diff --git a/Makefile b/Makefile
index 0f88c0e5..fb4da13a 100644
--- a/Makefile
+++ b/Makefile
@@ -105,7 +105,7 @@ MODULE_NAMES := administration\
antibody-purification\
assays\
biopsy\
- biobank-specimens\
+ specimens\
organizations\
data-sets\
data-transformations\
diff --git a/README.md b/README.md
index 4610d168..b5059048 100644
--- a/README.md
+++ b/README.md
@@ -20,7 +20,7 @@ Our ontology terms come in three groups. Depending on what type of term you want
- [`assays.tsv`](src/ontology/templates/assays.tsv) for general assays
- [`epitope-assays.tsv`](src/ontology/templates/epitope-assays.tsv) specifically for immune epitope assays
- [`value-specifications.tsv`](src/ontology/templates/value-specifications.tsv)
- - [`biobank-specimens.tsv`](src/ontology/templates/biobank-specimens.tsv)
+ - [`specimens.tsv`](src/ontology/templates/specimens.tsv) for specimens
- [`medical-history.tsv`](src/ontology/templates/medical-history.tsv) for medical history classifications and related selection criteria
- [`study-designs.tsv`](src/ontology/templates/study-designs.tsv) for study designs
- [`data-sets.tsv`](src/ontology/templates/data-sets.tsv) for data sets
diff --git a/src/ontology/OntoFox_inputs/Uberon_input.txt b/src/ontology/OntoFox_inputs/Uberon_input.txt
index f8d66599..9c704777 100755
--- a/src/ontology/OntoFox_inputs/Uberon_input.txt
+++ b/src/ontology/OntoFox_inputs/Uberon_input.txt
@@ -14,6 +14,7 @@ http://purl.obolibrary.org/obo/UBERON_0000010 # peripheral nervous system
http://purl.obolibrary.org/obo/UBERON_0000029
http://purl.obolibrary.org/obo/UBERON_0000057 # urethra
http://purl.obolibrary.org/obo/UBERON_0000105
+http://purl.obolibrary.org/obo/UBERON_0000162 # cloaca
http://purl.obolibrary.org/obo/UBERON_0000165
http://purl.obolibrary.org/obo/UBERON_0000165 # mouth
http://purl.obolibrary.org/obo/UBERON_0000173
diff --git a/src/ontology/OntoFox_outputs/Uberon_imports.owl b/src/ontology/OntoFox_outputs/Uberon_imports.owl
index 30aedb96..8473f492 100644
--- a/src/ontology/OntoFox_outputs/Uberon_imports.owl
+++ b/src/ontology/OntoFox_outputs/Uberon_imports.owl
@@ -149,6 +149,18 @@
+
+
+
+
+ cloaca
+ Common chamber into which the intestines and excretory system opens. Arises during development in all vertebrates, but in many it becomes subdivided, lost or incorporated into other structures.
+
+ cloaca
+
+
+
+
diff --git a/src/ontology/catalog-v001.xml b/src/ontology/catalog-v001.xml
index 37551192..870c1343 100755
--- a/src/ontology/catalog-v001.xml
+++ b/src/ontology/catalog-v001.xml
@@ -30,7 +30,6 @@
-
@@ -43,6 +42,7 @@
+
diff --git a/src/ontology/modules/biobank-specimens.owl b/src/ontology/modules/specimens.owl
similarity index 61%
rename from src/ontology/modules/biobank-specimens.owl
rename to src/ontology/modules/specimens.owl
index bfbb4222..75682009 100644
--- a/src/ontology/modules/biobank-specimens.owl
+++ b/src/ontology/modules/specimens.owl
@@ -1,13 +1,13 @@
-
-
+
@@ -46,6 +46,12 @@
+
+
+
+
+
+
@@ -64,6 +70,12 @@
+
+
+
+
+
+
@@ -93,6 +105,12 @@
+
+
+
+
+
+
@@ -105,12 +123,36 @@
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
@@ -152,362 +218,1527 @@
-
+
-
+
-
+
-
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
-
-
-
-
-
-
-
-
-
-
-
+
+
+
+
+
-
- A specimen that is derived from amniotic fluid.
- Chris Stoeckert
- Chris Stoeckert, Penn Medicine Biobank
- amniotic fluid specimen
+ urine specimen
+
+ a portion of urine collected from an organism
+ 4/10/2011BP: It seems to me that the editor notes refer to a previous version, and are no longer relevant.
+ This could be instead a kind of collection of secreted stuff. Among secreted stuff there is passive, and active. urine is secreted, passiv. lavage is secreted, active
+ are we happy calling collection of urine a material separation?
+ urine specimen
-
+
-
+
+
+
+
+
+
+
+
-
-
-
-
-
-
-
-
-
-
-
+
+
+
+
+
+ blood specimen
+ blood drawn from a human for glucose assay
- A specimen that is derived from bile.
- Chris Stoeckert
- Chris Stoeckert, Penn Medicine Biobank
- bile specimen
+ a material entity derived from a portion of blood collected from an organism
+ Bjoern Peters
+ Bjoern Peters
+ blood specimen
-
+
-
+
+
+
+
+
+
+
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
+
+
+
+
+
-
- A specimen that is derived from cerbrospinal fluid.
- Chris Stoeckert
- Chris Stoeckert, Penn Medicine Biobank
- cerebrospinal fluid specimen
+ sample from organism
+
+ a material obtained from an organism in order to be a representative of the whole
+ 5/29: This is a helper class for now
+ we need to work on this: Is taking a urine sample a material separation process? If not, we will need to specify what 'taking a sample from organism' entails. We can argue that the objective to obtain a urine sample from a patient is enough to call it a material separation process, but it could dilute what material separation was supposed to be about.
+ sample from organism
-
+
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- A specimen that is derived from feces.
- Chris Stoeckert
- stool specimen
- Chris Stoeckert, Penn Medicine Biobank
- feces specimen
+
+
+
+
+
+
+
+
+ whole organism preparation
+ putting a mouse in the blender. Not: putting a mouse on a scale
+
+ A material entity which is the output of a process in which one or more whole organisms are prepared in a way to make it easier to study them, and in which the great majority of organismal parts are maintained
+ does this include injecting a dye to a patient to be able to visualize parts of his brain? If not, we should state that the components of the organism are substantially re-arranged.
+ whole organism preparation
-
+
-
+
+
+
+
+
+
+
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
+
+
+
+
+
-
- A specimen that is derived from digestive system fluid or secretion.
- Chris Stoeckert
- gastric fluid specimen
- Chris Stoeckert, Penn Medicine Biobank
- digestive system fluid or secretion specimen
+ material sample
+ blood drawn from patient to measure his systemic glucose level. A population of humans with HIV enrolled in a study taken to represent patients with HIV in general.
+
+ A material entity that has the material sample role
+ OBI: workshop
+ sample
+ sample population
+ https://github.com/obi-ontology/obi/issues/1013
+ material sample
-
+
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- A specimen that is derived from milk.
- Chris Stoeckert
- Chris Stoeckert, Penn Medicine Biobank
- milk specimen
+
+
+ high molecular weight DNA extract
+ Extraction of chromosomal DNA from mammalian cells by first isolating nucei
+
+ The output of an extraction process in which DNA molecules above a molecular weight cutoff are purified in order to exclude DNA from organellas.
+ PERSON:Chris Stoeckert
+ OBI
+ high molecular weight DNA extract
-
+
-
-
-
-
-
-
-
-
-
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ nuclear RNA extract
+ Isolation and purification of nuclear RNA from animal cells using Norgen Bioteck corp. cytoplasmic and nuclear RNA purification kit (http://www.norgenbiotek.com/display-product.php?ID=30)
+
+ A RNA extract that is the output of an extraction process in which RNA molecules found in the nucleus, including mRNA precursors (pre-mRNA), are extracted.
+ PERSON: Chris Stoeckert
+ PERSON: Jie Zheng
+ UPenn Group
+ nuclear RNA extract
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ polyA RNA extract
+ Preparation of polyA RNA by cellulose-bound oligo-dT (Aviv, H., Leder, P. 1972. Purification of biologically active globin messenger RNA by chromatography on oligothymidylic acid-cellulose. Proc. Nat. Acad. Sci. USA 69, 1408-1412.)
+
+ A RNA extract that is the output of an extraction process in which RNA molecules with poly A tail at its 3' end are purified.
+ PERSON: Chris Stoeckert
+ PERSON: Jie Zheng
+ UPenn Group
+ polyA RNA extract
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ pre-mortem specimen
+ material obtained through a liver biopsy from a human patient
+
+ a specimen that was taken from a live organism
+ Bjoern Peters
+ MO_705 premortem
+ pre-mortem specimen
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ cytoplasmic RNA extract
+ Cytoplasmic RNA extraction from mammalian tissues to create cDNA library (Carninci P, Nakamura M, Sato K, Hayashizaki Y, Brownstein MJ. Cytoplasmic RNA extraction from fresh and frozen mammalian tissues. Biotechniques. 2002;33:306–309.)
+
+ A RNA extract that is the output of a RNA extraction process in which RNA molecules found in the cytoplasm are extracted.
+ PERSON:Chris Stoeckert
+ UPenn Group
+ cytoplasmic RNA extract
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ RNA extract
+
+ an extract which is the output of an extraction process in which RNA molecules are isolated from a specimen.
+ PERSON: Chris Stoeckert
+ PERSON: Jie Zheng
+ Group: UPenn Group
+ RNA extract
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ total RNA extract
+ Extraction of total RNA from cells with Qiagen mini RNeasy kit
+
+ A RNA extract that is the output of an extraction process in which total celluar and organelle RNA molecules are isolated from a specimen.
+ PERSON: Chris Stoeckert
+ PERSON: Jie Zheng
+ UPenn Group
+ total RNA extract
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ organellar RNA extract
+ Extraction of organellar RNA from plant cells using organellar RNA binding protein.
+
+ A RNA extract that is the output of an extraction process in which RNA molecules found in an organelle, e.g., mitochondrion, ER, or chloroplast, excluding the nucleus, are extracted.
+ PERSON: Chris Stoeckert
+ PERSON: Jie Zheng
+ UPenn Group
+ organellar RNA extract
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ post mortem specimen
+ the spleen taken from a dead mouse
+
+ a specimen that was taken from a dead organism
+ Bjoern Peters
+ MO_416 postmortem
+ post mortem specimen
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ labeled DNA extract
+
+ a labeled specimen that is the output of a labeling process and has grain labeled DNA to be able to detect DNA in future experiments.
+ Need to find out if we consider labeled nucleotides still nucleotides. It is after consulting with ChEBI group. Added duirng Mar 1, 2010 dev call
+ Group: OBI group
+ Group: OBI group
+ labeled DNA extract
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ cell specimen
+ type of sample used in the PCIRN influenza network
+
+ A specimen obtained by inserting a swab deeply into the vent of the cloaca of an organism and vigorously swabbing the wall. The swab should be deeply stained with fecal material and is then placed in transport medium.
+ PERSON: Melanie Courtot
+ WEB: http://www.wpro.who.int/NR/rdonlyres/EFD2B9A7-2265-4AD0-BC98-97937B4FA83C/0/manualonanimalaidiagnosisandsurveillance.pdf
+ cloacal specimen
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ nasopharyngeal aspirate specimen
+ type of sample used in the PCIRN influenza network
+
+ A specimen which derives from nasopharyngeal mucosa after aspiration.
+ PERSON: Melanie Courtot
+ WEB: http://www.wpro.who.int/NR/rdonlyres/EFD2B9A7-2265-4AD0-BC98-97937B4FA83C/0/manualonanimalaidiagnosisandsurveillance.pdf
+ nasopharyngeal aspirate specimen
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ nasal swab specimen
+ type of sample used in the PCIRN influenza network
+
+ A specimen obtained using a cotton swab on a stick, passed up the nostril to obtain a sample of exudate and epithelial debris for microbiological or cellular examination.
+ PERSON: Melanie Courtot
+ WEB: http://www.wpro.who.int/NR/rdonlyres/EFD2B9A7-2265-4AD0-BC98-97937B4FA83C/0/manualonanimalaidiagnosisandsurveillance.pdf
+ nasal swab specimen
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ labeled RNA extract
+
+ a labeled specimen that is the output of a labeling process and has grain labeled RNA to be able to detect RNA in future experiments.
+ Need to find out if we consider labeled nucleotides still nucleotides. It is after consulting with ChEBI group. Added duirng Mar 1, 2010 dev call
+ Group: OBI group
+ Group: OBI group
+ labeled RNA extract
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ frozen specimen
+ Frozen blood plasma
+
+ A specimen that has been frozen in order to store it.
+ Person:Alan Ruttenberg
+ MO_610 frozen_sample
+ frozen specimen
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ labeled specimen
+
+ A specimen that has been modified in order to be able to detect it in future experiments
+ added during call 3/1/2010
+ OBI group
+ labeled specimen
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ paraffin specimen
+ liver tissue embedded in paraffin
+
+ a specimen that is output of a paraffin storage process in which specimen is embedded in paraffin
+ PERSON: Chris Stoeckert
+ PERSON: Jie Zheng
+ MO_990 paraffin_sample
+ paraffin specimen
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ processed specimen
+
+ A specimen that has been intentionally physically modified.
+ A tissue sample that has been sliced and stained for a histology study.
+ Bjoern Peters
+ Bjoern Peters
+ processed specimen
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ lyophilized specimen
+ freezing dried DNA
+
+ a specimen that is output of a lyophilization storage process in which specimen is lyophilized for storage.
+ PERSON: Chris Stoeckert
+ PERSON: Jie Zheng
+ MO_589 freeze_dried_sample
+ lyophilized specimen
+
+
+
+
+
+
+
+
+ fresh specimen
+ a liver freshly removed from a rat
+
+ a specimen that is output of a specimen creation process used for an investigation without storage.
+ PERSON: Chris Stoeckert
+ PERSON: Jie Zheng
+ MO_730 fresh_sample
+ fresh specimen
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ agar stab specimen
+
+ a specimen that is output of a process that cell culture inoculated into agar for long term storage.
+ PERSON: Chris Stoeckert
+ PERSON: Jie Zheng
+ MO_971 agar_stab
+ agar stab specimen
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ nucleic acid extract
+
+ An extract that is the output of an extraction process in which nucleic acid molecules are isolated from a specimen.
+ Person: Jie Zheng
+ UPenn Group
+ nucleic acid extract
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ DNA extract
+
+ The output of an extraction process in which DNA molecules are purified in order to exclude DNA from organellas.
+ Person: Jie Zheng
+ Group: UPenn group
+ DNA extract
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ labeled nucleic acid extract
+
+ a labeled specimen that is the output of a labeling process and has grain labeled nucleic acid for detection of the nucleic acid in future experiments.
+ Person: Jie Zheng
+ labeled extract
+ MO_221 labeledExtract
+ labeled nucleic acid extract
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ cell specimen
+
+ A specimen primarily composed of a cell or cells collected from a multicellular organism or a cell culture.
+ Discussed on obi call Jan 23, 2017. To improve cell specimen that include single cell specimen. Details see tracker: https://sourceforge.net/p/obi/obi-terms/828
+ PERSON: Chris Stoeckert, Jie Zheng, Alexander Diehl
+ MO_612 cell
+ cell specimen
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ specimen with known storage state
+
+ A specimen for which it is known whether it has been subjected to storage of a specified type.
