool" +#lead "Lead in soil, paint or water" +#well "Well water" +#mold "Mold" +#noise "Excessive noise" +#no_internet "No internet" +#no_electricity "Unreliable electricity supply" +#air_quality "Poor air quality" +#water_quality "Poor drinking water quality" +#crime "Neighborhood crime" +#traffic "Neighborhood traffic" +#unwalkable "Neighborhood unwalkable" +#insects "Insect infestation" +#rodents "Rodent infestation" +#asbestos "Asbestos" +#disrepair "Home in disrepair" +#clutter "Clutter or hoarding" +#fire_hazard "No fire escape or other fire hazard" +#stairs "Steps hard to navigate" +#bathroom "Bathroom facilities hard to utilize, e.g., on another floor or lacking accomodations" +#crowding "Overcrowded" +#isolated "Too far away from things" +#transportation "Hard to access transportation resources" +#radiation "Radiation" +#asbestos "Asbestos" +#pesticides "Pesticides" +#motorcycle "Rides a motorcycle" +#contact_sports "Plays contact sports" +#seat_belt "Does not wear seat belts" +#sun_exposure "Spends excessive time in the sun" +#tanning "Uses tanning bed" + +ValueSet: SubstanceOfAbuseVS +Includes codes descending from SCT#312417001 "substance of abuse" + +ValueSet: TeratogenVS +//DISEASES +#chlamydia "Chlamydia" +#pneumonia "Pneumonia" +#gonorrhea "Gonorrhea" +#rubella "Rubella (German Measles)" +#herpes "Herpes" +#scarlet "Scarlet Fever" +#hiv "HIV" +#syphilis "Syphilis" +#mumps "Mumps" +#toxoplasmosis "Toxoplasmosis" +#tuberculosis "Tuberculosis" +#influenza "Influenza" +//DRUGS +#accutane "Accutane" +#hexachlorophene "Hexachlorophene" +#alcohol "Alcohol" +#iodides "Iodides" +#amphetamines "Amphetamines" +#lithium "Lithium" +#antibiotics "Antibiotics" +#lsd "LSD" +#anti-cancer "Anti-cancer drugs" +#opiates "Opiates" +#anticoagulant "Anticoagulant drugs" +#quinine "Quinine" +#aspirin "Aspirin" +#sedatives "Sedatives" +#barbiturates "Barbiturates" +#smallpox "Smallpox vaccination" +#caffeine "Caffeine" +#thalidomide "Thalidomide" +#nicotine "Nicotine" +#tranquilizers "Tranquilizers" +#cocaine "Cocaine" +#vitamins "Vitamins in excess" +#des "Diethylstilbestrol (DES)" +#marijuana "Marijuana " +//ENVIRONMENTAL FACTORS +#cadmium "Cadmium" +#mercury "Mercury" +#cat "Cat feces" +#nickel "Nickel" +#fumes "Fumes from paints, solvents, glues, dry-cleaning fluids" +#pesticides "Pesticides" +#insecticides "Insecticides" +#herbicides "Herbicides" +#manganese "Manganese" +#radiation "Radiation (X-rays, Video Display Terminals)" +#hair "Hair dyes" +#polychlorinated "Polychlorinated Biphenyls (PCBs)" +#lead "Lead" +//NONINFECTIOUS MATERNAL CONDITIONS +#alcoholism "Alcoholism" +#chemical "Chemical dependency" +#phenylketonuria "Phenylketonuria" +#rh "Rh + factor" +#anemia "Anemia" +#stress "Stress" +#diabetes "Diabetes Mellitus" + +ValueSet: AlcoholUseScreeningToolVS +Description: "Common alcohol use screening instruments." +#audit "AUDIT" +#audit_c "AUDIT-C" +#crafft "CRAFFT" + +/* not used (using LL1069 instead) +ValueSet: EducationalAttainmentVS +#no_formal "No schooling completed, or ages 0-4" +#elementary "Elementary (grades 1-8)" +#high_school_some "High school (grades 9-12, no degree)" +#high_school_grad "High school graduate (or equivalent)" +#college "Some college (1-4 years, no degree)" +#assoc "Associate’s degree (including vocational, occupational or academic degrees)" +#bachelor "Bachelor’s degree (BA, BS, AB, etc)" +#master "Master’s degree (MA, MS, MENG, MSW, etc)" +#prof "Professional school degree (MD, DDC, JD, etc)" +#doc "Doctorate degree (PhD, EdD, etc)" +*/ \ No newline at end of file diff --git a/spec/shr_familyhistory.txt b/spec/shr_familyhistory.txt new file mode 100644 index 00000000..48fe935c --- /dev/null +++ b/spec/shr_familyhistory.txt @@ -0,0 +1,35 @@ +Grammar: DataElement 5.0 +Namespace: fhx +Description: "Contains elements related to the health history of a patient's family members." +Uses: shr.core, shr.base, entity + CodeSystem: LNC = http://loinc.org + +EntryElement: FamilyMember +Based on: RelatedPerson +Description: "A related person that is a family member of the patient. This includes biological and non-biological family, as well as extended family." +1..1 RelationshipToPatient // from https://vsac.nlm.nih.gov/valueset/2.16.840.1.113883.1.11.19579/expansion +// Family member value VS used in CCDA. 2015 Ed ONC Cert Criteria indicate relationship to patient should be coded in SCT, and allows for pre- or post-coordination with condition. TODO: consider SCT value set (maybe allow both?) +// Not feasible. Cannot override value set constraint from http://hl7.org/fhir/ValueSet/relatedperson-relationshiptype to https://vsac.nlm.nih.gov/valueset/2.16.840.1.113883.1.11.19579/expansion. ERROR_CODE:13029 + + +EntryElement: FamilyMemberHistory +Based on: ClinicalStatement +Concept: LNC#54114-4 "Family member health history [USSG-FHT] Family member" //This is part of a US General Surgeon general family health LOINC panel +Description: "The health history of a patient's family member." +1..1 SubjectOfRecord value is type ref(Patient) +1..1 FamilyMember + StatusOrActive is type Status +1..1 Status from http://hl7.org/fhir/ValueSet/history-status +0..* FamilyMemberCondition + + +Element: FamilyMemberCondition +Concept: LNC#8670-2 "History of family member diseases" +0..1 Onset +0..1 ConditionOutcome +1..1 Code from http://hl7.org/fhir/us/core/ValueSet/us-core-problem if covered + + Element: ConditionOutcome + Concept: TBD#TBD + Description: "The lasting effects of a disease, e.g. death, functional impairment." + Value: CodeableConcept could be from http://hl7.org/fhir/ValueSet/condition-outcome \ No newline at end of file diff --git a/spec/shr_financial.txt b/spec/shr_financial.txt index 3f394cbf..e9ad038f 100644 --- a/spec/shr_financial.txt +++ b/spec/shr_financial.txt @@ -1,27 +1,38 @@ Grammar: DataElement 5.0 -Namespace: shr.financial -Description: "The SHR Demographics domain contains definitions that describe basic characteristics of the person of record, such as name, address, and date of birth. Elements in the demographics domains are used for unique identification and patient matching." -Uses: shr.core, shr.base, cimi.core, cimi.entity, cimi.element +Namespace: shr.core Path: FHIR = http://hl7.org/fhir/ValueSet // ------------ TODO: move to Payment domain ------------ EntryElement: Coverage -Based on: InformationEntry +Based on: DomainResource Concept: MTH#C0021682 "HealthInsurance" Description: "Health insurance coverage available (even if not used for payment for a given encounter)." + StatusOrActive is type Status 0..1 Status from http://hl7.org/fhir/ValueSet/fm-status -1..1 Type should be from http://hl7.org/fhir/ValueSet/coverage-type -0..1 InsuranceMemberId +0..1 CoverageType should be from http://hl7.org/fhir/ValueSet/coverage-type +0..1 Subscriber +0..1 SubscriberId +0..1 Beneficiary 0..1 PolicyHolder 0..1 EffectiveTimePeriod -// TODO: complete this! - Element: InsuranceMemberId - Concept: TBD - Description: "Patient identifier at a healthcare provider, insurer, or other related organization." - Value: string // should be id, but FHIR uses string + Element: CoverageType + Description: "Coverage category such as medical or accident." + Value: CodeableConcept + + Element: Subscriber + Description: "The party who has signed-up for or 'owns' the contractual relationship to the policy or to whom the benefit of the policy for services rendered to them or their family is due." + Value: ref(Patient) or ref(RelatedPerson) + + Element: SubscriberId + Description: "The insurer assigned ID for the Subscriber." + Value: string or Identifier // string in STU3, Identifier in STU2 + + Element: Beneficiary + Description: "The party who benefits from the insurance coverage., the patient when services are provided." + Value: ref(Patient) Element: PolicyHolder Description: "Owner of the policy" diff --git a/spec/shr_financial_map.txt b/spec/shr_financial_map.txt deleted file mode 100644 index 7ec6beed..00000000 --- a/spec/shr_financial_map.txt +++ /dev/null @@ -1,11 +0,0 @@ -Grammar: Map 5.0 -Namespace: shr.financial -Target: FHIR_STU_3 - - -Coverage maps to Coverage: - Status maps to status - Type maps to type - InsuranceMemberId maps to subscriberId - EffectiveTimePeriod maps to period - PolicyHolder maps to policyHolder \ No newline at end of file diff --git a/spec/shr_financial_map_dstu2.txt b/spec/shr_financial_map_dstu2.txt new file mode 100644 index 00000000..93097af7 --- /dev/null +++ b/spec/shr_financial_map_dstu2.txt @@ -0,0 +1,14 @@ +Grammar: Map 5.0 +Namespace: shr.core +Target: FHIR_DSTU_2 + + +Coverage maps to Coverage: + Identifier maps to identifier + Status maps to extension + CoverageType maps to type + Subscriber maps to subscriber + SubscriberId maps to subscriberId + Beneficiary maps to extension + PolicyHolder maps to extension + EffectiveTimePeriod maps to period \ No newline at end of file diff --git a/spec/shr_financial_map_stu3.txt b/spec/shr_financial_map_stu3.txt new file mode 100644 index 00000000..eae0f735 --- /dev/null +++ b/spec/shr_financial_map_stu3.txt @@ -0,0 +1,15 @@ +Grammar: Map 5.0 +Namespace: shr.core +Target: FHIR_STU_3 + + +Coverage maps to Coverage: + Identifier maps to identifier + Status maps to status + CoverageType maps to type + Subscriber maps to subscriber + SubscriberId maps to subscriberId + Beneficiary maps to beneficiary + PolicyHolder maps to policyHolder + EffectiveTimePeriod maps to period + \ No newline at end of file diff --git a/spec/shr_finding.txt b/spec/shr_finding.txt new file mode 100644 index 00000000..5df5de33 --- /dev/null +++ b/spec/shr_finding.txt @@ -0,0 +1,392 @@ +Grammar: DataElement 5.0 +Namespace: shr.core +Description: "Contains the SHR Entry definition -- the metadata added to any independent item in the SHR." + + +Abstract Element: ObservationComponent +Description: "A sub-observation contributing to the parent observation, expressed as separate code value pairs that share the same attributes. Examples include systolic and diastolic component observations for blood pressure measurement and multiple component observations for genetics observations. Component observations share the same attributes in the Observation resource as the primary observation and are always treated a part of a single observation (they are not separable). However, the reference range for the primary observation value is not inherited by the component values and is required when appropriate for each component observation." +// should an observation component have additional properties, such as protocol, circumstance, or interpretation? +// how do we handle a normal? (physical exam normal) +// exclusions? (diabetes excluded) +1..1 Code +0..1 DataValue +0..1 DataAbsentReason +0..1 ReferenceRange +0..1 Interpretation + + Element: DataValue + Description: "The value or result of a test, evaluation, or judgment, for example, a systolic blood pressure, or if a condition or body structure is present or absent." + Value: CodeableConcept or Quantity or string or Range or Ratio or time or dateTime or TimePeriod + // exclude boolean because FHIR STU3 component doesn't include it, although Observation does; exclude Attachment because it is not present in FHIR v4 + + Element: DataAbsentReason + Concept: TBD + Description: "Reason that a value associated with a test or other finding is missing." + Value: CodeableConcept from http://hl7.org/fhir/ValueSet/data-absent-reason if covered + + Element: ReferenceRange + Concept: MTH#C0883335 + Description: "The usual or acceptable range for a test result." + 0..1 Range // TODO: align this with FHIR + 0..1 Type from http://hl7.org/fhir/ValueSet/referencerange-meaning if covered + 0..1 ApplicableSubpopulation + 0..1 ApplicableAgeRange + + Element: ApplicableSubpopulation + Concept: MTH#C0039309 "Target Population" + Description: "Codes to indicate the target population this reference range applies to. For example, a reference range may be based on the normal population or a particular sex or race." + Value: CodeableConcept from http://hl7.org/fhir/ValueSet/referencerange-appliesto if covered + + Element: ApplicableAgeRange + Concept: TBD + Description: "The age at which this reference range is applicable. This is a neonatal age (e.g. number of weeks at term) if the meaning says so." // FHIR: how exactly does one indicate a neonatal or prenatal age? + Value: Range + +Abstract Element: CodedObservationComponent +Based on: ObservationComponent +Description: "A non-independent finding whose result is a concept code." + DataValue value is type CodeableConcept +0..0 ReferenceRange + +Abstract Element: QuantitativeObservationComponent +Based on: ObservationComponent +Description: "A non-independent finding whose result is a quantity." + DataValue value is type Quantity + +Abstract Element: ConditionOrObservation +Based on: ClinicalStatement +Description: "An assertion, determination, opinion, evaluation, result, observation, or measurement made by a person or device." +1..1 Code + StatusOrActive is type Status + + +EntryElement: Observation +Based on: ConditionOrObservation +Concept: TBD +Description: "Represents the result of evaluations (measurements, tests, or questions) that have been performed. +Observation has a value representing the result (answer), or an DataAbsentReason indicating why the value is not present. Things observed about the subject can include social and behavioral factors, subjective and objective observations, and assessments. +For an Observation, the Code describes the aspect or property of the subject being observed or measured. The Code is the 'question code' that pairs to the 'answer' contained in the Value." +0..1 DataValue +0..1 DataAbsentReason +0..1 Method +0..1 RelevantTime +1..1 Status from http://hl7.org/fhir/ValueSet/observation-status +0..1 Category from http://hl7.org/fhir/ValueSet/observation-category if covered // MK Category cardinality from 0..* to 0..1 to be compatible with DSTU 2 +0..1 SubjectOfInformation +0..1 BodySite +0..1 CommentOrDescription +0..1 Interpretation +0..1 Device +0..1 ReferenceRange +0..1 Components +0..1 PanelMembers +1..1 SubjectOfRecord value is type PatientOrGroupOrDeviceOrLocation + Author value is type PersonOrOrganization + InformationSource value is type PersonOrOrganization + CareContext value is type ref(Encounter) + + Element: RelevantTime + Concept: TBD + Description: "The time or time period that the statement addresses. + The clinically relevant time is not necessarily when the information is gathered or when a test is carried out, but for example, when a specimen was collected, or the time period referred to by the question. Use a TimePeriod for a measurement or specimen collection continued over a significant period of time (e.g. 24 hour Urine Sodium)." + Value: dateTime or TimePeriod + + Element: SubjectOfInformation + Description: "The entity this condition or observation relates to, for example, a person related to the SubjectOfRecord. The SubjectOfInformation is only required if the person or thing observed is different than the SubjectOfRecord. SubjectOfInformation should not be an anatomical location. Examples: The focus for cancer progression would be the cancer condition; for wound length, an instance of a wound (a condition). In the case where the SubjectOfInformation is a related person, the value may be a RelatedPerson resource or a concept code with the relationship to the SubjectOfRecord (e.g., wife)" + Value: ref(DomainResource) or CodeableConcept + + Element: Interpretation + Concept: MTH#C0420833 + Description: "A clinical interpretation of a finding (applies to both assertions and observation)." + Value: CodeableConcept from http://hl7.org/fhir/ValueSet/observation-interpretation if covered + + Element: PanelMembers + Concept: TBD + Description: "PanelMembers represent the elements of a group of a related but independent evaluations. + + Examples are the measurements that compose a complete blood count (CBC), or the elements of a pathology report. Each member is an independent evaluation, but the grouping reflects a composite lab order, shared specimen, or a single report author. Typically the Category and ReasonCode are not given for individual findings that are part of the panel, but rather given at the level of the panel itself." + 0..* ref(Observation) + + Element: Components + Concept: TBD + Description: "Sub-observations that are part of this observation. A sub-observation contributs to the parent observation and are always treated a part of a single observation (they are not separable). However, the reference range for the primary observation value is not inherited by the component values and is required when appropriate for each component observation." + 0..* ref(ObservationComponent) + + +/* commented out but it might need to come back, so please save + Element: Precondition + Concept: TBD + Description: "A description of the conditions or context of an observation, for example, under sedation, fasting or post-exercise. Body position and body site are also qualifiers, but handled separately. A qualifier cannot modify the measurement type; for example, a fasting blood sugar is still a blood sugar. " + Value: CodeableConcept or ref(Observation) + + + Element: DeltaFlag + Concept: MTH#C1705241 + Description: "Indicator of significant change (delta) from the last or previous measurement." + Value: CodeableConcept from DeltaFlagVS +*/ +// Element: Issued +// Description: "The date and time this observation was made available to providers, typically after the results have been reviewed and verified." +// Value: instant + + +// Non-Laboratory Results + +EntryElement: NonLaboratoryObservation +Based on: Observation +Description: "An observation not based on a specimen." + +EntryElement: SimpleNonLaboratoryObservation +Based on: NonLaboratoryObservation +Description: "An observation having no components or panel members" +0..0 Components +0..0 PanelMembers + +EntryElement: CodedNonLaboratoryObservation +Based on: NonLaboratoryObservation +Concept: TBD +Description: "The result of evaluations (measurements, tests, or questions) whose answer is expressed as a code." + DataValue value is type CodeableConcept +0..0 ReferenceRange + +EntryElement: QuantitativeNonLaboratoryObservation +Based on: NonLaboratoryObservation +Concept: TBD +Description: "The result of evaluations (measurements, tests, or questions) whose answer is expressed as a code." + DataValue value is type Quantity + +EntryElement: SimpleCodedNonLaboratoryObservation +Based on: CodedNonLaboratoryObservation +Description: "An observation whose result is a code, and also having no components or panel members" +0..0 Components +0..0 PanelMembers + +EntryElement: ComponentOnlyNonLaboratoryObservation +Based on: NonLaboratoryObservation +Description: "An observation with components, but without a result value or panel members." +0..0 DataValue +0..0 DataAbsentReason +0..0 PanelMembers +0..0 ReferenceRange + +// Laboratory Measurements and Results + +EntryElement: LaboratoryObservation +Based on: Observation +Description: "A coded finding based on a specimen collected from a patient." + Code from http://hl7.org/fhir/ValueSet/observation-codes if covered +1..1 Category // MK changed from 1..* to 1..1 to be compatible with DSTU 2 +1..1 SubjectOfRecord +0..1 Specimen +0..0 BodySite // BodySite is determined indirectly from Specimen.CollectionSite + Category is OBSCAT#laboratory + +EntryElement: CodedLaboratoryObservation +Based on: LaboratoryObservation +Description: "A coded result from a laboratory test." + DataValue value is type CodeableConcept +0..0 ReferenceRange + +EntryElement: SimpleLaboratoryObservation +Based on: LaboratoryObservation +Description: "A coded result from a laboratory test without further panel members or components." +0..0 Components +0..0 PanelMembers + +EntryElement: SimpleCodedLaboratoryObservation +Based on: CodedLaboratoryObservation +Description: "A coded result from a laboratory test without further panel members or components." +0..0 Components +0..0 PanelMembers + +EntryElement: QuantitativeLaboratoryObservation +Based on: LaboratoryObservation +Description: "A quantiative result from a laboratory test." + DataValue value is type Quantity + +EntryElement: Panel +Based on: Observation +Description: "A set of independent but related observations that are often presented together to facilitate interpretation, such as a lipid panel." +0..0 Components +0..0 BodySite +0..0 Specimen +0..0 Device + + +EntryElement: HeadlessPanel +Based on: Panel +Description: "A panel that does not have an overall value that summarizes the entire panel." +0..0 DataValue +0..0 DataAbsentReason +0..0 ReferenceRange + +Element: SocialHistoryObservation +Based on: NonLaboratoryObservation +Description: "A simplified observation for social histories." +1..1 SubjectOfRecord value is type PatientOnly + Category is OBSCAT#social-history "Social History" +0..0 Method +0..0 BodySite +0..0 ReferenceRange +0..0 PanelMembers +0..0 Device +0..0 DataAbsentReason + +Element: CodedSocialHistoryObservation +Based on: SocialHistoryObservation +Description: "The result of social history questions, whose answer is expressed as a code." + DataValue value is type CodeableConcept + +EntryElement: Condition +Based on: ConditionOrObservation +Description: "A condition that is or may be present in a subject. 'Condition' is interpreted broadly and could be a disorder, abnormality, problem, injury, complaint, functionality, illness, disease, ailment, sickness, affliction, upset, difficulty, disorder, symptom, worry, or trouble. +SHR Condition uses the SHR BodySite structure that includes not only a code, but optional laterality, direction, clock direction, and distance. If included, the distance is measured from the location specified by the code, laterality, and direction." + Code from http://hl7.org/fhir/us/core/ValueSet/us-core-problem if covered // cannot make the binding weaker because US Core requires an extensible binding + InformationSource value is type PatientOrPractitionerOrRelatedPerson +1..1 SubjectOfRecord value is type ref(Patient) // restricted in DSTU 2 (from Patient or Group) +1..1 Category from ConditionCategoryVS // DSTU 2 change - category is 1..1 in Argonaut +0..* BodySite +1..1 Status from http://hl7.org/fhir/ValueSet/condition-ver-status +1..1 ClinicalStatus from http://hl7.org/fhir/ValueSet/condition-clinical +0..1 Severity from http://hl7.org/fhir/ValueSet/condition-severity +0..1 StageInformation +0..1 Onset +0..1 Abatement +0..1 Evidence +// Stuff from CIMI eliminated +//0..1 WhenClinicallyRecognized +//0..1 PresentOnAdmission +//0..* ConditionCause +//0..1 Criticality + + Element: Evidence + Description: "Supporting evidence / manifestations that are the basis of the Condition's verification status, such as evidence that confirmed or refuted the condition." + 0..* Manifestation + 0..* DomainResource + + Element: Manifestation + Description: "Clinical symptoms/signs." + Value: CodeableConcept could be from http://hl7.org/fhir/ValueSet/clinical-findings + + Element: ConditionCause + Description: "The cause of the condition. This includes such causes as disease vectors and endogenous states (e.g., macular degeneration due to diabetes), substances, medications, micro-organisms, and forces associated with the occurrence of a Condition from temporal or causative perspectives" + Value: CodeableConcept or ref(Entity) or ref(ConditionOrObservation) + // probably other attributes needed, such as likelihood or type of cause + + Element: ClinicalStatus + Concept: TBD + Description: "A flag indicating whether the condition is active or inactive, recurring, in remission, or resolved (as of the last update of the Condition)." + Value: CodeableConcept + + Element: WhenClinicallyRecognized + Concept: TBD + Description: "The time at which a condition or condition was first identified in a healthcare context." + Value: date + + Element: PresentOnAdmission + Concept: LNC#89251-3 "Condition present on admission" + Description: "If the problem or condition existed before the current episode of care." + Value: CodeableConcept from YesNoUnknownVS + + Element: Severity + Concept: MTH#C0392364 + Description: "Degree of harshness or extent of a symptom, disorder, or condition." + Value: CodeableConcept + + Element: Criticality + Concept: MTH#C3858539 "Criticality" + Description: "The potential clinical harm associated with a condition. When the worst case result is assessed to have a life-threatening or organ system threatening potential, it is considered to be of high criticality." + Value: CodeableConcept from http://hl7.org/fhir/ValueSet/allergy-intolerance-criticality + + Element: StageInformation + Concept: MTH#C0699749 + Description: "The relative advancement in the course of a disease. The StageCode is the summary stage or stage group. StageDetail optionally contains the full staging information." + 0..1 StageSummary + 0..1 StageDetail + + Element: StageSummary + Concept: TBD + Description: "A code representing the current stage of a disease." + Value: CodeableConcept + + Element: StageDetail + Concept: TBD + Description: "The full staging information" + Value: ref(Observation) + + Element: AlleviatingFactor + Concept: LNC#55258-8 + Description: "Activities that reduce the severity of the pathology" + Value: CodeableConcept + + Element: ExacerbatingFactor + Concept: LNC#55258-8 + Description: "Activities that increase the severity of the pathology" + Value: CodeableConcept + + Element: Onset + Concept: LNC#85585-8 + Description: "The beginning or first appearance of a mental or physical disorder." + Value: dateTime or Age or TimePeriod or Range or string + + Element: Abatement + Concept: LNC#88878-4 + Description: "The end, remission or resolution." + Value: dateTime or Age or boolean or TimePeriod or Range or string + + + +EntryElement: BodyStructure +Based on: Condition +Description: "A body structure such as wound or tumor, observed to be present in a patient. The body structure is a condition that persists over time. The Code represents the body structure itself (the morphology), while the BodySiteCode is the location of that structure. This corresponds to FHIR R4, where the BodyStructure resource has morphology (corresponding to Code) and location (corresponding to BodySite.BodySiteCode. For example, the Code could be blunt force injury (SCT 3821009) and location left knee." + Code from BodyStructureVS if covered +0..0 ReferenceRange + +EntryElement: CongenitalAbnormality +Concept: MTH#C0000768 "Congenital Abnormality" +Based on: Condition +Description: "Any abnormality, genetic, anatomical, biochemical, evident at birth or during the neonatal period. Includes malformations, deformations, and chromosomal abnormalities." + Code from CongenitalAbnormalitiesVS if covered + + +EntryElement: DiagnosticReport +Based on: ConditionOrObservation // TODO: need a new term for ConditionOrObservation +0..