From efae02e6c9d4293f42c8981754e051e6cfead1b5 Mon Sep 17 00:00:00 2001
From: Sebastian Duesing <66700705+sebastianduesing@users.noreply.github.com>
Date: Fri, 1 Nov 2024 17:00:06 -0500
Subject: [PATCH] Rename biobank-specimens to specimens

---
 Makefile                                                    | 2 +-
 README.md                                                   | 2 +-
 src/ontology/catalog-v001.xml                               | 2 +-
 .../modules/{biobank-specimens.owl => specimens.owl}        | 6 +++---
 src/ontology/obi-edit.owl                                   | 2 +-
 .../templates/{biobank-specimens.tsv => specimens.tsv}      | 0
 6 files changed, 7 insertions(+), 7 deletions(-)
 rename src/ontology/modules/{biobank-specimens.owl => specimens.owl} (99%)
 rename src/ontology/templates/{biobank-specimens.tsv => specimens.tsv} (100%)

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/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 @@
     <uri name="http://purl.obolibrary.org/obo/obi/dev/modules/antibody-purification.owl" uri="modules/antibody-purification.owl"/>
     <uri name="http://purl.obolibrary.org/obo/obi/dev/modules/assays.owl" uri="modules/assays.owl"/>
     <uri name="http://purl.obolibrary.org/obo/obi/dev/modules/biopsy.owl" uri="modules/biopsy.owl"/>
-    <uri name="http://purl.obolibrary.org/obo/obi/dev/modules/biobank-specimens.owl" uri="modules/biobank-specimens.owl"/>
     <uri name="http://purl.obolibrary.org/obo/obi/dev/modules/biobank-tissue-specimen.owl" uri="modules/biobank-tissue-specimen.owl"/>
     <uri name="http://purl.obolibrary.org/obo/obi/dev/modules/data-sets.owl" uri="modules/data-sets.owl"/>
     <uri name="http://purl.obolibrary.org/obo/obi/dev/modules/data-transformations.owl" uri="modules/data-transformations.owl"/>
@@ -43,6 +42,7 @@
     <uri name="http://purl.obolibrary.org/obo/obi/dev/modules/sample-collection.owl" uri="modules/sample-collection.owl"/>
     <uri name="http://purl.obolibrary.org/obo/obi/dev/modules/sequence-analysis.owl" uri="modules/sequence-analysis.owl"/>
     <uri name="http://purl.obolibrary.org/obo/obi/dev/modules/specimen-assay-data.owl" uri="modules/specimen-assay-data.owl"/>
+    <uri name="http://purl.obolibrary.org/obo/obi/dev/modules/specimens.owl" uri="modules/specimens.owl"/>
     <uri name="http://purl.obolibrary.org/obo/obi/dev/modules/study-designs.owl" uri="modules/study-designs.owl"/>
     <uri name="http://purl.obolibrary.org/obo/obi/dev/modules/value-specifications.owl" uri="modules/value-specifications.owl"/>
 </catalog>
diff --git a/src/ontology/modules/biobank-specimens.owl b/src/ontology/modules/specimens.owl
similarity index 99%
rename from src/ontology/modules/biobank-specimens.owl
rename to src/ontology/modules/specimens.owl
index e8734fc8..c9841718 100644
--- a/src/ontology/modules/biobank-specimens.owl
+++ b/src/ontology/modules/specimens.owl
@@ -1,13 +1,13 @@
 <?xml version="1.0"?>
-<rdf:RDF xmlns="http://purl.obolibrary.org/obo/obi/dev/modules/biobank-specimens.owl#"
-     xml:base="http://purl.obolibrary.org/obo/obi/dev/modules/biobank-specimens.owl"
+<rdf:RDF xmlns="http://purl.obolibrary.org/obo/obi/dev/modules/specimens.owl#"
+     xml:base="http://purl.obolibrary.org/obo/obi/dev/modules/specimens.owl"
      xmlns:obo="http://purl.obolibrary.org/obo/"
      xmlns:owl="http://www.w3.org/2002/07/owl#"
      xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
      xmlns:xml="http://www.w3.org/XML/1998/namespace"
      xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
      xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#">
-    <owl:Ontology rdf:about="http://purl.obolibrary.org/obo/obi/dev/modules/biobank-specimens.owl"/>
+    <owl:Ontology rdf:about="http://purl.obolibrary.org/obo/obi/dev/modules/specimens.owl"/>
     
 
 
diff --git a/src/ontology/obi-edit.owl b/src/ontology/obi-edit.owl
index 780b734e..5c276597 100644
--- a/src/ontology/obi-edit.owl
+++ b/src/ontology/obi-edit.owl
@@ -44,7 +44,6 @@
         <owl:imports rdf:resource="http://purl.obolibrary.org/obo/obi/dev/modules/administration.owl"/>
         <owl:imports rdf:resource="http://purl.obolibrary.org/obo/obi/dev/modules/antibody-purification.owl"/>
         <owl:imports rdf:resource="http://purl.obolibrary.org/obo/obi/dev/modules/assays.owl"/>
-        <owl:imports rdf:resource="http://purl.obolibrary.org/obo/obi/dev/modules/biobank-specimens.owl"/>
         <owl:imports rdf:resource="http://purl.obolibrary.org/obo/obi/dev/modules/biopsy.owl"/>
         <owl:imports rdf:resource="http://purl.obolibrary.org/obo/obi/dev/modules/data-sets.owl"/>
         <owl:imports rdf:resource="http://purl.obolibrary.org/obo/obi/dev/modules/data-transformations.owl"/>
@@ -56,6 +55,7 @@
         <owl:imports rdf:resource="http://purl.obolibrary.org/obo/obi/dev/modules/physical-examination.owl"/>
         <owl:imports rdf:resource="http://purl.obolibrary.org/obo/obi/dev/modules/sample-collection.owl"/>
         <owl:imports rdf:resource="http://purl.obolibrary.org/obo/obi/dev/modules/sequence-analysis.owl"/>
+        <owl:imports rdf:resource="http://purl.obolibrary.org/obo/obi/dev/modules/specimens.owl"/>
         <owl:imports rdf:resource="http://purl.obolibrary.org/obo/obi/dev/modules/specimen-assay-data.owl"/>
         <owl:imports rdf:resource="http://purl.obolibrary.org/obo/obi/dev/modules/study-designs.owl"/>
         <owl:imports rdf:resource="http://purl.obolibrary.org/obo/obi/dev/modules/value-specifications.owl"/>
diff --git a/src/ontology/templates/biobank-specimens.tsv b/src/ontology/templates/specimens.tsv
similarity index 100%
rename from src/ontology/templates/biobank-specimens.tsv
rename to src/ontology/templates/specimens.tsv