+ PERSON: Chris Stoeckert, Jie Zheng
+ MO_95 BiosourceType
+ specimen with known storage state
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ A specimen that derives from an anatomical part or substance arising from an organism. Examples of tissue specimen include tissue, organ, physiological system, blood, or body location (arm).
+ PERSON: Chris Stoeckert, Jie Zheng
+ tissue specimen
+ MO_954 organism_part
+ specimen from organism
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ specimen with pre- or post-mortem status
+
+ A specimen that has been established to be taken from a live (pre-mortem) or dead (post-mortem) organism.
+ organizational term, used in description of specimen that is created from known pre- or post-mortem status
+ PERSON: Chris Stoeckert, Jie Zheng
+ MO_84 OrganismStatus
+ specimen with pre- or post-mortem status
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ H&E-stained fixed tissue slide specimen
+
+ A fixed tissue slide specimen that is the output of H&E slide staining.
+ Chris Stoeckert, Ned Haubein
+ OBIB, OBI
+ H&E-stained fixed tissue slide specimen
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ IHC-stained fixed tissue slide specimen
+
+ A fixed tissue slide specimen that is the output of immunohistochemistry slide staining.
+ Chris Stoeckert, Ned Haubein
+ OBIB, OBI
+ IHC-stained fixed tissue slide specimen
+
+
+
+
+
+
+
+
+
+ A cell specimen that contains only one cell.
+ Requested by Sirarat Sarntivijai (EBI). Details see tracker: https://sourceforge.net/p/obi/obi-terms/828/
+ PERSON: Jie Zheng, Alexander Diehl
+ PERSON: Jie Zheng, Alexander Diehl
+ single cell specimen
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ A specimen that is derived from amniotic fluid.
+ Chris Stoeckert
+ Chris Stoeckert, Penn Medicine Biobank
+ amniotic fluid specimen
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ A specimen that is derived from bile.
+ Chris Stoeckert
+ Chris Stoeckert, Penn Medicine Biobank
+ bile specimen
+
+
+
+
+
+
+
+
+
+
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+
+
+
+
+
+ A specimen that is derived from cerbrospinal fluid.
+ Chris Stoeckert
+ Chris Stoeckert, Penn Medicine Biobank
+ cerebrospinal fluid specimen
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
-
+
+
+
+
+
+
+
+
+
+ A specimen that is derived from feces.
+ Chris Stoeckert
+ stool specimen
+ Chris Stoeckert, Penn Medicine Biobank
+ feces specimen
+
+
+
+
+
+
+
+
+
+
+
-
-
+
+
+
+
+
+
+
+
+
- A specimen that is derived from pericardial fluid.
+ A specimen that is derived from digestive system fluid or secretion.
Chris Stoeckert
+ gastric fluid specimen
Chris Stoeckert, Penn Medicine Biobank
- pericardial fluid specimen
+ digestive system fluid or secretion specimen
-
+
-
+
+
-
-
+
+
+
+
+
+
+
+
+
+ A specimen that is derived from milk.
+ Chris Stoeckert
+ Chris Stoeckert, Penn Medicine Biobank
+ milk specimen
+
+
+
+
+
+
+
+
+
+
+
-
-
+
+
+
+
+
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+
+
+
- A specimen that is derived from saliva.
+ A specimen that is derived from pericardial fluid.
Chris Stoeckert
Chris Stoeckert, Penn Medicine Biobank
- saliva specimen
+ pericardial fluid specimen
-
+
-
+
+
-
-
+
+
+
+
+
+
+
+
+
+ A specimen that is derived from saliva.
+ Chris Stoeckert
+ Chris Stoeckert, Penn Medicine Biobank
+ saliva specimen
+
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-
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+
+
+
+
+
+
+
+
+ A specimen that is derived from vagina.
+ Chris Stoeckert
+ Chris Stoeckert, NCI BBRB
+ vagina specimen
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ A RNA extract that is the output of an extraction process in which RNA molecules lacking poly A tails at thier 3' ends are purified.
+ Mark A. Miller, based on http://purl.obolibrary.org/obo/OBI_0000869
+ PERSON: Chris Stoeckert
+ PERSON: Jie Zheng
+ UPenn Group
+ polyA depleted RNA extract
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ swab specimen
- A specimen that is derived from vagina.
+ A specimen that is stored on a swab as the output of a collecting specimen with swab process.
Chris Stoeckert
- Chris Stoeckert, NCI BBRB
- vagina specimen
+ OBIB/OBI
+ https://github.com/obi-ontology/obi/issues/910
+ OBIB
+ swab specimen
@@ -2760,34 +3813,25 @@
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@@ -3261,19 +4215,89 @@
-
+
+
+
+
+ ribosomal RNA-depleted RNA extract
+ Looking at the reads for each ribosomal RNA-depleted RNA extract, the vast majority align to protein coding genes based on the ENSEMBL annotation.
+
+ An extract of RNA which is produced through rRNA (ribosomal RNA) depletion (the removal of highly abundant rRNA species).
+ Dan Berrios
+ https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-018-4585-1
+ ribosomal RNA-depleted RNA extract
+
+
+
+
+
+
+
+
+
+
+
+
+
+ 1
+
+
+
+
+
+ A specimen composed of an individual organism to be studied in an investigation.
+ Person: Jie Zheng
+ EFO_0000542 individual
+ https://github.com/obi-ontology/obi/issues/1092
+ individual organism specimen
+
+
+
+
+
+
+
+
+
+
+
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+
+
+
+
+
+
+
+
+ A specimen used in a blood meal assay to determine what is the source of blood ingested by a mosquito.
+
+ A specimen of the blood ingested by an arthropod.
+ The mosquito feeds on a human for example, ingests the blood of the human, this blood is then taken from the tummy of a mosquito and a PCR may be run on this specimen to identify that the mosquito definitely fed on a human.
+ Chris Stoeckert
+ Jie Zheng
+ blood meal
+ VEuPathDB
+ https://github.com/obi-ontology/obi/issues/1117
+ VEuPathDB
+ arthropod meal of blood specimen
+
+
+
+
+
-
+
+
-
@@ -3286,15 +4310,10 @@
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+
A sputum specimen that is collected from an organism following its inhalation of a nebulized salt solution.
John Judkins
@@ -3304,40 +4323,42 @@
+
+
+
+
+ A blood plasma specimen that is the output of some platelet-poor plasma preparation and is the portion of plasma that contains fewer than 10,000 platelets per microliter.
+ PERSON: Matthew Diller
+ platelet-poor plasma specimen
+
+
+
+
+
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+
A specimen that is collected with a suctioning tube from the trachea.
Asiyah Yu Lin ORCID:0000-0003-2620-0345
@@ -3354,34 +4375,25 @@
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@@ -3537,7 +4522,7 @@
-
+
@@ -3555,48 +4540,39 @@
- A specimen that is derived from the lower respiratory tract.
- Asiyah Yu Lin ORCID:0000-0003-2620-0345
- Asiyah Yu Lin ORCID:0000-0003-2620-0345
- lower respiratory tract specimen
-
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+ A specimen that is derived from the lower respiratory tract.
+ Asiyah Yu Lin ORCID:0000-0003-2620-0345
+ Asiyah Yu Lin ORCID:0000-0003-2620-0345
+ lower respiratory tract specimen
+
+
+
+
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@@ -3617,10 +4593,10 @@
+
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@@ -3633,15 +4609,10 @@
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+
+
A specimen that derives from a biofilm that forms on the inner surface of an endotracheal tube while the tube is in the trachea. The specimen is collected upon removal of the tube from the trachea.
John Judkins ORCID:0000-0001-6595-0902
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A specimen that derives from a biofilm that forms on the inner surface of an endotracheal tube while the tube is in the trachea. The specimen is collected by suction without removing the tube.
John Judkins ORCID:0000-0001-6595-0902
@@ -3691,10 +4657,10 @@
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A blood specimen that is located in a vacutainer.
John Judkins
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A blood specimen that is located on a filter paper.
Chris Stoeckert
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A processed specimen that is extracted from whole blood using gradient centrifugation that separates the blood into a layer of peripheral blood mononuclear cells under the top layer of plasma. It contains lymphocytes, monocytes or macrophages that are critical components in the immune system.
Chris Stoeckert
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A specimen that is derived from a portion of lymph collected from an organism.
John Judkins ORCID:0000-0001-6595-0902
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+
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+
+
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+
+ A specimen that is derived from part of a digestive tract.
+ John Judkins ORCID:0000-0001-6595-0902
+ VEuPathDB
+ digestive tract specimen
+
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+ A specimen collected through nasal cavity lavage that contains the reagents used to for the lavage process, organisms, cells, cellular secretions, and other biomaterials present in the nasal cavity space.
+ Randi Vita
+ Sebastian Duesing
+ nasal lavage fluid
+
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+
+ albumin-free serum
+ A blood serum specimen that contains no albumin.
+ Sebastian Duesing
+ https://github.com/obi-ontology/obi/issues/493
+ Philippe Rocca-Serra
+ albumin-free serum
+
+
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+ lavage fluid specimen
+ The collection of bronchoalveolar lavage fluid (BAL) from the lungs of mice in order to study the cytokines present.
+ A specimen obtained through a lavage process which includes fluid in addition to cells and/or cellular secretions.
+ Sebastian Duesing
+ https://github.com/obi-ontology/obi/issues/1803
+ lavage fluid specimen
+
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+ oral lavage fluid
+ A specimen collected through oral cavity lavage that contains the reagents used to for the lavage process, organisms, cells, cellular secretions, and other biomaterials present in the oral cavity space.
+ Sebastian Duesing
+ mouth rinse specimen
+ https://github.com/obi-ontology/obi/issues/1803
+ Anna Maria Masci
+ oral lavage fluid
+
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- A specimen that is derived from part of a digestive tract.
- John Judkins ORCID:0000-0001-6595-0902
- VEuPathDB
- digestive tract specimen
+ blood plasma specimen
+ PMID: 18217225.Sex Transm Dis. 2008 Jan;35(1):55-60. Review.Human immunodeficiency virus viral load in blood plasma and semen: review and implications of empirical findings.
+
+ a material entity which corresponds to the liquid component of blood, in which the blood cells are suspended.
+ 03/21/2010: BP, blood plasma is defined as the output of certain separation processes, so this is in the domain of OBI, not FMA.
+ PERSON: Maura Gasparetto
+ PERSON: Melanie Courtot
+ PERSON: Philippe Rocca-Serra
+ plasma
+ WEB: http://en.wikipedia.org/wiki/Blood_plasma
+ blood plasma specimen
+
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+ blood serum specimen
+ PMID: 18229666.Adv Med Sci. 2007;52 Suppl 1:204-6.Antioxidant activity of blood serum and saliva in patients with periodontal disease treated due to epilepsy.
+
+ A material entity which derives from blood and corresponds to blood plasma without fibrinogen or the other clotting factors.
+ PERSON: Maura Gasparetto
+ PERSON: Melanie Courtot
+ PERSON: Philippe Rocca-Serra
+ WEB: http://en.wikipedia.org/wiki/Blood_plasma
+ blood serum specimen
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- A specimen collected through nasal cavity lavage that contains the reagents used to for the lavage process, organisms, cells, cellular secretions, and other biomaterials present in the nasal cavity space.
- Randi Vita
- Sebastian Duesing
- nasal lavage fluid
+ bronchial alveolar lavage
+ solution containing lung derived T cells, eosinophils, and TNFa.
+
+ Group of biomaterials present in the bronchial aveolar space of an organism which are collected through lavage including the reagents used to for the lavage process, organisms, cells, and cellular secretions present in the bronchial aveolar space.
+ PERSON: Bjoern Peters
+ BAL
+ GROUP: IEDB
+ bronchial alveolar lavage
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- lavage fluid specimen
- The collection of bronchoalveolar lavage fluid (BAL) from the lungs of mice in order to study the cytokines present.
- A specimen obtained through a lavage process which includes fluid in addition to cells and/or cellular secretions.
- Sebastian Duesing
- https://github.com/obi-ontology/obi/issues/1803
- lavage fluid specimen
+ pool of specimens
+
+ A pool of specimens is a mixture of a population of samples which have been gathered from one or more sample populations, obtained by the physical process of mixing individual specimens, e.g. mixing the DNA collected from the individual fish.
+ check with advisors as to how to represent multiple instances of any class? a set of specimens which have been gathered from one or more sample_populations, obtained by the physical process of mixing individual specimens, e.g. mixing the DNA collected from the individual fish
+ PERSON: Jennifer Fostel
+ GROUP: CEBS
+ pool of specimens
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+ whole mount tissue
+
+ A whole organism preparation resulting from a histological preparation known as whole mount preparation where the whole specimen is mounted or spread on the microscope (glass) slide
+ PERSON: Helen Parkinson
+ PERSON: Philippe Rocca-Serra
+ whole mount sample
+ GROUP: OBI
+ PRS:22-02-2008: indicates the need to create a protocol application and distinguish it from this entity
+ PRS:22-02-2008: is a material which has output_role during whole mount preparation protocol-application
+ whole mount tissue
+
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- oral lavage fluid
- A specimen collected through oral cavity lavage that contains the reagents used to for the lavage process, organisms, cells, cellular secretions, and other biomaterials present in the oral cavity space.
- Sebastian Duesing
- mouth rinse specimen
- https://github.com/obi-ontology/obi/issues/1803
- Anna Maria Masci
- oral lavage fluid
+ lymph node cell specimen
+
+ A cell specimen comprised of a mixed population of cells obtained by processing whole lymph node into individual cells, typically performed using a sieve. This population includes T cells, B cells, macrophages, and other cell types.
+ IEDB
+ IEDB
+ lymph node cell specimen
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+ splenocyte specimen
+
+ A cell specimen comprised of a mixed cell population obtained by processing whole spleen into individual cells, typically performed using a sieve or blender. This population includes T cells, B cells, macrophages, and other cell types.
+ IEDB
+ IEDB
+ splenocyte specimen
+
-
+
-
+
+
+ FFPE specimen
+ Many of today’s researchers prefer to use Formalin-Fixed Paraffin-Embedded samples of tissues for their IHC, histological or in-situ genomic analyses. Professionally fixed and embedded FFPE samples and the biomolecules they contain are reasonably stable at ambient temperatures. -based on https://lab-ally.com/histopathology-resources/ffpe-samples/
+ A specimen that has been fixed in formalin and embedded in paraffin.
+ MIABIS
+ formalin-fixed paraffin-embeded specimen
+ https://www.biochain.com/general/what-is-ffpe-tissue/
+ https://github.com/obi-ontology/obi/issues/1019
+ FFPE specimen
+
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A specimen that is derived from some erythrocytes
Christian Stoeckert ORCID:0000-0002-5714-991X
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A specimen that is derived from some reticulocytes
Christian Stoeckert ORCID:0000-0002-5714-991X
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A specimen that is derived from some leukocytes
Christian Stoeckert ORCID:0000-0002-5714-991X
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diff --git a/src/ontology/obi-edit.owl b/src/ontology/obi-edit.owl
index 1b85d742..8d7cd215 100644
--- a/src/ontology/obi-edit.owl
+++ b/src/ontology/obi-edit.owl
@@ -44,7 +44,6 @@
-
@@ -57,6 +56,7 @@
+
@@ -4207,7 +4207,7 @@ editor = PRS
specimen role
liver section; a portion of a culture of cells; a nemotode or other animal once no longer a subject (generally killed); portion of blood from a patient.