* RelatedRequest value is type ReferralOrProcedureOrMedicationRequest // CarePlan | ImmunizationRecommendation | MedicationRequest | NutritionOrder | ProcedureRequest | ReferralRequest +1..1 Status from http://hl7.org/fhir/ValueSet/diagnostic-report-status +0..1 ServiceCategory +0..1 SubjectOfRecord value is type PatientOrGroupOrDeviceOrLocation +1..1 Code should be from http://hl7.org/fhir/ValueSet/report-codes +0..1 CareContext +0..1 RelevantTime +0..1 StatementDateTime +0..* Participation + Participation.Participant value is type PractitionerOrOrganization +0..0 Participation.ParticipationPeriod +0..0 Participation.OnBehalfOf +0..* ref(Specimen) +0..* ref(Observation) // Panel members? +//0..* ref(ImagingStudy) +0..* ref(Media) +0..1 Conclusion +0..* DiagnosisCode +0..* OriginalReport + + Element: ReferralOrProcedureOrMedicationRequest + Based on: ActionRequested + Value: ref(ReferralRequest) or ref(ProcedureRequest) or ref(MedicationRequest) // CarePlan not yet implemented + + Element: Conclusion + Description: "Concise and clinically contextualized impression / summary of the diagnostic report." + Value: string + + Element: OriginalReport + Description: "Fully formatted representation of the entire result as issued by the diagnostic service. Multiple formats are allowed but they SHALL be semantically equivalent." + Value: ref(Attachment) + + + +EntryElement: ClinicalNote +Based on: DocumentReference +Description: "An entry concerning a patient where the result is a narrative text." +1..1 Type from http://hl7.org/fhir/ValueSet/c80-doc-typecodes +1..1 Category from http://fhir.org/guides/argonaut-clinicalnotes/ValueSet/documentreference-category diff --git a/spec/shr_finding_map_dstu2.txt b/spec/shr_finding_map_dstu2.txt new file mode 100644 index 00000000..288ca96d --- /dev/null +++ b/spec/shr_finding_map_dstu2.txt @@ -0,0 +1,86 @@ +Grammar: Map 5.1 +Namespace: shr.core +Target: FHIR_DSTU_2 + + +Observation maps to Observation: + Identifier maps to identifier + SubjectOfRecord maps to subject + Author maps to performer + Code maps to code + Method maps to method + // dstu 2 change (name change) + CommentOrDescription maps to comments + Category maps to category + BodySite.BodySiteCode maps to bodySite + BodySite.Laterality maps to bodySite.extension + BodySite.AnatomicalDirection maps to bodySite.extension + BodySite.ClockDirection maps to bodySite.extension + BodySite.CommentOrDescription maps to bodySite.extension + BodySite.Attachment maps to bodySite.extension + BodySite.DistanceFromLandmark maps to bodySite.extension + Device maps to device + StatementDateTime maps to issued + ReferenceRange maps to referenceRange + ReferenceRange.Range.LowerBound maps to referenceRange.low + ReferenceRange.Range.UpperBound maps to referenceRange.high + // dstu 2 change + ReferenceRange.Type maps to referenceRange.meaning + // dstu 2 change (no such attribute) +// ReferenceRange.ApplicableSubpopulation maps to referenceRange.appliesTo +// dstu 2 change (no such attribute) +// ReferenceRange.ApplicableAgeRange maps to referenceRange.age + Components maps to component + Components.ObservationComponent.Code maps to component.code (slice on = code.coding.code; slice strategy = includes) + Components.ObservationComponent.DataValue maps to component.value[x] + Components.ObservationComponent.DataAbsentReason maps to component.dataAbsentReason + // dstu 2 change (no such attribute) + //Components.ObservationComponent.Interpretation maps to component.interpretation + Components.ObservationComponent.ReferenceRange maps to component.referenceRange + fix related.type to #has-member + PanelMembers maps to related + PanelMembers.Observation maps to related.target (slice at = related; slice on = target.reference.resolve(); slice on type = profile; slice strategy = includes) + DataValue maps to value[x] + DataAbsentReason maps to dataAbsentReason + Interpretation maps to interpretation +// Issued maps to issued + Status maps to status + RelevantTime maps to effective[x] + // dstu 2 change (name change) + CareContext maps to encounter +// DeltaFlag maps to http://hl7.org/fhir/StructureDefinition/observation-delta + +NonLaboratoryObservation maps to Observation: + constrain specimen to 0..0 + +LaboratoryObservation maps to http://fhir.org/guides/argonaut/StructureDefinition/argo-observationresults: + Specimen maps to specimen + +Condition maps to http://fhir.org/guides/argonaut/StructureDefinition/argo-condition: +// dstu 2 change (different mapping target) + Identifier maps to identifier + StatementDateTime maps to dateRecorded + InformationSource maps to asserter + SubjectOfRecord maps to patient + Category maps to category + Identifier maps to identifier + Code maps to code + BodySite.BodySiteCode maps to bodySite + BodySite.Laterality maps to bodySite.extension + BodySite.AnatomicalDirection maps to bodySite.extension + BodySite.ClockDirection maps to bodySite.extension + BodySite.CommentOrDescription maps to bodySite.extension + BodySite.Attachment maps to bodySite.extension + BodySite.DistanceFromLandmark maps to bodySite.extension + CareContext maps to encounter + ClinicalStatus maps to clinicalStatus + Status maps to verificationStatus + Onset maps to onset[x] + Abatement maps to abatement[x] + Severity maps to severity + StageInformation maps to stage + StageInformation.StageSummary maps to stage.summary + StageInformation.StageDetail maps to stage.assessment + Evidence.Manifestation maps to evidence.code + Evidence.DomainResource maps to evidence.detail + diff --git a/spec/shr_finding_map_stu3.txt b/spec/shr_finding_map_stu3.txt new file mode 100644 index 00000000..b55a599f --- /dev/null +++ b/spec/shr_finding_map_stu3.txt @@ -0,0 +1,101 @@ +Grammar: Map 5.1 +Namespace: shr.core +Target: FHIR_STU_3 + + +// do not map Observation to US Core Results -- Brett says that's meant for for lab observations +Observation maps to Observation: + Identifier maps to identifier + SubjectOfRecord maps to subject + Author maps to performer + Code maps to code + Method maps to method + CommentOrDescription maps to comment + Category maps to category + BodySite.BodySiteCode maps to bodySite + BodySite.Laterality maps to bodySite.extension + //(slice on = url; slice strategy = value) + BodySite.AnatomicalDirection maps to bodySite.extension + BodySite.CommentOrDescription maps to bodySite.extension + BodySite.ClockDirection maps to bodySite.extension + BodySite.Attachment maps to bodySite.extension + BodySite.DistanceFromLandmark maps to bodySite.extension + Device maps to device + StatementDateTime maps to issued + ReferenceRange maps to referenceRange + ReferenceRange.Range.LowerBound maps to referenceRange.low + ReferenceRange.Range.UpperBound maps to referenceRange.high + ReferenceRange.Type maps to referenceRange.type + ReferenceRange.ApplicableSubpopulation maps to referenceRange.appliesTo + ReferenceRange.ApplicableAgeRange maps to referenceRange.age + Components maps to component + Components.ObservationComponent.Code maps to component.code (slice on = code.coding.code; slice strategy = includes) + Components.ObservationComponent.DataValue maps to component.value[x] + Components.ObservationComponent.DataAbsentReason maps to component.dataAbsentReason + //Components.ObservationComponent.Interpretation maps to component.interpretation + Components.ObservationComponent.ReferenceRange maps to component.referenceRange + fix related.type to #has-member + PanelMembers maps to related + PanelMembers.Observation maps to related.target (slice at = related; slice on = target.reference.resolve(); slice on type = profile; slice strategy = includes) + DataValue maps to value[x] + DataAbsentReason maps to dataAbsentReason + Interpretation maps to interpretation +// Issued maps to issued + Status maps to status + RelevantTime maps to effective[x] + CareContext maps to context + SubjectOfInformation maps to extension +// DeltaFlag maps to http://hl7.org/fhir/StructureDefinition/observation-delta + +NonLaboratoryObservation maps to Observation: + constrain specimen to 0..0 + +LaboratoryObservation maps to http://hl7.org/fhir/us/core/StructureDefinition/us-core-observationresults: + Specimen maps to specimen + +Condition maps to http://hl7.org/fhir/us/core/StructureDefinition/us-core-condition: + Identifier maps to identifier + StatementDateTime maps to assertedDate + InformationSource maps to asserter + SubjectOfRecord maps to subject + Category maps to category + Identifier maps to identifier + Code maps to code + BodySite.BodySiteCode maps to bodySite + BodySite.Laterality maps to bodySite.extension + BodySite.AnatomicalDirection maps to bodySite.extension + BodySite.CommentOrDescription maps to bodySite.extension + BodySite.ClockDirection maps to bodySite.extension + BodySite.Attachment maps to bodySite.extension + BodySite.DistanceFromLandmark maps to bodySite.extension + CareContext maps to context + ClinicalStatus maps to clinicalStatus + Status maps to verificationStatus + Onset maps to onset[x] + Abatement maps to abatement[x] + Severity maps to severity + StageInformation maps to stage + StageInformation.StageSummary maps to stage.summary + StageInformation.StageDetail maps to stage.assessment + Evidence.Manifestation maps to evidence.code + Evidence.DomainResource maps to evidence.detail + +DiagnosticReport maps to DiagnosticReport: + Identifier maps to identifier + RelatedRequest maps to basedOn + Status maps to status + SubjectOfRecord maps to subject + Code maps to code + CareContext maps to context + RelevantTime maps to effective[x] + StatementDateTime maps to issued + Participation maps to performer + Participation.ParticipationType maps to performer.role + Participation.Participant maps to performer.actor + Specimen maps to specimen + Observation maps to result +// ref(ImagingStudy) or imaging manifest + Media maps to image.link + Conclusion maps to conclusion + DiagnosisCode maps to codedDiagnosis + OriginalReport maps to presentedForm \ No newline at end of file diff --git a/spec/shr_foundation.txt b/spec/shr_foundation.txt new file mode 100644 index 00000000..58ab7302 --- /dev/null +++ b/spec/shr_foundation.txt @@ -0,0 +1,462 @@ +Grammar: DataElement 5.0 +Namespace: shr.core + +CodeSystem: MTH = http://ncimeta.nci.nih.gov +CodeSystem: LNC = http://loinc.org +CodeSystem: SCT = http://snomed.info/sct +CodeSystem: NCI = https://evs.nci.nih.gov/ftp1/CDISC/SDTM/ +CodeSystem: OBSCAT = http://hl7.org/fhir/observation-category + +Abstract Element: Resource +Description: "Parent class for any item in clinical or administrative health-related system. Contains metadata attributes that apply to any item represented in the standard health record. An DomainResource can belong to a single person's health record, or represent an entity that surfaces in multiple records, such as organizations, providers, payments, decision support artifacts, etc." +0..1 Metadata +0..1 Language // from http://hl7.org/fhir/ValueSet/languages +// language has required binding in Argonaut in DSTU 2 that is different than the extensible binding in us-core-patient. Not able to resolve this. +0..1 ImplicitRules + + Element: Language + Concept: MTH#C0023008 + Description: "A human language, spoken or written." + Value: CodeableConcept + + Element: ImplicitRules + Description: "A set of rules under which this content was created" + Value: uri + + +Abstract Element: DomainResource +Based on: Resource +Description: "Parent class for any item in clinical or administrative health-related system. A DomainResource can belong to a single person's health record, or represent an entity that surfaces in multiple records, such as organizations, providers, payments, decision support artifacts, etc." +0..1 Narrative +0..1 StatusOrActive +0..* Identifier + + Element: Narrative + Concept: TBD + Description: "A human-readable narrative, potentially including images, that contains a summary of the resource, and may be used to represent the content of the resource to a human." + 1..1 NarrativeText + 1..1 NarrativeQualifier + + Element: NarrativeText + Description: "Text of narrative, in xhtml." + Value: xhtml + + Element: NarrativeQualifier + Description: "Additional information on how the narrative was generated, and the scope of information contained." + Value: CodeableConcept from http://hl7.org/fhir/ValueSet/narrative-status + + Abstract Element: StatusOrActive + Description: "Abstract class for a property that defines either the status of the recource, or whether the resource is active." + Value: boolean or CodeableConcept + + Element: Status + Based on: StatusOrActive + Description: "A state that relates to the workflow or interpretation of this resource. Certain status values can modify the meaning of the resource, for example, entered-in-error. When a boolean value is used, Status of true indicates the record is active, false means inactive." + Value: CodeableConcept // should be from http://hl7.org/fhir/ValueSet/resource-status + // cannot specify the preferred value set here because there are conflicting required value sets in some status attributes, particularly Encounter. It will generate an error to map preferred to required. + + Element: Active + Based on: StatusOrActive + Description: "A flag that indicates whether the resource record is active, or inactive and ignored for all but historical purposes." + Value: boolean + + +Element: Metadata +Description: "Elements that belong to all information items." +0..1 VersionId +0..1 LastUpdated +//0..1 SourceSystem // R4 only +0..* SecurityLabel +0..* Tag + + Element: VersionId + Concept: MTH#C0333052 + Description: "An identifier associated with the product that denotes a particular release iteration." + Value: id + + Element: LastUpdated + Description: "The most recent date the information item was changed." + Value: dateTime + +/* + Element: SourceSystem + Description: "FHIR: This provides a minimal amount of Provenance information that can be used to track or differentiate the source of information in the resource. The source may identify another FHIR server, document, message, database, etc. + FHIM: Identifies the computer system that created the medical record. This optional field may also be used to indicate that the medical record was originally created by a different organization from the one that is currently storing or utilizing the record in that the assigning authority of the Id could be set to that originating organization. This property is optional, as some systems will assume that all records that it contains originated in that system, however it is anticipated that it will become increasingly commonplace for records from multiple systems and organizations will be comingled in order to provide a complete picture of the patient's health record." + Value: uri +*/ + Element: SecurityLabel + Concept: MTH#C3858779 "security classification" + Description: "A code that connects the entry to a security policy. Security labels can be updated when the resource changes, or whenever the security sub-system chooses to." + Value: CodeableConcept + + Element: Tag + Concept: MTH#C4280044 "Metatags" + Description: "A code used to relate entries to categories or workflows. Applications are not required to consider the tags when interpreting the meaning of an entry." + Value: CodeableConcept + + +Abstract Element: ClinicalStatement +Based on: DomainResource +Description: "This abstract class provides properties and behaviors common to entries in a medical record. Patient and Encounter are ubiquitous in clinical statements. This class also allows for common representation of simple data provenance elements asserter, recorder, and creation date." +0..1 SubjectOfRecord +0..1 CareContext +0..1 StatementDateTime +0..1 Author +0..1 InformationSource +0..1 Recorder + + + Element: SubjectOfRecord + Description: "The subject of a clinical statement, often called the Patient or the Subject. The SubjectOfRecord typically identifies the clinical record in which this statement is contained. If the statement should be in John Doe's patient record, then John Doe is the subject of record. The SubjectOfRecord can also be a location, group, or other entity that statements can pertain to. For example, observations concerning a hospital floor would have a Location as the SubjectOfRecord. + + Note that the word 'Subject' is used in the sense of a person or entity subjected to observations or actions, not subject as in a conceptual topic, like heart disease." + Value: ref(EntityOrRole) + + Element: StatementDateTime + Concept: MTH#C3669169 + Description: "The point in time when the statement was created." + Value: dateTime // we can map to instant from dateTime + + Element: Author + Description: "The actor who created the item and it responsible for the content (regardless of the information source or who recorded it). If only the author is given, it is assumed the author is the information source and the recorder." + Value: ref(EntityOrRole) + + Element: InformationSource + Description: "The originator or source of the information or request: a practitioner, patient, related person, organization, an algorithm, device, etc." + Value: ref(EntityOrRole) + + Element: Recorder + Concept: TBD + Description: "The recorder of the information, if other than the author. For example, the nurse taking a list of medications reported by the patient." + Value: ref(EntityOrRole) + + Element: Participant + Concept: MTH#C1550369 + Description: "An entity (usually a Practitioner, Patient, or Organization but potentially a device or other entity) that participates in a healthcare task or activity. A code can be used to indicate a generic type of participant, e.g., mother, EMT, or social worker." + Value: ref(EntityOrRole) + + +EntryElement: Composition +Based on: DomainResource +Description: "A composition represents a set of Entries sharing common provenance, a document such as an extract from a patient record, a knowledge artifact, or a catalog definition." +0..1 Identifier // FHIR inconsistency -- usually 0..* + StatusOrActive is type Status +1..1 Status from http://hl7.org/fhir/ValueSet/composition-status +1..1 Type should be from http://hl7.org/fhir/ValueSet/doc-typecodes +0..* Section + + Element: Section + Description: "Represents a section containing entries in a composition." + //0..1 Title + 0..* DomainResource + 0..* Section + +// Combined participant roles + + Element: PatientOrPractitioner + Based on: EntityOrRole + Description: "A choice of Patient or Practitioner. Needed for mapping to FHIR." + Value: ref(Patient) or ref(Practitioner) + + Element: PatientOrPractitionerOrRelatedPerson + Based on: EntityOrRole + Description: "A choice of Patient, Practitioner and RelatedPerson. Needed for mapping to FHIR, for example, mapping AdverseEvent.SignedBy to FHIR AdverseEvent." + Value: ref(Patient) or ref(Practitioner) or ref(RelatedPerson) + + Element: PractitionerOrRelatedPerson + Based on: EntityOrRole + Description: "A choice of Practitioner and RelatedPerson. Needed for mapping to FHIR, for example, mapping EncounterPerformed.Participant to FHIR Encounter.participant.individual" + Value: ref(Practitioner) or ref(RelatedPerson) + + Element: PersonOrOrganization + Based on: EntityOrRole + Description: "A choice of Person (in any role) or Organization. Needed for mapping to FHIR." + Value: ref(Patient) or ref(Practitioner) or ref(RelatedPerson) or ref(Organization) + + Element: PersonOrDevice + Based on: EntityOrRole + Description: "A choice of Person (in any role) or Organization. Needed for mapping to FHIR." + Value: ref(Patient) or ref(Practitioner) or ref(RelatedPerson) or ref(Device) + + Element: PersonOrDeviceOrLocation + Based on: EntityOrRole + Description: "A choice of Person (in any role) or Organization. Needed for mapping to FHIR." + Value: ref(Patient) or ref(Practitioner) or ref(RelatedPerson) or ref(Device) or ref(Location) + + Element: PersonOrOrganizationOrDevice + Based on: EntityOrRole + Description: "Constrains participants to classes that are accepted by FHIR as actors in procedures in STU 3." + Value: ref(Practitioner) or ref(Organization) or ref(Patient) or ref(RelatedPerson) or ref(Device) + + Element: PractitionerOrDevice + Based on: EntityOrRole + Description: "A choice of Practitioner or Device. Needed for mapping to FHIR." + Value: ref(Practitioner) or ref(Device) + + Element: PractitionerOrOrganization + Based on: EntityOrRole + Description: "A choice of Practitioner or Organization. Needed for mapping to FHIR." + Value: ref(Practitioner) or ref(Organization) + + Element: PatientOrPractitionerOrGroupOrDevice + Based on: EntityOrRole + Description: "A choice of Patient, Practitioner, Group or Device. Needed for mapping to FHIR." + Value: ref(Patient) or ref(Practitioner) or ref(Group) or ref(Device) + + Element: PatientOrGroupOrDeviceOrLocation + Based on: EntityOrRole + Description: "A choice of Patient, Group, Device, or Location. Needed for mapping to FHIR." + Value: ref(Patient) or ref(Group) or ref(Device) or ref(Location) + + Element: PatientOrResearchSubjectOrMedicationOrDevice + Based on: EntityOrRole + Description: "A choice of Patient, ResearchSubject, Medication, or Device. Needed for mapping to FHIR." + Value: ref(Patient) or ref(ResearchSubject) or ref(Medication) or ref(Device) + + Element: PatientOrGroup + Based on: EntityOrRole + Description: "A choice of Patient or Group. Needed for mapping to FHIR." + Value: ref(Patient) or ref(Group) + + Element: PatientOrPractitionerOrGroupOrDeviceOrSpecimen + Based on: EntityOrRole + Description: "A choice of Patient, Practitioner, Group, Device or Specimen. Needed for mapping to FHIR." + Value: ref(Patient) or ref(Practitioner) or ref(Group) or ref(Device) or ref(Specimen) + + Element: PatientOnly + Based on: PatientOrGroupOrDeviceOrLocation + Description: "A choice of Patient or nothing. Used to further restrict the SubjectOfRecord of Observations. This is a hack!" + Value: ref(Patient) +/* + Element: HealthRecordId + Concept: MTH#C1549718 + Description: "A unique, persistent, permanent identifier for a health record." + Value: id + + Element: DerivedFrom + Concept: TBD + Description: "Indicates the source of information in the case the Entry has been created by logical extension or modification of one or more source entries." + Value: ref(DomainResource) + + Element: SignedBy + Description: "Provenance information specific to the signing of the clinical statement." + Value: Participant + + Element: CosignedBy + Description: "Provenance information specific to the cosigning of the clinical statement." + Value: Participant + + Element: VerifiedBy + Description: "Provenance information specific to the verification process associated with this statement (e.g., verifier, when verified, etc.)" + Value: Participant +*/ + + + +EntryElement: ValueSet +Based on: DomainResource +Description: "A set of codes drawn from one or more code systems" +0..1 Url +0..1 VersionString +0..1 NameAsText +0..1 Title +1..1 Status from http://hl7.org/fhir/ValueSet/publication-status +0..1 IsExperimental +0..* SubjectType +0..1 LastUpdated +0..1 PublisherName +0..* ContactDetail +0..1 DescriptionMarkdown +0..* UseContext +0..* Jurisdiction +0..1 IsImmutable +0..1 PurposeMarkdown +0..1 Copyright +0..1 IsExtensible +0..1 ContentLogicalDefinition +0..1 ValueSetExpansion + + Element: IsImmutable + Description: "Indicates whether or not any change to the content logical definition may occur" Value: boolean + + Element: IsExtensible + Description: "Whether this is intended to be used with an extensible binding" + Value: boolean + + Element: ContentLogicalDefinition + Description: "Definition of the content of the value set." + 0..1 LockedDate + 0..1 IncludeInactiveCodes + 1..* IncludeCodes + 0..* ExcludeCodes + + Element: LockedDate + Description: "If a locked date is defined, then the Content Logical Definition must be evaluated using the current version as of the locked date for referenced code system(s) and value set instances where ValueSet.compose.include.version is not defined." + Value: date + + Element: IncludeInactiveCodes + Description: "Whether inactive codes - codes that are not approved for current use - are in the value set. If inactive = true, inactive codes are to be included in the expansion, if inactive = false, the inactive codes will not be included in the expansion. If absent, the behavior is determined by the implementation, or by the applicable ExpansionProfile (but generally, inactive codes would be expected to be included)." + Value: boolean + + Element: IncludeCodes + Description: "Include one or more codes from a code system or other value set(s)." + Value: CodeSet + + Element: ExcludeCodes + Description: "Exclude one or more codes from the value set based on code system filters and/or other value sets." + Value: CodeSet + + Element: CodeSet + Description: "A description of a set of codes, to be included or excluded from a value set." + 0..1 CodeSystem + 0..1 CodeSystemVersion + 0..* CodeSetConcept + 0..* CodeSetFilter + 0..* ValueSetUri + + Element: CodeSetConcept + Description: "Specifies a concept to be included or excluded." + 0..1 CodeValue + 0..1 DisplayText + 0..* Designation + + Element: Designation + Description: "Additional representations for this concept when used in this value set - other languages, aliases, specialized purposes, used for particular purposes, etc." + 0..1 Language + 0..1 Type from http://hl7.org/fhir/ValueSet/designation-use if covered + 1..1 DisplayText + + Element: CodeSetFilter + Description: "Select concepts by specify a matching criteria based on the properties (including relationships) defined by the system. If multiple filters are specified, they SHALL all be true." + 1..1 Property + 1..1 Operation + 1..1 CodeValue + + Element: Property + Description: "A code that identifies a property or a filter defined in the code system." + Value: CodeableConcept + + Element: Operation + Description: "The kind of operation to perform as a part of the filter criteria." + Value: CodeableConcept from http://hl7.org/fhir/ValueSet/filter-operator + + Element: ValueSetUri + Description: "Selects the concepts found in this value set (based on its value set definition). This is an absolute URI that is a reference to ValueSet.url. If multiple value sets are specified this includes the union of the contents of all of the referenced value sets." + Value: uri + + Element: ValueSetExpansion + Description: "The value set turned into a simple collection of enumerated codes. This element holds the expansion, if it has been performed." + 0..1 Url + 1..1 CreationDateTime + 0..1 TotalCount + 0..1 Offset + 0..* ExpansionParameter + 0..