- a role borne by a material entity that is gained during a specimen collection process and that can be realized by use of the specimen in an investigation
+ A role borne by a material entity that is obtained during a specimen collection process and that can be realized by performing measurements or observations on the specimen.
22Jun09. The definition includes whole organisms, and can include a human. The link between specimen role and study subject role has been removed. A specimen taken as part of a case study is not considered to be a population representative, while a specimen taken as representing a population, e.g. person taken from a cohort, blood specimen taken from an animal) would be considered a population representative and would also bear material sample role.
Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation.
blood taken from animal: animal continues in study, whereas blood has role specimen.
@@ -7368,39 +7368,6 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094
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- urine specimen
-
- a portion of urine collected from an organism
- 4/10/2011BP: It seems to me that the editor notes refer to a previous version, and are no longer relevant.
- This could be instead a kind of collection of secreted stuff. Among secreted stuff there is passive, and active. urine is secreted, passiv. lavage is secreted, active
- are we happy calling collection of urine a material separation?
- urine specimen
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- blood specimen
- blood drawn from a human for glucose assay
-
- a material entity derived from a portion of blood collected from an organism
- Bjoern Peters
- Bjoern Peters
- blood specimen
-
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-
-
@@ -7571,9 +7505,10 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094
- drawing blood from a patient for analysis, collecting a piece of a plant for depositing in a herbarium, buying meat from a butcher in order to measure its protein content in an investigation
+ drawing blood from a patient for analysis, collecting a piece of a plant for depositing in a herbarium, buying meat from a butcher in order to measure its protein content in an investigation, collecting a stone from a site
- A planned process with the objective of collecting a specimen.
+ A planned process with the objective to obtain a material entity for potential use as an input upon which measurements or observations are performed.
+ Definition updated following discussion on 2024-10-07 OBI dev call.
Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation.
Philly2013: A specimen collection can have as part a material entity acquisition, such as ordering from a bank. The distinction is that specimen collection necessarily involves the creation of a specimen role. However ordering cell lines cells from ATCC for use in an investigation is NOT a specimen collection, because the cell lines already have a specimen role.
Philly2013: The specimen_role for the specimen is created during the specimen collection process.
@@ -7706,40 +7641,6 @@ http://sourceforge.net/p/obi/obi-terms/716/
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- sample from organism
-
- a material obtained from an organism in order to be a representative of the whole
- 5/29: This is a helper class for now
- we need to work on this: Is taking a urine sample a material separation process? If not, we will need to specify what 'taking a sample from organism' entails. We can argue that the objective to obtain a urine sample from a patient is enough to call it a material separation process, but it could dilute what material separation was supposed to be about.
- sample from organism
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- whole organism preparation
- putting a mouse in the blender. Not: putting a mouse on a scale
-
- A material entity which is the output of a process in which one or more whole organisms are prepared in a way to make it easier to study them, and in which the great majority of organismal parts are maintained
- does this include injecting a dye to a patient to be able to visualize parts of his brain? If not, we should state that the components of the organism are substantially re-arranged.
- whole organism preparation
-
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@@ -7909,7 +7773,8 @@ http://sourceforge.net/p/obi/obi-terms/716/
The objective to collect bits of excrement in the rainforest. The objective to obtain a blood sample from a patient.
- A objective specification to obtain a material entity for potential use as an input during an investigation.
+ A objective specification that is fulfilled by obtaining a material entity for potential use as an input upon which measurements or observations are performed.
+ OBI recommends against subclassing this term in order to avoid further parallel hierarchies between this term and specimen collection process.
Bjoern Peters
Bjoern Peters
specimen collection objective
@@ -8921,33 +8786,6 @@ the role 'adjuvant role' inheres in some 'material entity' a
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- material sample
- blood drawn from patient to measure his systemic glucose level. A population of humans with HIV enrolled in a study taken to represent patients with HIV in general.
-
- A material entity that has the material sample role
- OBI: workshop
- sample population
-
- sample
- material sample
-
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@@ -9748,21 +9586,6 @@ http://en.wikipedia.org/wiki/Survival_rate
-
-
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- high molecular weight DNA extract
- Extraction of chromosomal DNA from mammalian cells by first isolating nucei
-
- The output of an extraction process in which DNA molecules above a molecular weight cutoff are purified in order to exclude DNA from organellas.
- PERSON:Chris Stoeckert
- OBI
- high molecular weight DNA extract
-
-
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- nuclear RNA extract
- Isolation and purification of nuclear RNA from animal cells using Norgen Bioteck corp. cytoplasmic and nuclear RNA purification kit (http://www.norgenbiotek.com/display-product.php?ID=30)
-
- A RNA extract that is the output of an extraction process in which RNA molecules found in the nucleus, including mRNA precursors (pre-mRNA), are extracted.
- PERSON: Chris Stoeckert
- PERSON: Jie Zheng
- UPenn Group
- nuclear RNA extract
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- polyA RNA extract
- Preparation of polyA RNA by cellulose-bound oligo-dT (Aviv, H., Leder, P. 1972. Purification of biologically active globin messenger RNA by chromatography on oligothymidylic acid-cellulose. Proc. Nat. Acad. Sci. USA 69, 1408-1412.)
-
- A RNA extract that is the output of an extraction process in which RNA molecules with poly A tail at its 3' end are purified.
- PERSON: Chris Stoeckert
- PERSON: Jie Zheng
- UPenn Group
- polyA RNA extract
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- pre-mortem specimen
- material obtained through a liver biopsy from a human patient
-
- a specimen that was taken from a live organism
- Bjoern Peters
- MO_705 premortem
- pre-mortem specimen
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- cytoplasmic RNA extract
- Cytoplasmic RNA extraction from mammalian tissues to create cDNA library (Carninci P, Nakamura M, Sato K, Hayashizaki Y, Brownstein MJ. Cytoplasmic RNA extraction from fresh and frozen mammalian tissues. Biotechniques. 2002;33:306–309.)
-
- A RNA extract that is the output of a RNA extraction process in which RNA molecules found in the cytoplasm are extracted.
- PERSON: Chris Stoeckert
- PERSON: Jie Zheng
- UPenn Group
- cytoplasmic RNA extract
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- RNA extract
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- an extract which is the output of an extraction process in which RNA molecules are isolated from a specimen.
- PERSON: Chris Stoeckert
- PERSON: Jie Zheng
- Group: UPenn Group
- RNA extract
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@@ -10391,28 +10079,6 @@ J Nutr. 2010 Feb;140(2):382-91. Epub 2009 Dec 23.
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- total RNA extract
- Extraction of total RNA from cells with Qiagen mini RNeasy kit.
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- A RNA extract that is the output of an extraction process in which total celluar and organelle RNA molecules are isolated from a specimen.
- PERSON: Chris Stoeckert
- PERSON: Jie Zheng
- UPenn Group
- total RNA extract
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@@ -10428,89 +10094,26 @@ J Nutr. 2010 Feb;140(2):382-91. Epub 2009 Dec 23.
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- organellar RNA extract
- Extraction of organellar RNA from plant cells using organellar RNA binding protein.
+
+
+ sequence feature annotation
- A RNA extract that is the output of an extraction process in which RNA molecules found in an organelle, e.g., mitochondrion, ER, or chloroplast, excluding the nucleus, are extracted.
- PERSON: Chris Stoeckert
- PERSON: Jie Zheng
- UPenn Group
- organellar RNA extract
+ Information about a sequence region
+ Bjoern Peters
+ Bjoern Peters
+ place holder for sequence ontology term
+ sequence feature annotation
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+
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- post mortem specimen
- the spleen taken from a dead mouse
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- a specimen that was taken from a dead organism
- Bjoern Peters
- MO_416 postmortem
- post mortem specimen
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- sequence feature annotation
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- Information about a sequence region
- Bjoern Peters
- Bjoern Peters
- place holder for sequence ontology term
- sequence feature annotation
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+
+
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- labeled DNA extract
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- a labeled specimen that is the output of a labeling process and has grain labeled DNA to be able to detect DNA in future experiments.
- Need to find out if we consider labeled nucleotides still nucleotides. It is after consulting with ChEBI group.
-Added duirng Mar 1, 2010 dev call
- Group: OBI group
- Group: OBI group
- labeled DNA extract
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- cloacal specimen
- type of sample used in the PCIRN influenza network
-
- A specimen obtained by inserting a swab deeply into the vent of the cloaca of
-an organism and vigorously swabbing the wall. The swab should be deeply
-stained with fecal material and is then placed in transport medium.
- PERSON: Melanie Courtot
- WEB: http://www.wpro.who.int/NR/rdonlyres/EFD2B9A7-2265-4AD0-BC98-97937B4FA83C/0/manualonanimalaidiagnosisandsurveillance.pdf
- cloacal specimen
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- nasopharyngeal aspirate specimen
- type of sample used in the PCIRN influenza network
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- A speciemn which derives from nasopharyngeal mucosa after
-aspiration.
- PERSON: Melanie Courtot
- WEB: http://www.wpro.who.int/NR/rdonlyres/EFD2B9A7-2265-4AD0-BC98-97937B4FA83C/0/manualonanimalaidiagnosisandsurveillance.pdf
- nasopharyngeal aspirate specimen
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- nasal swab specimen
- type of sample used in the PCIRN influenza network
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- A specimen obtained using a cotton swab on a stick, passed up the nostril to obtain a sample of
-exudate and epithelial debris for microbiological or cellular examination.
- PERSON: Melanie Courtot
- WEB: http://www.wpro.who.int/NR/rdonlyres/EFD2B9A7-2265-4AD0-BC98-97937B4FA83C/0/manualonanimalaidiagnosisandsurveillance.pdf
- nasal swab specimen
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@@ -10783,128 +10267,6 @@ exudate and epithelial debris for microbiological or cellular examination.
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- labeled RNA extract
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- a labeled specimen that is the output of a labeling process and has grain labeled RNA to be able to detect RNA in future experiments.
- Need to find out if we consider labeled nucleotides still nucleotides. It is after consulting with ChEBI group.
-Added duirng Mar 1, 2010 dev call
- Group: OBI group
- Group: OBI group
- labeled RNA extract
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- frozen specimen
- Frozen blood plasma
-
- A specimen that has been frozen in order to store it.
- Person:Alan Ruttenberg
- MO_610 frozen_sample
- frozen specimen
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- labeled specimen
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- A specimen that has been modified in order to be able to detect it in future experiments
- added during call 3/1/2010
- OBI group
- labeled specimen
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@@ -11189,78 +10551,6 @@ Biochimie. 2010 Feb 18.
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- paraffin specimen
- liver tissue embedded in paraffin
-
- a specimen that is output of a paraffin storage process in which specimen is embedded in paraffin
- PERSON: Chris Stoeckert
- PERSON: Jie Zheng
- MO_990 paraffin_sample
- paraffin specimen
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- processed specimen
- A tissue sample that has been sliced and stained for a histology study.
-A blood specimen that has been centrifuged to obtain the white blood cells.
-
- A specimen that has been intentionally physically modified.
- Bjoern Peters
- Bjoern Peters
- A tissue sample that has been sliced and stained for a histology study.
- processed specimen
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@@ -11322,53 +10612,6 @@ A blood specimen that has been centrifuged to obtain the white blood cells.
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- lyophilized specimen
- freezing dried DNA
-
- a specimen that is output of a lyophilization storage process in which specimen is lyophilized for storage.
- PERSON: Chris Stoeckert
- PERSON: Jie Zheng
- MO_589 freeze_dried_sample
- lyophilized specimen
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@@ -11462,23 +10705,6 @@ In the examples above, a reagent is an operational component of a device, but th
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- fresh specimen
- a liver freshly removed from a rat
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- a specimen that is output of a specimen creation process used for an investigation without storage.
- PERSON: Chris Stoeckert
- PERSON: Jie Zheng
- MO_730 fresh_sample
- fresh specimen
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- paraffin storage
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- a storage process with input organism or anatomical entity and paraffin and output material embedded in paraffin for long term storage
- PERSON: Chris Stoeckert
- PERSON: Jie Zheng
- UPenn Group
- need to specify paraffin or wax is one of specified input of the process
- paraffin storage
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- agar stab specimen
-
- a specimen that is output of a process that cell culture inoculated into agar for long term storage.
+
+ paraffin storage
+
+
+ a storage process with input organism or anatomical entity and paraffin and output material embedded in paraffin for long term storage
PERSON: Chris Stoeckert
PERSON: Jie Zheng
- MO_971 agar_stab
- agar stab specimen
+ UPenn Group
+ need to specify paraffin or wax is one of specified input of the process
+ paraffin storage
@@ -11833,40 +11023,6 @@ JZ: based on textual definition of edited document, it can be defined as N&S
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- nucleic acid extract
-
- An extract that is the output of an extraction process in which nucleic acid molecules are isolated from a specimen.
- PERSON: Jie Zheng
- UPenn Group
- nucleic acid extract
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@@ -11996,32 +11152,6 @@ JZ: based on textual definition of edited document, it can be defined as N&S
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- DNA extract
-
- The output of an extraction process in which DNA molecules are purified in order to exclude DNA from organellas.
- Person: Jie Zheng
- Group: UPenn group
- DNA extract
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@@ -12106,52 +11236,6 @@ JZ: based on textual definition of edited document, it can be defined as N&S
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- labeled nucleic acid extract
-
- a labeled specimen that is the output of a labeling process and has grain labeled nucleic acid for detection of the nucleic acid in future experiments.
- Person: Jie Zheng
- labeled extract
- MO_221 labeledExtract
- labeled extract
- labeled nucleic acid extract
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@@ -13855,33 +12939,6 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html
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- cell specimen
-
- A specimen primarily composed of a cell or cells collected from a multicellular organism or a cell culture.
- Discussed on obi call Jan 23, 2017. To improve cell specimen that include single cell specimen. Details see tracker: https://sourceforge.net/p/obi/obi-terms/828/
- PERSON: Chris Stoeckert, Jie Zheng, Alexander Diehl
- MO_612 cell
- cell specimen
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@@ -13922,36 +12979,6 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html
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- specimen with known storage state
-
- A specimen for which it is known whether it has been subjected to storage of a specified type.
- PERSON: Chris Stoeckert, Jie Zheng
- MO_95 BiosourceType
- specimen with known storage state
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@@ -13986,41 +13013,6 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html
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- A specimen that derives from an anatomical part or substance arising from an organism. Examples of tissue specimen include tissue, organ, physiological system, blood, or body location (arm).
- PERSON: Chris Stoeckert, Jie Zheng
- tissue specimen
- MO_954 organism_part
- specimen from organism
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@@ -14304,54 +13296,6 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html
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- specimen with pre- or post-mortem status
-
- A specimen that has been established to be taken from a live (pre-mortem) or dead (post-mortem) organism.
- organizational term, used in description of specimen that is created from known pre- or post-mortem status
- PERSON: Chris Stoeckert, Jie Zheng
- MO_84 OrganismStatus
- specimen with pre- or post-mortem status
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@@ -18784,69 +17728,6 @@ https://www.doi.org/
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- H&E-stained fixed tissue slide specimen
-
- A fixed tissue slide specimen that is the output of H&E slide staining.
- Chris Stoeckert, Ned Haubein
- OBIB, OBI
- H&E-stained fixed tissue slide specimen
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- IHC-stained fixed tissue slide specimen
-
- A fixed tissue slide specimen that is the output of immunohistochemistry slide staining.