* ExpansionCoding + + Element: TotalCount + Description: "Total number of items." + Value: integer + + Element: Offset + Description: "If paging is being used, the offset at which this resource starts. I.e. this resource is a partial view into the expansion. If paging is not being used, this element SHALL NOT be present." + Value: integer + + Element: ExpansionParameter + Description: "A parameter that controlled the expansion process. These parameters may be used by users of expanded value sets to check whether the expansion is suitable for a particular purpose, or to pick the correct expansion." + 1..1 NameAsText + 0..1 ParameterValue + + Element: ParameterValue + Description: "The value of the parameter." + Value: string or boolean or integer or decimal or uri or code or dateTime + + Element: ExpansionCoding + Based on: Coding + Description: "The codes that are contained in the value set expansion." + // Inherits CodeValue, CodeSystem, CodeSystemVersion, DisplayText + 0..1 Inactive + 0..1 NonSelectable + 0..* Designation + 0..* ExpansionCoding + + Element: Inactive + Description: "A flag that indicates whether the item is inactive." + Value: boolean + + Element: NonSelectable + Description: "A flag that indicates whether the use cannot select this item." + Value: boolean + +EntryElement: DocumentReference +Based on: DomainResource +Description: "A reference to a document, used to describe a document that is made available to a healthcare system. A document is some sequence of bytes that is identifiable, establishes its own context (e.g., what subject, author, etc. can be displayed to the user), and has defined update management. The DocumentReference resource can be used with any document format that has a recognized mime type and that conforms to this definition." +0..1 MasterIdentifier + StatusOrActive is type Status +1..1 Status from http://hl7.org/fhir/ValueSet/document-reference-status +0..1 DocumentStatus from http://hl7.org/fhir/ValueSet/composition-status +1..1 Type from http://hl7.org/fhir/ValueSet/c80-doc-typecodes +0..1 Category from http://hl7.org/fhir/ValueSet/c80-doc-classcodes +0..1 SubjectOfRecord value is type ref(Patient) // us core restriction +0..1 CreationDateTime +1..1 StatementDateTime +0..* Author value is type PersonOrOrganizationOrDevice +0..1 Authenticator +0..1 ManagingOrganization +1..* DocumentReferenced +0..* RelatedDocument +0..1 CommentOrDescription +0..* SecurityLabel from http://hl7.org/fhir/ValueSet/security-labels if covered +0..1 ClinicalContext + + Element: MasterIdentifier + Description: "Document identifier as assigned by the source of the document. This identifier is specific to this version of the document. This unique identifier may be used elsewhere to identify this version of the document." + Value: Identifier + + Element: DocumentStatus + Description: "The status of the underlying document." + Value: CodeableConcept + + Element: Authenticator + Description: "Who authenticated the document" + Value: ref(Practitioner) or ref(Organization) + + Element: DocumentReferenced + Description: "The document referenced." + 1..1 Attachment + 1..1 Attachment.ContentType // constraint from us-core + 1..1 Attachment.ResourceLocation // constraint from us-core + 0..1 Type from http://hl7.org/fhir/ValueSet/formatcodes if covered // us-core extensible binding + + Element: RelatedDocument + Description: "Documents related to this one." + 1..1 Relationship from http://hl7.org/fhir/ValueSet/document-relationship-type + 1..1 ref(DocumentReference) + + Element: Relationship + Description: "A description of the association between two items." + Value: CodeableConcept + + Element: ClinicalContext + Description: "Clinical context of document" + 0..1 ref(Encounter) // in 4, changes to CareContext (Encounter or EpisodeOfCare) + 0..* Event + 0..1 TimePeriod + 0..1 FacilityType + 0..1 Setting + 0..1 ContemporaneousPatientInformation + 0..* RelatedInformation + 0..* Identifier + + Element: Event + Description: "Main clinical acts documented" + Value: CodeableConcept could be from http://hl7.org/fhir/ValueSet/v3-ActCode + + Element: FacilityType + Description: "Kind of facility where patient was seen" + Value: CodeableConcept could be from http://hl7.org/fhir/ValueSet/c80-facilitycodes + + Element: ContemporaneousPatientInformation + Description: "he Patient Information as known when the document was published. May be a reference to a version specific, or contained." + Value: ref(Patient) + + diff --git a/spec/shr_foundation_map_dstu2.txt b/spec/shr_foundation_map_dstu2.txt new file mode 100644 index 00000000..4590500e --- /dev/null +++ b/spec/shr_foundation_map_dstu2.txt @@ -0,0 +1,28 @@ +Grammar: Map 5.1 +Namespace: shr.core +Target: FHIR_DSTU_2 + + +DomainResource maps to DomainResource: + _Entry.EntryId maps to id + Language maps to language + Narrative maps to text + ImplicitRules maps to implicitRules + Metadata.VersionId maps to meta.versionId +// Metadata.SourceSystem maps to meta.extension + // _Entry.EntryType maps to meta.profile // (this will force a profile -- don't do it) + Metadata.LastUpdated maps to meta.lastUpdated + Metadata.SecurityLabel maps to meta.security + Metadata.Tag maps to meta.tag + +Composition maps to Composition: + Identifier maps to identifier + Status maps to status + Type maps to type + Section maps to section + Section.DomainResource maps to section.entry (slice on = reference.resolve(); slice on type = profile; slice strategy = includes) + Section.Section maps to section.section + +Narrative maps to Narrative: + NarrativeText maps to div + NarrativeQualifier maps to status \ No newline at end of file diff --git a/spec/shr_foundation_map_stu3.txt b/spec/shr_foundation_map_stu3.txt new file mode 100644 index 00000000..a05e7f3f --- /dev/null +++ b/spec/shr_foundation_map_stu3.txt @@ -0,0 +1,136 @@ +Grammar: Map 5.1 +Namespace: shr.core +Target: FHIR_STU_3 + + +DomainResource maps to DomainResource: +// _Entry.EntryId maps to id + Language maps to language + Narrative maps to text + ImplicitRules maps to implicitRules + Metadata.VersionId maps to meta.versionId +// Metadata.SourceSystem maps to meta.extension + // in R4, this will be meta.source + // _Entry.EntryType maps to meta.profile // (this will force a profile -- don't do it) + Metadata.LastUpdated maps to meta.lastUpdated + Metadata.SecurityLabel maps to meta.security + Metadata.Tag maps to meta.tag + +Composition maps to Composition: + Identifier maps to identifier + Status maps to status + Type maps to type + Section maps to section + Section.DomainResource maps to section.entry (slice on = reference.resolve(); slice on type = profile; slice strategy = includes) + Section.Section maps to section.section + +Narrative maps to Narrative: + NarrativeText maps to div + NarrativeQualifier maps to status + + +ValueSet maps to ValueSet: + Url maps to url + Identifier maps to identifier + VersionString maps to version + NameAsText maps to name + Title maps to title + Status maps to status + IsExperimental maps to experimental + LastUpdated maps to date + PublisherName maps to publisher + ContactDetail maps to contact + DescriptionMarkdown maps to description + UseContext.Code maps to useContext.code + UseContext.ContextValue maps to useContext.value[x] + Jurisdiction maps to jurisdiction + IsImmutable maps to immutable + PurposeMarkdown maps to purpose + Copyright maps to copyright + constrain extensible to 0..0 + ContentLogicalDefinition maps to compose + ContentLogicalDefinition.LockedDate maps to compose.lockedDate + ContentLogicalDefinition.IncludeInactiveCodes maps to compose.inactive + ContentLogicalDefinition.IncludeCodes maps to compose.include + ContentLogicalDefinition.IncludeCodes.CodeSet.CodeSystem maps to compose.include.system + ContentLogicalDefinition.IncludeCodes.CodeSet.CodeSystemVersion maps to compose.include.version + ContentLogicalDefinition.IncludeCodes.CodeSet.CodeSetConcept maps to compose.include.concept + ContentLogicalDefinition.IncludeCodes.CodeSet.CodeSetConcept.CodeValue maps to compose.include.concept.code + ContentLogicalDefinition.IncludeCodes.CodeSet.CodeSetConcept.DisplayText maps to compose.include.concept.display + ContentLogicalDefinition.IncludeCodes.CodeSet.CodeSetConcept.Designation maps to compose.include.concept.designation + ContentLogicalDefinition.IncludeCodes.CodeSet.CodeSetConcept.Designation.Language maps to compose.include.concept.designation.language + ContentLogicalDefinition.IncludeCodes.CodeSet.CodeSetConcept.Designation.Type maps to compose.include.concept.designation.use + ContentLogicalDefinition.IncludeCodes.CodeSet.CodeSetConcept.Designation.DisplayText maps to compose.include.concept.designation.value + ContentLogicalDefinition.IncludeCodes.CodeSet.CodeSetFilter maps to compose.include.filter + ContentLogicalDefinition.IncludeCodes.CodeSet.CodeSetFilter.Property maps to compose.include.filter.property + ContentLogicalDefinition.IncludeCodes.CodeSet.CodeSetFilter.Operation maps to compose.include.filter.op + ContentLogicalDefinition.IncludeCodes.CodeSet.CodeSetFilter.CodeValue maps to compose.include.filter.value + ContentLogicalDefinition.IncludeCodes.CodeSet.ValueSetUri maps to compose.include.valueSet + // ExcludeCodes + ContentLogicalDefinition.ExcludeCodes maps to compose.exclude + ContentLogicalDefinition.ExcludeCodes.CodeSet.CodeSystem maps to compose.exclude.system + ContentLogicalDefinition.ExcludeCodes.CodeSet.CodeSystemVersion maps to compose.exclude.version + ContentLogicalDefinition.ExcludeCodes.CodeSet.CodeSetConcept maps to compose.exclude.concept + ContentLogicalDefinition.ExcludeCodes.CodeSet.CodeSetConcept.CodeValue maps to compose.exclude.concept.code + ContentLogicalDefinition.ExcludeCodes.CodeSet.CodeSetConcept.DisplayText maps to compose.exclude.concept.display + ContentLogicalDefinition.ExcludeCodes.CodeSet.CodeSetConcept.Designation maps to compose.exclude.concept.designation + ContentLogicalDefinition.ExcludeCodes.CodeSet.CodeSetConcept.Designation.Language maps to compose.exclude.concept.designation.language + ContentLogicalDefinition.ExcludeCodes.CodeSet.CodeSetConcept.Designation.Type maps to compose.exclude.concept.designation.use + ContentLogicalDefinition.ExcludeCodes.CodeSet.CodeSetConcept.Designation.DisplayText maps to compose.exclude.concept.designation.value + ContentLogicalDefinition.ExcludeCodes.CodeSet.CodeSetFilter maps to compose.exclude.filter + ContentLogicalDefinition.ExcludeCodes.CodeSet.CodeSetFilter.Property maps to compose.exclude.filter.property + ContentLogicalDefinition.ExcludeCodes.CodeSet.CodeSetFilter.Operation maps to compose.exclude.filter.op + ContentLogicalDefinition.ExcludeCodes.CodeSet.CodeSetFilter.CodeValue maps to compose.exclude.filter.value + ContentLogicalDefinition.ExcludeCodes.CodeSet.ValueSetUri maps to compose.exclude.valueSet + // expansion + ValueSetExpansion maps to expansion + ValueSetExpansion.Url maps to expansion.identifier + ValueSetExpansion.CreationDateTime maps to expansion.timestamp + ValueSetExpansion.TotalCount maps to expansion.total + ValueSetExpansion.Offset maps to expansion.offset + ValueSetExpansion.ExpansionParameter maps to expansion.parameter + ValueSetExpansion.ExpansionParameter.NameAsText maps to expansion.parameter.name + ValueSetExpansion.ExpansionParameter.ParameterValue maps to expansion.parameter.value[x] + ValueSetExpansion.ExpansionCoding maps to expansion.contains + ValueSetExpansion.ExpansionCoding.CodeValue maps to expansion.contains.code + ValueSetExpansion.ExpansionCoding.CodeSystem maps to expansion.contains.system + ValueSetExpansion.ExpansionCoding.CodeSystemVersion maps to expansion.contains.version + ValueSetExpansion.ExpansionCoding.DisplayText maps to expansion.contains.display + ValueSetExpansion.ExpansionCoding.Inactive maps to expansion.contains.inactive + ValueSetExpansion.ExpansionCoding.NonSelectable maps to expansion.contains.abstract + ValueSetExpansion.ExpansionCoding.Designation maps to expansion.contains.designation + ValueSetExpansion.ExpansionCoding.ExpansionCoding maps to expansion.contains.contains + +DocumentReference maps to DocumentReference: +// http://hl7.org/fhir/us/core/StructureDefinition/us-core-documentreference: Not sure why this is not found +//ERROR shr: Invalid FHIR target: http://hl7.org/fhir/us/core/StructureDefinition/us-core-documentreference. ERROR_CODE:13001 (module=shr-fhir-export, shrId=shr.core.DocumentReference) +// target: http://hl7.org/fhir/us/core/StructureDefinition/us-core-documentreference + MasterIdentifier maps to masterIdentifier + Identifier maps to identifier + Status maps to status + DocumentStatus maps to docStatus + Type maps to type + Category maps to class + SubjectOfRecord maps to subject + CreationDateTime maps to created + StatementDateTime maps to indexed + Author maps to author + Authenticator maps to authenticator + ManagingOrganization maps to custodian + RelatedDocument maps to relatesTo + RelatedDocument.Relationship maps to relatesTo.code + RelatedDocument.DocumentReference maps to relatesTo.target + CommentOrDescription maps to description + SecurityLabel maps to securityLabel + DocumentReferenced maps to content + DocumentReferenced.Attachment maps to content.attachment + DocumentReferenced.Type maps to content.format + ClinicalContext maps to context + ClinicalContext.Encounter maps to context.encounter + ClinicalContext.Event maps to context.event + ClinicalContext.TimePeriod maps to context.period + ClinicalContext.FacilityType maps to context.facilityType + ClinicalContext.Setting maps to context.practiceSetting + ClinicalContext.ContemporaneousPatientInformation maps to context.sourcePatientInfo + ClinicalContext.Identifier maps to context.related.identifier + ClinicalContext.RelatedInformation maps to context.related.ref diff --git a/spec/shr_foundation_vs.txt b/spec/shr_foundation_vs.txt new file mode 100644 index 00000000..7978e8c3 --- /dev/null +++ b/spec/shr_foundation_vs.txt @@ -0,0 +1,121 @@ +Grammar: ValueSet 5.0 +Namespace: shr.core + +CodeSystem: SCT = http://snomed.info/sct +CodeSystem: MTH = http://ncimeta.nci.nih.gov +CodeSystem: LNC = http://loinc.org +CodeSystem: HL7DAR = http://terminology.hl7.org/CodeSystem/data-absent-reason + + +ValueSet: ConditionCategoryVS +Description: "A category assigned to the condition, for example, a disease, concern, symptom, adverse reaction, functional impairment, or structural abnormality." +#disease "A disorder of structure or function in a human, animal, or plant, especially one that produces specific signs or symptoms or that affects a specific location and is not simply a direct result of physical injury." +#functional_impairment "A disability experienced by the subject." +#structural_abnormality "An abnormality of physiologic structure." +#concern "Something the subject is worried about, which may or may not have yet been manifested. The object of the concern does not have to be a medical disorder." +#symptom "A sign or manifestation of a deeper cause, of known or unknown etiology, e.g. pain or ringing in the ears." +#adverse_reaction "An adverse reaction to an intervention." + +ValueSet: BodyStructureVS +Description: "A normal or abnormal physiology." +Includes codes descending from SCT#123037004 "Body Structure (body structure)" + +ValueSet: CongenitalAbnormalitiesVS +Includes codes descending from SCT#66091009 "Congenital Disease" // ICD10 Q00-Q99 + +/* +ValueSet: PresenceCertaintyVS +Description: "A code describing whether the finding in question is present, possible, suspected, etc." +//SCT#36692007 "Known" +//SCT#410605003 "Confirmed present" +//SCT#410591008 "Definitely present" +SCT#410515003 "Known present" +SCT#410592001 "Probably present" +SCT#410590009 "Known possible" +SCT#415684004 "Suspected" +//SCT#410593006 "Probably not present" // should be reported as Absence +//SCT#261665006 "Unknown" + +ValueSet: AbsenceCertaintyVS +Description: "A code describing whether the finding is question is absent, unknown, or not suspected." +//SCT#410516002 "Known absent" MK - commented out - same as "Definitely not present" +SCT#410594000 "Definitely not present" +SCT#410593006 "Probably not present" +SCT#428263003 "NOT suspected" +SCT#443508001 "No history of clinical finding in subject (situation)" + +ValueSet: AtRiskContextVS +Description: "A code describing the sense in which the subject has risk of a hypothetical (future) finding. At present, this value set contains only one code, but it is presented as a value set to allow for more nuanced meanings in the future." +SCT#410519009 "At risk" + +ValueSet: ExpectationContextVS +Description: "A code describing the sense in which a finding is expected." +SCT#410517006 "Expected" +SCT#410596003 "Likely outcome" +SCT#410595004 "Prognosis" +SCT#71033007 "Impending" + +ValueSet: GoalContextVS +Description: "A code describing the sense in which a finding is a goal or objective." +SCT#703039001 "Health objective" +SCT#410518001 "Goal" + +ValueSet: DeltaFlagVS +Concept: MTH#C1705241 +Description: "Change patterns and trends, including resolved." +Includes codes descending from SCT#385634002 "Change patterns (qualifier value)" +//SCT#58158008 "Stable (qualifier value)" +//SCT#385633008 "Improving (qualifier value)" +//SCT#230993007 "Worsening (qualifier value)" +//SCT#260369004 "Increasing (qualifier value)" +//SCT#260371004 "Decreasing (qualifier value)" +SCT#723506003 "Resolved (qualifier value)" + +ValueSet: DeltaFlagVS +Description: "Indicators for degree of change (delta) from the last or previous measurement." + Includes codes descending from SCT#263703002 "Changed status (qualifier value)" +// has values decreased, decreased relative to previous, improved, increased, increased relative to previous, maintained stablized, worse +// Also see LOINC #89253-9 Trend ... has values improved, deteriorated, stablized, resolved + +ValueSet: DiagnosticServiceVS +Description: "The type of laboratory service used in producing a laboratory result. Note -- we may want to include additional descendants of SCT#224891009 (Healthcare services)" +SCT#310078000 "Microbiology service (qualifier) -- Laboratory concerned with cultures, to look for suspected pathogens." +SCT#706900000 "Parasitology service (qualifier) -- Laboratory responsible for examining parasites, feces samples may be examined for evidence of intestinal parasites such as tapeworms or hookworms and others." +SCT#708185002 "Virology service (qualifier) -- Laboratory concerned with identification of viruses in specimens such as blood, urine, and cerebrospinal fluid." +SCT#708196005 "Hematology service (qualifier) -- Laboratory that works with whole blood to do full blood counts, and blood films as well as many other specialised tests." +SCT#310076001 "Biochemistry service (qualifier) -- Laboratory that usually receives serum or plasma and tests the serum for chemicals present in blood." +SCT#708191000 "Toxicology service (qualifier) -- Laboratory that mainly tests for pharmaceutical and recreational drugs. Urine and blood samples are submitted to this lab." +SCT#708190004 "Immunology service (qualifier) -- Immunology/Serology laboratory uses the concept of antigen-antibody interaction as a diagnostic tool. Compatibility of transplanted organs is also determined." +//#urinalysis "Laboratory tests urine for many analytes. Some health care providers have a urinalysis laboratory, while others don't." +SCT#310074003 "Pathology service (qualifier)-- Surgical, cytopathology, or histopathology laboratory. Surgical pathology examines organs, limbs, tumors, fetuses, and other tissues biopsied in surgery such as breast mastectomies." +SCT#310048009 "Genetics service (procedure) - note: should be in the Snomed (qualifier) hierarchy - Laboratory that mainly performs DNA analysis." +SCT#708178001 "Cytogenetics service (qualifier) -- Laboratory that uses blood and other cells to get a karyotype. This can be helpful in prenatal diagnosis (e.g. Down's syndrome) as well as in cancer (some cancers have abnormal chromosomes)." + +ValueSet: DataAbsentReasonVS +Description: "Reasons that a value associated with a test or other finding is missing. Includes all codes from http://hl7.org/fhir/ValueSet/data-absent-reason version 3.3.0 and additional codes covering other missing value circumstances." +HL7DAR#unknown "Unknown" +HL7DAR#asked-unknown "Asked But Unknown" +HL7DAR#temp-unknown "Temporarily Unknown" +HL7DAR#not-asked "Not Asked" +HL7DAR#asked-declined "Asked But Declined" +HL7DAR#masked "Masked" +HL7DAR#not-applicable "Not Applicable" +HL7DAR#unsupported "Unsupported" +HL7DAR#as-text "As Text" +HL7DAR#error "Error" +HL7DAR#not-a-number "Not a Number (NaN)" +HL7DAR#negative-infinity "Negative Infinity (NINF)" +HL7DAR#positive-infinity "Positive Infinity (PINF)" +HL7DAR#not-performed "Not Performed" +HL7DAR#not-permitted "Not Permitted" + +RM: these came from CIMI/Intermountain, commenting out until proven necessary. +MK - Insufficient-evidence is redundant with "unsupported" +#insufficient-evidence "There is insufficient information to make a determination." +#indeterminate-value "The value could not be determined or established with accuracy or certainty." +#no-further-explanation "The reason the information is not present is not known." +#null-answer "The answer is appears missing because the correct answer is null or empty; e.g., a question that asks for a list of the names of siblings applied to an only child." +#specimen-unavailable "Missing due to a problem collecting, identifying, or locating the specimen, including patient refusal or unable to provide specimen" +#specimen-inadequate "Missing due to a problem with the specimen, e.g. inadequate specimen, contamination, clotting, improper tube type, improper storage, too small, etc." +#instrument-malfunction "Missing due to instrument malfunction." +*/ diff --git a/spec/shr_medication.txt b/spec/shr_medication.txt new file mode 100644 index 00000000..3f8cb647 --- /dev/null +++ b/spec/shr_medication.txt @@ -0,0 +1,187 @@ +Grammar: DataElement 5.0 +Namespace: shr.core + +/* Taking out for now since Plan has not been defined +EntryElement: MedicationRegimen // Definitional +Concept: MTH#C0237125 +Description: "Defines a specific application of over-the-counter and prescribed/recommended medications and infusions to meet guidelines for therapeutic action, safety, and schedule." +1..* MedicationUsePlanned +*/ + +Element: Dosage +Concept: MTH#C0178602 +Description: "The dosage of the medication. The data structure is flexible and can describe a dosage prescribed, administered, or reported." +0..1 DoseAmount +0..1 TimingOfDoses +0..1 AsNeededIndicator +0..1 DosageInstructionsText +0..* AdditionalDosageInstruction from http://hl7.org/fhir/ValueSet/additional-instruction-codes +0..1 RouteIntoBody from http://hl7.org/fhir/ValueSet/route-codes +0..1 DosageMethod from http://hl7.org/fhir/ValueSet/administration-method-codes +0..1 DosageBodySite +0..1 MaximumDosePerTimePeriod + + Element: DoseAmount + Concept: TBD + Description: "The amount of medication taken per dose, as a quantity or range. Relative dose (e.g., per kg body weight or surface area) are indicated by specifying appropriate units (e.g., mg/kg or mg/m2 etc)." + Value: SimpleQuantity or Range + + Element: TimingOfDoses + Concept: TBD + Description: "When doses of medication should be administered." + Value: Timing + + Element: AsNeededIndicator + Concept: MTH#C1883728 + Description: "Indicates the pre-condition under which the drug or intervention should be used." + Value: boolean or CodeableConcept could be from http://hl7.org/fhir/ValueSet/medication-as-needed-reason + + Element: DosageInstructionsText + Concept: TBD + Description: "The directions (signetur) on the drug prescription or dispensing record." + Value: string + + Element: AdditionalDosageInstruction + Concept: MTH#C1644714 + Description: "Supplemental instructions - e.g. 'with meals'." + Value: CodeableConcept + + Element: DosageMethod + Concept: MTH#C1547585 + Description: "Technique for administering medication." + Value: CodeableConcept + + Element: DosageBodySite + Concept: MTH#C0229986 + Description: "The anatomic site at which medical intervention is applied." + Value: BodySiteCode + + Element: MaximumDosePerTimePeriod + Concept: TBD + Description: "The maximum amount of a medication to be taken in a given period of time (e.g., no more than x in any 24-hour period)" + Value: Ratio + + +Abstract Element: MedicationExposure +Based on: ActionPerformed +Description: "Abstract class representing medication exposure, independent of whether reported in a medication statement or medication administration. Does not include medication requests (prescriptions)." +1..1 Medication +0..1 Dosage +0..0 Method // because of Dosage.Method + + +EntryElement: MedicationStatement +Based on: MedicationExposure +Concept: SCT#416608005 "Drug therapy (procedure)" // TODO: investigate whether we need a new code or use a drug concept. +Description: "A record of the use of a medication. If the medication is given as part of a course of treatment, the PartOf attribute should refer to the CourseOfTreatment. +Although FHIR supports the asserter (information source) and date asserted, it does not have a place for the recorder (who recorded the statement). SHR adds the recorder as an extension, as part of standardizing clinical statements. +Medication not taken has changed from DSTU2 and STU3 to R4. In R4, status and statusReason are used to indicate medications not taken. SHR does not allow the MedicationStatement to represent not taking a drug, fixing taken to yes (y), and setting the cardinality for reasonNotTaken to 0..0. Status values can be used to indicated 'stopped' or 'not taken' if those values are available in a given FHIR version. +ReasonCode is a choice of CodeableConcept or ref(Condition) in DSTU2, and limited to one reason. In STU3 and R4, there can be multiple reason codes, and multiple reason references, simultaneously." + InformationSource value is type PersonOrOrganization + SubjectOfRecord value is type ref(Patient) // no Group in DSTU2 +1..1 StatementDateTime // us-core required +0..1 Category should be from http://hl7.org/fhir/ValueSet/medication-statement-category + Status from http://hl7.org/fhir/ValueSet/medication-statement-status +0..1 ReasonCode // Upper cardinality imposed by DSTU 2 +0..1 ReasonReference value is type ref(Condition) +0..0 Participation + RelatedRequest value is type ReferralOrProcedureOrMedicationRequest // or CarePlan +0..* TreatmentIntent +0..