- Chris Stoeckert, Ned Haubein
- immunohistochemistry slide specimen
- OBIB, OBI
- IHC-stained fixed tissue slide specimen
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-
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-
-
- A cell specimen that contains only one cell.
- Requested by Sirarat Sarntivijai (EBI). Details see tracker: https://sourceforge.net/p/obi/obi-terms/828/
- PERSON: Jie Zheng, Alexander Diehl
- PERSON: Jie Zheng, Alexander Diehl
- single cell specimen
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@@ -19632,37 +18513,15 @@ https://www.doi.org/
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- "include only Hispanic individuals"
- An inclusion criteria that defines and states one or more ethnicities which, if met, makes an entity suitable for a given task or participation in a given process.
- Mathias Brochhausen
- ethnicity inclusion criterion
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- polyA depleted RNA extract
- A RNA extract that is the output of an extraction process in which RNA molecules lacking poly A tails at thier 3' ends are purified.
- Mark A. Miller, based on http://purl.obolibrary.org/obo/OBI_0000869
- PERSON: Chris Stoeckert
- PERSON: Jie Zheng
- UPenn Group
- 2018-05-11T16:35:11Z
- polyA depleted RNA extract
+
+
+
+
+
+ "include only Hispanic individuals"
+ An inclusion criteria that defines and states one or more ethnicities which, if met, makes an entity suitable for a given task or participation in a given process.
+ Mathias Brochhausen
+ ethnicity inclusion criterion
@@ -19736,28 +18595,6 @@ https://www.doi.org/
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- swab specimen
-
- A specimen that is stored on a swab as the output of a collecting specimen with swab process.
- Chris Stoeckert
- OBIB/OBI
- https://github.com/obi-ontology/obi/issues/910
- OBIB
- swab specimen
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@@ -19879,41 +18716,6 @@ https://www.doi.org/
-
-
-
-
- ribosomal RNA-depleted RNA extract
- Looking at the reads for each ribosomal RNA-depleted RNA extract, the vast majority align to protein coding genes based on the ENSEMBL annotation.
-
- An extract of RNA which is produced through rRNA (ribosomal RNA) depletion (the removal of highly abundant rRNA species).
- Dan Berrios
- https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-018-4585-1
- ribosomal RNA-depleted RNA extract
-
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- 1
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- A specimen composed of an individual organism to be studied in an investigation.
- Person: Jie Zheng
- EFO_0000542 individual
- https://github.com/obi-ontology/obi/issues/1092
- individual organism specimen
-
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@@ -20058,25 +18860,6 @@ https://www.doi.org/
-
-
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-
- A specimen used in a blood meal assay to determine what is the source of blood ingested by a mosquito.
-
- A specimen of the blood ingested by an arthropod.
- The mosquito feeds on a human for example, ingests the blood of the human, this blood is then taken from the tummy of a mosquito and a PCR may be run on this specimen to identify that the mosquito definitely fed on a human.
- Chris Stoeckert
- Jie Zheng
- blood meal
- VEuPathDB
- https://github.com/obi-ontology/obi/issues/1117
- VEuPathDB
- arthropod meal of blood specimen
-
-
-
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@@ -20250,17 +19033,6 @@ b) that the amount of analyte/measurand detected is over some predetermined thre
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- A blood plasma specimen that is the output of some platelet-poor plasma preparation and is the portion of plasma that contains fewer than 10,000 platelets per microliter.
- PERSON: Matthew Diller
- platelet-poor plasma specimen
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- albumin-free serum
- A blood serum specimen that contains no albumin.
- Sebastian Duesing
- https://github.com/obi-ontology/obi/issues/493
- Philippe Rocca-Serra
- albumin-free serum
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- blood plasma specimen
- PMID: 18217225.Sex Transm Dis. 2008 Jan;35(1):55-60. Review.Human immunodeficiency virus viral load in blood plasma and semen: review and implications of empirical findings.
-
- a material entity which corresponds to the liquid component of blood, in which the blood cells are suspended.
- 03/21/2010: BP, blood plasma is defined as the output of certain separation processes, so this is in the domain of OBI, not FMA.
- PERSON: Maura Gasparetto
- PERSON: Melanie Courtot
- PERSON: Philippe Rocca-Serra
- plasma
- WEB: http://en.wikipedia.org/wiki/Blood_plasma
- blood plasma specimen
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- blood serum specimen
- PMID: 18229666.Adv Med Sci. 2007;52 Suppl 1:204-6.Antioxidant activity of blood serum and saliva in patients with periodontal disease treated due to epilepsy.
-
- A material entity which derives from blood and corresponds to blood plasma without fibrinogen or the other clotting factors.
- PERSON: Maura Gasparetto
- PERSON: Melanie Courtot
- PERSON: Philippe Rocca-Serra
- WEB: http://en.wikipedia.org/wiki/Blood_plasma
- blood serum specimen
-
-
-
-
@@ -22318,10 +20975,9 @@ This issue is outside the scope of OBI.
specimen
- Biobanking of blood taken and stored in a freezer for potential future investigations stores specimen.
+ Biobanking of blood taken and stored in a freezer for potential future investigations stores specimen; collecting a stone from a site.
- A material entity that has the specimen role.
- Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation.
+ A material entity that is collected for potential use as an input upon which measurements or observations are performed.
PERSON: James Malone
PERSON: Philippe Rocca-Serra
GROUP: OBI Biomaterial Branch
@@ -22539,34 +21195,6 @@ Thyroidectomy during laryngectomy for advanced laryngeal carcinoma--whole organ
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- bronchial alveolar lavage
- solution containing lung derived T cells, eosinophils, and TNFa.
-
- Group of biomaterials present in the bronchial aveolar space of an organism which are collected through lavage including the reagents used to for the lavage process, organisms, cells, and cellular secretions present in the bronchial aveolar space.
- PERSON: Bjoern Peters
- BAL
- GROUP: IEDB
- bronchial alveolar lavage
-
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@@ -26526,42 +25154,6 @@ determinations of compounds.
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- pool of specimens
-
- A pool of specimens is a mixture of a population of samples which have been gathered from one or more sample populations, obtained by the physical process of mixing individual specimens, e.g. mixing the DNA collected from the individual fish.
- check with advisors as to how to represent multiple instances of any class? a set of specimens which have been gathered from one or more sample_populations, obtained by the physical process of mixing individual specimens, e.g. mixing the DNA collected from the individual fish
- PERSON: Jennifer Fostel
- GROUP: CEBS
- pool of specimens
-
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- whole mount tissue
-
- A whole organism preparation resulting from a histological preparation known as whole mount preparation where the whole specimen is mounted or spread on the microscope (glass) slide
- PERSON: Helen Parkinson
- PERSON: Philippe Rocca-Serra
- whole mount sample
- GROUP: OBI
- PRS:22-02-2008: indicates the need to create a protocol application and distinguish it from this entity
- PRS:22-02-2008: is a material which has output_role during whole mount preparation protocol-application
- whole mount tissue
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- lymph node cell specimen
-
- A cell specimen comprised of a mixed population of cells obtained by processing whole lymph node into individual cells, typically performed using a sieve. This population includes T cells, B cells, macrophages, and other cell types.
- IEDB
- IEDB
- lymph node cell specimen
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@@ -31392,36 +29924,6 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it
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- splenocyte specimen
-
- A cell specimen comprised of a mixed cell population obtained by processing whole spleen into individual cells, typically performed using a sieve or blender. This population includes T cells, B cells, macrophages, and other cell types.
- IEDB
- IEDB
- splenocyte specimen
-
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@@ -31850,24 +30352,6 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10
-
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- FFPE specimen
- Many of today’s researchers prefer to use Formalin-Fixed Paraffin-Embedded samples of tissues for their IHC, histological or in-situ genomic analyses. Professionally fixed and embedded FFPE samples and the biomolecules they contain are reasonably stable at ambient temperatures.
-
--based on https://lab-ally.com/histopathology-resources/ffpe-samples/
- A specimen that has been fixed in formalin and embedded in paraffin.
- MIABIS
- formalin-fixed paraffin-embeded specimen
-
-
- FFPE specimen
-
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-ontology ID label editor preferred term has curation status alternative term definition definition source example of usage term editor editor note curator note ontology term requester term tracker item logical type specimen collection process gross anatomical part collection process input URI
-ID A rdfs:label A editor preferred term AI has curation status A alternative term SPLIT=| AL definition@en A definition source SPLIT=| A example of usage SPLIT=| A term editor SPLIT=| A editor note SPLIT=| A curator note SPLIT=| A ontology term requester A term tracker item CLASS_TYPE C specimen and (is_specified_output_of some %) C specimen and (is_specified_output_of some 'specimen collection process') and ('derives from' some %) C specimen and (is_specified_output_of some ('specimen collection process' and has_specified_input some %))
-OBI:0002500 amniotic fluid specimen ready for release A specimen that is derived from amniotic fluid. Chris Stoeckert, Penn Medicine Biobank Chris Stoeckert equivalent collecting specimen from organism amniotic fluid UBERON_0000173
-OBI:0002501 bile specimen ready for release A specimen that is derived from bile. Chris Stoeckert, Penn Medicine Biobank Chris Stoeckert equivalent collecting specimen from organism bile UBERON_0001970
-OBI:0002502 cerebrospinal fluid specimen ready for release A specimen that is derived from cerbrospinal fluid. Chris Stoeckert, Penn Medicine Biobank Chris Stoeckert equivalent collecting specimen from organism cerebrospinal fluid UBERON_0001359
-OBI:0002503 feces specimen ready for release stool specimen A specimen that is derived from feces. Chris Stoeckert, Penn Medicine Biobank Chris Stoeckert equivalent collecting specimen from organism feces UBERON_0001988
-OBI:0002504 digestive system fluid or secretion specimen ready for release gastric fluid specimen A specimen that is derived from digestive system fluid or secretion. Chris Stoeckert, Penn Medicine Biobank Chris Stoeckert equivalent collecting specimen from organism digestive system secreted substance UBERON_0006911
-OBI:0002505 milk specimen ready for release A specimen that is derived from milk. Chris Stoeckert, Penn Medicine Biobank Chris Stoeckert equivalent collecting specimen from organism milk UBERON_0001913
-OBI:0002506 pericardial fluid specimen ready for release A specimen that is derived from pericardial fluid. Chris Stoeckert, Penn Medicine Biobank Chris Stoeckert equivalent collecting specimen from organism pericardial fluid UBERON_0002409
-OBI:0002507 saliva specimen ready for release A specimen that is derived from saliva. Chris Stoeckert, Penn Medicine Biobank Chris Stoeckert equivalent collecting specimen from organism saliva UBERON_0001836
-OBI:0002508 sputum specimen ready for release A specimen that is derived from sputum. Chris Stoeckert, Penn Medicine Biobank Chris Stoeckert equivalent collecting specimen from organism sputum UBERON_0007311
-OBI:0002509 sweat specimen ready for release A specimen that is derived from sweat. Chris Stoeckert, Penn Medicine Biobank Chris Stoeckert equivalent collecting specimen from organism sweat UBERON_0001089
-OBI:0002510 synovial fluid specimen ready for release A specimen that is derived from synovial fluid. Chris Stoeckert, Penn Medicine Biobank Chris Stoeckert equivalent collecting specimen from organism synovial fluid UBERON_0001090
-OBI:0002511 vitreous humor specimen ready for release vitreous fluid specimen A specimen that is derived from vireous humor. Chris Stoeckert, Penn Medicine Biobank Chris Stoeckert equivalent collecting specimen from organism (tissue and ('part of' some 'vitreous humor')) UBERON_0001797
-OBI:0002512 bone marrow specimen ready for release A specimen that is derived from bone marrow. Chris Stoeckert, Penn Medicine Biobank Chris Stoeckert equivalent bone marrow biopsy bone marrow UBERON_0002371
-OBI:0002513 placenta specimen ready for release A specimen that is derived from placenta. Chris Stoeckert, Penn Medicine Biobank Chris Stoeckert equivalent collecting specimen from organism (tissue and ('part of' some placenta)) UBERON_0001987
-OBI:0002514 peritoneal fluid specimen ready for release A specimen that is derived from peritoneal fluid. Chris Stoeckert, Penn Medicine Biobank Chris Stoeckert equivalent collecting specimen from organism peritoneal fluid UBERON_0001268
-OBI:0002515 pleural fluid specimen ready for release A specimen that is derived from pleural fluid. Chris Stoeckert, Penn Medicine Biobank Chris Stoeckert equivalent collecting specimen from organism pleural fluid UBERON_0001087
-OBI:0002516 brain specimen ready for release A specimen that is derived from brain. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent collecting specimen from organism (tissue and ('part of' some brain)) UBERON_0000955
-OBI:0002517 hair specimen ready for release A specimen that is derived from hair. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent collecting specimen from organism strand of hair UBERON_0001037
-OBI:0002518 prostate gland specimen ready for release A specimen that is derived from prostate gland. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent collecting specimen from organism (tissue and ('part of' some 'prostate gland')) UBERON_0002367
-OBI:0002519 skeletal muscle tissue specimen ready for release A specimen that is derived from skeletal muscle. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent collecting specimen from organism skeletal muscle tissue UBERON_0001134
-OBI:0002520 heart specimen ready for release A specimen that is derived from heart. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent collecting specimen from organism (tissue and ('part of' some heart)) UBERON_0000948
-OBI:0002521 renal medulla specimen ready for release kidney medulla specimen A specimen that is derived from renal medulla. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent collecting specimen from organism (tissue and ('part of' some 'renal medulla')) UBERON_0000362
-OBI:0002522 adrenal gland specimen ready for release A specimen that is derived from adrenal gland. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent collecting specimen from organism (tissue and ('part of' some 'adrenal gland')) UBERON_0002369
-OBI:0002523 breast specimen ready for release mammary tissue specimen A specimen that is derived from breast. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent collecting specimen from organism (tissue and ('part of' some breast)) UBERON_0000310
-OBI:0002524 urinary bladder specimen ready for release A specimen that is derived from urinary bladder. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent collecting specimen from organism (tissue and ('part of' some 'urinary bladder')) UBERON_0001255
-OBI:0002525 tibial artery specimen ready for release A specimen that is derived from tibial artery. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent collecting specimen from organism (tissue and ('part of' some 'tibial artery')) UBERON_0007610
-OBI:0002526 skin of body specimen ready for release skin specimen A specimen that is derived from skin. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent collecting specimen from organism (tissue and ('part of' some 'skin of body')) UBERON_0002097
-OBI:0002527 pancreas specimen ready for release A specimen that is derived from pancreas. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent collecting specimen from organism (tissue and ('part of' some pancreas)) UBERON_0001264
-OBI:0002528 stomach specimen ready for release A specimen that is derived from stomach. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent collecting specimen from organism (tissue and ('part of' some stomach)) UBERON_0000945
-OBI:0002529 pituitary gland specimen ready for release A specimen that is derived from pituitary gland. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent collecting specimen from organism (tissue and ('part of' some 'pituitary gland')) UBERON_0000007
-OBI:0002530 adipose tissue specimen ready for release A specimen that is derived from adipose tissue. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent collecting specimen from organism adipose tissue UBERON_0001013
-OBI:0002531 cortex of kidney specimen ready for release kidney cortex specimen A specimen that is derived from cortex of kidney. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent collecting specimen from organism (tissue and ('part of' some 'cortex of kidney')) UBERON_0001225
-OBI:0002532 esophagus mucosa specimen ready for release A specimen that is derived from esophagus mucosa. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent collecting specimen from organism (tissue and ('part of' some 'esophagus mucosa')) UBERON_0002469
-OBI:0002533 colon specimen ready for release A specimen that is derived from colon. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent collecting specimen from organism (tissue and ('part of' some colon)) UBERON_0001155
-OBI:0002534 lung specimen ready for release A specimen that is derived from lung. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent collecting specimen from organism (tissue and ('part of' some lung)) UBERON_0002048
-OBI:0002535 esophagus muscularis mucosa specimen ready for release esophagus muscularis specimen A specimen that is derived from esophagus muscularis mucosa. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent collecting specimen from organism (tissue and ('part of' some 'esophagus muscularis mucosa')) UBERON_0004648
-OBI:0002536 cerebral cortex specimen ready for release brain cortex specimen A specimen that is derived from cerebral cortex. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent collecting specimen from organism (tissue and ('part of' some 'cerebral cortex')) UBERON_0000956
-OBI:0002537 thyroid gland specimen ready for release A specimen that is derived from thyroid gland. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent collecting specimen from organism (tissue and ('part of' some 'thyroid gland')) UBERON_0002046
-OBI:0002538 cerebellum specimen ready for release brain cerebellum specimen A specimen that is derived from cerebellum. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent collecting specimen from organism (tissue and ('part of' some cerebellum)) UBERON_0002037
-OBI:0002539 tibial nerve specimen ready for release A specimen that is derived from tibial nerve. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent collecting specimen from organism (tissue and ('part of' some 'tibial nerve')) UBERON_0001323
-OBI:0002540 coronary artery specimen ready for release A specimen that is derived from coronary artery. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent collecting specimen from organism (tissue and ('part of' some 'coronary artery')) UBERON_0001621
-OBI:0002541 spleen specimen ready for release A specimen that is derived from spleen. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent collecting specimen from organism (tissue and ('part of' some spleen)) UBERON_0002106
-OBI:0002542 aorta specimen ready for release A specimen that is derived from aorta. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent collecting specimen from organism (tissue and ('part of' some aorta)) UBERON_0000947
-OBI:0002543 atrial appendage specimen ready for release A specimen that is derived from the atrium auricular region. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent collecting specimen from organism (tissue and ('part of' some 'atrium auricular region')) UBERON_0006618
-OBI:0002544 esophagogastric junction specimen ready for release A specimen that is derived from the esophagogastric junction. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent collecting specimen from organism (tissue and ('part of' some 'esophagogastric junction')) UBERON_0007650
-OBI:0002545 ileum specimen ready for release A specimen that is derived from ileum. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent collecting specimen from organism (tissue and ('part of' some ileum)) UBERON_0002116
-OBI:0002546 liver specimen ready for release A specimen that is derived from liver. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent collecting specimen from organism (tissue and ('part of' some liver)) UBERON_0002107
-OBI:0002547 minor salivary gland specimen ready for release A specimen that is derived from minor salivary gland. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent collecting specimen from organism (tissue and ('part of' some 'minor salivary gland')) UBERON_0001830
-OBI:0002548 omentum specimen ready for release A specimen that is derived from omentum. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent collecting specimen from organism (tissue and ('part of' some omentum)) UBERON_0003688
-OBI:0002549 ovary specimen ready for release A specimen that is derived from female gonad. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent collecting specimen from organism (tissue and ('part of' some ovary)) UBERON_0000992
-OBI:0002550 sigmoid colon specimen ready for release A specimen that is derived from sigmoid colon. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent collecting specimen from organism (tissue and ('part of' some 'sigmoid colon')) UBERON_0001159
-OBI:0002551 suprapubic skin specimen ready for release A specimen that is derived from suprapubic skin. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent collecting specimen from organism (tissue and ('part of' some 'suprapubic skin')) UBERON_0036149
-OBI:0002552 testis specimen ready for release A specimen that is derived from testis. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent collecting specimen from organism (tissue and ('part of' some testis)) UBERON_0000473
-OBI:0002553 uterus specimen ready for release A specimen that is derived from uterus. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent collecting specimen from organism (tissue and ('part of' some uterus)) UBERON_0000995
-OBI:0002554 vagina specimen ready for release A specimen that is derived from vagina. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent collecting specimen from organism (tissue and ('part of' some vagina)) UBERON_0000996
-OBI:0002603 areolar swab specimen ready for release A specimen that is collected with a swab from the surface of an areola of a breast. Chris Stoeckert, OBIB Chris Stoeckert equivalent collecting specimen with swab areola UBERON_0002032
-OBI:0002604 breast swab specimen ready for release A specimen that is collected with a swab from the surface of a breast. Chris Stoeckert, OBIB Chris Stoeckert equivalent collecting specimen with swab breast UBERON_0000310
-OBI:0002605 cheek swab specimen ready for release A specimen that is collected with a swab from the cheek portion of the inside surface of a mouth. Chris Stoeckert, OBIB Chris Stoeckert equivalent collecting specimen with swab cheek UBERON_0001567
-OBI:0002606 nasopharyngeal swab specimen ready for release A specimen that is collected with a swab from the surface of a nasopharynx. Chris Stoeckert, OBIB Chris Stoeckert equivalent collecting specimen with swab nasopharynx UBERON_0001728
-OBI:0002607 oral swab specimen ready for release A specimen that is collected with a swab from the inside surface of a mouth. Chris Stoeckert, OBIB Chris Stoeckert equivalent collecting specimen with swab mouth UBERON_0000165
-OBI:0002608 oropharyngeal swab specimen ready for release A specimen that is collected with a swab from the surface of a oropharynx. Chris Stoeckert, OBIB Chris Stoeckert equivalent collecting specimen with swab oropharynx UBERON_0001729
-OBI:0002609 rectal swab specimen ready for release A specimen that is collected with a swab from the surface of a rectum. Chris Stoeckert, OBIB Chris Stoeckert equivalent collecting specimen with swab rectum UBERON_0001052
-OBI:0002610 tongue swab specimen ready for release A specimen that is collected with a swab from the surface of a tongue. Chris Stoeckert, OBIB Chris Stoeckert equivalent collecting specimen with swab tongue UBERON_0001723
-OBI:0002611 vagina swab specimen ready for release A specimen that is collected with a swab from the surface of a vagina. Chris Stoeckert, OBIB Chris Stoeckert equivalent collecting specimen with swab vagina UBERON_0000996
-OBI:0002612 fecal swab specimen ready for release stool swab specimen A specimen that is collected with a swab from the surface of a feces. Chris Stoeckert, OBIB Chris Stoeckert equivalent collecting specimen with swab feces UBERON_0001988
-OBI:0002613 environmental swab specimen ready for release A specimen that is collected with a swab from the surface of an environmenal material. Chris Stoeckert, OBIB Chris Stoeckert equivalent collecting specimen with swab environmental material ENVO_00010483
-OBI:0002746 induced sputum specimen A sputum specimen that is collected from an organism following its inhalation of a nebulized salt solution. PMC3297553 John Judkins subclass collecting specimen from organism sputum UBERON_0007311
-OBI:0002778 tracheal aspirate specimen tracheal wash specimen A specimen that is collected with a suctioning tube from the trachea. PMID:25338241 Asiyah Yu Lin ORCID:0000-0003-2620-0345 subclass aspiration specimen collection trachea UBERON_0003126
-OBI:0002779 mid-turbinate nasal swab specimen A specimen that is collected with a mid-turbinate nasal swab from the turbinate area of the nasal cavity. https://seattlechildrenslab.testcatalog.org/catalogs/185/files/11633 Asiyah Yu Lin ORCID:0000-0003-2620-0345 equivalent collecting specimen with swab middle nasal concha UBERON_0005921
-OBI:0002780 nasal aspirate specimen nasal wash specimen|nasopharyngeal aspirate A specimen that is collected with a suctioning tube from the nasal cavity. Asiyah Yu Lin ORCID:0000-0003-2620-0345 Asiyah Yu Lin ORCID:0000-0003-2620-0345 equivalent aspiration specimen collection nasal cavity mucosa UBERON_0001826
-OBI:0002781 lower respiratory tract aspirate specimen lower respiratory tract wash specimen A specimen that is collected with a suctioning tube from the lower respiratory tract. Asiyah Yu Lin ORCID:0000-0003-2620-0345 Asiyah Yu Lin ORCID:0000-0003-2620-0345 equivalent aspiration specimen collection lower respiratory tract UBERON_0001558
-OBI:0002782 upper respiratory specimen A specimen that is derived from the upper respiratory tract Asiyah Yu Lin ORCID:0000-0003-2620-0345 Asiyah Yu Lin ORCID:0000-0003-2620-0345 equivalent collecting specimen with swab upper respiratory tract UBERON_0001557
-OBI:0002783 lower respiratory tract specimen A specimen that is derived from the lower respiratory tract. Asiyah Yu Lin ORCID:0000-0003-2620-0345 Asiyah Yu Lin ORCID:0000-0003-2620-0345 equivalent lower respiratory tract UBERON_0001558
-OBI:0002784 anterior nasal swab specimen A specimen that is derived from the anterior nasal wall Asiyah Yu Lin ORCID:0000-0003-2620-0345 Asiyah Yu Lin ORCID:0000-0003-2620-0345 equivalent collecting specimen with swab anterior nasal wall UBERON_3000016
-OBI:0002971 endotracheal tube specimen A specimen that derives from a biofilm that forms on the inner surface of an endotracheal tube while the tube is in the trachea. The specimen is collected upon removal of the tube from the trachea. https://bmcpulmmed.biomedcentral.com/articles/10.1186/s12890-019-0926-3 John Judkins ORCID:0000-0001-6595-0902 subclass collecting specimen from organism respiratory system fluid/secretion UBERON_0006538
-OBI:0002972 endotracheal aspirate specimen A specimen that derives from a biofilm that forms on the inner surface of an endotracheal tube while the tube is in the trachea. The specimen is collected by suction without removing the tube. https://bmcpulmmed.biomedcentral.com/articles/10.1186/s12890-019-0926-3 John Judkins ORCID:0000-0001-6595-0902 subclass collecting specimen from organism respiratory system fluid/secretion UBERON_0006538
-OBI:0003054 blood specimen in vacutainer Vacutainer sample A blood specimen that is located in a vacutainer. VEuPathDB John Judkins collecting specimen from organism blood UBERON_0000178
-OBI:0003055 blood specimen on filter paper Filter paper sample A blood specimen that is located on a filter paper. Penn Group Jie Zheng|Chris Stoeckert collecting specimen from organism blood UBERON_0000178
-OBI:0003380 placental blood specimen A specimen that is derived from placental blood. VEuPathDB John Judkins equivalent collecting specimen from organism placental blood UBERON_8470000
-OBI:0003415 peripheral blood mononuclear cell specimen PBMC specimen A processed specimen that is extracted from whole blood using gradient centrifugation that separates the blood into a layer of peripheral blood mononuclear cells under the top layer of plasma. It contains lymphocytes, monocytes or macrophages that are critical components in the immune system. http://en.wikipedia.org/wiki/Peripheral_blood_mononuclear_cell Jie Zheng|Chris Stoeckert subclass collecting specimen from organism peripheral blood mononuclear cell CL_2000001
-OBI:0003482 lymph specimen A specimen that is derived from a portion of lymph collected from an organism. VEuPathDB John Judkins ORCID:0000-0001-6595-0902 collecting specimen from organism (tissue and ('part of' some lymph)) UBERON_0002391
-OBI:0003483 digestive tract specimen A specimen that is derived from part of a digestive tract. VEuPathDB John Judkins ORCID:0000-0001-6595-0902 collecting specimen from organism (tissue and ('part of' some 'digestive tract')) UBERON_0001555
-OBI:0003595 nasal lavage fluid A specimen collected through nasal cavity lavage that contains the reagents used to for the lavage process, organisms, cells, cellular secretions, and other biomaterials present in the nasal cavity space. Sebastian Duesing|Randi Vita equivalent lavage nasal cavity mucosa UBERON_0001826
-OBI:0003666 lavage fluid specimen lavage fluid specimen A specimen obtained through a lavage process which includes fluid in addition to cells and/or cellular secretions. The collection of bronchoalveolar lavage fluid (BAL) from the lungs of mice in order to study the cytokines present. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1803 equivalent lavage
-OBI:0003667 oral lavage fluid oral lavage fluid mouth rinse specimen A specimen collected through oral cavity lavage that contains the reagents used to for the lavage process, organisms, cells, cellular secretions, and other biomaterials present in the oral cavity space. Sebastian Duesing Anna Maria Masci https://github.com/obi-ontology/obi/issues/1803 equivalent lavage mouth UBERON_0000165
-OBI:2000000 uterine cervix specimen A specimen that is derived from some uterine cervix Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X equivalent collecting specimen from organism (tissue and ('part of' some 'uterine cervix')) UBERON_0000002
-OBI:2000001 urethra specimen A specimen that is derived from some urethra Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X equivalent collecting specimen from organism (tissue and ('part of' some urethra)) UBERON_0000057
-OBI:2000002 cervical mucus specimen A specimen that is derived from some cervical mucus Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X equivalent collecting specimen from organism cervical mucus UBERON_0000316
-OBI:2000003 throat specimen A specimen that is derived from some throat Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X equivalent collecting specimen from organism (tissue and ('part of' some throat)) UBERON_0000341
-OBI:2000004 eye specimen A specimen that is derived from some eye Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X equivalent collecting specimen from organism (tissue and ('part of' some eye)) UBERON_0000970
-OBI:2000005 respiratory system specimen A specimen that is derived from some respiratory system Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X equivalent collecting specimen from organism (tissue and ('part of' some 'respiratory system')) UBERON_0001004
-OBI:2000006 upper respiratory tract specimen A specimen that is derived from some upper respiratory tract Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X equivalent collecting specimen from organism (tissue and ('part of' some 'upper respiratory tract')) UBERON_0001557
-OBI:2000007 nasopharynx specimen A specimen that is derived from some nasopharynx Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X equivalent collecting specimen from organism (tissue and ('part of' some nasopharynx)) UBERON_0001728
-OBI:2000008 semen specimen A specimen that is derived from some semen Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X equivalent collecting specimen from organism semen UBERON_0001968
-OBI:2000009 bodily fluid specimen A specimen that is derived from some bodily fluid Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X equivalent collecting specimen from organism bodily fluid UBERON_0006314
-OBI:2000010 chorionic villus specimen A specimen that is derived from some chorionic villus Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X equivalent collecting specimen from organism (tissue and ('part of' some 'chorionic villus')) UBERON_0007106
-OBI:2000011 meconium specimen A specimen that is derived from some meconium Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X equivalent collecting specimen from organism meconium UBERON_0007109
-OBI:2000012 umbilical cord blood specimen A specimen that is derived from some umbilical cord blood Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X equivalent collecting specimen from organism umbilical cord blood UBERON_0012168