* TerminationReason from MedicationTerminationReasonVS + + +EntryElement: MedicationAdministration +Based on: MedicationExposure +Description: "A record of the use of a medication. If the medication is given as part of a course of treatment, the PartOf attribute should refer to the CourseOfTreatment. +Although FHIR MedicationAdministration supports date of administration and performer, it lacks common provenance elements, creation date, asserter, and recorder. These are supported as optional extensions. +FHIR DSTU2 lacks a category attribute, which is provided as an extension in that version. +SHR does not allow the 'not given' attributes from DSTU2 and STU3, since they are dropped in R4. The status element is used to document medications not given." + SubjectOfRecord value is type ref(Patient) // no Group in DSTU2 +0..1 Category should be from http://hl7.org/fhir/ValueSet/medication-admin-category + Status from http://hl7.org/fhir/ValueSet/medication-admin-status +0..1 Participation + Participation.Participant value is type PatientOrPractitionerOrRelatedPerson // DSTU 2 change (max cardinality = 1), also, DSTU 2 participant excludes Device +0..0 Participation.ParticipationType + RelatedRequest value is type ref(MedicationRequest) + +Element: MedicationDispense +Based on: MedicationExposure +Description: "Indicates that a medication product has been dispensed for a named person/patient. This includes a description of the medication product (supply) provided and the instructions for administering the medication. The medication dispense is the result of a pharmacy system responding to a medication order." +// TODO: Attributes from FHIR needed +// TODO: Mapping needed + +// Move to behavior? +EntryElement: MedicationNonadherence +Based on: CodedNonLaboratoryObservation // possibly Condition, with start/stop, severity of nonadherence? +Description: "Information on the ability and cooperation of the patient in taking medicine or supplement as recommended or prescribed. This includes correct timing, dosage, and frequency. The SubjectOfInformation can reference a specific medication. + +Modeling note: MedicationAdherence could be attached to MedicationStatement directly as an extension, but modeling as an observation avoids creating an extension and allows this observation to be made at any time, independent of any specific medication." + Code is MTH#C0746935 "Medication Nonadherence" + DataValue from QualitativeFrequencyVS +0..1 SubjectOfInformation value is type ref(MedicationExposure) + Components.ObservationComponent +includes 0..* MedicationNonAdherenceReason + + Element: MedicationNonAdherenceReason + Based on: CodedObservationComponent + Description: "Reason that patient did not adhere to a medication regimen." + Code is TBD#TBD + DataValue from MedicationNonAdherenceReasonVS + + +EntryElement: MedicationRequest +Based on: ActionRequested +Description: "An order for a medication to be dispensed and instructions for use. +Value sets for status are in direct conflict between DSTU2 Argonaut and STU3 US-Core. +Category does not exist in DSTU2 and is provided as an extension. +Intent was added in STU3 and is provided as an extension with required binding." + SubjectOfRecord value is type ref(Patient) +1..1 Medication +0..1 Dosage +1..1 Author value is type ref(Practitioner) + Status //from http://hl7.org/fhir/ValueSet/medication-request-status + // incompatible value sets between DSTU2 Argonaut and STU3 + // Cannot override value set constraint from http://hl7.org/fhir/ValueSet/medication-order-status to http://hl7.org/fhir/ValueSet/medication-request-status + PriorityCode from http://hl7.org/fhir/ValueSet/medication-request-priority + Type should be from http://hl7.org/fhir/ValueSet/medication-admin-category + RequestIntent from http://hl7.org/fhir/ValueSet/medication-request-intent +1..1 StatementDateTime + ExpectedPerformanceTime value is type TimePeriod +0..0 ExpectedPerformerType + Recipient value is type ref(Organization) +0..1 NumberOfRefillsAllowed +0..1 QuantityPerDispense +0..1 SupplyDuration +0..1 SubstitutionAllowed +0..1 SubstitutionReason from +http://hl7.org/fhir/ValueSet/v3-SubstanceAdminSubstitutionReason +0..1 ReasonCode could be from http://hl7.org/fhir/ValueSet/condition-code // Upper cardinality of 1 imposed by DSTU 2 +0..1 ReasonReference value is type ref(Condition) +0..0 CommunicationMethod // not needed +0..1 Annotation // upper card restricted by us-core-medicationrequest + + Element: NumberOfRefillsAllowed + Concept: TBD + Description: "The maximum number of times the dispense can be repeated. For medication dispense, this integer does NOT include the original order dispense. This means that if an order indicates dispense 30 tablets plus 3 repeats, then the order can be dispensed a total of 4 times and the patient can receive a total of 120 tablets." + Value: positiveInt // should be unsignedInt, but that causes a mapping error in FHIR 3.0 + + Element: QuantityPerDispense + Concept: TBD + Description: "The amount that is to be dispensed for one fill." + Value: SimpleQuantity + + Element: SupplyDuration + Concept: TBD + Description: "Identifies the period time over which the supplied product is expected to be used, or the length of time the dispense is expected to last." + Value: Duration + + Element: SubstitutionAllowed + Concept: TBD + Description: "Whether substitution is allowed or not." + Value: boolean + + Element: SubstitutionReason + Concept: TBD + Description: "Why should (not) substitution be made." + Value: CodeableConcept + \ No newline at end of file diff --git a/spec/shr_medication_map_dstu2.txt b/spec/shr_medication_map_dstu2.txt new file mode 100644 index 00000000..c0ff0d95 --- /dev/null +++ b/spec/shr_medication_map_dstu2.txt @@ -0,0 +1,123 @@ +Grammar: Map 5.1 +Namespace: shr.core +Target: FHIR_DSTU_2 + +/* DSTU 2 change (mapping target does not exist) +Dosage maps to Dosage: + DoseAmount maps to dose[x] + TimingOfDoses maps to timing + AsNeededIndicator maps to asNeeded[x] + DosageInstructionsText maps to text + AdditionalDosageInstruction maps to additionalInstruction + RouteIntoBody maps to route + DosageMethod maps to method + DosageBodySite.BodySiteCode maps to site + MaximumDosePerTimePeriod maps to maxDosePerPeriod +*/ + +MedicationStatement maps to http://fhir.org/guides/argonaut/StructureDefinition/argo-medicationstatement: + Identifier maps to identifier + InformationSource maps to informationSource + StatementDateTime maps to dateAsserted // slight semantic difference? + SubjectOfRecord maps to patient + constrain wasNotTaken to 0..0 + constrain reasonNotTaken to 0..0 + constrain dosage to 0..1 +// DSTU 2 change (mapping target does not exist) +// Dosage maps to dosage + Medication maps to medication[x] +// DSTU 2 change (no such attribute) +// Category maps to category +// DSTU 2 change (no such attribute) +// fix taken to #y + ReasonCode maps to reasonForUse[x] +// ReasonReference maps to reasonForUse[x] +// ReasonReference maps to reason[x] +// TODO: above mapping triggers a bug: ERROR shr: Cannot make choice element explicit at MedicationOrder:medication-MedicationRequest.reason[x]. Could not find compatible type match for: Condition. ERROR_CODE:????? (module=shr-fhir-export, shrId=medication.MedicationRequest, mappingRule="ReasonReference maps to reasonForUse[x]") + OccurrenceTimeOrPeriod maps to effective[x] + Status maps to status +// DSTU 2 change (added Dosage as in-line element) + Dosage.DoseAmount maps to dosage.quantity[x] + Dosage.TimingOfDoses maps to dosage.timing + Dosage.AsNeededIndicator maps to dosage.asNeeded[x] + Dosage.DosageInstructionsText maps to dosage.text +// DSTU 2 change (no such attribute) +// AdditionalDosageInstruction maps to additionalInstruction + Dosage.RouteIntoBody maps to dosage.route + Dosage.DosageMethod maps to dosage.method + Dosage.DosageBodySite.BodySiteCode maps to dosage.site[x] + Dosage.MaximumDosePerTimePeriod maps to dosage.maxDosePerPeriod + +MedicationAdministration maps to MedicationAdministration: + Identifier maps to identifier + SubjectOfRecord maps to patient + // DSTU 2 change (name change) + CareContext maps to encounter + RelatedRequest maps to prescription + // DSTU 2 change (name change) + constrain wasNotGiven to 0..0 + constrain reasonNotGiven to 0..0 + // DSTU 2 change (mapping target does not exist) +// Dosage maps to dosage + Medication maps to medication[x] + // DSTU 2 change (no such attribute) +// Category maps to category +// DSTU 2 change (name change) + ReasonCode maps to reasonGiven + OccurrenceTimeOrPeriod maps to effectiveTime[x] + Status maps to status + // DSTU 2 change (more restrictive type) + Participation.Participant maps to practitioner + // DSTU 2 change (no such attribute) +// Participation.OnBehalfOf maps to performer.onBehalfOf +// DSTU 2 change (added Dosage as in-line element) + Dosage.DoseAmount.SimpleQuantity maps to dosage.quantity + Dosage.RouteIntoBody maps to dosage.route + Dosage.DosageMethod maps to dosage.method + Dosage.DosageBodySite.BodySiteCode maps to dosage.site[x] +// TODO - represent rate and DosageBodySite ref(BodySite) + + +MedicationRequest maps to http://fhir.org/guides/argonaut/StructureDefinition/argo-medicationorder: + SubjectOfRecord maps to patient + CareContext maps to encounter + StatementDateTime maps to dateWritten + Identifier maps to identifier + Author maps to prescriber + RequestIntent maps to extension + Medication maps to medication[x] + NumberOfRefillsAllowed maps to dispenseRequest.numberOfRepeatsAllowed + QuantityPerDispense maps to dispenseRequest.quantity + SupplyDuration maps to dispenseRequest.expectedSupplyDuration + constrain dosageInstruction to 0..1 + // DSTU 2 change (name change) + ReasonCode maps to reason[x] +// ReasonReference maps to reason[x] +// TODO: above mapping triggers a bug: ERROR shr: Cannot make choice element explicit at MedicationOrder:medication-MedicationRequest.reason[x]. Could not find compatible type match for: Condition. ERROR_CODE:????? (module=shr-fhir-export, shrId=medication.MedicationRequest, mappingRule="ReasonReference maps to reason[x]") + Status maps to status + ExpectedPerformanceTime maps to dispenseRequest.validityPeriod + // DSTU 2 change (no such attribute) +// PriorityCode maps to priority +// DSTU 2 change (different data type) + Annotation.Text maps to note + // DSTU 2 change (no such attribute) + constrain note to 0..1 + // DSTU 2 change (mapping target does not exist) +// Dosage maps to dosageInstruction +// DSTU 2 change (added Dosage as in-line element) + Dosage.DoseAmount maps to dosageInstruction.dose[x] + Dosage.TimingOfDoses maps to dosageInstruction.timing + Dosage.AsNeededIndicator maps to dosageInstruction.asNeeded[x] + Dosage.DosageInstructionsText maps to dosageInstruction.text + // DSTU 2 change (no such attribute) +// AdditionalDosageInstruction maps to additionalInstruction + Dosage.RouteIntoBody maps to dosageInstruction.route + Dosage.DosageMethod maps to dosageInstruction.method + Dosage.DosageBodySite.BodySiteCode maps to dosageInstruction.site[x] + Dosage.MaximumDosePerTimePeriod maps to dosageInstruction.maxDosePerPeriod + SubstitutionAllowed maps to substitution.extension + SubstitutionReason maps to substitution.reason + + + + \ No newline at end of file diff --git a/spec/shr_medication_map_stu3.txt b/spec/shr_medication_map_stu3.txt new file mode 100644 index 00000000..7da53a5f --- /dev/null +++ b/spec/shr_medication_map_stu3.txt @@ -0,0 +1,75 @@ +Grammar: Map 5.1 +Namespace: shr.core +Target: FHIR_STU_3 + +Dosage maps to Dosage: + DoseAmount maps to dose[x] + TimingOfDoses maps to timing + AsNeededIndicator maps to asNeeded[x] + DosageInstructionsText maps to text + AdditionalDosageInstruction maps to additionalInstruction + RouteIntoBody maps to route + DosageMethod maps to method + DosageBodySite.BodySiteCode maps to site + MaximumDosePerTimePeriod maps to maxDosePerPeriod + +MedicationStatement maps to http://hl7.org/fhir/us/core/StructureDefinition/us-core-medicationstatement: + Identifier maps to identifier + InformationSource maps to informationSource + StatementDateTime maps to dateAsserted + SubjectOfRecord maps to subject + constrain reasonNotTaken to 0..0 + constrain dosage to 0..1 + Dosage maps to dosage + Medication maps to medication[x] + Category maps to category + fix taken to #y + ReasonCode maps to reasonCode + OccurrenceTimeOrPeriod maps to effective[x] + Status maps to status + CareContext maps to context + RelatedRequest maps to basedOn + +MedicationAdministration maps to MedicationAdministration: + Identifier maps to identifier + SubjectOfRecord maps to subject + CareContext maps to context + RelatedRequest maps to prescription + constrain notGiven to 0..0 + constrain reasonNotGiven to 0..0 + Dosage maps to dosage + Medication maps to medication[x] + Category maps to category + ReasonCode maps to reasonCode + OccurrenceTimeOrPeriod maps to effective[x] + Status maps to status + Participation maps to performer + Participation.Participant maps to performer.actor +// Participation.ParticipationType maps to performer.role (no role in med administration!) + Participation.OnBehalfOf maps to performer.onBehalfOf + + +MedicationRequest maps to http://hl7.org/fhir/us/core/StructureDefinition/us-core-medicationrequest: + SubjectOfRecord maps to subject + CareContext maps to context + StatementDateTime maps to authoredOn + Identifier maps to identifier + Author maps to requester + RequestIntent maps to intent + Medication maps to medication[x] + NumberOfRefillsAllowed maps to dispenseRequest.numberOfRepeatsAllowed + QuantityPerDispense maps to dispenseRequest.quantity + SupplyDuration maps to dispenseRequest.expectedSupplyDuration + constrain dosageInstruction to 0..1 + Dosage maps to dosageInstruction + ReasonCode maps to reasonCode + Status maps to status + ExpectedPerformanceTime maps to dispenseRequest.validityPeriod + PriorityCode maps to priority + Annotation maps to note + Recipient maps to dispenseRequest.performer + constrain note to 0..1 + SubstitutionAllowed maps to substitution.allowed + SubstitutionReason maps to substitution.reason + Type maps to category + \ No newline at end of file diff --git a/spec/cimi_medication_vs.txt b/spec/shr_medication_vs.txt similarity index 97% rename from spec/cimi_medication_vs.txt rename to spec/shr_medication_vs.txt index 864670ea..e7c784bb 100644 --- a/spec/cimi_medication_vs.txt +++ b/spec/shr_medication_vs.txt @@ -1,5 +1,5 @@ Grammar: ValueSet 5.0 -Namespace: cimi.medication +Namespace: shr.core CodeSystem: MTH = http://ncimeta.nci.nih.gov CodeSystem: RXN = http://www.nlm.nih.gov/research/umls/rxnorm @@ -38,7 +38,7 @@ ValueSet: MedicationChangeTypeVS #swap "Switch from one medication (or set of medications) to another" #stop "Medication stopped" -ValueSet: MedicationChangeReasonVS +ValueSet: MedicationTerminationReasonVS #not_needed "Do not need it any more, condition abated" #finished "Course of treatment complete" #ineffective "MTH #C3661846 Medication not effective." diff --git a/spec/shr_occupation.txt b/spec/shr_occupation.txt deleted file mode 100644 index 5583c5b1..00000000 --- a/spec/shr_occupation.txt +++ /dev/null @@ -1,308 +0,0 @@ -Grammar: DataElement 5.0 -Namespace: shr.occupation -Description: "Patient’s or family member's work information." -Uses: shr.core, shr.base, cimi.core, cimi.context, cimi.topic, cimi.statement, cimi.composition, cimi.entity, cimi.element, cimi.encounter - -CodeSystem: LNC = http://loinc.org -CodeSystem: MTH = http://ncimeta.nci.nih.gov -CodeSystem: UCUM = http://unitsofmeasure.org -CodeSystem: OBSCAT = http://hl7.org/fhir/observation-category - -EntryElement: OccupationalDataComposition -Concept: LNC#74166-0 -Based on: Composition -Description: "Current and past activities for profit, wages, salary, or as a service to others." -1..1 Section is type OccupationalDataSection - -Element: OccupationalDataSection -Concept: TBD -Based on: Section -Description: "Single section in the current OccupationalDataComposition, containing the person's history of employment and occupation, past and present." - ClinicalStatement -includes 0..* HistoryOfEmploymentStatus -includes 0..* DateOfRetirement -includes 0..* CombatZonePeriod -includes 0..1 UsualOccupation -includes 0..* PastOrPresentOccupation - -EntryElement: HistoryOfEmploymentStatus -Based on: CodedSocialHistoryObservation -Concept: LNC#74165-2 "HistoryOfEmploymentStatus" -Description: "A person’s state of being employed during the time period specified. -Generally, employment status refers to whether or not a person has a job (e.g. employed, unemployed, not in labor force). In a healthcare setting employment status may be used to determine appropriate probing questions for occupational hazards and occupational history. For example, someone who is unemployed or has chosen not to work may be prompted to provide information about previous jobs. Employment status is not the same as work classification, which describes characteristics of a given job such as self-employed." -0..0 SubjectIfNotPersonOfRecord - ObservationTopic.TopicCode is LNC#74165-2 "HistoryOfEmploymentStatus" - ObservationContext.ResultValue value is type CodeableConcept - ObservationContext.ResultValue from http://hl7.org/fhir/ValueSet/employment-status-odh -0..0 ObservationTopic.EvaluationComponent -0..0 ObservationTopic.Focus - -EntryElement: DateOfRetirement -Based on: SocialHistoryObservation -Concept: LNC#87510-4 "Date of Retirement" -Description: "If present, the patient is retired, and this observation records the retirement date. -This is a self-identified statement about the date of being retired as self-identified by the patient. A person can be both retired and employed; most often, a person would be retired from one job and employed in another job." -0..0 SubjectIfNotPersonOfRecord - ObservationTopic.TopicCode is LNC#87510-4 "Date of Retirement" - ObservationContext.ResultValue value is type dateTime -0..0 ObservationTopic.EvaluationComponent -0..0 ObservationContext.RelevantTime // The result value contains the date of retirement, so having a relevant time would be redundant. -0..0 ObservationTopic.Focus - -EntryElement: CombatZonePeriod -Based on: SocialHistoryObservation -Concept: LNC#87511-2 -Description: "Indicates the date range(s) an individual hs worked in what is considered a combat or hazardous duty zone; both civilian and military." -0..0 SubjectIfNotPersonOfRecord - ObservationTopic.TopicCode is LNC#87511-2 - ObservationContext.ResultValue value is type TimePeriod -0..0 ObservationTopic.EvaluationComponent -0..0 ObservationContext.RelevantTime // The result value contains the time period of combat zone activity, so the relevant time would be redundant. -0..0 ObservationTopic.Focus // only patient - - -EntryElement: UsualOccupation -Based on: CodedSocialHistoryObservation -Concept: LNC#21843-8 -Description: "The type of work a person has held for the longest duration during his or her working history at the point in time the statement is recorded." -// We'll need to determine the fix here -- US Core requires Subject to be a patient, but ODH allows patient or related person - ObservationTopic.TopicCode is LNC#21843-8 - ObservationContext.ResultValue could be from http://hl7.org/fhir/ValueSet/occupation-cdc-census-2010 // defined in FHIR 3.2 and not found in 3.0.1 - ObservationTopic.Focus value is type CodeableConcept - ObservationTopic.Focus from http://hl7.org/fhir/ValueSet/relatedperson-relationshiptype - ObservationTopic.EvaluationComponent -includes 1..1 UsualIndustry -includes 0..1 UsualOccupationDuration -1..1 ObservationContext.RelevantTime - ObservationContext.RelevantTime value is type TimePeriod - - -/* UsualOccupation is in the value element - Element: UsualOccupation - Based on: CodedEvaluationComponent - Concept: LNC#21843-8 "History of Usual Occupation" // Occupation is LNC#74287-4 - Description: "A person's work or business" - Value: CodeableConcept could be from http://hl7.org/fhir/ValueSet/occupation-cdc-census-2010 // VS defined in FHIR 3.2 and not found in 3.0.1 -*/ - Element: UsualIndustry - Based on: CodedEvaluationComponent - Concept: LNC#21844-6 "History of Usual industry" - Description: "The industry (type of business) which the subject has worked in for the longest duration while in the usual occupation. - For example, a person who has spent 30 years as a secretary in various industries, but mostly in construction, would record a usual occupation of secretary and a usual industry of construction." // "A history of this observation is not retained. Actually past versions of the observation could be retained, but the panel should refer to the latest one only. - Value: CodeableConcept could be from http://hl7.org/fhir/ValueSet/industry-cdc-census-2010 // defined in FHIR 3.2 and not found in 3.0.1 - TopicCode is LNC#21844-6 "History of Usual industry" - - Element: UsualOccupationDuration - Based on: EvaluationComponent - Concept: LNC#74163-7 "Usual occupation duration" - Description: "The total time spent on an activity, inclusive of all time intervals, whether continuous or interrupted." - Value: Quantity with units UCUM#a - TopicCode is LNC#74163-7 "Usual occupation duration" - -EntryElement: PastOrPresentOccupation -Based on: CodedSocialHistoryObservation -Concept: LNC#11341-5 "History of Occupation" -Description: "A single job, past or present. The relevant time is the period the job was held." - ObservationTopic.TopicCode is LNC#11341-5 "History of Occupation" - ObservationContext.ResultValue could be from http://hl7.org/fhir/ValueSet/occupation-cdc-census-2010 -0..1 Employer // must be extension; cannot be a result value or an evaluation component because the value is a reference to Person or Organization - ObservationTopic.Focus value is type CodeableConcept - ObservationTopic.Focus from http://hl7.org/fhir/ValueSet/relatedperson-relationshiptype - ObservationTopic.EvaluationComponent -includes 0..1 PastOrPresentIndustry -includes 0..1 WorkClassification -includes 0..1 SupervisoryLevel -includes 0..* JobDuty -includes 0..* OccupationalHazard -includes 0..1 WorkSchedule -includes 0..1 WeeklyWorkDays -includes 0..1 DailyWorkHours -1..1 ObservationContext.RelevantTime - ObservationContext.RelevantTime value is type TimePeriod - -// Question -- organization only, or person or organization - Element: Employer - Based on: Role - Concept: SCT#394571004 "Employer (person)" - Description: "A person or organization that hires the services of another." - Value: ref(Person) or ref(Organization) - - Element: PastOrPresentIndustry - Based on: CodedEvaluationComponent - Concept: LNC#86188-0 - Description: "The type of business (industry) in which the subject currently holds or has held a job in the past." - Value: CodeableConcept could be from http://hl7.org/fhir/ValueSet/industry-cdc-census-2010 // defined in FHIR 3.2 and not found in 3.0.1 - TopicCode is LNC#86188-0 - - Element: WorkClassification - Based on: CodedEvaluationComponent - Concept: LNC#85104-8 "Compensation and sector employment type" - Description: "Employment attributes for a given job. - This specifies information about the worker’s job, such as self-employed or unpaid, and is similar to the U.S. Bureau of Labor Statistics ‘class of worker’ and the International Labor Organization ‘classification of status in employment’. Knowing a patient is self-employed, for example, can assist in discussing return-to-work options." - Value: CodeableConcept could be from http://hl7.org/fhir/ValueSet/work-classification-odh - TopicCode is LNC#85104-8 "Compensation and sector employment type" - - Element: SupervisoryLevel - Based on: CodedEvaluationComponent - Concept: LNC#87707-6 - Description: "The supervisory or management responsibilities for an individual’s job. For military jobs, this is pay grade." - Value: CodeableConcept could be from http://hl7.org/fhir/ValueSet/supervisory-level-odh-us - TopicCode is LNC#87707-6 - - Element: JobDuty - Based on: EvaluationComponent - Concept: LNC#63761-1 - Description: "Regular actions performed at work. A person may have the occupation of 'construction laborer' and his specific job duty to carry construction supplies." - Value: string - 0..0 ReferenceRange - TopicCode is LNC#63761-1 - - Element: OccupationalHazard - Based on: EvaluationComponent - Concept: LNC#87729-0 - Description: "Actual contact or interaction with a specific hazard that increases an individual’s risk of a detrimental physical or mental health outcome (e.g., ingestion or inhalation of a toxic chemical). - Information on an exposure may include the measurement of duration/intensity of contact or interaction with the specific hazard." - Value: string - 0..0 ReferenceRange - TopicCode is LNC#87729-0 - - Element: WorkSchedule - Based on: CodedEvaluationComponent - Concept: LNC#74159-5 - Description: "An individual's typical arrangement of working hours for an occupation. - For example, work schedule may capture that an individual typically works a regular day shift, evening shift, or night shift. It can also specify if an individual has another type of schedule, such as a rotating shift, split shift, etc." - Value: CodeableConcept could be from http://hl7.org/fhir/ValueSet/work-schedule-odh - TopicCode is LNC#74159-5 - - Element: WeeklyWorkDays - Based on: EvaluationComponent - Concept: LNC#74160-3 - Description: "The typical number of days per week that a person spends performing their duties for work. - This information is most useful coupled with daily work hours and helps to reveal compressed schedules or a 7-day work-week." - Value: Quantity with units UCUM#d - 0..0 ReferenceRange - TopicCode is LNC#74160-3 - - Element: DailyWorkHours - Based on: EvaluationComponent - Concept: LNC#87512-0 - Description: "The typical number of hours in a day that a person spends performing their duties for work. - This information is most useful coupled with weekly work days and helps to reveal compressed schedules, long work hours, and overtime." - Value: Quantity with units UCUM#h - 0..0 ReferenceRange - TopicCode is LNC#87512-0 - -Element: SocialHistoryObservation -Based on: FindingStatement -Description: "A simplified observation for social histories." -// 0..0 SourceOfInformation -0..0 Recorded -0..0 Signed - StatementTopic is type ObservationTopic - StatementContext is type ObservationContext - SubjectIfNotPersonOfRecord value is type ref(RelatedPerson) - SourceOfInformation value is type AnyPersonOrOrganization // mapped to performer (who made the observation) - ObservationTopic.Category is OBSCAT#social-history -0..0 ObservationTopic.FindingMethod -0..0 ObservationTopic.AnatomicalLocation -0..0 ObservationTopic.Precondition -0..0 ObservationTopic.ReferenceRange -0..0 ObservationTopic.PanelMembers -0..0 ObservationContext.ExceptionValue -0..0 ObservationContext.Interpretation -0..0 ObservationContext.Encounter -0..0 ObservationContext.DeltaFlag -0..0 ObservationTopic.Device -0..0 ObservationTopic.Specimen -0..0 ObservationTopic.Media - - -Element: CodedSocialHistoryObservation -Based on: SocialHistoryObservation -Description: "The result of social history questions, whose answer is expressed as a code." - ObservationContext.ResultValue value is type CodeableConcept -0..0 ObservationTopic.ReferenceRange - -/* -EntryElement: MilitaryServiceHistory -Based on: ComponentOnlyNonLaboratoryObservation -Description: "History of service in the US military." - ObservationTopic.Category is OBSCAT#social-history - ObservationTopic.TopicCode is MTH#C3714797 - ObservationTopic.EvaluationComponent -includes 1..1 MilitaryStatus -includes 0..1 MilitaryServiceDischargeStatus -includes 0..1 MilitaryBranch -includes 0..