-OBI:2000013 arterial blood specimen A specimen that is derived from some arterial blood Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X equivalent collecting specimen from organism arterial blood UBERON_0013755
-OBI:2000014 venous blood specimen A specimen that is derived from some venous blood Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X equivalent collecting specimen from organism venous blood UBERON_0013756
-OBI:2000015 capillary blood specimen A specimen that is derived from some capillary blood Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X equivalent collecting specimen from organism capillary blood UBERON_0013757
-OBI:2000016 erythrocyte specimen A specimen that is derived from some erythrocytes Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X subclass collecting specimen with swab erythrocyte CL_0000232
-OBI:2000017 reticulocyte specimen A specimen that is derived from some reticulocytes Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X subclass collecting specimen with swab reticulocyte CL_0000558
-OBI:2000018 leukocyte specimen A specimen that is derived from some leukocytes Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X subclass collecting specimen with swab leukocyte CL_0000738
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+ontology ID label editor preferred term has curation status alternative term definition definition source example of usage term editor editor note curator note ontology term requester term tracker item logical type parent class specimen collection process gross anatomical part collection process input associated axioms URI
+ID A rdfs:label A editor preferred term AI has curation status A alternative term SPLIT=| AL definition@en A definition source SPLIT=| A example of usage SPLIT=| A term editor SPLIT=| A editor note SPLIT=| A curator note SPLIT=| A ontology term requester A term tracker item CLASS_TYPE C % C is_specified_output_of some % C (is_specified_output_of some 'specimen collection process') and ('derives from' some %) C is_specified_output_of some ('specimen collection process' and has_specified_input some %) C % SPLIT=|
+OBI:0000651 urine specimen urine specimen metadata complete a portion of urine collected from an organism This could be instead a kind of collection of secreted stuff. Among secreted stuff there is passive, and active. urine is secreted, passiv. lavage is secreted, active|are we happy calling collection of urine a material separation?|4/10/2011BP: It seems to me that the editor notes refer to a previous version, and are no longer relevant. equivalent specimen from organism collecting specimen from organism urine
+OBI:0000655 blood specimen blood specimen ready for release a material entity derived from a portion of blood collected from an organism Bjoern Peters blood drawn from a human for glucose assay Bjoern Peters equivalent specimen from organism collecting specimen from organism blood
+OBI:0000671 sample from organism sample from organism example to be eventually removed a material obtained from an organism in order to be a representative of the whole we need to work on this: Is taking a urine sample a material separation process? If not, we will need to specify what 'taking a sample from organism' entails. We can argue that the objective to obtain a urine sample from a patient is enough to call it a material separation process, but it could dilute what material separation was supposed to be about.|5/29: This is a helper class for now equivalent specimen from organism 'has role' some 'material sample role'
+OBI:0000680 whole organism preparation whole organism preparation metadata incomplete A material entity which is the output of a process in which one or more whole organisms are prepared in a way to make it easier to study them, and in which the great majority of organismal parts are maintained putting a mouse in the blender. Not: putting a mouse on a scale does this include injecting a dye to a patient to be able to visualize parts of his brain? If not, we should state that the components of the organism are substantially re-arranged. subclass specimen 'derives from' some 'organism'
+OBI:0000747 material sample material sample metadata incomplete sample|sample population A material entity that has the material sample role blood drawn from patient to measure his systemic glucose level. A population of humans with HIV enrolled in a study taken to represent patients with HIV in general. OBI: workshop https://github.com/obi-ontology/obi/issues/1013 equivalent specimen 'has role' some 'material sample role'
+OBI:0000834 high molecular weight DNA extract high molecular weight DNA extract metadata complete The output of an extraction process in which DNA molecules above a molecular weight cutoff are purified in order to exclude DNA from organellas. OBI Extraction of chromosomal DNA from mammalian cells by first isolating nucei PERSON:Chris Stoeckert subclass DNA extract
+OBI:0000862 nuclear RNA extract nuclear RNA extract metadata complete A RNA extract that is the output of an extraction process in which RNA molecules found in the nucleus, including mRNA precursors (pre-mRNA), are extracted. UPenn Group Isolation and purification of nuclear RNA from animal cells using Norgen Bioteck corp. cytoplasmic and nuclear RNA purification kit (http://www.norgenbiotek.com/display-product.php?ID=30) PERSON: Chris Stoeckert|PERSON: Jie Zheng subclass RNA extract nuclear RNA extraction
+OBI:0000869 polyA RNA extract polyA RNA extract metadata complete A RNA extract that is the output of an extraction process in which RNA molecules with poly A tail at its 3' end are purified. UPenn Group Preparation of polyA RNA by cellulose-bound oligo-dT (Aviv, H., Leder, P. 1972. Purification of biologically active globin messenger RNA by chromatography on oligothymidylic acid-cellulose. Proc. Nat. Acad. Sci. USA 69, 1408-1412.) PERSON: Chris Stoeckert|PERSON: Jie Zheng subclass RNA extract polyA RNA extraction
+OBI:0000873 pre-mortem specimen pre-mortem specimen metadata complete a specimen that was taken from a live organism MO_705 premortem material obtained through a liver biopsy from a human patient Bjoern Peters equivalent specimen with pre- or post-mortem status ('organism' and ('has quality' some 'alive'))
+OBI:0000876 cytoplasmic RNA extract cytoplasmic RNA extract metadata complete A RNA extract that is the output of a RNA extraction process in which RNA molecules found in the cytoplasm are extracted. UPenn Group Cytoplasmic RNA extraction from mammalian tissues to create cDNA library (Carninci P, Nakamura M, Sato K, Hayashizaki Y, Brownstein MJ. Cytoplasmic RNA extraction from fresh and frozen mammalian tissues. Biotechniques. 2002;33:306–309.) PERSON:Chris Stoeckert subclass RNA extract cytoplasmic RNA extraction
+OBI:0000880 RNA extract RNA extract metadata complete an extract which is the output of an extraction process in which RNA molecules are isolated from a specimen. Group: UPenn Group PERSON: Chris Stoeckert|PERSON: Jie Zheng subclass nucleic acid extract RNA extraction 'has grain' some 'ribonucleic acid'
+OBI:0000895 total RNA extract total RNA extract metadata complete A RNA extract that is the output of an extraction process in which total celluar and organelle RNA molecules are isolated from a specimen. UPenn Group Extraction of total RNA from cells with Qiagen mini RNeasy kit PERSON: Chris Stoeckert|PERSON: Jie Zheng subclass RNA extract total RNA extraction
+OBI:0000899 organellar RNA extract organellar RNA extract metadata complete A RNA extract that is the output of an extraction process in which RNA molecules found in an organelle, e.g., mitochondrion, ER, or chloroplast, excluding the nucleus, are extracted. UPenn Group Extraction of organellar RNA from plant cells using organellar RNA binding protein. PERSON: Chris Stoeckert|PERSON: Jie Zheng subclass RNA extract organellar RNA extraction
+OBI:0000902 post mortem specimen post mortem specimen metadata complete a specimen that was taken from a dead organism MO_416 postmortem the spleen taken from a dead mouse Bjoern Peters equivalent specimen with pre- or post-mortem status ('organism' and ('has quality' some 'dead'))
+OBI:0000908 labeled DNA extract labeled DNA extract metadata complete a labeled specimen that is the output of a labeling process and has grain labeled DNA to be able to detect DNA in future experiments. Group: OBI group Group: OBI group Need to find out if we consider labeled nucleotides still nucleotides. It is after consulting with ChEBI group. Added duirng Mar 1, 2010 dev call equivalent labeled nucleic acid extract ('addition of molecular label' and ('has_specified_input' some 'DNA extract')) 'has grain' some 'deoxyribonucleic acid'
+OBI:0000909 cloacal specimen cell specimen metadata complete A specimen obtained by inserting a swab deeply into the vent of the cloaca of an organism and vigorously swabbing the wall. The swab should be deeply stained with fecal material and is then placed in transport medium. WEB: http://www.wpro.who.int/NR/rdonlyres/EFD2B9A7-2265-4AD0-BC98-97937B4FA83C/0/manualonanimalaidiagnosisandsurveillance.pdf type of sample used in the PCIRN influenza network PERSON: Melanie Courtot equivalent specimen from organism collecting specimen from organism cloaca
+OBI:0000914 nasopharyngeal aspirate specimen nasopharyngeal aspirate specimen metadata complete A specimen which derives from nasopharyngeal mucosa after aspiration. WEB: http://www.wpro.who.int/NR/rdonlyres/EFD2B9A7-2265-4AD0-BC98-97937B4FA83C/0/manualonanimalaidiagnosisandsurveillance.pdf type of sample used in the PCIRN influenza network PERSON: Melanie Courtot subclass specimen from organism collecting specimen from organism nasopharynx
+OBI:0000917 nasal swab specimen nasal swab specimen metadata complete A specimen obtained using a cotton swab on a stick, passed up the nostril to obtain a sample of exudate and epithelial debris for microbiological or cellular examination. WEB: http://www.wpro.who.int/NR/rdonlyres/EFD2B9A7-2265-4AD0-BC98-97937B4FA83C/0/manualonanimalaidiagnosisandsurveillance.pdf type of sample used in the PCIRN influenza network PERSON: Melanie Courtot equivalent specimen from organism collecting specimen with swab nasal cavity mucosa
+OBI:0000921 labeled RNA extract labeled RNA extract metadata complete a labeled specimen that is the output of a labeling process and has grain labeled RNA to be able to detect RNA in future experiments. Group: OBI group Group: OBI group Need to find out if we consider labeled nucleotides still nucleotides. It is after consulting with ChEBI group. Added duirng Mar 1, 2010 dev call equivalent labeled nucleic acid extract ('addition of molecular label' and ('has_specified_input' some 'RNA extract')) 'has grain' some 'ribonucleic acid'
+OBI:0000922 frozen specimen frozen specimen metadata incomplete A specimen that has been frozen in order to store it. MO_610 frozen_sample Frozen blood plasma Person:Alan Ruttenberg equivalent specimen ('freezing storage' and ('has_specified_input' some ('has role' some 'specimen role')))
+OBI:0000924 labeled specimen labeled specimen metadata incomplete A specimen that has been modified in order to be able to detect it in future experiments OBI group added during call 3/1/2010 equivalent specimen addition of molecular label 'has part' some 'molecular label'
+OBI:0000950 paraffin specimen paraffin specimen metadata incomplete a specimen that is output of a paraffin storage process in which specimen is embedded in paraffin MO_990 paraffin_sample liver tissue embedded in paraffin PERSON: Chris Stoeckert|PERSON: Jie Zheng equivalent specimen ('paraffin storage' and ('has_specified_input' some ('has role' some 'specimen role')))
+OBI:0000953 processed specimen processed specimen ready for release A specimen that has been intentionally physically modified. Bjoern Peters Bjoern Peters A tissue sample that has been sliced and stained for a histology study. equivalent specimen 'processed material' and 'specimen'
+OBI:0000965 lyophilized specimen lyophilized specimen metadata incomplete a specimen that is output of a lyophilization storage process in which specimen is lyophilized for storage. MO_589 freeze_dried_sample freezing dried DNA PERSON: Chris Stoeckert|PERSON: Jie Zheng equivalent specimen ('lyophilization storage' and ('has_specified_input' some ('has role' some 'specimen role')))
+OBI:0000971 fresh specimen fresh specimen metadata incomplete a specimen that is output of a specimen creation process used for an investigation without storage. MO_730 fresh_sample a liver freshly removed from a rat PERSON: Chris Stoeckert|PERSON: Jie Zheng subclass specimen with known storage state
+OBI:0000981 agar stab specimen agar stab specimen metadata incomplete a specimen that is output of a process that cell culture inoculated into agar for long term storage. MO_971 agar_stab PERSON: Chris Stoeckert|PERSON: Jie Zheng equivalent specimen ('agar stab storage' and ('has_specified_input' some ('has role' some 'specimen role')))
+OBI:0001010 nucleic acid extract nucleic acid extract metadata complete An extract that is the output of an extraction process in which nucleic acid molecules are isolated from a specimen. UPenn Group Person: Jie Zheng subclass specimen nucleic acid extraction
+OBI:0001051 DNA extract DNA extract metadata complete The output of an extraction process in which DNA molecules are purified in order to exclude DNA from organellas. Group: UPenn group Person: Jie Zheng subclass nucleic acid extract DNA extraction 'has grain' some 'deoxyribonucleic acid'
+OBI:0001143 labeled nucleic acid extract labeled nucleic acid extract metadata complete labeled extract a labeled specimen that is the output of a labeling process and has grain labeled nucleic acid for detection of the nucleic acid in future experiments. MO_221 labeledExtract Person: Jie Zheng equivalent labeled specimen ('addition of molecular label' and ('has_specified_input' some 'nucleic acid extract')) 'has grain' some 'nucleic acid'
+OBI:0001468 cell specimen cell specimen metadata incomplete A specimen primarily composed of a cell or cells collected from a multicellular organism or a cell culture. MO_612 cell PERSON: Chris Stoeckert, Jie Zheng, Alexander Diehl Discussed on obi call Jan 23, 2017. To improve cell specimen that include single cell specimen. Details see tracker: https://sourceforge.net/p/obi/obi-terms/828 equivalent specimen from organism 'has part' some 'cell'
+OBI:0001472 specimen with known storage state specimen with known storage state metadata incomplete A specimen for which it is known whether it has been subjected to storage of a specified type. MO_95 BiosourceType PERSON: Chris Stoeckert, Jie Zheng equivalent specimen 'fresh specimen' or ('specimen' and ('is_specified_output_of' some 'storage'))
+OBI:0001479 specimen from organism ready for release tissue specimen A specimen that derives from an anatomical part or substance arising from an organism. Examples of tissue specimen include tissue, organ, physiological system, blood, or body location (arm). MO_954 organism_part PERSON: Chris Stoeckert, Jie Zheng equivalent specimen ('organism' or 'material anatomical entity' or 'anatomical cluster')
+OBI:0001506 specimen with pre- or post-mortem status specimen with pre- or post-mortem status metadata complete A specimen that has been established to be taken from a live (pre-mortem) or dead (post-mortem) organism. MO_84 OrganismStatus PERSON: Chris Stoeckert, Jie Zheng organizational term, used in description of specimen that is created from known pre- or post-mortem status equivalent specimen ('organism' and ('has quality' some ('alive' or 'dead')))
+OBI:0002125 H&E-stained fixed tissue slide specimen H&E-stained fixed tissue slide specimen pending final vetting A fixed tissue slide specimen that is the output of H&E slide staining. OBIB, OBI Chris Stoeckert, Ned Haubein equivalent fixed tissue slide specimen H&E slide staining
+OBI:0002126 IHC-stained fixed tissue slide specimen IHC-stained fixed tissue slide specimen pending final vetting A fixed tissue slide specimen that is the output of immunohistochemistry slide staining. OBIB, OBI Chris Stoeckert, Ned Haubein equivalent fixed tissue slide specimen IHC slide staining
+OBI:0002127 single cell specimen metadata complete A cell specimen that contains only one cell. PERSON: Jie Zheng, Alexander Diehl PERSON: Jie Zheng, Alexander Diehl Requested by Sirarat Sarntivijai (EBI). Details see tracker: https://sourceforge.net/p/obi/obi-terms/828/ subclass cell specimen
+OBI:0002500 amniotic fluid specimen ready for release A specimen that is derived from amniotic fluid. Chris Stoeckert, Penn Medicine Biobank Chris Stoeckert equivalent specimen from organism collecting specimen from organism amniotic fluid UBERON_0000173
+OBI:0002501 bile specimen ready for release A specimen that is derived from bile. Chris Stoeckert, Penn Medicine Biobank Chris Stoeckert equivalent specimen from organism collecting specimen from organism bile UBERON_0001970
+OBI:0002502 cerebrospinal fluid specimen ready for release A specimen that is derived from cerbrospinal fluid. Chris Stoeckert, Penn Medicine Biobank Chris Stoeckert equivalent specimen from organism collecting specimen from organism cerebrospinal fluid UBERON_0001359
+OBI:0002503 feces specimen ready for release stool specimen A specimen that is derived from feces. Chris Stoeckert, Penn Medicine Biobank Chris Stoeckert equivalent specimen from organism collecting specimen from organism feces UBERON_0001988
+OBI:0002504 digestive system fluid or secretion specimen ready for release gastric fluid specimen A specimen that is derived from digestive system fluid or secretion. Chris Stoeckert, Penn Medicine Biobank Chris Stoeckert equivalent specimen from organism collecting specimen from organism digestive system secreted substance UBERON_0006911
+OBI:0002505 milk specimen ready for release A specimen that is derived from milk. Chris Stoeckert, Penn Medicine Biobank Chris Stoeckert equivalent specimen from organism collecting specimen from organism milk UBERON_0001913
+OBI:0002506 pericardial fluid specimen ready for release A specimen that is derived from pericardial fluid. Chris Stoeckert, Penn Medicine Biobank Chris Stoeckert equivalent specimen from organism collecting specimen from organism pericardial fluid UBERON_0002409
+OBI:0002507 saliva specimen ready for release A specimen that is derived from saliva. Chris Stoeckert, Penn Medicine Biobank Chris Stoeckert equivalent specimen from organism collecting specimen from organism saliva UBERON_0001836
+OBI:0002508 sputum specimen ready for release A specimen that is derived from sputum. Chris Stoeckert, Penn Medicine Biobank Chris Stoeckert equivalent specimen from organism collecting specimen from organism sputum UBERON_0007311
+OBI:0002509 sweat specimen ready for release A specimen that is derived from sweat. Chris Stoeckert, Penn Medicine Biobank Chris Stoeckert equivalent specimen from organism collecting specimen from organism sweat UBERON_0001089
+OBI:0002510 synovial fluid specimen ready for release A specimen that is derived from synovial fluid. Chris Stoeckert, Penn Medicine Biobank Chris Stoeckert equivalent specimen from organism collecting specimen from organism synovial fluid UBERON_0001090
+OBI:0002511 vitreous humor specimen ready for release vitreous fluid specimen A specimen that is derived from vireous humor. Chris Stoeckert, Penn Medicine Biobank Chris Stoeckert equivalent specimen from organism collecting specimen from organism (tissue and ('part of' some 'vitreous humor')) UBERON_0001797
+OBI:0002512 bone marrow specimen ready for release A specimen that is derived from bone marrow. Chris Stoeckert, Penn Medicine Biobank Chris Stoeckert equivalent specimen from organism bone marrow biopsy bone marrow UBERON_0002371
+OBI:0002513 placenta specimen ready for release A specimen that is derived from placenta. Chris Stoeckert, Penn Medicine Biobank Chris Stoeckert equivalent specimen from organism collecting specimen from organism (tissue and ('part of' some placenta)) UBERON_0001987
+OBI:0002514 peritoneal fluid specimen ready for release A specimen that is derived from peritoneal fluid. Chris Stoeckert, Penn Medicine Biobank Chris Stoeckert equivalent specimen from organism collecting specimen from organism peritoneal fluid UBERON_0001268
+OBI:0002515 pleural fluid specimen ready for release A specimen that is derived from pleural fluid. Chris Stoeckert, Penn Medicine Biobank Chris Stoeckert equivalent specimen from organism collecting specimen from organism pleural fluid UBERON_0001087
+OBI:0002516 brain specimen ready for release A specimen that is derived from brain. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent specimen from organism collecting specimen from organism (tissue and ('part of' some brain)) UBERON_0000955
+OBI:0002517 hair specimen ready for release A specimen that is derived from hair. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent specimen from organism collecting specimen from organism strand of hair UBERON_0001037
+OBI:0002518 prostate gland specimen ready for release A specimen that is derived from prostate gland. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent specimen from organism collecting specimen from organism (tissue and ('part of' some 'prostate gland')) UBERON_0002367
+OBI:0002519 skeletal muscle tissue specimen ready for release A specimen that is derived from skeletal muscle. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent specimen from organism collecting specimen from organism skeletal muscle tissue UBERON_0001134
+OBI:0002520 heart specimen ready for release A specimen that is derived from heart. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent specimen from organism collecting specimen from organism (tissue and ('part of' some heart)) UBERON_0000948
+OBI:0002521 renal medulla specimen ready for release kidney medulla specimen A specimen that is derived from renal medulla. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent specimen from organism collecting specimen from organism (tissue and ('part of' some 'renal medulla')) UBERON_0000362
+OBI:0002522 adrenal gland specimen ready for release A specimen that is derived from adrenal gland. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent specimen from organism collecting specimen from organism (tissue and ('part of' some 'adrenal gland')) UBERON_0002369
+OBI:0002523 breast specimen ready for release mammary tissue specimen A specimen that is derived from breast. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent specimen from organism collecting specimen from organism (tissue and ('part of' some breast)) UBERON_0000310
+OBI:0002524 urinary bladder specimen ready for release A specimen that is derived from urinary bladder. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent specimen from organism collecting specimen from organism (tissue and ('part of' some 'urinary bladder')) UBERON_0001255
+OBI:0002525 tibial artery specimen ready for release A specimen that is derived from tibial artery. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent specimen from organism collecting specimen from organism (tissue and ('part of' some 'tibial artery')) UBERON_0007610
+OBI:0002526 skin of body specimen ready for release skin specimen A specimen that is derived from skin. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent specimen from organism collecting specimen from organism (tissue and ('part of' some 'skin of body')) UBERON_0002097
+OBI:0002527 pancreas specimen ready for release A specimen that is derived from pancreas. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent specimen from organism collecting specimen from organism (tissue and ('part of' some pancreas)) UBERON_0001264
+OBI:0002528 stomach specimen ready for release A specimen that is derived from stomach. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent specimen from organism collecting specimen from organism (tissue and ('part of' some stomach)) UBERON_0000945
+OBI:0002529 pituitary gland specimen ready for release A specimen that is derived from pituitary gland. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent specimen from organism collecting specimen from organism (tissue and ('part of' some 'pituitary gland')) UBERON_0000007
+OBI:0002530 adipose tissue specimen ready for release A specimen that is derived from adipose tissue. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent specimen from organism collecting specimen from organism adipose tissue UBERON_0001013
+OBI:0002531 cortex of kidney specimen ready for release kidney cortex specimen A specimen that is derived from cortex of kidney. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent specimen from organism collecting specimen from organism (tissue and ('part of' some 'cortex of kidney')) UBERON_0001225
+OBI:0002532 esophagus mucosa specimen ready for release A specimen that is derived from esophagus mucosa. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent specimen from organism collecting specimen from organism (tissue and ('part of' some 'esophagus mucosa')) UBERON_0002469
+OBI:0002533 colon specimen ready for release A specimen that is derived from colon. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent specimen from organism collecting specimen from organism (tissue and ('part of' some colon)) UBERON_0001155
+OBI:0002534 lung specimen ready for release A specimen that is derived from lung. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent specimen from organism collecting specimen from organism (tissue and ('part of' some lung)) UBERON_0002048
+OBI:0002535 esophagus muscularis mucosa specimen ready for release esophagus muscularis specimen A specimen that is derived from esophagus muscularis mucosa. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent specimen from organism collecting specimen from organism (tissue and ('part of' some 'esophagus muscularis mucosa')) UBERON_0004648
+OBI:0002536 cerebral cortex specimen ready for release brain cortex specimen A specimen that is derived from cerebral cortex. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent specimen from organism collecting specimen from organism (tissue and ('part of' some 'cerebral cortex')) UBERON_0000956
+OBI:0002537 thyroid gland specimen ready for release A specimen that is derived from thyroid gland. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent specimen from organism collecting specimen from organism (tissue and ('part of' some 'thyroid gland')) UBERON_0002046
+OBI:0002538 cerebellum specimen ready for release brain cerebellum specimen A specimen that is derived from cerebellum. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent specimen from organism collecting specimen from organism (tissue and ('part of' some cerebellum)) UBERON_0002037
+OBI:0002539 tibial nerve specimen ready for release A specimen that is derived from tibial nerve. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent specimen from organism collecting specimen from organism (tissue and ('part of' some 'tibial nerve')) UBERON_0001323
+OBI:0002540 coronary artery specimen ready for release A specimen that is derived from coronary artery. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent specimen from organism collecting specimen from organism (tissue and ('part of' some 'coronary artery')) UBERON_0001621
+OBI:0002541 spleen specimen ready for release A specimen that is derived from spleen. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent specimen from organism collecting specimen from organism (tissue and ('part of' some spleen)) UBERON_0002106
+OBI:0002542 aorta specimen ready for release A specimen that is derived from aorta. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent specimen from organism collecting specimen from organism (tissue and ('part of' some aorta)) UBERON_0000947
+OBI:0002543 atrial appendage specimen ready for release A specimen that is derived from the atrium auricular region. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent specimen from organism collecting specimen from organism (tissue and ('part of' some 'atrium auricular region')) UBERON_0006618
+OBI:0002544 esophagogastric junction specimen ready for release A specimen that is derived from the esophagogastric junction. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent specimen from organism collecting specimen from organism (tissue and ('part of' some 'esophagogastric junction')) UBERON_0007650
+OBI:0002545 ileum specimen ready for release A specimen that is derived from ileum. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent specimen from organism collecting specimen from organism (tissue and ('part of' some ileum)) UBERON_0002116
+OBI:0002546 liver specimen ready for release A specimen that is derived from liver. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent specimen from organism collecting specimen from organism (tissue and ('part of' some liver)) UBERON_0002107
+OBI:0002547 minor salivary gland specimen ready for release A specimen that is derived from minor salivary gland. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent specimen from organism collecting specimen from organism (tissue and ('part of' some 'minor salivary gland')) UBERON_0001830
+OBI:0002548 omentum specimen ready for release A specimen that is derived from omentum. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent specimen from organism collecting specimen from organism (tissue and ('part of' some omentum)) UBERON_0003688
+OBI:0002549 ovary specimen ready for release A specimen that is derived from female gonad. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent specimen from organism collecting specimen from organism (tissue and ('part of' some ovary)) UBERON_0000992
+OBI:0002550 sigmoid colon specimen ready for release A specimen that is derived from sigmoid colon. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent specimen from organism collecting specimen from organism (tissue and ('part of' some 'sigmoid colon')) UBERON_0001159
+OBI:0002551 suprapubic skin specimen ready for release A specimen that is derived from suprapubic skin. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent specimen from organism collecting specimen from organism (tissue and ('part of' some 'suprapubic skin')) UBERON_0036149
+OBI:0002552 testis specimen ready for release A specimen that is derived from testis. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent specimen from organism collecting specimen from organism (tissue and ('part of' some testis)) UBERON_0000473
+OBI:0002553 uterus specimen ready for release A specimen that is derived from uterus. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent specimen from organism collecting specimen from organism (tissue and ('part of' some uterus)) UBERON_0000995
+OBI:0002554 vagina specimen ready for release A specimen that is derived from vagina. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent specimen from organism collecting specimen from organism (tissue and ('part of' some vagina)) UBERON_0000996
+OBI:0002573 polyA depleted RNA extract A RNA extract that is the output of an extraction process in which RNA molecules lacking poly A tails at thier 3' ends are purified. UPenn Group PERSON: Chris Stoeckert|PERSON: Jie Zheng|Mark A. Miller, based on http://purl.obolibrary.org/obo/OBI_0000869 subclass RNA extract RNA extraction with polyA depletion
+OBI:0002599 swab specimen swab specimen ready for release A specimen that is stored on a swab as the output of a collecting specimen with swab process. OBIB/OBI Chris Stoeckert OBIB https://github.com/obi-ontology/obi/issues/910 equivalent specimen collecting specimen with swab
+OBI:0002603 areolar swab specimen ready for release A specimen that is collected with a swab from the surface of an areola of a breast. Chris Stoeckert, OBIB Chris Stoeckert equivalent specimen from organism collecting specimen with swab areola UBERON_0002032
+OBI:0002604 breast swab specimen ready for release A specimen that is collected with a swab from the surface of a breast. Chris Stoeckert, OBIB Chris Stoeckert equivalent specimen from organism collecting specimen with swab breast UBERON_0000310
+OBI:0002605 cheek swab specimen ready for release A specimen that is collected with a swab from the cheek portion of the inside surface of a mouth. Chris Stoeckert, OBIB Chris Stoeckert equivalent specimen from organism collecting specimen with swab cheek UBERON_0001567
+OBI:0002606 nasopharyngeal swab specimen ready for release A specimen that is collected with a swab from the surface of a nasopharynx. Chris Stoeckert, OBIB Chris Stoeckert equivalent specimen from organism collecting specimen with swab nasopharynx UBERON_0001728
+OBI:0002607 oral swab specimen ready for release A specimen that is collected with a swab from the inside surface of a mouth. Chris Stoeckert, OBIB Chris Stoeckert equivalent specimen from organism collecting specimen with swab mouth UBERON_0000165
+OBI:0002608 oropharyngeal swab specimen ready for release A specimen that is collected with a swab from the surface of a oropharynx. Chris Stoeckert, OBIB Chris Stoeckert equivalent specimen from organism collecting specimen with swab oropharynx UBERON_0001729
+OBI:0002609 rectal swab specimen ready for release A specimen that is collected with a swab from the surface of a rectum. Chris Stoeckert, OBIB Chris Stoeckert equivalent specimen from organism collecting specimen with swab rectum UBERON_0001052
+OBI:0002610 tongue swab specimen ready for release A specimen that is collected with a swab from the surface of a tongue. Chris Stoeckert, OBIB Chris Stoeckert equivalent specimen from organism collecting specimen with swab tongue UBERON_0001723
+OBI:0002611 vagina swab specimen ready for release A specimen that is collected with a swab from the surface of a vagina. Chris Stoeckert, OBIB Chris Stoeckert equivalent specimen from organism collecting specimen with swab vagina UBERON_0000996
+OBI:0002612 fecal swab specimen ready for release stool swab specimen A specimen that is collected with a swab from the surface of a feces. Chris Stoeckert, OBIB Chris Stoeckert equivalent specimen from organism collecting specimen with swab feces UBERON_0001988
+OBI:0002613 environmental swab specimen ready for release A specimen that is collected with a swab from the surface of an environmenal material. Chris Stoeckert, OBIB Chris Stoeckert equivalent specimen collecting specimen with swab environmental material ENVO_00010483
+OBI:0002627 ribosomal RNA-depleted RNA extract ribosomal RNA-depleted RNA extract pending final vetting An extract of RNA which is produced through rRNA (ribosomal RNA) depletion (the removal of highly abundant rRNA species). https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-018-4585-1 Looking at the reads for each ribosomal RNA-depleted RNA extract, the vast majority align to protein coding genes based on the ENSEMBL annotation. Dan Berrios subclass RNA extract