* MilitaryServiceEra -includes 0..1 ServiceConnectedDisability -//includes 0..1 TBD "MilitaryRank" -0..0 ObservationTopic.FindingMethod -0..0 ObservationTopic.AnatomicalLocation -0..0 ObservationTopic.Focus -0..0 ObservationTopic.Device -0..0 ObservationTopic.Precondition -0..0 ObservationContext.Interpretation -0..0 ObservationContext.RelevantTime -0..0 ObservationContext.Encounter -0..0 ObservationContext.DeltaFlag - - Element: MilitaryStatus - Concept: MTH#C1550416 - Based on: CodedEvaluationComponent - Description: "The current connection to the US military." - Value: CodeableConcept from MilitaryStatusVS - - Element: MilitaryServiceDischargeStatus - Concept: TBD - Based on: CodedEvaluationComponent - Description: "How the subject was formally discharged from the US Military." - Value: CodeableConcept from MilitaryServiceDischargeStatusVS - - Element: MilitaryBranch - Concept: MTH#C2129058 - Based on: CodedEvaluationComponent - Description: "The branch of the US military that the subject has served." - Value: CodeableConcept from USMilitaryBranchVS - - Element: MilitaryServiceEra - Concept: TBD - Based on: CodedEvaluationComponent - Description: "The time period of US military service." - Value: CodeableConcept from MilitaryServiceEraVS - - Element: ServiceConnectedDisability - Based on: EvaluationComponent - Concept: TBD - Description: "Percentage disability resulting from US Military Service." - Value: Quantity with units UCUM#% - 0..0 ReferenceRange - - -EntryElement: OccupationalDataSummary -Concept: LNC#74166-0 -Based on: Observation // Overall outer container could be a Composition. -Description: "Current and past activities for profit, wages, salary, or as a service to others." - ObservationTopic.TopicCode is LNC#74166-0 - ObservationTopic.Category is OBSCAT#social-history -0..0 ObservationTopic.EvaluationComponent - ObservationTopic.PanelMembers.Observation -includes 0..* HistoryOfEmploymentStatus -includes 0..* DateOfRetirement -includes 0..* CombatZonePeriod -includes 0..1 UsualOccupation -includes 0..* PastOrPresentOccupation -0..0 ObservationTopic.FindingMethod -0..0 ObservationTopic.AnatomicalLocation -0..0 ObservationTopic.Focus -0..0 ObservationTopic.Device -0..0 ObservationTopic.Specimen -0..0 ObservationTopic.Precondition -0..0 ObservationTopic.ReferenceRange -0..0 ObservationContext.ResultValue -0..0 ObservationContext.ExceptionValue -0..0 ObservationContext.Interpretation -0..0 ObservationContext.RelevantTime -0..0 ObservationContext.DeltaFlag -*/ - - diff --git a/spec/shr_occupation_map.txt b/spec/shr_occupation_map.txt deleted file mode 100644 index 457ab2d8..00000000 --- a/spec/shr_occupation_map.txt +++ /dev/null @@ -1,35 +0,0 @@ -Grammar: Map 5.1 -Namespace: shr.occupation -Target: FHIR_STU_3 - -// do not map to US Core Results -- Brett says that is only for labs -SocialHistoryObservation maps to Observation: - PersonOfRecord maps to subject -// SubjectIfNotPersonOfRecord.RelationshipToPersonOfRecord maps to http://hl7.org/fhir/StructureDefinition/observation-focal-subject - ObservationTopic.TopicCode maps to code - ObservationTopic.FindingMethod maps to method - ObservationTopic.Details maps to comment -// ObservationTopic.Media maps to extension - ObservationTopic.Category maps to category -// ObservationTopic.Precondition maps to extension - ObservationTopic.ReferenceRange maps to referenceRange - ObservationTopic.ReferenceRange.Range.LowerBound maps to referenceRange.low - ObservationTopic.ReferenceRange.Range.UpperBound maps to referenceRange.high - ObservationTopic.ReferenceRange.Type maps to referenceRange.type - ObservationTopic.ReferenceRange.ApplicableSubpopulation maps to referenceRange.appliesTo - ObservationTopic.ReferenceRange.ApplicableAgeRange maps to referenceRange.age - ObservationTopic.EvaluationComponent maps to component (slice on = coding.code; slice strategy = includes) - ObservationTopic.EvaluationComponent._Concept maps to component.code - ObservationTopic.EvaluationComponent.Value maps to component.value[x] - ObservationTopic.EvaluationComponent.ExceptionValue maps to component.dataAbsentReason - ObservationTopic.EvaluationComponent.Interpretation maps to component.interpretation - ObservationTopic.EvaluationComponent.ReferenceRange maps to component.referenceRange - constrain related to 0..0 -// ObservationContext.ContextCode maps to nothing // drop - ObservationContext.ResultValue maps to value[x] - ObservationContext.ExceptionValue maps to dataAbsentReason - ObservationContext.Interpretation maps to interpretation - ObservationContext.Issued maps to issued - ObservationContext.FindingStatus maps to status - ObservationContext.RelevantTime maps to effective[x] - ObservationContext.Encounter maps to context diff --git a/spec/shr_oncology.txt b/spec/shr_oncology.txt deleted file mode 100644 index cc0f3e66..00000000 --- a/spec/shr_oncology.txt +++ /dev/null @@ -1,545 +0,0 @@ -Grammar: DataElement 5.0 -Namespace: shr.oncology -Description: "SHR implementation of ASCO requirements." -Uses: shr.core, shr.base, cimi.core, cimi.element, cimi.context, cimi.topic, cimi.statement, cimi.entity - -CodeSystem: SCT = http://snomed.info/sct -CodeSystem: LNC = http://loinc.org -CodeSystem: MTH = http://ncimeta.nci.nih.gov -CodeSystem: UCUM = http://unitsofmeasure.org -CodeSystem: HGNC = http://www.genenames.org -CodeSystem: CAP = https://sdt.cap.org -CodeSystem: OBSCAT = http://hl7.org/fhir/observation-category - -EntryElement: BreastSite -Based on: AnatomicalLocation -Description: "A body site specific to the breast structure." -Value: CodeableConcept from BreastSiteVS -0..1 ClockDirection -0..1 DistanceFromBreastSiteToNipple -0..0 AnatomicalDirection - - Element: DistanceFromBreastSiteToNipple - Description: "Distance between the feature of interest (e.g., the tumor) and the nipple." - Value: Quantity with units UCUM#cm - -EntryElement: BreastSpecimen -Based on: Specimen -Description: "Specimen resulting from biopsy or excision of breast and surrounding tissue." - Type from BreastSpecimenTypeVS - CollectionSite value is type BreastSite - CollectionMethod from BreastSpecimenCollectionMethodVS - SourceSpecimen value is type BreastSpecimen -0..1 ColdIschemiaTime - - Element: ColdIschemiaTime - Concept: LNC#44778-9 - Description: "The time period between the chilling of a tissue or tissue sample and the time it is warmed. - CIMI Alignment: In CIMI Version 0.0.4, specimen processing is represented as a 'SpecimenProcessingPerformed' clinical statement, mapped to FHIR Procedure. However, specimen processing should actually map to FHIR Specimen.processing, part of the Specimen resource. It would be a difficult mapping exercise (beyond the scope of this IG) to express the mapping rule that any CIMI SpecimenProcessingPerformed clinical statement needs to mapped to FHIR by (1) finding the corresponding Specimen entity, and (2) mapping the content of (possibly multiple) SpecimenProcessingPerformed into the FHIR Specimen resource. To avoid this complexity, the breast cancer model expresses the cold ischemia time as an attribute of the BreastSpecimen rather than a separate procedure." - Value: TimePeriod - -EntryElement: BreastCancerPresenceStatement -Based on: ConditionPresenceStatement -Concept: SCT#126926005 "Neoplasm of breast (disorder)" -Description: "Diagnosis of cancer originating in the tissues of the breast, and potentially spread to other organs of the body." - ConditionTopic.TopicCode from BreastCancerTypeVS - ConditionPresenceContext.Stage.StageDetail value is type BreastCancerStage - ConditionTopic.FindingMethod should be from BreastCancerDetectionVS // can't change to 'could be' because us-core uses preferred binding - ConditionTopic.AnatomicalLocation is type BreastSite -0..1 MorphologyBehavior from MorphologyBehaviorVS - - Element: MorphologyBehavior - Concept: TBD - Description: "A description of the morphology and behavioral characteristics of the cancer." - Value: CodeableConcept - -// We need to add an example to the IG! -// Perhaps move timing prefix to component -// Perhaps make T, N, M separate observations -// Do we want to follow Travis' approach of putting the Cancer Staging Encounter Phase in Encounter? -Element: BreastCancerStageTopic -Based on: ObservationTopic -Description: "The topic class for describing a breast cancer staging observation." - TopicCode is MTH#C2216702 "Malignant Neoplasm of Breast Staging" -0..1 StageTimingPrefix - EvaluationComponent -includes 0..1 BreastCancerPrimaryTumorClassification -includes 0..1 BreastCancerRegionalNodesClassification -includes 0..1 BreastCancerDistantMetastasesClassification - PanelMembers.Observation -includes 0..1 HER2ReceptorStatus -includes 0..1 EstrogenReceptorStatus -includes 0..1 ProgesteroneReceptorStatus -includes 0..1 DCISNuclearGrade -includes 0..1 BreastCancerHistologicGrade -0..0 Focus // only one breast cancer per patient -0..0 ref(Device) -0..0 ref(Specimen) -0..0 Precondition -0..0 ReferenceRange - - Element: StageTimingPrefix - Concept: SCT#260869008 "Timing of stage" - Description: "Indicates when the staging was done, in terms of treatment landmarks." - Value: CodeableConcept from StageTimingPrefixVS - - Element: BreastCancerPrimaryTumorClassification - Concept: SCT#78873005 "T category" - Based on: CodedEvaluationComponent - Description: "The size and extent of the primary tumor, based on criteria defined by the staging system being used." - Value: CodeableConcept - 0..1 StageSuffix - - Element: BreastCancerRegionalNodesClassification - Concept: SCT#277206009 "N category" //RMB: was LNC#59525-6, which is specific to AJCC 7th edition - Based on: CodedEvaluationComponent - Description: "The presence of metastases in regional lymph nodes, based on criteria defined by the staging system being used." - Value: CodeableConcept - 0..1 StageSuffix - - Element: StageSuffix - Concept: TBD - Description: "A suffix used in conjuction with certain breast cancer stages, based on criteria defined by the staging system being used." - Value: CodeableConcept - - Element: BreastCancerDistantMetastasesClassification - Concept: SCT#277208005 "M category (observable entity)" //RMB: was LNC#59522-3, which is specific to AJCC 7th edition - Based on: CodedEvaluationComponent - Description: "The presence of distant metastases, based on criteria defined by the staging system being used." - Value: CodeableConcept - -EntryElement: BreastCancerStage -Based on: Observation -Concept: MTH#C2216702 "Malignant Neoplasm of Breast Staging" //Not LNC#21908-9 since that is AJCC-specific and also not breast cancer specific. We do however, give the LOINC list of stage values as the preferred codes. -Description: "The stage of a breast cancer. Different staging systems use different staging groups, so there are currently no terminology bindings associated with this class." - ObservationTopic is type BreastCancerStageTopic - ObservationContext.ResultValue value is type CodeableConcept - ObservationContext.ResultValue should be from http://loinc.org/vs/LL240-3 - - -EntryElement: DCISNuclearGrade -Concept: MTH#C18513 // What is the proper LOINC code? -Based on: SimpleCodedLaboratoryObservation -Description: "An evaluation of the size and shape of the nucleus in tumor cells and the percentage of tumor cells that are in the process of dividing or growing. Cancers with low nuclear grade grow and spread less quickly than cancers with high nuclear grade." - ObservationContext.ResultValue value is type CodeableConcept - ObservationContext.ResultValue.CodeableConcept from NuclearGradeVS - LaboratoryObservationTopic.Specimen is type BreastSpecimen - LaboratoryObservationTopic.TopicCode is MTH#C18513 - LaboratoryObservationTopic.DiagnosticService is #pathology - - -EntryElement: BreastCancerHistologicGrade -Concept: LNC#44648-4 -Based on: CodedLaboratoryObservation -Description: "The Elston Grade/Nottingham Score, representative of the aggressive potential of the tumor. Well differentiated cells (Grade 1) look similar to normal cells and are usually slow growing, while poorly differentiated cells (Grade 3) look very different than normal and are fast-growing." - ObservationContext.ResultValue value is type CodeableConcept - ObservationContext.ResultValue.CodeableConcept from NottinghamCombinedGradeVS - ObservationContext.ExceptionValue from NottinghamNullVS - LaboratoryObservationTopic.TopicCode is LNC#44648-4 - LaboratoryObservationTopic.Specimen is type BreastSpecimen - LaboratoryObservationTopic.DiagnosticService is #pathology - LaboratoryObservationTopic.EvaluationComponent -includes 0..1 TubuleFormationScore -includes 0..1 NuclearPleomorphismScore -includes 0..1 MitoticCountScore -0..0 LaboratoryObservationTopic.PanelMembers - -//RMB: the CAP form has two additional options for each of these subcomponents: "only microinvasion present" and "no residual invasive carcinoma", both of which are situations where a histologic grade wouldn't be assigned. Because the our exceptions value set doesn't handle these options (and possibly others related to other data elements, should we allow for a string option to contain reasons for missing data? Otherwise the expection value set might become unruly. - Element: TubuleFormationScore - Concept: LNC#85321-8 "Granular differentiation" // SHOULD BE LOINC - Based on: CodedEvaluationComponent - Description: "Glandular differentiation [Score] in Breast cancer specimen Qualitative by Nottingham." - Value: CodeableConcept from TubuleFormationScoreVS //TODO: Determine if it is better to use codes as opposed to a number 1, 2 or 3. Observations don't support integer or posInteger - ExceptionValue from NottinghamComponentNullVS - - Element: NuclearPleomorphismScore - Concept: LNC#44645-0 - Based on: CodedEvaluationComponent - Description: "Nuclear pleomorphism in Breast tumor Qualitative by Nottingham." - Value: CodeableConcept from NuclearPleomorphismScoreVS - ExceptionValue from NottinghamComponentNullVS - - Element: MitoticCountScore - Concept: LNC#85300-2 - Based on: CodedEvaluationComponent - Description: "Mitotic rate [Score] in Breast cancer specimen Qualitative by Nottingham." - Value: CodeableConcept from MitoticCountScoreVS // 1 to 3 //RMB: this shouldn't be different from TubuleFormationScore and NuclearPleomorphismScore. They have the same scoring mechanism. Suggest using local codes. - ExceptionValue from MitoticCountScoreNullVS - -EntryElement: EstrogenReceptorStatus -Based on: CodedLaboratoryObservation -Concept: LNC#16112-5 "Estrogen receptor [Interpretation] in Tissue" -Description: "Estrogen receptor alpha is the predominant estrogen receptor expressed in breast tissue and is overexpressed in around 50% of breast carcinomas. ER status (positive=present or overexpressed; negative=absent) is a factor in determining prognosis and treatment options. -The current approach is that positive/negative designation is a value, even though that value is (in fact) an interpretation of evidence (NuclearPositivity and AverageStainingIntensity)." - ObservationContext.ResultValue value is type CodeableConcept - ObservationContext.ResultValue.CodeableConcept from PositiveNegativeVS - LaboratoryObservationTopic.TopicCode is LNC#16112-5 - LaboratoryObservationTopic.DiagnosticService is #pathology - LaboratoryObservationTopic.Specimen is type BreastSpecimen - LaboratoryObservationTopic.EvaluationComponent -includes 0..1 NuclearPositivity -includes 0..1 AverageStainingIntensity -0..0 LaboratoryObservationTopic.PanelMembers -/* additional components from CAP form -includes 0..1 StainingControl -includes 0..1 PrimaryAntibody //from EstrogenAntibodyVS if covered -includes 0..1 AllredProportionScore -includes 0..1 AllredIntensityScore -includes 0..1 AllredTotalScore -includes 0..1 OtherReceptorScoringSystem -*/ - -EntryElement: ProgesteroneReceptorStatus -Based on: CodedLaboratoryObservation -Concept: LNC#16113-3 -Description: "Progesterone receptor status is a factor in determining prognosis and treatment options. The value is the percentage of cells that test (stain) positive for the presence of a receptor. The interpretation of positive or negative (found in the interpretation property) is based on the staining percentage, and may take into account the staining intensity. -Based on discussion with Cancer Interoperability Group subject matter experts, there was insufficient rationale to include the following components in the data model: StainingControl, PrimaryAntibody, Allred Score (both total and component scores). We are seeking feedback on whether or not those components should be included in this model." - ObservationContext.ResultValue value is type CodeableConcept - ObservationContext.ResultValue.CodeableConcept from PositiveNegativeVS - LaboratoryObservationTopic.TopicCode is LNC#16113-3 "Progesterone receptor [Interpretation] in Tissue" - LaboratoryObservationTopic.DiagnosticService is #pathology - LaboratoryObservationTopic.Specimen is type BreastSpecimen - LaboratoryObservationTopic.EvaluationComponent -includes 0..1 NuclearPositivity -includes 0..1 AverageStainingIntensity -0..0 LaboratoryObservationTopic.PanelMembers - - Element: NuclearPositivity - Based on: EvaluationComponent - Concept: TBD // apparently no LOINC code - Description: "The percentage of cells that test (stain) positive for the presence of a receptor. - We are seeking feedback on whether nuclear positivity should be an exact percentage or a range of percentages. As currently defined, an exact nuclear positivity could be represented by a zero-width range, where the lower and upper bounds would be the same number." - Value: Range - 0..0 ReferenceRange - - Element: AverageStainingIntensity - Concept: SCT#444775005 "Average intensity of positive staining neoplastic cells (observable entity)" - Based on: CodedEvaluationComponent - Description: "The degree or magnitude of staining (nuclear positivity) across cells in the specimen." - Value: CodeableConcept from StainingIntensityVS - -EntryElement: HER2ReceptorStatus -Based on: CodedLaboratoryObservation -Concept: LNC#48676-1 "HER2 [Interpretation] in Tissue" -Description: "HER2 receptor status. HER2 is a member of the human epidermal growth factor receptor family of proteins and is encoded by the ERBB2 oncogene. HER2 is overexpressed in 20-30% of breast tumors, and is associated with an aggressive clinical course and poor prognosis. HER2 status (positive=present or overexpressed; negative=absent) is a factor in determining prognosis and treatment options." - ObservationContext.ResultValue.CodeableConcept from PositiveNegativeEquivocalVS - LaboratoryObservationTopic.TopicCode is LNC#48676-1 "HER2 [Interpretation] in Tissue" - LaboratoryObservationTopic.DiagnosticService is #pathology - LaboratoryObservationTopic.Specimen is type BreastSpecimen -0..0 LaboratoryObservationTopic.Precondition -0..0 LaboratoryObservationTopic.FindingMethod -0..0 LaboratoryObservationTopic.EvaluationComponent - LaboratoryObservationTopic.PanelMembers.Observation -includes 0..* HER2byIHC -includes 0..* HER2byFISH - -EntryElement: HER2byIHC -// MK 7/14/2018 separated null value from non-null values. -Based on: CodedLaboratoryObservation -Concept: LNC#85319-2 -Description: "HER2 presence in Breast cancer specimen by Immunohistochemistry (IHC). " - ObservationContext.ResultValue.CodeableConcept from HER2byIHCScoreVS - ObservationContext.ExceptionValue from HER2byIHCScoreNullVS - ObservationContext.Interpretation from PositiveNegativeEquivocalVS - LaboratoryObservationTopic.TopicCode is LNC#85319-2 "HER2 [Presence] in Breast cancer specimen by Immune stain" -0..0 LaboratoryObservationTopic.FindingMethod // pre-coordinated in the TopicCode - LaboratoryObservationTopic.DiagnosticService is #pathology -0..0 LaboratoryObservationTopic.Precondition - LaboratoryObservationTopic.Specimen is type BreastSpecimen - LaboratoryObservationTopic.EvaluationComponent -includes 0..1 CompleteMembraneStainingPercent -0..0 LaboratoryObservationTopic.PanelMembers - - Element: CompleteMembraneStainingPercent - Based on: EvaluationComponent - Concept: LNC#85328-3 "Cells.HER2 uniform intense membrane staining/100 cells" - Description: "Percentage of cells with uniform intense complete membrane staining." - Value: Quantity with units UCUM#% // TODO: Percentage causes CLI error - 0..0 ReferenceRange - 0..0 Interpretation - -EntryElement: HER2byFISH -Based on: LaboratoryObservation -Concept: LNC#85318-4 // Corrected 5/12/2018 by MK -Description: "HER2 receptor status as determined by single-probe or dual-probe Fluorescence In Situ Hybridization (FISH)." -0..0 ObservationContext.ResultValue -0..0 ObservationContext.ExceptionValue - LaboratoryObservationTopic.TopicCode is LNC#85318-4 "HER2 [Presence] in Breast cancer specimen by FISH" - LaboratoryObservationTopic.FindingMethod from HER2FISHMethodVS // single or double probe - ObservationContext.Interpretation from PositiveNegativeEquivocalVS - LaboratoryObservationTopic.DiagnosticService is #pathology -0..0 LaboratoryObservationTopic.Precondition - LaboratoryObservationTopic.Specimen is type BreastSpecimen - LaboratoryObservationTopic.EvaluationComponent -includes 0..1 AverageHER2SignalsPerCell -includes 0..1 AverageCEP17SignalsPerCell -includes 0..1 HER2toCEP17Ratio -0..0 LaboratoryObservationTopic.PanelMembers - - Element: AverageHER2SignalsPerCell - Based on: EvaluationComponent - Concept: LNC#74860-8 - Description: "Average number of HER2 signals per cell" - Value: Quantity - 0..0 ReferenceRange - - Element: AverageCEP17SignalsPerCell - Based on: EvaluationComponent - Concept: LNC#74861-6 - Description: "Average number CEP17 signals per cell (dual probe only)" - Value: Quantity - 0..0 ReferenceRange - - Element: HER2toCEP17Ratio - Based on: EvaluationComponent - Concept: LNC#49683-6 - Description: "HER2 to CEP17 Ratio (dual probe only)" - Value: Quantity - 0..0 ReferenceRange - -EntryElement: OncotypeDxInvasiveRecurrenceScore -Based on: SimpleLaboratoryObservation -Concept: MTH#C1709318 -Description: "The Oncotype DX test for invasive breast cancer examines the activity of 21 genes in a patient’s breast tumor tissue to provide personalized information for tailoring treatment based on the biology of their individual disease. The value from 0 to 100 indicates the estimated risk of recurrence, with the highest risk indicated by a score greater than 31. -No LOINC code currently exists for this test. We are seeking feedback on the value of separating OncotypeDx scores for DCIS and invasive breast carcinomas. Does it make more sense to report the OncotypeDx as a single score, regardless of the type of cancer?" - ObservationContext.ResultValue value is type Quantity - ObservationContext.ResultValue.Quantity with units UCUM#1 - LaboratoryObservationTopic.TopicCode is MTH#C1709318 - ObservationContext.Interpretation from RecurrenceRiskScoreInterpretationVS - LaboratoryObservationTopic.DiagnosticService is #pathology - LaboratoryObservationTopic.Specimen is type BreastSpecimen - - -EntryElement: OncotypeDxDCISRecurrenceScore -Based on: SimpleLaboratoryObservation -Concept: MTH#C3898101 -Description: "The Oncotype DX test for DCIS (Ductal Carcinoma in Situ) breast cancer. Risk scores range from 0 to 100 with the following interpretations: 0-38: Low-Risk, 39-54: Intermediate-Risk, 55+: High-Risk. -No LOINC code currently exists for this test. We are seeking feedback on the value of separating OncotypeDx scores for DCIS and invasive breast carcinomas. Does it make more sense to report the OncotypeDx as a single score, regardless of the type of cancer?" - ObservationContext.ResultValue value is type Quantity - ObservationContext.ResultValue.Quantity with units UCUM#1 - LaboratoryObservationTopic.TopicCode is MTH#C3898101 - ObservationContext.Interpretation from RecurrenceRiskScoreInterpretationVS - LaboratoryObservationTopic.DiagnosticService is #pathology - LaboratoryObservationTopic.Specimen is type BreastSpecimen - -EntryElement: ProsignaRecurrenceScore -Based on: SimpleLaboratoryObservation -Concept: LNC#76544-6 -Description: "Breast cancer genomic signature assay for 10-year risk of distant recurrence score calculated by Prosigna. -The Prosigna Score is reported on a 0-100 scale (referred to as ROR Score or Risk of Recurrence Score in the literature), which is correlated with the probability of distant recurrence at ten years for post-menopausal women with hormone receptor positive, early stage breast cancer." - ObservationContext.ResultValue value is type Quantity - ObservationContext.ResultValue.Quantity with units UCUM#1 - LaboratoryObservationTopic.TopicCode is LNC#76544-6 - ObservationContext.Interpretation from RecurrenceRiskScoreInterpretationVS - LaboratoryObservationTopic.DiagnosticService is #pathology - LaboratoryObservationTopic.Specimen is type BreastSpecimen - -EntryElement: MammaprintRecurrenceScore -Based on: SimpleLaboratoryObservation -Concept: MTH#C2827401 -Description: "Breast cancer genomic signature assay for 10-year risk of distant recurrence score calculated by Mammaprint. -In the United States, MammaPrint can only be used on cancers that are stage I or stage II, invasive, smaller than 5 centimeters, and estrogen-receptor-positive or -negative. Scores range from -1.0 to +1.0, with scores less than 0 indicating high risk, and scores greater than 0 indicating low risk. -The is currently no LOINC code for Mammaprint test." - ObservationContext.ResultValue value is type Quantity - LaboratoryObservationTopic.TopicCode is MTH#C2827401 - ObservationContext.Interpretation from RecurrenceRiskScoreInterpretationVS - LaboratoryObservationTopic.DiagnosticService is #pathology - LaboratoryObservationTopic.Specimen is type BreastSpecimen - - -/* - Element: Aneusomy - Based on: CodedEvaluationComponent - Concept: CAP#30478 - Description: "Aneusomy (as defined by vendor kit used)" - Value: CodeableConcept from YesNoVS - - Element: HeterogeneousSignals - Based on: CodedEvaluationComponent - Concept: CAP#30482 - Description: "Whether In Situ Hybridization signals were heterogeneous." - Value: CodeableConcept from YesNoVS - - Element: PercentageAmplified - Based on: EvaluationComponent - Concept: CAP#31073 - Description: "Percentage of cells with amplified HER2 signals" - Value: Quantity with units UCUM#% - - Element: NuclearPositivity - Based on: EvaluationComponent - Concept: TBD - Description: "The percentage of cells that test (stain) positive for the presence of a receptor." - Value: Range - - - Element: PrimaryAntibody - Based on: CodedEvaluationComponent - Concept: CAP#31092 - Description: "" - Value: CodeableConcept - - Element: StainingControl - Based on: CodedEvaluationComponent - Concept: CAP#25895 - Description: "Whether control cells were present." - Value: CodeableConcept from StainingControlVS if covered - - Element: AllredProportionScore - Concept: CAP#31054 - Based on: EvaluationComponent - Description: "Part of Allred scoring, based on the percentage of cells that stain for a receptor, on a scale of 0 to 5." - Value: Quantity with units UCUM#1 - - Element: AllredIntensityScore - Concept: CAP#29749 - Based on: EvaluationComponent - Description: "Part of the Allred scoring, based on the intensity of that staining, on a scale of 0 to 3." - Value: Quantity with units UCUM#1 - - Element: AllredTotalScore - Concept: CAP#31056 - Based on: EvaluationComponent - Description: "The total Allred score, the total of proportion and intensity scores, from 0 to 8." - Value: Quantity with units UCUM#1 // unsignedInt - limit to max of 8 - - Element: OtherReceptorScoringSystem - Concept: CAP#31062 - Based on: CodedEvaluationComponent - Description: "A scoring system other than Allred." - -EntryElement: TumorDimensions -Based on: SimpleCodedObservation -Concept: MTH#C4086369 -0..0 Value - TopicCode is TBD#TBD - ObservationTopic.DiagnosticService is #pathology - EvaluationComponent -includes 0..1 TumorPrimaryDimensionSize -includes 0..1 TumorSecondaryDimensionSize -includes 0..1 SizeOfGrossTumorBed - - Element: TumorPrimaryDimensionSize - Description: "The longest diameter of the primary tumor." - Based on: EvaluationComponent - Concept: TBD - Value: Quantity with units UCUM#mm - - Element: TumorSecondaryDimensionSize - Description: "The longest perpendicular diameter of the primary tumor." - Based on: EvaluationComponent - Concept: TBD - Value: Quantity with units UCUM#mm - - Element: SizeOfGrossTumorBed - Based on: EvaluationComponent - Concept: TBD - Description: "The largest dimension of the gross tumor bed/fibrotic area." - Value: Quantity with units UCUM#mm - - -EntryElement: TumorMargins -Based on: SimpleCodedObservation -Concept: MTH#C4086369 -Description: "The edge or border of the tissue removed in cancer surgery. The margin is described as negative or clean when the pathologist finds no cancer cells at the edge of the tissue, suggesting that all of the cancer has been removed. The margin is described as positive or involved when the pathologist finds cancer cells at the edge of the tissue, suggesting that all of the cancer has not been removed." -Value: CodeableConcept from PositiveNegativeVS - TopicCode is MTH#C4086369 - ObservationTopic.DiagnosticService is #pathology - EvaluationComponent -includes 0..1 TumorMarginDescription -includes 0..1 Cellularity // not sure this belongs here -includes 0..1 PercentageInSituCarcinoma // not sure this belongs here -// Do we need to record the method? whether the result of imaging, or study of a removed tumor after lumpectomy? - - Element: TumorMarginDescription - Concept: TBD - Based on: CodedEvaluationComponent - Description: "Description of the edge or border of tumor in situ by radiologist or of removed tumor by pathologist." - Value: CodeableConcept from TumorMarginDescriptionVS - - Element: Cellularity - Concept: MTH#C4055283 - Based on: EvaluationComponent - Description: "Percentage of cells in a sample that are cancerous" - Value: Quantity with units UCUM#% - - Element: PercentageInSituCarcinoma - Based on: EvaluationComponent - Concept: TBD - Description: "The percentage of the cancer that is in situ, as opposed to invading other tissues." - Value: Quantity with units UCUM#% - - - - Element: Ki-67LabelingIndex - Based on: SimpleCodedObservation - Concept: MTH#C4049944 - Description: "Ki-67 is a protein phosphatase whose expression is strongly associated with cell proliferation and encoded by the MKI67 gene. The Ki67 labeling index is the fraction of Ki-67-positive cells to total cells in a tumor specimen and may be useful for determining prognosis with respect to survival and disease recurrence. The more positive cells there are, the more quickly they are dividing and forming new cells. ReferenceRange: Low <10, Intermediate 10-20, >20 High" - Value: Quantity with units UCUM#% - TopicCode is LNC#29593-1 - ObservationTopic.DiagnosticService is #pathology - EvaluationComponent - includes 0..1 PrimaryAntibody //from Ki67AntibodyVS if covered - - Element: S-PhaseFraction - Based on: SimpleCodedObservation - Concept: MTH#C0812425 - Description: "An expression of the number of mitoses found in a stated number of cells. The S-phase fraction number tells you what percentage of cells in the tissue sample are in the process of copying their genetic information (DNA). This S-phase, short for synthesis phase, happens just before a cell divides into two new cells. ReferenceRange: Low <6, Intermediate 6-10, >10 High." - Value: Quantity with units UCUM#% - ObservationTopic.DiagnosticService is #pathology - TopicCode is LNC#29593-1 - -EntryElement: GeneticVariant -Based on: Observation -Concept: MTH#C0678941 -Description: "Whether a subject carries a mutation in a particular gene." -Value: CodeableConcept from PositiveNegativeVS - Focus.CodeableConcept from GeneIdentifierVS - ObservationTopic.DiagnosticService is #genetics -0..0 Precondition -0..0 ReferenceRange -0..0 DeltaFlag -0..0 AnatomicalLocation - EvaluationComponent -includes 0..1 Refseq - - Element: Refseq - Based on: EvaluationComponent - Concept: TBD - Description: "The Reference Sequence (RefSeq) collection provides a comprehensive, integrated, non-redundant, well-annotated set of sequences, including genomic DNA, transcripts, and proteins. RefSeq sequences form a foundation for medical, functional, and diversity studies. They provide a stable reference for genome annotation, gene identification and characterization, mutation and polymorphism analysis (especially RefSeqGene records), expression studies, and comparative analyses." - Value: CodeableConcept from RefseqVS - -EntryElement: BreastCancerGeneticAnalysisObservation -Concept: TBD -Based on: Observation -Description: "The status of genes known or suspected to play a role in breast cancer risk, for example, the tumor suppressor genes, BRCA1 and BRCA2." - Observation.TopicCode is TBD#TBD - ObservationTopic.DiagnosticService is #genetics -0..0 EvaluationComponent - PanelMembers.EvaluationresultRecorded -includes 1..1 BRCA1Variant -includes 1..1 BRCA2Variant - - Element: BRCA1Variant - Concept: TBD - Based on: GeneticVariant - Description: "Whether the patient has a mutation in the BRCA1 gene." - Value: CodeableConcept from PositiveNegativeVS - Focus.CodeableConcept is HGNC#BRCA1Gene - - - Element: BRCA2Variant - Concept: TBD - Based on: GeneticVariant - Description: "Whether the patient has a mutation in the BRCA2 gene." - Value: CodeableConcept from PositiveNegativeVS - Focus.CodeableConcept is HGNC#BRCA2Gene - - -FHIR Genomics: -https://www.hl7.org/FHIR/2016Jan/obs-genetics-example3-bcr1%20and%20bcr2%20sequencing%20with%20FamilyHistory%20-1.json.html -https://www.hl7.org/FHIR/2016Jan/observation-genetics-cg-prf-1a.html -https://www.hl7.org/FHIR/2016Jan/observation-genetics.html -https://www.hl7.org/FHIR/2016Jan/obs-genetics-example2-germline.html -*/ - diff --git a/spec/shr_oncology_map.txt b/spec/shr_oncology_map.txt deleted file mode 100644 index 045b7836..00000000 --- a/spec/shr_oncology_map.txt +++ /dev/null @@ -1,20 +0,0 @@ -Grammar: Map 5.1 -Namespace: shr.oncology -Target: FHIR_STU_3 - - -BreastSpecimen maps to Specimen: - ColdIschemiaTime maps to processing (slice on = procedure) - ColdIschemiaTime.TimePeriod maps to processing.time[x] - ColdIschemiaTime._Concept maps to processing.procedure - constrain processing.additive to 0..0 -// fix processing.description to "ColdIschemiaTime" - - -/* -GeneticVariant: - constrain related to 0..0 - -LymphaticInvolvement: - constrain related to 0..0 -*/ \ No newline at end of file diff --git a/spec/shr_onconew.txt b/spec/shr_onconew.txt deleted file mode 100644 index 9ef4a79f..00000000 --- a/spec/shr_onconew.txt +++ /dev/null @@ -1,59 +0,0 @@ -Grammar: DataElement 5.0 -Namespace: shr.onconew -Description: "SHR implementation of ASCO requirements." -Uses: shr.core, shr.base, cimi.core, cimi.element, cimi.context, cimi.topic, cimi.statement, cimi.entity - - -/* -EntryElement: LymphNodeBodySite -Based on: AnatomicalLocation -Description: "A body site specific to the lymph node structure." -Value: CodeableConcept from LymphNodeGroupVS -1..1 Laterality -0..0 AnatomicalDirection - - -EntryElement: LymphNodeMobility -Based on: Observation -Concept: TBD -Description: "The degree to which the lymph node is moveable upon palpation." -Value: CodeableConcept from LymphNodeMobilityVS -1..* LymphNode -*/ - - -/* -EntryElement: LymphaticInvolvement -Based on: Observation -Concept: MTH#C0746333 -Description: "Description of lymph nodes contain cancer cells." -Value: CodeableConcept from PositiveNegativeVS -1..1 AnatomicalLocatoin from LymphSystemSubdivisionVS - ObservationTopic.DiagnosticService is #pathology -0..0 Focus -0..0 Precondition -0..0 ReferenceRange -0..0 DeltaFlag - EvaluationComponent -includes 0..1 LargestLymphNodeSize -includes 0..1 NumberOfLymphNodesInvolved -includes 0..1 DegreeOfLymphaticInvolvement - - Element: LargestLymphNodeSize - Based on: EvaluationComponent - Concept: MTH#C1285847 - Description: "The largest dimension of the largest lymph node invaded by cancer cells." - Value: Quantity with units UCUM#mm - - Element: NumberOfLymphNodesInvolved - Based on: EvaluationComponent - Concept: TBD - Description: "A count of lymph nodes invaded by cancer cells of those examined." - Value: Quantity with units UCUM#1 - - Element: DegreeOfLymphaticInvolvement - Based on: CodedEvaluationComponent - Concept: TBD - Description: "Assessment of how much cancer is in a lymph node." - Value: CodeableConcept from DegreeOfLymphaticInvolvementVS -*/ diff --git a/spec/shr_onconew_vs.txt b/spec/shr_onconew_vs.txt deleted file mode 100644 index 83967356..00000000 --- a/spec/shr_onconew_vs.txt +++ /dev/null @@ -1,28 +0,0 @@ -Grammar: ValueSet 5.0 -Namespace: shr.onconew - -CodeSystem: SCT = http://snomed.info/sct - -/* -ValueSet: LymphNodeMobilityVS -Description: "Values expressing the degree of moveability of lymph node upon palpation." -SCT#261010008 "Fixed (qualifier)" -SCT#300824007 "Moveable (qualifier)" - -//ValueSet: LymphNodeGroupVS -//Description: - - - - - -ValueSet: LymphSystemSubdivisionVS -Description: "A lymph node area or nodal group; a subdivision of the entire lymphatic system. For breast cancer, this includes 5 areas: internal mammary lymph nodes, axillary lymph nodes level I, II, and III, and the supraclavicular lymph nodes." -Includes codes descending from SCT#122490001 "Lymphoid system structure (body structure)" - -ValueSet: DegreeOfLymphaticInvolvementVS -#microscopic "Only a few cancer cells are in the node." -#gross "The cancer can be seen or felt without aid of microscopy." -#extracapsular "Cancer has pread outside the wall of the node." - -*/ \ No newline at end of file diff --git a/spec/shr_procedure.txt b/spec/shr_procedure.txt new file mode 100644 index 00000000..954e44a6 --- /dev/null +++ b/spec/shr_procedure.txt @@ -0,0 +1,144 @@ +Grammar: DataElement 5.0 +Namespace: shr.core + +CodeSystem: OBSCAT = http://hl7.org/fhir/observation-category + + +EntryElement: Procedure +Based on: ActionPerformed +Description: "A procedure that has been performed." + SubjectOfRecord value is type PatientOrGroup +1..1 Code from http://hl7.org/fhir/us/core/ValueSet/us-core-procedure-code if covered +0..* BodySite +0..1 PartOf value is type ref(Procedure) +0..1 Category // this is a constraint on the cardinality of Action.Category +0..* Annotation +0..1 ReasonCode +0..1 ReasonReference +0..0 Method // Procedure doesn't have Method +0..* TreatmentIntent + Participation.OnBehalfOf value is type ref(Organization) + // TODO: StatusReason + // Status from http://hl7.org/fhir/ValueSet/event-status + // Conflict V2 V3: Cannot override value set constraint from http://hl7.org/fhir/ValueSet/procedure-status to http://hl7.org/fhir/ValueSet/event-status +// Participation.Participant.EntityOrRole is type ref(Practitioner) + Participation.Participant value is type PersonOrOrganizationOrDevice + RelatedRequest value is type ref(ProcedureRequest) +0..1 ref(Location) +0..1 Outcome +0..* MaterialUsed + + Element: MaterialUsed + Description: "Items used during procedure" + Value: ref(Device) or ref(Medication) or ref(Substance) + + Element: TreatmentIntent + Concept: SCT#395077000 "Treatment intent (situation)" // TODO: Needs a new LOINC number" + Description: "The intended result from a given treatment. Examples include curative, palliative, and supportive." + Value: CodeableConcept from TreatmentIntentVS + + +EntryElement: ProcedureRequest +Based on: ActionRequested +Description: "A request for a procedure to be performed. May be a proposal or an order." + SubjectOfRecord value is type PatientOrGroup + PriorityCode // must be from http://hl7.org/fhir/ValueSet/request-priority + // DSTU 2 change (different required value sets in v2 and v3) + Status // from http://hl7.org/fhir/ValueSet/request-status + // DSTU 2 change(different required value sets in v2 and v3) +0..1 Author value is type PractitionerOrDevice // this is the intersection between DSTU 2 and STU 3. DSTU 2 allows Organization, and STU 3 allows Patient and RelatedPerson. Both allow Practitioner and Device. +1..1 Type from http://hl7.org/fhir/us/core/ValueSet/us-core-procedure-code if covered +0..* BodySite +0..1 PartOf value is type ref(Procedure) +0..1 Category // this is a constraint on the cardinality of Action.Category +0..* Annotation +0..1 ReasonCode +0..1 Method + RequestIntent from http://hl7.org/fhir/ValueSet/request-intent +//0..* InputFinding -- covered by Reason +//0..* Indication +0..1 ref(Location) +0..1 Recipient value is type PersonOrOrganizationOrDevice // TODO: why is Recipient equated with Performer? + + + +//---------- Specialized Types of Procedure Topics ---------------- + +EntryElement: ImagingProcedure +Based on: Procedure +Concept: TBD +Description: "Experimental class for an imaging procedure. This class is still incomplete at this time." +0..* ImagingSubstance + + Element: ImagingSubstance + Concept: TBD + Description: "Substance used for this imaging procedure such as a contrast agent." + Value: CodeableConcept + + +EntryElement: LaboratoryProcedure +Based on: Procedure +Concept: MTH#C0456984 +Description: "A procedure performed on a collected specimen such as a blood panel or a biopsy." +1..1 Code from http://hl7.org/fhir/ValueSet/observation-codes // ?? + Category is OBSCAT#laboratory +0..1 ref(Specimen) +//0..1 ref(Device) // constraint from 0..* + + +EntryElement: SurgicalProcedure +Based on: Procedure +Concept: TBD +Description: "A surgical action, independent of action context." +0..* DirectSite +0..* IndirectSite +0..* SurgicalApproach + + Element: DirectSite + Description: "The site where the procedure is performed." + Value: BodySite + + Element: IndirectSite + Description: "The indirect site for this procedure." + Value: BodySite + + Element: SurgicalApproach + Description: "The technique used to reach the site of the procedure. Approaches may be through the skin or mucous membrane, through an orifice or external." + Value: CodeableConcept + + +EntryElement: RadiationProcedure +Based on: Procedure +Description: "A radiation oncology procedure. If the treatment is part of a larger course of treatment, the PartOf attribute should indicate that." + Code from RadiationProcedureVS +0..1 RadiationDosePerFraction +0..1 RadiationFractionsDelivered +0..1 TotalRadiationDoseDelivered + +Element: RadiationDosePerFraction +Concept: TBD#TBD // TODO: Needs new LOINC and/or SNOMED codes +Description: "The total number of treatment sessions (fractions) administered during a course of radiation therapy therapy. A fraction is a portion of the total radiation dose, delivered as a series of treatments that make up the full course of radiotherapy. (source: LOINC)" +Value: Ratio + +Element: RadiationFractionsDelivered +Concept: LNC#21959-2 "Number of radiation treatment" +Description: "The total number of treatment sessions (fractions) administered during a course of radiation therapy therapy. A fraction is a portion of the total radiation dose, delivered as a series of treatments that make up the full course of radiotherapy. (source: LOINC)" +Value: Quantity with units UCUM#1 + +Element: TotalRadiationDoseDelivered +Concept: SCT#445461008 "Total radiation dose delivered (observable entity)" +Description: "The total amount of radiation dose delivered for the course of therapy. (source: SNOMED, ASTRO)" +Value: Quantity with units UCUM#Gy + + +EntryElement: DiagnosticImaging +Based on: ImagingProcedure +Description: "Diagnostic imaging procedure performed." + Code from DiagnosticImagingVS + +/* +EntryElement: SubstanceAbuseTreatment +Based on: ProcedurePerformed +Description: "The treatment program used to address a substance abuse problem." + Code from SubstanceAbuseTreatmentTypeVS +*/ \ No newline at end of file diff --git a/spec/shr_procedure_map_dstu2.txt b/spec/shr_procedure_map_dstu2.txt new file mode 100644 index 00000000..c38cd67d --- /dev/null +++ b/spec/shr_procedure_map_dstu2.txt @@ -0,0 +1,75 @@ +Grammar: Map 5.1 +Namespace: shr.core +Target: FHIR_DSTU_2 + +Procedure maps to http://fhir.org/guides/argonaut/StructureDefinition/argo-procedure: // DSTU 2 change (different mapping target) + Identifier maps to identifier + Code maps to code + SubjectOfRecord maps to subject + Category maps to category + // DSTU 2 change (name change) + constrain notPerformed to 0..0 + // DSTU 2 change (name change) + constrain reasonNotPerformed to 0..0 + BodySite.BodySiteCode maps to bodySite + BodySite.Laterality maps to bodySite.extension + BodySite.AnatomicalDirection maps to bodySite.extension + BodySite.ClockDirection maps to bodySite.extension + BodySite.CommentOrDescription maps to bodySite.extension + BodySite.Attachment maps to bodySite.extension + BodySite.DistanceFromLandmark maps to bodySite.extension + // DSTU 2 change (no such attribute) +// PartOf maps to partOf + Annotation maps to notes + CareContext maps to encounter + ReasonCode maps to reason[x] + OccurrenceTimeOrPeriod maps to performed[x] + Participation maps to performer + Participation.Participant maps to performer.actor + Participation.ParticipationType maps to performer.role + // DSTU 2 change (no such attribute) +// Participation.OnBehalfOf maps to performer.onBehalfOf + Status maps to status +// TODO The following statement is failing it might be a bug +// Method maps to http://hl7.org/fhir/StructureDefinition/procedure-method + RelatedRequest.Value maps to request +// RelatedPlan maps to definition + Outcome maps to outcome + Location maps to location + MaterialUsed maps to used + + +SurgicalProcedure maps to http://fhir.org/guides/argonaut/StructureDefinition/argo-procedure: // DSTU 2 change (different mapping target) + DirectSite maps to http://hl7.org/fhir/StructureDefinition/procedure-targetBodySite + IndirectSite maps to http://hl7.org/fhir/StructureDefinition/procedure-approachBodySite + + +ProcedureRequest maps to ProcedureRequest: + Identifier maps to identifier + StatementDateTime maps to orderedOn + Author maps to orderer + Type maps to code + // DSTU 2 change (no such attribute) +// Category maps to category +// DSTU 2 change (no such attribute) +// constrain doNotPerform to 0..0 + SubjectOfRecord maps to subject + BodySite.BodySiteCode maps to bodySite + BodySite.Laterality maps to bodySite.extension + BodySite.AnatomicalDirection maps to bodySite.extension + BodySite.ClockDirection maps to bodySite.extension + BodySite.CommentOrDescription maps to bodySite.extension + BodySite.Attachment maps to bodySite.extension + BodySite.DistanceFromLandmark maps to bodySite.extension + CareContext maps to encounter + ReasonCode maps to reason[x] + Status maps to status +// DSTU 2 change (no such attribute) + RequestIntent maps to extension +// DSTU 2 change (name change) + ExpectedPerformanceTime maps to scheduled[x] +// DSTU 2 change (no such attribute) + ExpectedPerformerType maps to extension + Recipient maps to performer + PriorityCode maps to priority + Annotation maps to notes diff --git a/spec/shr_procedure_map_stu3.txt b/spec/shr_procedure_map_stu3.txt new file mode 100644 index 00000000..2e232cd2 --- /dev/null +++ b/spec/shr_procedure_map_stu3.txt @@ -0,0 +1,68 @@ +Grammar: Map 5.1 +Namespace: shr.core +Target: FHIR_STU_3 + + +Procedure maps to http://hl7.org/fhir/us/core/StructureDefinition/us-core-procedure: + Identifier maps to identifier + Code maps to code + SubjectOfRecord maps to subject + Category maps to category + constrain notDone to 0..0 + constrain notDoneReason to 0..0 + BodySite.BodySiteCode maps to bodySite + BodySite.Laterality maps to bodySite.extension + BodySite.AnatomicalDirection maps to bodySite.extension + BodySite.ClockDirection maps to bodySite.extension + BodySite.CommentOrDescription maps to bodySite.extension + BodySite.Attachment maps to bodySite.extension + BodySite.DistanceFromLandmark maps to bodySite.extension + PartOf maps to partOf + Annotation maps to note + CareContext maps to context + ReasonCode maps to reasonCode + ReasonReference maps to reasonReference + OccurrenceTimeOrPeriod maps to performed[x] + Participation maps to performer + Participation.Participant maps to performer.actor + Participation.ParticipationType maps to performer.role + Participation.OnBehalfOf maps to performer.onBehalfOf + Status maps to status +// TODO The following statement is failing it might be a bug +// Method maps to http://hl7.org/fhir/StructureDefinition/procedure-method + RelatedRequest.Value maps to basedOn +// RelatedPlan maps to definition + Outcome maps to outcome + Location maps to location + MaterialUsed maps to usedReference + +SurgicalProcedure maps to http://hl7.org/fhir/us/core/StructureDefinition/us-core-procedure: + DirectSite maps to http://hl7.org/fhir/StructureDefinition/procedure-targetBodySite + IndirectSite maps to http://hl7.org/fhir/StructureDefinition/procedure-approachBodySite + SurgicalApproach maps to http://hl7.org/fhir/StructureDefinition/procedure-approachBodySite + + +ProcedureRequest maps to ProcedureRequest: + Identifier maps to identifier + StatementDateTime maps to authoredOn + Author maps to requester.agent + Type maps to code + Category maps to category + constrain doNotPerform to 0..0 + SubjectOfRecord maps to subject + BodySite.BodySiteCode maps to bodySite + BodySite.Laterality maps to bodySite.extension + BodySite.AnatomicalDirection maps to bodySite.extension + BodySite.ClockDirection maps to bodySite.extension + BodySite.CommentOrDescription maps to bodySite.extension + BodySite.Attachment maps to bodySite.extension + BodySite.DistanceFromLandmark maps to bodySite.extension + CareContext maps to context + ReasonCode maps to reasonCode + Status maps to status + RequestIntent maps to intent + ExpectedPerformanceTime maps to occurrence[x] + ExpectedPerformerType maps to performerType + Recipient maps to performer + PriorityCode maps to priority + Annotation maps to note diff --git a/spec/shr_procedure_vs.txt b/spec/shr_procedure_vs.txt new file mode 100644 index 00000000..39880117 --- /dev/null +++ b/spec/shr_procedure_vs.txt @@ -0,0 +1,39 @@ + +Grammar: ValueSet 5.0 +Namespace: shr.core + +CodeSystem: LNC = http://loinc.org +CodeSystem: SCT = http://snomed.info/sct +CodeSystem: MTH = http://ncimeta.nci.nih.gov +CodeSystem: RXN = http://www.nlm.nih.gov/research/umls/rxnorm + +ValueSet: TreatmentIntentVS +Description: "The purpose of a treatment. Examples include curative, palliative, and supportive." +Includes codes descending from SCT#363675004 "Intents (nature of procedure values) (qualifier value)" + +ValueSet: SurgicalProcedureVS +Description: "Surgical procedure (procedure)" +Includes codes descending from SCT#387713003 "Surgical procedure (procedure)" + +ValueSet: DiagnosticImagingVS +Description: "Imaging procedures." +Includes codes descending from SCT#363679005 "Imaging (procedure)" + +ValueSet: RadiationProcedureVS +Description: "Radiation oncology AND/OR radiotherapy (procedure)" +Includes codes descending from SCT#108290001 "Radiation oncology AND/OR radiotherapy (procedure)" + +/* +ValueSet: SubstanceAbuseTreatmentTypeVS +#day_treatment "Day Treatment Services" +#inpatient "Inpatient/Hospital" +#inpatient_detox "Hospital Inpatient Detoxification Services" +#ambulatory "Outpatient services" +#ambulatory_detox "Ambulatory Detoxification Services" +#outreach "Outreach Services" +#intensive_outpatient "Intensive Outpatient Services" +#methadone_treatment "Methadone Treatment Services" +#residental_rehab "Residential/Rehabilitation Services" +#after_care "After Care Services" +#recovery_support "Recovery Support Services" +*/ \ No newline at end of file diff --git a/spec/shr_questionnaire.txt b/spec/shr_questionnaire.txt new file mode 100644 index 00000000..32de0ec3 --- /dev/null +++ b/spec/shr_questionnaire.txt @@ -0,0 +1,197 @@ +Grammar: DataElement 5.0 +Namespace: shr.core + +/* +Abstract Element: PublishedArtifact +Based on: DomainResource +Description: "Abstract class with common elements for information items that are published." +0..1 Url +0..1 VersionString +0..1 NameAsText +0..1 Title +1..1 Status from http://hl7.org/fhir/ValueSet/publication-status +0..1 IsExperimental +0..* SubjectType +0..1 LastUpdated +0..1 PublisherName +0..* ContactDetail +0..1 DescriptionMarkdown +0..* UseContext +0..* Jurisdiction +0..1 PurposeMarkdown +0..1 Copyright +*/ + +EntryElement: Questionnaire +Based on: DomainResource +Description: "A structured set of questions intended to guide the collection of answers from end-users. Questionnaires provide detailed control over order, presentation, phraseology and grouping to allow coherent, consistent data collection." +0..1 Url +0..1 VersionString +0..1 NameAsText +0..1 Title + StatusOrActive is type Status +1..1 Status from http://hl7.org/fhir/ValueSet/publication-status +0..1 IsExperimental +0..* SubjectType +0..1 LastUpdated +0..1 PublisherName +0..* ContactDetail +0..1 DescriptionMarkdown +0..* UseContext +0..* Jurisdiction +0..1 PurposeMarkdown +0..1 Copyright +0..1 LastReviewedDate +0..1 ApprovalDate +0..1 EffectiveTimePeriod +0..* Code could be from http://hl7.org/fhir/ValueSet/questionnaire-questions +0..* QuestionnaireItem + + Element: IsExperimental + Description: "A Boolean value to indicate that the item is for testing purposes (or education/evaluation/marketing) and is not intended to be used for genuine usage." + Value: boolean + + Element: SubjectType + Description: "Resource that can be subject of QuestionnaireResponse" + Value: CodeableConcept from http://hl7.org/fhir/ValueSet/resource-types + + Element: PublisherName + Description: "The name of the organization or individual that published this item." + Value: string + + Element: DescriptionMarkdown + Description: "A description of the purpose of the item." + Value: markdown + + Element: UseContext + Description: "The content was developed with a focus and intent of supporting the contexts that are listed. These contexts may be general categories (gender, age, ...) or may be references to specific programs (insurance plans, studies, ...) and may be used to assist with indexing and searching for appropriate questionnaire instances." + 1..1 Code + 1..1 ContextValue + + Element: ContextValue + Description: "A value that defines the context specified in this context of use. The interpretation of the value is defined by the code." + Value: CodeableConcept or Quantity or Range or ref(ResearchStudy) or ref(Group) or ref(Location) or ref(Organization) // or PlanDefinition, InsurancePlan, HealthcareSerice + + Element: PurposeMarkdown + Description: "A description of the purpose of the item." + Value: markdown + + Element: Copyright + Description: "A rights statement relating legal restrictions on the use and publishing of the item." + Value: markdown + + Element: LastReviewedDate + Description: "The most recent date the item was reviewed." + Value: date + + Element: ApprovalDate + Description: "The date on which the item was officiallly deemed acceptable by the publisher." + Value: date + + Element: QuestionnaireItem + Description: "Questions and sections within the Questionnaire." + 1..1 IdentifierString + 0..1 DetailsLink + 0..