+OBI:0002648 individual organism specimen A specimen composed of an individual organism to be studied in an investigation. EFO_0000542 individual Person: Jie Zheng https://github.com/obi-ontology/obi/issues/1092 equivalent specimen 'has component' exactly 1 'organism'
+OBI:0002691 arthropod meal of blood specimen metadata complete blood meal A specimen of the blood ingested by an arthropod. VEuPathDB A specimen used in a blood meal assay to determine what is the source of blood ingested by a mosquito. Chris Stoeckert|Jie Zheng The mosquito feeds on a human for example, ingests the blood of the human, this blood is then taken from the tummy of a mosquito and a PCR may be run on this specimen to identify that the mosquito definitely fed on a human. VEuPathDB https://github.com/obi-ontology/obi/issues/1117 subclass specimen from organism collecting specimen from organism
+OBI:0002746 induced sputum specimen A sputum specimen that is collected from an organism following its inhalation of a nebulized salt solution. PMC3297553 John Judkins subclass specimen from organism collecting specimen from organism sputum UBERON_0007311
+OBI:0002774 platelet-poor plasma specimen A blood plasma specimen that is the output of some platelet-poor plasma preparation and is the portion of plasma that contains fewer than 10,000 platelets per microliter. PERSON: Matthew Diller subclass blood plasma specimen
+OBI:0002778 tracheal aspirate specimen tracheal wash specimen A specimen that is collected with a suctioning tube from the trachea. PMID:25338241 Asiyah Yu Lin ORCID:0000-0003-2620-0345 subclass specimen from organism aspiration specimen collection trachea UBERON_0003126
+OBI:0002779 mid-turbinate nasal swab specimen A specimen that is collected with a mid-turbinate nasal swab from the turbinate area of the nasal cavity. https://seattlechildrenslab.testcatalog.org/catalogs/185/files/11633 Asiyah Yu Lin ORCID:0000-0003-2620-0345 equivalent specimen from organism collecting specimen with swab middle nasal concha UBERON_0005921
+OBI:0002780 nasal aspirate specimen nasal wash specimen|nasopharyngeal aspirate A specimen that is collected with a suctioning tube from the nasal cavity. Asiyah Yu Lin ORCID:0000-0003-2620-0345 Asiyah Yu Lin ORCID:0000-0003-2620-0345 equivalent specimen from organism aspiration specimen collection nasal cavity mucosa UBERON_0001826
+OBI:0002781 lower respiratory tract aspirate specimen lower respiratory tract wash specimen A specimen that is collected with a suctioning tube from the lower respiratory tract. Asiyah Yu Lin ORCID:0000-0003-2620-0345 Asiyah Yu Lin ORCID:0000-0003-2620-0345 equivalent specimen from organism aspiration specimen collection lower respiratory tract UBERON_0001558
+OBI:0002782 upper respiratory specimen A specimen that is derived from the upper respiratory tract Asiyah Yu Lin ORCID:0000-0003-2620-0345 Asiyah Yu Lin ORCID:0000-0003-2620-0345 equivalent specimen from organism collecting specimen with swab upper respiratory tract UBERON_0001557
+OBI:0002783 lower respiratory tract specimen A specimen that is derived from the lower respiratory tract. Asiyah Yu Lin ORCID:0000-0003-2620-0345 Asiyah Yu Lin ORCID:0000-0003-2620-0345 equivalent specimen from organism lower respiratory tract UBERON_0001558
+OBI:0002784 anterior nasal swab specimen A specimen that is derived from the anterior nasal wall Asiyah Yu Lin ORCID:0000-0003-2620-0345 Asiyah Yu Lin ORCID:0000-0003-2620-0345 equivalent specimen from organism collecting specimen with swab anterior nasal wall UBERON_3000016
+OBI:0002971 endotracheal tube specimen A specimen that derives from a biofilm that forms on the inner surface of an endotracheal tube while the tube is in the trachea. The specimen is collected upon removal of the tube from the trachea. https://bmcpulmmed.biomedcentral.com/articles/10.1186/s12890-019-0926-3 John Judkins ORCID:0000-0001-6595-0902 subclass specimen from organism collecting specimen from organism respiratory system fluid/secretion UBERON_0006538
+OBI:0002972 endotracheal aspirate specimen A specimen that derives from a biofilm that forms on the inner surface of an endotracheal tube while the tube is in the trachea. The specimen is collected by suction without removing the tube. https://bmcpulmmed.biomedcentral.com/articles/10.1186/s12890-019-0926-3 John Judkins ORCID:0000-0001-6595-0902 subclass specimen from organism collecting specimen from organism respiratory system fluid/secretion UBERON_0006538
+OBI:0003054 blood specimen in vacutainer Vacutainer sample A blood specimen that is located in a vacutainer. VEuPathDB John Judkins specimen from organism collecting specimen from organism blood UBERON_0000178
+OBI:0003055 blood specimen on filter paper Filter paper sample A blood specimen that is located on a filter paper. Penn Group Jie Zheng|Chris Stoeckert specimen from organism collecting specimen from organism blood UBERON_0000178
+OBI:0003380 placental blood specimen A specimen that is derived from placental blood. VEuPathDB John Judkins equivalent specimen from organism collecting specimen from organism placental blood UBERON_8470000
+OBI:0003415 peripheral blood mononuclear cell specimen PBMC specimen A processed specimen that is extracted from whole blood using gradient centrifugation that separates the blood into a layer of peripheral blood mononuclear cells under the top layer of plasma. It contains lymphocytes, monocytes or macrophages that are critical components in the immune system. http://en.wikipedia.org/wiki/Peripheral_blood_mononuclear_cell Jie Zheng|Chris Stoeckert subclass specimen from organism collecting specimen from organism peripheral blood mononuclear cell CL_2000001
+OBI:0003482 lymph specimen A specimen that is derived from a portion of lymph collected from an organism. VEuPathDB John Judkins ORCID:0000-0001-6595-0902 specimen from organism collecting specimen from organism (tissue and ('part of' some lymph)) UBERON_0002391
+OBI:0003483 digestive tract specimen A specimen that is derived from part of a digestive tract. VEuPathDB John Judkins ORCID:0000-0001-6595-0902 specimen from organism collecting specimen from organism (tissue and ('part of' some 'digestive tract')) UBERON_0001555
+OBI:0003595 nasal lavage fluid A specimen collected through nasal cavity lavage that contains the reagents used to for the lavage process, organisms, cells, cellular secretions, and other biomaterials present in the nasal cavity space. Sebastian Duesing|Randi Vita equivalent lavage fluid specimen lavage nasal cavity mucosa UBERON_0001826
+OBI:0003652 albumin-free serum albumin-free serum A blood serum specimen that contains no albumin. Sebastian Duesing Philippe Rocca-Serra https://github.com/obi-ontology/obi/issues/493 equivalent blood serum specimen 'has part' only (not ('albumin'))
+OBI:0003666 lavage fluid specimen lavage fluid specimen A specimen obtained through a lavage process which includes fluid in addition to cells and/or cellular secretions. The collection of bronchoalveolar lavage fluid (BAL) from the lungs of mice in order to study the cytokines present. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1803 equivalent specimen from organism lavage
+OBI:0003667 oral lavage fluid oral lavage fluid mouth rinse specimen A specimen collected through oral cavity lavage that contains the reagents used to for the lavage process, organisms, cells, cellular secretions, and other biomaterials present in the oral cavity space. Sebastian Duesing Anna Maria Masci https://github.com/obi-ontology/obi/issues/1803 equivalent lavage fluid specimen lavage mouth UBERON_0000165
+OBI:0100016 blood plasma specimen blood plasma specimen metadata complete plasma a material entity which corresponds to the liquid component of blood, in which the blood cells are suspended. WEB: http://en.wikipedia.org/wiki/Blood_plasma PMID: 18217225.Sex Transm Dis. 2008 Jan;35(1):55-60. Review.Human immunodeficiency virus viral load in blood plasma and semen: review and implications of empirical findings. PERSON: Maura Gasparetto|PERSON: Melanie Courtot|PERSON: Philippe Rocca-Serra 03/21/2010: BP, blood plasma is defined as the output of certain separation processes, so this is in the domain of OBI, not FMA. subclass blood specimen ('material component separation' and ('has_specified_input' some 'blood specimen'))
+OBI:0100017 blood serum specimen blood serum specimen metadata complete A material entity which derives from blood and corresponds to blood plasma without fibrinogen or the other clotting factors. WEB: http://en.wikipedia.org/wiki/Blood_plasma PMID: 18229666.Adv Med Sci. 2007;52 Suppl 1:204-6.Antioxidant activity of blood serum and saliva in patients with periodontal disease treated due to epilepsy. PERSON: Maura Gasparetto|PERSON: Melanie Courtot|PERSON: Philippe Rocca-Serra subclass blood plasma specimen (('filtration' or 'centrifugation' or 'dialysis') and ('has_specified_input' some 'blood specimen'))
+OBI:0100067 bronchial alveolar lavage bronchial alveolar lavage metadata complete BAL Group of biomaterials present in the bronchial aveolar space of an organism which are collected through lavage including the reagents used to for the lavage process, organisms, cells, and cellular secretions present in the bronchial aveolar space. GROUP: IEDB solution containing lung derived T cells, eosinophils, and TNFa. PERSON: Bjoern Peters equivalent lavage fluid specimen lavage lung
+OBI:0302716 pool of specimens pool of specimens metadata complete A pool of specimens is a mixture of a population of samples which have been gathered from one or more sample populations, obtained by the physical process of mixing individual specimens, e.g. mixing the DNA collected from the individual fish. GROUP: CEBS PERSON: Jennifer Fostel check with advisors as to how to represent multiple instances of any class? a set of specimens which have been gathered from one or more sample_populations, obtained by the physical process of mixing individual specimens, e.g. mixing the DNA collected from the individual fish equivalent specimen ('material combination' and ('has_specified_input' only 'specimen'))
+OBI:1000049 whole mount tissue whole mount tissue metadata complete whole mount sample A whole organism preparation resulting from a histological preparation known as whole mount preparation where the whole specimen is mounted or spread on the microscope (glass) slide GROUP: OBI PERSON: Helen Parkinson|PERSON: Philippe Rocca-Serra PRS:22-02-2008: indicates the need to create a protocol application and distinguish it from this entity|PRS:22-02-2008: is a material which has output_role during whole mount preparation protocol-application subclass whole organism preparation histological sample preparation 'derives from' some 'material anatomical entity'
+OBI:1110041 lymph node cell specimen lymph node cell specimen metadata incomplete A cell specimen comprised of a mixed population of cells obtained by processing whole lymph node into individual cells, typically performed using a sieve. This population includes T cells, B cells, macrophages, and other cell types. IEDB IEDB equivalent cell specimen ('organ harvesting' and ('has_specified_input' some 'lymph node'))
+OBI:1110116 splenocyte specimen splenocyte specimen metadata complete A cell specimen comprised of a mixed cell population obtained by processing whole spleen into individual cells, typically performed using a sieve or blender. This population includes T cells, B cells, macrophages, and other cell types. IEDB IEDB equivalent cell specimen ('organ harvesting' and ('has_specified_input' some 'spleen'))
+OBI:1200000 FFPE specimen FFPE specimen formalin-fixed paraffin-embeded specimen A specimen that has been fixed in formalin and embedded in paraffin. https://www.biochain.com/general/what-is-ffpe-tissue/ Many of today’s researchers prefer to use Formalin-Fixed Paraffin-Embedded samples of tissues for their IHC, histological or in-situ genomic analyses. Professionally fixed and embedded FFPE samples and the biomolecules they contain are reasonably stable at ambient temperatures. -based on https://lab-ally.com/histopathology-resources/ffpe-samples/ MIABIS https://github.com/obi-ontology/obi/issues/1019 subclass paraffin specimen
+OBI:2000000 uterine cervix specimen A specimen that is derived from some uterine cervix Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X equivalent specimen from organism collecting specimen from organism (tissue and ('part of' some 'uterine cervix')) UBERON_0000002
+OBI:2000001 urethra specimen A specimen that is derived from some urethra Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X equivalent specimen from organism collecting specimen from organism (tissue and ('part of' some urethra)) UBERON_0000057
+OBI:2000002 cervical mucus specimen A specimen that is derived from some cervical mucus Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X equivalent specimen from organism collecting specimen from organism cervical mucus UBERON_0000316
+OBI:2000003 throat specimen A specimen that is derived from some throat Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X equivalent specimen from organism collecting specimen from organism (tissue and ('part of' some throat)) UBERON_0000341
+OBI:2000004 eye specimen A specimen that is derived from some eye Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X equivalent specimen from organism collecting specimen from organism (tissue and ('part of' some eye)) UBERON_0000970
+OBI:2000005 respiratory system specimen A specimen that is derived from some respiratory system Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X equivalent specimen from organism collecting specimen from organism (tissue and ('part of' some 'respiratory system')) UBERON_0001004
+OBI:2000006 upper respiratory tract specimen A specimen that is derived from some upper respiratory tract Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X equivalent specimen from organism collecting specimen from organism (tissue and ('part of' some 'upper respiratory tract')) UBERON_0001557
+OBI:2000007 nasopharynx specimen A specimen that is derived from some nasopharynx Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X equivalent specimen from organism collecting specimen from organism (tissue and ('part of' some nasopharynx)) UBERON_0001728
+OBI:2000008 semen specimen A specimen that is derived from some semen Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X equivalent specimen from organism collecting specimen from organism semen UBERON_0001968
+OBI:2000009 bodily fluid specimen A specimen that is derived from some bodily fluid Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X equivalent specimen from organism collecting specimen from organism bodily fluid UBERON_0006314
+OBI:2000010 chorionic villus specimen A specimen that is derived from some chorionic villus Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X equivalent specimen from organism collecting specimen from organism (tissue and ('part of' some 'chorionic villus')) UBERON_0007106
+OBI:2000011 meconium specimen A specimen that is derived from some meconium Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X equivalent specimen from organism collecting specimen from organism meconium UBERON_0007109
+OBI:2000012 umbilical cord blood specimen A specimen that is derived from some umbilical cord blood Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X equivalent specimen from organism collecting specimen from organism umbilical cord blood UBERON_0012168
+OBI:2000013 arterial blood specimen A specimen that is derived from some arterial blood Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X equivalent specimen from organism collecting specimen from organism arterial blood UBERON_0013755
+OBI:2000014 venous blood specimen A specimen that is derived from some venous blood Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X equivalent specimen from organism collecting specimen from organism venous blood UBERON_0013756
+OBI:2000015 capillary blood specimen A specimen that is derived from some capillary blood Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X equivalent specimen from organism collecting specimen from organism capillary blood UBERON_0013757
+OBI:2000016 erythrocyte specimen A specimen that is derived from some erythrocytes Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X subclass specimen from organism collecting specimen with swab erythrocyte CL_0000232
+OBI:2000017 reticulocyte specimen A specimen that is derived from some reticulocytes Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X subclass specimen from organism collecting specimen with swab reticulocyte CL_0000558
+OBI:2000018 leukocyte specimen A specimen that is derived from some leukocytes Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X subclass specimen from organism collecting specimen with swab leukocyte CL_0000738
diff --git a/src/sparql/specimen-violation-modules.rq b/src/sparql/specimen-violation-modules.rq
new file mode 100644
index 00000000..94cf8fcf
--- /dev/null
+++ b/src/sparql/specimen-violation-modules.rq
@@ -0,0 +1,11 @@
+# 'specimen' should have no asserted children in obi-edit.owl
+# Any descendant of specimen that has a label is asserted in obi-edit.owl
+
+PREFIX obo:
+PREFIX rdfs:
+
+SELECT ?s WHERE {
+ ?s rdfs:subClassOf* obo:OBI_0100051 ;
+ rdfs:label ?label .
+ FILTER (str(?s) != "http://purl.obolibrary.org/obo/OBI_0100051")
+}