* Code could be from http://hl7.org/fhir/ValueSet/questionnaire-questions + 0..1 Prefix + 0..1 Question + 1..1 Type from http://hl7.org/fhir/ValueSet/item-type + 0..* EnableWhen + 0..1 IsRequired + 0..1 MayRepeat + 0..1 IsReadOnly + 0..1 MaxTextLength + 0..1 AnswerValueSet + 0..* AnswerOption + 0..* PrepopulateValue + 0..* QuestionnaireItem + + Element: DetailsLink + Description: "The date on which the item was officiallly deemed acceptable by the publisher." + Value: uri + + Element: Question + Description: "The text of the question." + Value: string + + Element: IsRequired + Description: "An indication, if true, that the item may occur multiple times in the response, collecting multiple answers answers for questions or multiple sets of answers for groups." + Value: boolean + + Element: MayRepeat + Description: "An indication, if true, that the item may occur multiple times in the response, collecting multiple answers answers for questions or multiple sets of answers for groups." + Value: boolean + + Element: IsReadOnly + Description: "An indication, when true, that the value cannot be changed by a human respondent to the Questionnaire." + Value: boolean + + Element: MaxTextLength + Description: "The maximum number of characters that are permitted in a text field." + Value: integer + + Element: AnswerValueSet + Description: "Valueset containing permitted answers." + Value: ref(ValueSet) + + Element: AnswerOption + Description: "One of the permitted answers for a 'choice' or 'open-choice' question." + Value: integer or date or time or string or Coding or ref(DomainResource) + + Element: PrepopulateValue + Description: "One or more values that should be pre-populated in the answer when initially rendering the questionnaire for user input." + Value: boolean or decimal or integer or date or dateTime or time or string or uri or Attachment or Coding or Quantity or ref(DomainResource) + + Element: EnableWhen + Description: "A constraint indicating that this item should only be enabled (displayed/allow answers to be captured) when the specified condition is true." + 1..1 Question + 0..1 HasAnswer + 0..1 AnswerValue + + Element: HasAnswer + Description: "An indication that this item should be enabled only if the specified question is answered (hasAnswer=true) or not answered (hasAnswer=false)." + Value: boolean + + Element: AnswerValue + Description: "The answer to a question." + Value: boolean or decimal or integer or date or dateTime or time or string or uri or Attachment or Coding or Quantity or ref(DomainResource) + + +EntryElement: QuestionnaireResponse +Based on: DomainResource +Description: "A structured set of questions and their answers. The questions are ordered and grouped into coherent subsets, corresponding to the structure of the grouping of the questionnaire being responded to." +0..1 Identifier +0..* RelatedRequest value is type ReferralOrProcedureRequest +0..* PartOf value is type ObservationOrProcedure +0..1 ref(Questionnaire) + StatusOrActive is type Status +1..1 Status from http://hl7.org/fhir/ValueSet/questionnaire-answers-status +0..1 SubjectOfInformation value is type ref(DomainResource) +0..1 CareContext +0..1 StatementDateTime +0..1 Author value is type PersonOrDevice +0..1 InformationSource value is type PatientOrPractitionerOrRelatedPerson +0..* QuestionnaireResponseItem + + + Element: QuestionnaireResponseItem + Description: "Questions and sections within the Questionnaire." + 1..1 IdentifierString + 0..1 DetailsLink + 0..1 Question + 0..1 SubjectOfInformation value is type ref(DomainResource) + 0..* Answer + 0..* QuestionnaireResponseItem + + Element: Answer + Description: "The respondent's answer(s) to the question." + 0..1 AnswerValue + 0..* QuestionnaireResponseItem + + Element: ReferralOrProcedureRequest + Based on: ActionRequested + Value: ref(ReferralRequest) or ref(ProcedureRequest) // CarePlan not yet implemented + + Element: ObservationOrProcedure + Based on: DomainResource + Value: ref(Observation) or ref(Procedure) \ No newline at end of file diff --git a/spec/shr_questionnaire_map_dstu2.txt b/spec/shr_questionnaire_map_dstu2.txt new file mode 100644 index 00000000..89cd17ee --- /dev/null +++ b/spec/shr_questionnaire_map_dstu2.txt @@ -0,0 +1,5 @@ +Grammar: Map 5.1 +Namespace: odh +Target: FHIR_DSTU_2 + +// NOT STARTED \ No newline at end of file diff --git a/spec/shr_questionnaire_map_stu3.txt b/spec/shr_questionnaire_map_stu3.txt new file mode 100644 index 00000000..f28b12a7 --- /dev/null +++ b/spec/shr_questionnaire_map_stu3.txt @@ -0,0 +1,70 @@ +Grammar: Map 5.1 +Namespace: shr.core +Target: FHIR_STU_3 + + +Questionnaire maps to Questionnaire: + Identifier maps to identifier + Url maps to url + VersionString maps to version + NameAsText maps to name + Title maps to title + Status maps to status + IsExperimental maps to experimental + SubjectType maps to subjectType + LastUpdated maps to date + PublisherName maps to publisher + ContactDetail maps to contact + DescriptionMarkdown maps to description + UseContext.Code maps to useContext.code + UseContext.ContextValue maps to useContext.value[x] + Jurisdiction maps to jurisdiction + PurposeMarkdown maps to purpose + Copyright maps to copyright + LastReviewedDate maps to lastReviewDate + ApprovalDate maps to approvalDate + EffectiveTimePeriod maps to effectivePeriod + Code maps to code + QuestionnaireItem maps to item + QuestionnaireItem.IdentifierString maps to item.linkId + QuestionnaireItem.DetailsLink maps to item.definition + QuestionnaireItem.Code maps to item.code + QuestionnaireItem.Prefix maps to item.prefix + QuestionnaireItem.Question maps to item.text + QuestionnaireItem.Type maps to item.type + QuestionnaireItem.EnableWhen maps to item.enableWhen + QuestionnaireItem.EnableWhen.Question maps to item.enableWhen.question + QuestionnaireItem.EnableWhen.HasAnswer maps to item.enableWhen.hasAnswer + QuestionnaireItem.EnableWhen.AnswerValue maps to item.enableWhen.answer[x] + QuestionnaireItem.IsRequired maps to item.required + QuestionnaireItem.MayRepeat maps to item.repeats + QuestionnaireItem.IsReadOnly maps to item.readOnly + QuestionnaireItem.MaxTextLength maps to item.maxLength +// QuestionnaireItem.AnswerValueSet maps to item. + QuestionnaireItem.AnswerOption maps to item.option.value[x] + QuestionnaireItem.PrepopulateValue maps to item.initial[x] + QuestionnaireItem.QuestionnaireItem maps to item.item + +QuestionnaireResponse maps to QuestionnaireResponse: + Identifier maps to identifier + RelatedRequest maps to basedOn + PartOf maps to parent + Questionnaire maps to questionnaire + Status maps to status + SubjectOfInformation maps to subject + CareContext maps to context + StatementDateTime maps to authored + Author maps to author + InformationSource maps to source + QuestionnaireResponseItem maps to item + QuestionnaireResponseItem.IdentifierString maps to item.linkId + QuestionnaireResponseItem.DetailsLink maps to item.definition + QuestionnaireResponseItem.Question maps to item.text + QuestionnaireResponseItem.SubjectOfInformation maps to item.subject + QuestionnaireResponseItem.Answer maps to item.answer + QuestionnaireResponseItem.QuestionnaireResponseItem maps to item.item + QuestionnaireResponseItem.Answer.AnswerValue maps to item.answer.value[x] + QuestionnaireResponseItem.Answer.QuestionnaireResponseItem maps to item.answer.item + + + diff --git a/spec/shr_research.txt b/spec/shr_research.txt index d062ee67..542e7306 100644 --- a/spec/shr_research.txt +++ b/spec/shr_research.txt @@ -1,29 +1,27 @@ Grammar: DataElement 5.0 -Namespace: shr.research +Namespace: shr.core Description: "The SHR research domain contains definitions related to the clinical trials and research studies." -Uses: shr.core, shr.base, cimi.core, cimi.element, cimi.context, cimi.topic, cimi.statement, cimi.entity - -EntryElement: Study +EntryElement: ResearchStudy Based on: Entity Concept: TBD Description: "A clinical trial or similar research study. Reference: list of FDA data elements describing a research study: prsinfo.clinicaltrials.gov/definitions.html " 1..1 Title 1..1 Identifier -0..1 Details -0..* PartOf value is type Study -1..1 Status from http://hl7.org/fhir/ValueSet/research-study-status +0..1 CommentOrDescription +0..1 PartOf value is type ResearchStudy 0..* Enrollment 0..1 EffectiveTimePeriod 0..1 Sponsor 0..1 Jurisdiction 0..* ContactDetail 0..1 PrincipalInvestigator -0..* Facility +0..* Location 0..1 TerminationReason 0..* Annotation 0..* StudyArm - + StatusOrActive is type Status +1..1 Status from http://hl7.org/fhir/ValueSet/research-study-status Element: Enrollment Concept: MTH#C4041024 @@ -31,38 +29,34 @@ Description: "A clinical trial or similar research study. Reference: list of FDA Value: ref(Group) Element: Sponsor - Concept: TBD Description: "The organization responsible for the execution of the study." Value: ref(Organization) Element: Jurisdiction - Concept: TBD Description: "The country, state or other region taking legal responsibility for the conduct of the study." Value: CodeableConcept from http://hl7.org/fhir/ValueSet/jurisdiction if covered Element: PrincipalInvestigator - Concept: TBD Description: "Indicates the individual who has primary oversite of the execution of the study." Value: ref(Practitioner) Element: TerminationReason - Concept: TBD Description: "A description and/or code explaining the premature termination of the study." Value: CodeableConcept Element: StudyArm - Concept: TBD Description: "Arm refers to pre-specified group or subgroup of participant(s) in a clinical trial assigned to receive specific intervention(s) (or no intervention) according to a protocol." 1..1 Title 0..1 Type from StudyArmTypeVS - 0..1 Details + 0..1 CommentOrDescription EntryElement: ResearchSubject -Based on: Entity +Based on: Role Description: "Record of a subject's enrollment and participation in a research study." +0..1 Identifier // cardinality constraint 1..1 ref(Patient) -1..1 ref(Study) +1..1 ref(ResearchStudy) + StatusOrActive is type Status 1..1 Status from http://hl7.org/fhir/ValueSet/research-subject-status 1..1 ParticipationPeriod 0..1 TerminationReason from ResearchSubjectTerminationReasonVS - \ No newline at end of file diff --git a/spec/shr_research_map_dstu2.txt b/spec/shr_research_map_dstu2.txt new file mode 100644 index 00000000..39bea5ba --- /dev/null +++ b/spec/shr_research_map_dstu2.txt @@ -0,0 +1,10 @@ +Grammar: Map 5.1 +Namespace: shr.core +Target: FHIR_DSTU_2 + + +ResearchStudy maps to Basic: +// dstu 2 change (no suitable target) + +ResearchSubject maps to Basic: +// dstu 2 change (no suitable target) diff --git a/spec/shr_research_map.txt b/spec/shr_research_map_stu3.txt similarity index 75% rename from spec/shr_research_map.txt rename to spec/shr_research_map_stu3.txt index f3ee8f2f..b047689a 100644 --- a/spec/shr_research_map.txt +++ b/spec/shr_research_map_stu3.txt @@ -1,12 +1,11 @@ Grammar: Map 5.1 -Namespace: shr.research +Namespace: shr.core Target: FHIR_STU_3 - -Study maps to ResearchStudy: - Title maps to title +ResearchStudy maps to ResearchStudy: Identifier maps to identifier + Title maps to title PartOf maps to partOf Status maps to status Enrollment maps to enrollment @@ -15,15 +14,16 @@ Study maps to ResearchStudy: Jurisdiction maps to jurisdiction ContactDetail maps to contact PrincipalInvestigator maps to principalInvestigator - Facility maps to site + Location maps to site TerminationReason maps to reasonStopped Annotation maps to note StudyArm.Title maps to arm.name StudyArm.Type maps to arm.code - StudyArm.Details maps to arm.description + StudyArm.CommentOrDescription maps to arm.description ResearchSubject maps to ResearchSubject: + Identifier maps to identifier Patient maps to individual - Study maps to study + ResearchStudy maps to study Status maps to status ParticipationPeriod maps to period diff --git a/spec/shr_research_vs.txt b/spec/shr_research_vs.txt index 5fa1a1e9..420de5a7 100644 --- a/spec/shr_research_vs.txt +++ b/spec/shr_research_vs.txt @@ -1,5 +1,5 @@ Grammar: ValueSet 5.0 -Namespace: shr.research +Namespace: shr.core ValueSet: StudyArmTypeVS Description: "The role of each arm in the clinical trial." @@ -14,7 +14,7 @@ ValueSet: ResearchSubjectTerminationReasonVS Description: "The reason for a research subject leaving a research study." #moved "Subject relocated" #died "Suject passed away" -#ended "Study ended" +#ended "ResearchStudy ended" #adverse "Subject could not tolerate treatement" #protocol "Subject could not follow protocol, e.g. required appointments, dosing schedule, etc." #other "Other reason" diff --git a/spec/shr_wound.txt b/spec/shr_wound.txt deleted file mode 100644 index 43f83919..00000000 --- a/spec/shr_wound.txt +++ /dev/null @@ -1,501 +0,0 @@ -Grammar: DataElement 5.0 -Namespace: shr.wound -Description: "SHR implementation of the HL7 Pressure Ulcer Prevention Domain Analysis Model (May, 2011)." -Uses: shr.core, shr.base, cimi.core, cimi.context, cimi.topic, cimi.statement, cimi.entity, cimi.element, cimi.encounter, shr.condition - -CodeSystem: UCUM = http://unitsofmeasure.org -CodeSystem: LNC = http://loinc.org -CodeSystem: OBSCAT = http://hl7.org/fhir/observation-category - -/* LOINC Wound Assessment Panel (LOINC 39135-9) -See https://s.details.loinc.org/LOINC/39135-9.html?sections=Comprehensive - - 39135-9 Wound assessment panel O - 81666-0 Wound number [Identifier] - 72300-7 Wound type R - 89250-5 Device or anatomic structure visible in wound - 89251-3 Condition present on admission - 11373-8 Injury cause - 88878-4 Date of condition abatement {mm/dd/yyyy} - 72170-4 Photographic image - 89252-1 Episode of Wound - 89253-9 Trend - 85585-8 Date of Onset of Impairment {mm/dd/yyyy} - 72369-2 Body site identification panel R - 39111-0 Body site R - 39112-8 Body location qualifier O - 20228-3 Anatomic part Laterality O - 72301-5 Description of Periwound C - 72527-5 Pressure ulcer stage NPUAP - 72372-6 Wound bed and edge panel C - 89254-7 Wound bed panel - 72371-8 Appearance of Wound base R - 72370-0 Area of identified wound bed appearance/Area of wound bed of Wound base C % - 39132-6 Color of Wound base O - 89255-4 Wound bed area identified by color/Area of wound bed % - 89256-2 Wound edge panel - 72304-9 Edge of wound description O - 39133-4 Color of Wound edge O - 72299-1 Wound tunneling and undermining panel C - 89257-0 Wound tunneling panel - 72298-3 Tunneling of Wound R - 72296-7 Tunneling [Length] of Wound C cm - 72297-5 Tunneling clock position of Wound C - 89258-8 Wound undermining panel - 72295-9 Undermining of Wound R - 72293-4 Undermining [Length] of Wound C cm - 72294-2 Undermining clock position of Wound C - 72292-6 Wound exudate panel C - 89259-6 Presence of wound exudate - 89260-4 Area of wound cm2 - 39116-9 Drainage amount of Wound C - 72288-4 Odor of Exudate from wound O - 72289-2 Color of Exudate from wound R - 72290-0 Appearance of Exudate from wound R - - 72287-6 Wound size panel C - 39125-0 Width of Wound R cm - 39127-6 Depth of Wound R cm - 39126-8 Length of Wound R cm - 80338-7 Wound assessment [Interpretation] - - -========================== - -Wound ASSERTION -- ONE ASSERTION PER WOUND - 0..1 72300-7 Wound type R - 0..1 89251-3 Condition present on admission - 0..1 11373-8 Injury cause - 0..1 85585-8 Date of Onset of Impairment {mm/dd/yyyy} - 0..1 88878-4 Date of condition abatement {mm/dd/yyyy} - 1..1 81666-0 Wound number [Identifier] - 1..1? 89252-1 Episode of Wound (aka ClinicalStatus) - 1..1 72369-2 Anatomical Location - 0..1 72527-5 Pressure ulcer stage NPUAP - -========================== - -Wound ASSESSMENT PANEL (MULTIPLE PANELS PER WOUND) -1..1 81666-0 Wound number [Identifier] -------> REFERENCE TO Wound Assertion -0..1 89253-9 Trend -0..* 72170-4 Photographic image [Media] -0..1 80338-7 Wound assessment [Interpretation] -Components: -0..1 72301-5 Description of Periwound -0..* 89250-5 Device or anatomic structure visible in wound -1..1 72298-3 Presence of Tunneling of Wound R -1..1 72295-9 Presence of Undermining of Wound R -1..1 89259-6 Presence of wound exudate -MemberObservations: - 0..* 89254-7 Wound bed appearance observation - 0..* xxxx Wound bed color observation - 0..1? 89256-2 Wound edge observation - 0..* 89257-0 Wound tunneling observation - 0..* 89258-8 Wound undermining observation - 0..1 72292-6 Wound exudate observation - 0..1 72287-6 Wound size observation - -=========================== - -Observation: 89254-7 Wound bed appearance observation - COMPONENT: 72371-8 Appearance of Wound base (bed) R - COMPONENT: 72370-0 Area of wound bed appearance/Entire Area of wound bed C % - -Observation: xxxx Wound bed color observation - COMPONENT: 39132-6 Color of Wound base O - COMPONENT: 89255-4 Wound bed area identified by color/Area of wound bed % - -Observation: 89256-2 Wound edge observation - COMPONENT: 72304-9 Edge of wound description O - COMPONENT: 39133-4 Color of Wound edge O - -Observation: 89257-0 Wound tunneling observation - COMPONENT: 72296-7 Tunneling [Length] of Wound C cm - COMPONENT: 72297-5 Tunneling clock position of Wound C - -Observation: 89258-8 Wound undermining observation - COMPONENT: 72293-4 Undermining [Length] of Wound C cm - COMPONENT: 72294-2 Undermining clock position of Wound C - -Observation: 72292-6 Wound exudate observation - COMPONENT: 39116-9 Drainage amount of Wound C - COMPONENT: 72288-4 Odor of Exudate from wound O - COMPONENT: 72289-2 Color of Exudate from wound R - COMPONENT: 72290-0 Appearance of Exudate from wound R - -Observation: 72287-6 Wound size observation - COMPONENT: 39125-0 Width of Wound R cm - COMPONENT: 39127-6 Depth of Wound R cm - COMPONENT: 39126-8 Length of Wound R cm - COMPONENT: 89260-4 Area of wound cm2 - -*/ - -Abstract Element: WoundTopic -Based on: BodyStructureTopic -Description: "A topic concerning a wound, independent of context of being present or absent." -1..1 TopicCode from http://loinc.org/vs/LL2215-3 if covered // 72300-7 Wound type -1..1 Category is OBSCAT#exam -1..1 Identifier is type WoundNumber // 81666-0 Wound number [Identifier] - Morphology from WoundMorphologyVS - ConditionCause is type InjuryCause // 11373-8 "Injury cause" -1..1 AnatomicalLocation -0..0 Device -0..0 Precondition - - Element: WoundNumber - Based on: Identifier - Concept: LNC#81666-0 - 0..0 Purpose - Type is LNC#81666-0 // not sure this is necessary - 0..0 CodeSystem // why do we have this attribute on Identifier? - 0..1 EffectiveTimePeriod - 0..1 Issuer - - Element: InjuryCause - Based on: ConditionCause - Concept: LNC#11373-8 "Injury cause" - Value: CodeableConcept should be from http://loinc.org/vs/LL4936-2 - - -Abstract Element: WoundPresenceContext -Based on: ConditionPresenceContext - Onset value is type dateTime // 85585-8 Date of Onset {mm/dd/yyyy} - Abatement value is type dateTime // 88878-4 Date of abatement {mm/dd/yyyy} - ClinicalStatus is type EpisodeOfWound // 89252-1 Episode of Wound (aka ClinicalStatus) - Stage is type PressureUlcerStageNPUAP -0..0 Severity // not sure if this should be prohibited, but it is not part of LOINC panel -0..0 Criticality -0..0 Certainty - - Element: PressureUlcerStageNPUAP - Based on: Stage - Concept: LNC#72527-5 - Value: CodeableConcept from http://loinc.org/vs/LL2337-5 - 0..0 StageDetail - - Element: EpisodeOfWound - Based on: ClinicalStatus - Concept: LNC#89252-1 "Episode of Wound" - Value: code from http://hl7.org/fhir/ValueSet/condition-clinical // wrong value set, preferred is LL4937-0 - - -EntryElement: WoundPresenceStatement -Based on: BodyStructurePresenceStatement -Concept: SCT#416462003 "Wound (disorder)" -Description: "A determination that a wound that exists at a particular body site. Multiple wound assessments can be associated with a single wound." -// LOINC: Some of the features of a wound are recorded once, such as the cause, onset, presence on admission, etc. These should be part of the initial assertion that a wound exists. Other parts of the LOINC panel are observed repeatedly throughout the treatment of the wound. These are part of the wound evaluation. These parts can be linked by wound number or direct references in the model. - BodyStructureTopic is type WoundTopic - ConditionPresenceContext is type WoundPresenceContext - -/* Hold off for now -EntryElement: WoundAbsenceStatement -Based on: BodyStructureAbsenceStatement -Concept: TBD -Description: "Documents the absence of a wounds of a particular type at a given body site. if the Value is SCT#416462003 (Wound) then there is no wound of any type at the site." - BodyStructureTopic is type WoundTopic -*/ - -// This is the main event -EntryElement: WoundEvaluationSummaryPanel -Based on: NonLaboratoryObservation -Concept: LNC#54574-9 -Description: "Group of observations regarding the properties and severity of a wound." - StatementTopic is type WoundEvaluationResultTopic - StatementContext is type WoundObservationContext - - -Abstract Element: WoundObservationContext -Based on: ObservationContext -Description: "Context for recording wound assessments." - Interpretation is type WoundAssessmentInterpretation - DeltaFlag is type WoundTrend -0..0 ResultValue -0..0 ExceptionValue - - Element: WoundAssessmentInterpretation - Based on: Interpretation - Concept: LNC#80338-7 - Description: "Overall assessement of whether the wound is within normal parameters." - Value: CodeableConcept from http://loinc.org/vs/LL3816-7 if covered // underpowered? 'normal' and 'other' - - Element: WoundTrend - Based on: DeltaFlag - Concept: LNC#89253-9 - Description: "Whether a condition is improving, worsening, stable, or resolved." - Value: CodeableConcept should be from http://loinc.org/vs/LL4938-8 // improved, deteriorated, stablized or resolved - - -Abstract Element: WoundEvaluationResultTopic -Based on: ObservationTopic -Description: "Topic for wound assessments, independent of context." - TopicCode is LNC#54574-9 -0..0 ReferenceRange - Focus value is type Identifier // WoundNumber - Media is type PhotographicImage // 72170-4 Photographic image [Media] - EvaluationComponent -includes 0..1 PeriwoundDescription // 72301-5 Description of Periwound -includes 0..* VisibleInternalStructure //89250-5 Device or anatomic structure visible in wound -includes 0..1 PresenceOfWoundTunneling // 72298-3 Tunneling of Wound R present/absent -includes 0..1 PresenceOfWoundUndermining // 72295-9 Undermining of Wound R -includes 0..1 PresenceOfWoundExudate // 89259-6 Presence of wound exudate - PanelMembers.Observation -includes 0..* WoundBedAppearanceObservation //89254-7 Wound bed appearance observation -includes 0..* WoundBedColorObservation // xxxx Wound color observation -includes 0..1 WoundEdgeObservation // 89256-2 Wound edge observation -includes 0..* WoundTunnelingObservation // 89257-0 Wound tunneling observation -includes 0..* WoundUnderminingObservation // 89258-8 Wound undermining observation -includes 0..1 WoundExudateObservation // 72292-6 Wound exudate observation -includes 0..1 WoundSizeObservation // 72287-6 Wound size observation - - Element: PeriwoundDescription - Based on: CodedEvaluationComponent - Concept: LNC#72301-5 - Description: "A description of the skin around the wound (periwound). Color, induration, warmth and edema should be assessed. Redness of the surrounding skin can be indicative of unrelieved pressure. Irritation of the surrounding skin can result from exposure to feces or urine, a reaction to the dressing or tape, or inappropriate removal of dressing or tape. Redness, tenderness, warmth and swelling are classical clinical signs of infection. [Reference: Brown, P., 2009]" - Value: CodeableConcept could be from http://loinc.org/vs/LL2216-1 // example - - Element: VisibleInternalStructure - Based on: CodedEvaluationComponent - Concept: LNC#89250-5 - Description: "Exposed body structures, devices, and/or foreign bodies visible by the naked eye in a wound." - Value: CodeableConcept should be from http://loinc.org/vs/LL4935-4 // preferred - - Element: PresenceOfWoundTunneling - Based on: CodedEvaluationComponent - Concept: LNC#72298-3 - Description: "The presence or absence of wound tunneling." - Value: CodeableConcept from PresentAbsentVS - // LOINC: should re-use the same Snomed codes for Present-Absent - // LOINC: why preferred? why not required? - - Element: PresenceOfWoundUndermining - Based on: CodedEvaluationComponent - Concept: LNC#72295-9 - Description: "The presence or absence of wound undermining." - Value: CodeableConcept from PresentAbsentVS - - Element: PresenceOfWoundExudate - Based on: CodedEvaluationComponent - Concept: LNC#89259-6 - Description: "The presence or absence of wound exudate." - Value: CodeableConcept from PresentAbsentVS - -// LOINC: The wound bed panel has to be factored in a way that the percentages pair unambiguously with the color/appearances. It should be a set of 2-tuples (pairs). The way it is done in LOINC doesn't allow pairing -EntryElement: WoundBedAppearanceObservation -Based on: ComponentOnlyNonLaboratoryObservation -Concept: LNC#89254-7 -Description: "The appearance of the base (bed) of the wound, together with the percentage of the bed with each type of appearance." - ObservationTopic.EvaluationComponent -includes 1..1 WoundBedAppearance -includes 1..1 WoundBedAppearancePercentage - - Element: WoundBedAppearance - Based on: CodedEvaluationComponent - Concept: LNC#72371-8 - Description: "Appearance of wound base (bed)." - Value: CodeableConcept could be from http://loinc.org/vs/LL2237-7 - - Element: WoundBedAppearancePercentage - Based on: EvaluationComponent - Concept: LNC#72370-0 - Description: "Area of wound bed appearance/Entire Area of wound bed." - Value: Quantity with units UCUM#% - -EntryElement: WoundBedColorObservation -Based on: ComponentOnlyNonLaboratoryObservation -Concept: TBD -Description: "Color of part or all of the wound base (bed), and the percentage of the area with that color." - ObservationTopic.EvaluationComponent -includes 1..1 WoundBedColor -includes 1..1 WoundBedColorAreaPercentage - -// LOINC: Why precoordinate a general concept such as 'color' with the concept of wound bed? - Element: WoundBedColor - Based on: CodedEvaluationComponent - Concept: LNC#39132-6 - Description: "Color of Wound base (bed)." - Value: CodeableConcept could be from http://loinc.org/vs/LL2338-3 - -// LOINC: Why precoordinate a general concept such as 'percentage of area' with the concept of wound bed? - Element: WoundBedColorAreaPercentage - Based on: EvaluationComponent - Concept: LNC#89255-4 - Description: "Wound bed area identified by color/Area of wound bed." - Value: Quantity with units UCUM#% - -EntryElement: WoundEdgeObservation -Based on: ComponentOnlyNonLaboratoryObservation -Concept: LNC#89256-2 -Description: "The state of the tissue at the edge of the wound." - ObservationTopic.EvaluationComponent -includes 1..1 WoundEdgeDescription -includes 0..1 WoundEdgeColor -// LOINC:Is the entire edge of the wound described by one color? Or should it be by percentage, similar to the wound bed? -// LOINC: Why precoordinate a general concept such as 'color' with the concept of wound edge? - - Element: WoundEdgeDescription - Based on: CodedEvaluationComponent - Concept: LNC#72304-9 - Description: "Edge of wound description." - Value: CodeableConcept could be from http://loinc.org/vs/LL2230-2 - - Element: WoundEdgeColor - Based on: CodedEvaluationComponent - Concept: LNC#39133-4 - Description: "Color of Wound edge." - Value: CodeableConcept could be from http://loinc.org/vs/LL2338-3 - -EntryElement: WoundTunnelingObservation -Based on: ComponentOnlyNonLaboratoryObservation -Concept: LNC#89257-0 -Description: "A discharging blind-ended track that extends from the surface of an organ to an underlying area or abscess cavity. The track is invariably lined with granulation tissue. In chronic cases this may be augmented with epithelial tissue." - ObservationTopic.EvaluationComponent -includes 0..1 WoundTunnelLength -includes 0..1 WoundTunnelClockDirection - -// LOINC: why precoordinate length + tunneling? -// LOINC: why precoordinate clock position + tunneling? - - Element: WoundTunnelLength - Based on: EvaluationComponent - Concept: LNC#72296-7 - Description: "Length of wound tunneling." - Value: Quantity with units UCUM#cm - -// LOINC: should require use the full clock position value set - Element: WoundTunnelClockDirection - Based on: CodedEvaluationComponent - Concept: LNC#72297-5 - Description: "Clock position of wound tunnel" - Value: CodeableConcept from ClockDirectionVS - - -EntryElement: WoundUnderminingObservation -Based on: ComponentOnlyNonLaboratoryObservation -Concept: LNC#89258-8 -Description: "Assessment of deep tissue (subcutaneous fat and muscle) damage around the wound margin. Undermining are narrow sinus tracts away from the wound margins and go downward into the wound." - ObservationTopic.EvaluationComponent -includes 0..1 WoundUnderminingLength -includes 0..1 WoundUnderminingClockDirection - - Element: WoundUnderminingLength - Based on: EvaluationComponent - Concept: LNC#72293-4 - Description: "Length of wound undermining." - Value: Quantity with units UCUM#cm - -// LOINC: should require use the full clock position value set - Element: WoundUnderminingClockDirection - Based on: CodedEvaluationComponent - Concept: LNC#72294-2 - Description: "Clock position of wound undermining" - Value: CodeableConcept from ClockDirectionVS - -EntryElement: WoundExudateObservation -Based on: ComponentOnlyNonLaboratoryObservation -Concept: LNC#72292-6 -Description: "Description of the fluid produced by a wound." - ObservationTopic.EvaluationComponent -includes 0..1 ExudateDrainageAmount -includes 0..1 ExudateOdor -includes 1..1 ExudateColor -includes 1..1 ExudateAppearance -// LOINC: Wound area should be in wound size panel, not wound exudate panel - - Element: ExudateDrainageAmount - Based on: CodedEvaluationComponent - Concept: LNC#39116-9 - Description:"Drainage amount of wound" - Value: CodeableConcept could be from http://loinc.org/vs/LL2222-9 - - Element: ExudateOdor - Based on: CodedEvaluationComponent - Concept: LNC#72288-4 - Description:"Odor of exudate from wound" - // LOINC: no value set for exudate odor defined - - Element: ExudateColor - Based on: CodedEvaluationComponent - Concept: LNC#72289-2 - Description:"Color of exudate from wound" - Value: CodeableConcept could be from http://loinc.org/vs/LL2219-5 - - Element: ExudateAppearance - Based on: CodedEvaluationComponent - Concept: LNC#72290-0 - Description:"Appearance of exudate from wound" - Value: CodeableConcept could be from http://loinc.org/vs/LL2220-3 - - -EntryElement: WoundSizeObservation -Based on: ComponentOnlyNonLaboratoryObservation -Concept: LNC#72287-6 -Description: "The estimated or measured dimensions of a wound." - ObservationTopic.EvaluationComponent -includes 1..1 WoundLength -includes 1..1 WoundWidth -includes 1..1 WoundDepth -includes 0..1 WoundArea - - Element: WoundLength - Based on: EvaluationComponent - Concept: LNC#39126-8 - Description: "Length of the wound (longest dimension)." - Value: Quantity with units UCUM#cm - - Element: WoundWidth - Based on: EvaluationComponent - Concept: LNC#39125-0 - Description: "Width of the wound (perpendicular to longest dimension)." - Value: Quantity with units UCUM#cm - - Element: WoundDepth - Based on: EvaluationComponent - Concept: LNC#39127-6 - Description: "Depth of the wound." - Value: Quantity with units UCUM#cm - - Element: WoundArea - Based on: EvaluationComponent - Concept: LNC#89260-4 - Description: "Area of the wound." - Value: Quantity with units UCUM#cm2 - -/* Old Stuff -Element: SupportSurface -Concept: SCT#272243001 -Based on: Device -Description: "A specific instance of a support surface used to distribute pressure and support a patient. The value is coding of the type of support surface." -Value: CodeableConcept from SupportSurfaceVS -0..1 SupportSurfaceCategory -0..1 SupportSurfaceBodyPosition -0..* SupportSurfaceComponent - - Element: SupportSurfaceCategory - Concept: TBD - Description: "The category of support surface." - Value: CodeableConcept from SupportSurfaceCategoryVS - - Element: SupportSurfaceBodyPosition - Concept: TBD - Description: "What body positions the surface can be used for, specifically, sitting or lying." - Value: CodeableConcept from SupportSurfaceBodyPositionVS - - Element: SupportSurfaceComponent - Concept: TBD - Description: "A physical material, structure, or system used alone or in combination with other components to fashion a support surface." - Value: CodeableConcept from SupportSurfaceComponentVS - -Element: SupportSurfaceUsed -Concept: TBD -Based on: DeviceUsed -Description: "A paricular instance of the use of a support surface in patient care." -Value: Device is type SupportSurface - Implanted is #no -0..1 ImmersionDepth - - Element: ImmersionDepth - Concept: TBD - Description: "Depth of penetration (sinking) into a support surface." - Value: Quantity with units UCUM#cm "cm" -*/ \ No newline at end of file diff --git a/spec/sw_wound.txt b/spec/sw_wound.txt new file mode 100644 index 00000000..c842ce92 --- /dev/null +++ b/spec/sw_wound.txt @@ -0,0 +1,429 @@ +Grammar: DataElement 5.0 +Namespace: sw +Description: "SHR implementation of wound assessment." +Uses: shr.core + +CodeSystem: UCUM = http://unitsofmeasure.org +CodeSystem: LNC = http://loinc.org +CodeSystem: OBSCAT = http://hl7.org/fhir/observation-category + +/* LOINC Wound Assessment Panel (LOINC 39135-9) +See https://s.details.loinc.org/LOINC/39135-9.html?sections=Comprehensive + + 39135-9 Wound assessment panel O + 81666-0 Wound number [Identifier] + 72300-7 Wound type R + 89250-5 Device or anatomic structure visible in wound + 89251-3 Condition present on admission + 11373-8 Injury cause + 88878-4 Date of condition abatement {mm/dd/yyyy} + 72170-4 Photographic image + 89252-1 Episode of Wound + 89253-9 Trend + 85585-8 Date of Onset of Impairment {mm/dd/yyyy} + 72369-2 Body site identification panel R + 39111-0 Body site R + 39112-8 Body location qualifier O + 20228-3 Anatomic part Laterality O + 72301-5 Description of Periwound C + 72527-5 Pressure ulcer stage NPUAP + 72372-6 Wound bed and edge panel C + 89254-7 Wound bed panel + 72371-8 Appearance of Wound base R + 72370-0 Area of identified wound bed appearance/Area of wound bed of Wound base C % + **MISSING** Wound bed color panel + 39132-6 Color of Wound base O + 89255-4 Wound bed area identified by color/Area of wound bed % + 89256-2 Wound edge panel + 72304-9 Edge of wound description O + 39133-4 Color of Wound edge O + 72299-1 Wound tunneling and undermining panel C + 89257-0 Wound tunneling panel + 72298-3 Tunneling of Wound R + 72296-7 Tunneling [Length] of Wound C cm + 72297-5 Tunneling clock position of Wound C + 89258-8 Wound undermining panel + 72295-9 Undermining of Wound R + 72293-4 Undermining [Length] of Wound C cm + 72294-2 Undermining clock position of Wound C + 72292-6 Wound exudate panel C + 89259-6 Presence of wound exudate + 89260-4 Area of wound cm2 + 39116-9 Drainage amount of Wound C + 72288-4 Odor of Exudate from wound O + 72289-2 Color of Exudate from wound R + 72290-0 Appearance of Exudate from wound R + + 72287-6 Wound size panel C + 39125-0 Width of Wound R cm + 39127-6 Depth of Wound R cm + 39126-8 Length of Wound R cm + 80338-7 Wound assessment [Interpretation] + +*/ + + +//------------- Wound Absence or Presence --------------- +EntryElement: WoundPresent +Based on: Condition // TODO: change to BodyStructure? +Concept: SCT#416462003 "Wound (disorder)" // LNC#72300-7 Wound Type? +Description: "A determination that a particular type of wound that exists at a particular body site. +The WoundIdentifier serves as a link between this assertion and assessments of the wound that might occur at later times. Multiple wound assessments can be associated with a single wound." + Onset value is type dateTime // nowhere to put code LOINC 85585-8 Date of Onset {mm/dd/yyyy} + Abatement value is type dateTime // nowhere to put code 88878-4 Date of abatement {mm/dd/yyyy} +1..1 Category is OBSCAT#exam +1..1 Code from https://vsac.nlm.nih.gov/valueset/2.16.840.1.113883.1.11.20.2.6/expansion if covered +1..1 Identifier is type WoundIdentifier +0..1 ConditionCause is type WoundTypeEtiology +1..1 BodySite is type WoundBodySite +0..0 Severity // not sure if zeroing it out is wise, but severity is not part of LOINC panel +0..0 Criticality +0..0 Device + + Element: WoundIdentifier + Based on: Identifier + Concept: LNC#81666-0 + Description: "A human-readable identifier for the lesion; e.g., a letter or integer." + + Element: WoundTypeEtiology + Based on: ConditionCause + Concept: LNC#11373-8 "Injury cause" + Description: "A specialization of condition cause, specific to the causes of injuries (or not having injury in the wound absent context)." + Value: CodeableConcept from https://vsac.nlm.nih.gov/valueset/2.16.840.1.113762.1.4.1181.3/expansion // should be from http://loinc.org/vs/LL4936-2 + + Element: WoundBodySite + Based on: BodySite + Concept: LNC#39111-0 "Body Site" + BodySiteCode from https://vsac.nlm.nih.gov/valueset/2.16.840.1.113762.1.4.1181.14/expansion + 0..1 Laterality + 0..0 AnatomicalDirection + 0..0 ClockDirection + +//--------------- Wound Assessment ------------------------- + +EntryElement: WoundAssessmentPanel +Based on: NonLaboratoryObservation +Description: "Group of observations regarding the properties and severity of a wound." + Code is LNC#39135-9 "Wound assessment panel" +0..0 DataValue +0..0 DataAbsentReason +1..1 WoundIdentifier + Interpretation is type WoundAssessmentInterpretation +0..0 BodySite // carried by wound assertion +0..0 Device +0..0 ReferenceRange +0..* Attachment is type PhotographicImage // 72170-4 Photographic image [Attachment] + Components.ObservationComponent +includes 0..1 WoundEpisode // very similar to Episodicity or ClinicalStatus, but value set is different. +includes 0..1 WoundTrend +includes 0..1 WoundPeriwoundDescription // 72301-5 Description of Periwound +includes 0..* WoundVisibleInternalStructure //89250-5 Device or anatomic structure visible in wound +includes 0..1 WoundPressureUlcerAssociation // missing LOINC code +includes 0..1 WoundTunnelingPresentOrAbsent // 72298-3 Tunneling of Wound R present/absent +includes 0..1 WoundUnderminingPresentOrAbsent // 72295-9 Undermining of Wound R +includes 0..1 WoundExudatePresentOrAbsent // 89259-6 Presence of wound exudate + PanelMembers.Observation +includes 0..1 WoundBedPanel +includes 0..1 WoundEdgePanel // 89256-2 Wound edge panel +includes 0..1 WoundTunnelingPanel // 89257-0 Wound tunneling panel +includes 0..1 WoundUnderminingPanel // 89258-8 Wound undermining panel +includes 0..1 WoundExudatePanel // 72292-6 Wound exudate panel +includes 0..1 WoundSizePanel // 72287-6 Wound size panel + + Element: WoundEpisode + Based on: CodedObservationComponent + Description: "Wound episode refers to a period of the wound, an incident in the course of a wound" + Code is LNC#89252-1 "Episode of Wound" + DataValue from https://vsac.nlm.nih.gov/valueset/2.16.840.1.113762.1.4.1181.4/expansion + + Element: WoundPeriwoundDescription + Based on: CodedObservationComponent + Description: "A description of the skin around the wound (periwound). Color, induration, warmth and edema should be assessed. Redness of the surrounding skin can be indicative of unrelieved pressure. Irritation of the surrounding skin can result from exposure to feces or urine, a reaction to the dressing or tape, or inappropriate removal of dressing or tape. Redness, tenderness, warmth and swelling are classical clinical signs of infection. [Reference: Brown, P., 2009]" + Code is LNC#72301-5 "Description of Periwound" + DataValue from https://vsac.nlm.nih.gov/valueset/2.16.840.1.113762.1.4.1181.2/expansion + //could be from http://loinc.org/vs/LL2216-1 + + Element: WoundVisibleInternalStructure + Based on: CodedObservationComponent + Description: "Exposed body structures, devices, and/or foreign bodies visible by the naked eye in a wound." + Code is LNC#89250-5 "Device or anatomic structure visible in wound" + DataValue from https://vsac.nlm.nih.gov/valueset/2.16.840.1.113762.1.4.1181.1/expansion +// should be from http://loinc.org/vs/LL4935-4 + + Element: WoundPressureUlcerAssociation + Based on: CodedObservationComponent + Description: "Is the wound associated with a device or pressure point?" + Code is TBD#TBD "Pressure Ulcer Association" + DataValue from YesNoUnknownVS + + Element: WoundTunnelingPresentOrAbsent + Based on: CodedObservationComponent + Description: "The presence or absence of wound tunneling." + Code is LNC#72298-3 "Tunneling of Wound" + DataValue from PresentAbsentVS + // LOINC: should re-use the same Snomed codes for Present-Absent + + Element: WoundUnderminingPresentOrAbsent + Based on: CodedObservationComponent + Description: "The presence or absence of wound undermining." + Code is LNC#72295-9 "Undermining of Wound" + DataValue from PresentAbsentVS + + Element: WoundExudatePresentOrAbsent + Based on: CodedObservationComponent + Description: "The presence or absence of wound exudate." + Code is LNC#89259-6 "Presence of wound exudate" + DataValue from PresentAbsentVS + + Element: WoundAssessmentInterpretation + Based on: Interpretation + Concept: LNC#80338-7 + Description: "Overall assessement of whether the wound is within normal parameters." + Value: CodeableConcept from http://loinc.org/vs/LL3816-7 if covered // underpowered? 'normal' and 'other' + + Element: WoundTrend + Based on: CodedObservationComponent + Description: "Whether a condition is improving, worsening, stable, or resolved." + Code is LNC#89253-9 "Trend" + DataValue from https://vsac.nlm.nih.gov/valueset/2.16.840.1.113762.1.4.1181.5/expansion // should be from http://loinc.org/vs/LL4938-8 with values improved, deteriorated, stablized or resolved. Resolved is missing from the VS in VSAC + + +EntryElement: WoundBedPanel +Based on: ComponentOnlyNonLaboratoryObservation +Description: "The appearance and color of the base (bed) of the wound, together with the percentage of the bed with each type of appearance and color. The appearance and appearance percentage arrays must be the same length, and the order in the arrays is significant*; the elements at the same array position shall be interpreted as pairs. The same rule applies to the color and color percentage arrays. The number of color areas and appearance areas do not have to be the same. + +*See https://www.hl7.org/fhir/xml.html: When an element is allowed to repeat, the elements are ordered, and the technical infrastructure needs to be able to access the items in the right order. https://www.hl7.org/fhir/json.html The order of properties of an object is not significant in the JSON representation, though order within an array SHALL be maintained." +1..1 WoundIdentifier + Code is LNC#89254-7 "Wound Bed Panel" +0..0 BodySite // body site is given in the wound assertion +0..0 Device + Components.ObservationComponent +includes 0..* WoundBedAppearance +includes 0..* WoundBedAppearancePercentage +includes 0..* WoundBedColor +includes 0..* WoundBedColorAreaPercentage + + Element: WoundBedAppearance + Based on: CodedObservationComponent + Description: "Appearance of wound base (bed)." + Code is LNC#72371-8 "Appearance of Wound base" + DataValue from https://vsac.nlm.nih.gov/valueset/2.16.840.1.113762.1.4.1181.6/expansion //could be from http://loinc.org/vs/LL2237-7 + + Element: WoundBedAppearancePercentage + Based on: QuantitativeObservationComponent + Description: "Area of wound bed appearance/Entire Area of wound bed." + Code is LNC#72370-0 "Area of identified wound bed appearance/Area of wound bed of Wound base" + DataValue.Quantity.Units is UCUM#% + 0..0 ReferenceRange + + Element: WoundBedColor + Based on: CodedObservationComponent + Description: "Color of Wound base (bed)." + Code is LNC#39132-6 "Color of Wound base (bed)." + DataValue from https://vsac.nlm.nih.gov/valueset/2.16.840.1.113762.1.4.1181.7/expansion //could be from http://loinc.org/vs/LL2338-3 + + Element: WoundBedColorAreaPercentage + Based on: QuantitativeObservationComponent + Description: "Wound bed area identified by color/Area of wound bed." + Code is LNC#89255-4 "Wound bed area identified by color/Area of wound bed." + DataValue.Quantity.Units is UCUM#% + 0..0 ReferenceRange + +EntryElement: WoundEdgePanel +Based on: ComponentOnlyNonLaboratoryObservation +Description: "The state of the tissue at the edge of the wound." +1..1 WoundIdentifier + Code is LNC#89256-2 "Wound edge panel" +0..0 BodySite // location is given by the wound assertion +0..0 Device + Components.ObservationComponent +includes 0..1 WoundEdgeDescription +includes 0..1 WoundEdgeColor +// LOINC:Is the entire edge of the wound described by one color? Or should it be by percentage, similar to the wound bed? +// LOINC: Why precoordinate a general concept such as 'color' with the concept of wound edge? + + Element: WoundEdgeDescription + Based on: CodedObservationComponent + Description: "Edge of wound description." + Code is LNC#72304-9 "Edge of wound description" + DataValue from https://vsac.nlm.nih.gov/valueset/2.16.840.1.113762.1.4.1181.8/expansion // could be from http://loinc.org/vs/LL2230-2 + + Element: WoundEdgeColor + Based on: CodedObservationComponent + Description: "Color of Wound edge." + Code is LNC#39133-4 "Color of Wound edge" + DataValue could be from http://loinc.org/vs/LL2338-3 + +EntryElement: WoundTunnelingPanel +Based on: ComponentOnlyNonLaboratoryObservation +Description: "Observation of wound tunnels. The tunnel length and clock direction arrays must be the same length, and the order in the arrays is significant*; the elements at the same array position shall be interpreted as pairs." +1..1 WoundIdentifier + Code is LNC#89257-0 "Wound tunneling panel" +0..0 BodySite // location is given by the wound assertion +0..0 Device + Components.ObservationComponent +includes 0..* WoundTunnelLength +includes 0..* WoundTunnelClockDirection + +// LOINC: why precoordinate length + tunneling? +// LOINC: why precoordinate clock position + tunneling? + + Element: WoundTunnelLength + Based on: QuantitativeObservationComponent + Description: "Length of wound tunneling." + Code is LNC#72296-7 "Length of wound tunneling." + DataValue.Quantity.Units is UCUM#cm + 0..0 ReferenceRange + +// LOINC: should require use the full clock position value set + Element: WoundTunnelClockDirection + Based on: CodedObservationComponent + Description: "Clock position of wound tunnel" + Code is LNC#72297-5 "Clock position of wound tunnel" + DataValue from ClockDirectionVS + + +EntryElement: WoundUnderminingPanel +Based on: ComponentOnlyNonLaboratoryObservation +Description: "Assessment of deep tissue (subcutaneous fat and muscle) damage around the wound margin. The undermining length and clock direction arrays must be the same length, and the order in the arrays is significant*; the elements at the same array position shall be interpreted as pairs." +1..1 WoundIdentifier +0..0 BodySite // location is given by the wound assertion +0..0 Device + Components.ObservationComponent +includes 0..1 WoundUnderminingLength +includes 0..1 WoundUnderminingClockDirection + + Element: WoundUnderminingLength + Based on: QuantitativeObservationComponent + Description: "Length of wound undermining." + Code is LNC#72293-4 "Undermining [Length] of Wound" + DataValue.Quantity.Units is UCUM#cm + 0..0 ReferenceRange + +// LOINC: should require use the full clock position value set + Element: WoundUnderminingClockDirection + Based on: CodedObservationComponent + Description: "Clock position of wound undermining" + Code is LNC#72294-2 "Undermining clock position of Wound" + DataValue from ClockDirectionVS + +EntryElement: WoundExudatePanel +Based on: ComponentOnlyNonLaboratoryObservation +Description: "Description of the fluid produced by a wound." + Code is LNC#72292-6 "Wound exudate panel" +1..1 WoundIdentifier +0..0 BodySite // location is given by the wound assertion +0..0 Device + Components.ObservationComponent +includes 0..1 WoundExudateAmount +includes 0..1 WoundExudateAppearance +includes 0..1 WoundExudateColor +includes 0..1 WoundExudateOdor + +// LOINC: Wound area should be in wound size panel, not wound exudate panel + + Element: WoundExudateAmount + Based on: CodedObservationComponent + Description:"Drainage amount of wound" + Code is LNC#39116-9 "Drainage amount of Wound" + DataValue from https://vsac.nlm.nih.gov/valueset/2.16.840.1.113762.1.4.1181.10/expansion //could be from http://loinc.org/vs/LL2222-9 + + Element: WoundExudateAppearance + Based on: CodedObservationComponent + Description:"Appearance of exudate from wound" + Code is LNC#72290-0 "Appearance of exudate from wound" + DataValue from https://vsac.nlm.nih.gov/valueset/2.16.840.1.113762.1.4.1181.11/expansion //could be from http://loinc.org/vs/LL2220-3 + + Element: WoundExudateColor + Based on: CodedObservationComponent + Description:"Color of exudate from wound" + Code is LNC#72289-2 "Color of exudate from wound" + DataValue from https://vsac.nlm.nih.gov/valueset/2.16.840.1.113762.1.4.1181.12/expansion + // could be from http://loinc.org/vs/LL2219-5 + + Element: WoundExudateOdor + Based on: CodedObservationComponent + Description:"Odor of exudate from wound" + Code is LNC#72288-4 "Odor of Exudate from wound" + DataValue from https://vsac.nlm.nih.gov/valueset/2.16.840.1.113762.1.4.1181.13/expansion + + +EntryElement: WoundSizePanel +Based on: ComponentOnlyNonLaboratoryObservation +Description: "The estimated or measured dimensions of a wound." + Code is LNC#72287-6 "Wound size panel" +1..1 WoundIdentifier +0..0 BodySite // location is given by the wound assertion +0..0 Device + Components.ObservationComponent +includes 1..1 WoundLength +includes 1..1 WoundWidth +includes 0..1 WoundDepth +includes 0..1 WoundArea + + Element: WoundLength + Based on: QuantitativeObservationComponent + Description: "Length of the wound (longest dimension)." + Code is LNC#39126-8 "Length of wound" + DataValue.Quantity.Units is UCUM#cm + 0..0 ReferenceRange + + Element: WoundWidth + Based on: QuantitativeObservationComponent + Description: "Width of the wound (perpendicular to longest dimension)." + Code is LNC#39125-0 "Width of wound" + DataValue.Quantity.Units is UCUM#cm + 0..0 ReferenceRange + + Element: WoundDepth + Based on: QuantitativeObservationComponent + Description: "Depth of the wound." + Code is LNC#39127-6 "Depth of the wound." + DataValue.Quantity.Units is UCUM#cm + 0..0 ReferenceRange + + Element: WoundArea + Based on: QuantitativeObservationComponent + Description: "Area of the wound." + Code is LNC#89260-4 "Area of the wound." + DataValue.Quantity.Units is UCUM#cm2 + 0..0 ReferenceRange + +/* Old Stuff +Element: SupportSurface +Concept: SCT#272243001 +Based on: Device +Description: "A specific instance of a support surface used to distribute pressure and support a patient. The value is coding of the type of support surface." +Value: CodeableConcept from SupportSurfaceVS +0..1 SupportSurfaceCategory +0..1 SupportSurfaceBodyPosition +0..* SupportSurfaceComponent + + Element: SupportSurfaceCategory + Concept: TBD + Description: "The category of support surface." + Value: CodeableConcept from SupportSurfaceCategoryVS + + Element: SupportSurfaceBodyPosition + Concept: TBD + Description: "What body positions the surface can be used for, specifically, sitting or lying." + Value: CodeableConcept from SupportSurfaceBodyPositionVS + + Element: SupportSurfaceComponent + Concept: TBD + Description: "A physical material, structure, or system used alone or in combination with other components to fashion a support surface." + Value: CodeableConcept from SupportSurfaceComponentVS + +Element: SupportSurfaceUsed +Concept: TBD +Based on: DeviceUsed +Description: "A paricular instance of the use of a support surface in patient care." +Value: Device is type SupportSurface + Implanted is #no +0..1 ImmersionDepth + + Element: ImmersionDepth + Concept: TBD + Description: "Depth of penetration (sinking) into a support surface." + DataValue.Quantity.Units is UCUM#cm "cm" +*/ \ No newline at end of file diff --git a/spec/shr_wound_vs.txt b/spec/sw_wound_vs.txt similarity index 87% rename from spec/shr_wound_vs.txt rename to spec/sw_wound_vs.txt index 6c53dafb..3eef4e74 100644 --- a/spec/shr_wound_vs.txt +++ b/spec/sw_wound_vs.txt @@ -1,5 +1,8 @@ Grammar: ValueSet 5.0 -Namespace: shr.wound +Namespace: sw + + +/* Not used ValueSet: WoundMorphologyVS Description: "The shape and nature of a wound." @@ -9,8 +12,12 @@ ValueSet: WoundTypeVS Description: "Disorders classified as types of wounds." Includes codes descending from SCT#416462003 "Wound (disorder)" +SCT#241000205101 "Wound exudate quantity - none (finding)" +SCT#251000205103 "Wound exudate quantity - scant (finding)" +SCT#261000205100 "Wound exudate quantity - small (finding)" +SCT#291000205107 "Wound exudate quantity - moderate (finding)" +SCT#271000205108 "Wound exudate quantity - large (finding)" -/* Old stuff ValueSet: WoundBodySiteVS SCT#43631005 "Back of head" SCT#23747009 "Chin"