Merge pull request #709 from vaccineontology/Rxnorm_HepatitisA

Added hepatitis A related vaccines defined in RxNorm Extension
vaccineontology · May 28, 2024 · 1513a81 · 1513a81
2 parents 629c129 + a85661f
commit 1513a81
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Showing 25 changed files with 41,600 additions and 7,286 deletions.
diff --git a/Makefile b/Makefile
@@ -73,8 +73,10 @@ src/modules/%.owl: src/templates/%.csv | build/robot.jar
 # Update all modules
 MODULE_NAMES := cancer_vaccine\
  vaccine\
+ vaccine_RxNorm\
  vaccine_adjuvant\
  vaccine_component\
+ brand_name\
  data_item\
  process\
  site\
@@ -85,6 +87,7 @@ MODULE_NAMES := cancer_vaccine\
  vo_annotationProp\
  vo_objectProp\
  vo_CVX_code\
+ vo_RxNorm\
  obsolete
 
 MODULE_FILES := $(foreach x,$(MODULE_NAMES),src/modules/$(x).owl)

diff --git a/src/Ontofox_input/IAO_import_input.txt b/src/Ontofox_input/IAO_import_input.txt
@@ -16,6 +16,7 @@ http://purl.obolibrary.org/obo/IAO_0000032 #scalar measurement datum
 http://purl.obolibrary.org/obo/IAO_0000003 #measurement unit label
 http://purl.obolibrary.org/obo/IAO_0000013 #journal article
 http://purl.obolibrary.org/obo/IAO_0000100 #data set
+http://purl.obolibrary.org/obo/IAO_0020000 #identifier
 
 [Top level source term URIs and target direct superclass URIs]
 http://purl.obolibrary.org/obo/IAO_0000030

diff --git a/src/VO.owl b/src/VO.owl
@@ -22,8 +22,10 @@
         <owl:imports rdf:resource="http://purl.obolibrary.org/obo/ro/core.owl"/>
         <owl:imports rdf:resource="http://purl.obolibrary.org/obo/vo/dev/cancer_vaccine.owl"/>
         <owl:imports rdf:resource="http://purl.obolibrary.org/obo/vo/dev/vaccine.owl"/>
+        <owl:imports rdf:resource="http://purl.obolibrary.org/obo/vo/dev/vaccine_RxNorm.owl"/>
         <owl:imports rdf:resource="http://purl.obolibrary.org/obo/vo/dev/vaccine_adjuvant.owl"/>
         <owl:imports rdf:resource="http://purl.obolibrary.org/obo/vo/dev/vaccine_component.owl"/>
+        <owl:imports rdf:resource="http://purl.obolibrary.org/obo/vo/dev/brand_name.owl"/>
         <owl:imports rdf:resource="http://purl.obolibrary.org/obo/vo/dev/data_item.owl"/>
         <owl:imports rdf:resource="http://purl.obolibrary.org/obo/vo/dev/gene.owl"/>
         <owl:imports rdf:resource="http://purl.obolibrary.org/obo/vo/dev/process.owl"/>
@@ -33,6 +35,7 @@
         <owl:imports rdf:resource="http://purl.obolibrary.org/obo/vo/dev/individuals.owl"/>
         <owl:imports rdf:resource="http://purl.obolibrary.org/obo/vo/dev/vo_annotationProp.owl"/>
         <owl:imports rdf:resource="http://purl.obolibrary.org/obo/vo/dev/vo_CVX_code.owl"/>
+        <owl:imports rdf:resource="http://purl.obolibrary.org/obo/vo/dev/vo_RxNorm.owl"/>
         <owl:imports rdf:resource="http://purl.obolibrary.org/obo/vo/dev/vo_objectProp.owl"/>
         <owl:imports rdf:resource="http://purl.obolibrary.org/obo/vo/dev/obsolete.owl"/>
         <owl:imports rdf:resource="http://purl.obolibrary.org/obo/vo/external/CHEBI_import.owl"/>

diff --git a/src/catalog-v001.xml b/src/catalog-v001.xml
@@ -3,8 +3,10 @@
     <uri name="http://purl.obolibrary.org/obo/vo/dev/ontorat.owl" uri="modules/ontorat.owl"/>
     <uri name="http://purl.obolibrary.org/obo/vo/dev/cancer_vaccine.owl" uri="modules/cancer_vaccine.owl"/>
     <uri name="http://purl.obolibrary.org/obo/vo/dev/vaccine.owl" uri="modules/vaccine.owl"/>
+    <uri name="http://purl.obolibrary.org/obo/vo/dev/vaccine_RxNorm.owl" uri="modules/vaccine_RxNorm.owl"/>
     <uri name="http://purl.obolibrary.org/obo/vo/dev/vaccine_adjuvant.owl" uri="modules/vaccine_adjuvant.owl"/>
     <uri name="http://purl.obolibrary.org/obo/vo/dev/vaccine_component.owl" uri="modules/vaccine_component.owl"/>
+    <uri name="http://purl.obolibrary.org/obo/vo/dev/brand_name.owl" uri="modules/brand_name.owl"/>
     <uri name="http://purl.obolibrary.org/obo/vo/dev/data_item.owl" uri="modules/data_item.owl"/>
     <uri name="http://purl.obolibrary.org/obo/vo/dev/gene.owl" uri="modules/gene.owl"/>
     <uri name="http://purl.obolibrary.org/obo/vo/dev/process.owl" uri="modules/process.owl"/>
@@ -14,6 +16,7 @@
     <uri name="http://purl.obolibrary.org/obo/vo/dev/individuals.owl" uri="modules/individuals.owl"/>
     <uri name="http://purl.obolibrary.org/obo/vo/dev/vo_annotationProp.owl" uri="modules/vo_annotationProp.owl"/>
     <uri name="http://purl.obolibrary.org/obo/vo/dev/vo_CVX_code.owl" uri="modules/vo_CVX_code.owl"/>
+    <uri name="http://purl.obolibrary.org/obo/vo/dev/vo_RxNorm.owl" uri="modules/vo_RxNorm.owl"/>
     <uri name="http://purl.obolibrary.org/obo/vo/dev/vo_objectProp.owl" uri="modules/vo_objectProp.owl"/>
     <uri name="http://purl.obolibrary.org/obo/vo/dev/obsolete.owl" uri="modules/obsolete.owl"/>
     <uri name="http://purl.obolibrary.org/obo/vo.owl" uri="VO.owl"/>

diff --git a/src/imports/IAO_import.owl b/src/imports/IAO_import.owl
@@ -1,6 +1,7 @@
 <?xml version="1.0"?>
 <rdf:RDF xmlns="http://purl.obolibrary.org/obo/vo/external/IAO_import.owl#"
      xml:base="http://purl.obolibrary.org/obo/vo/external/IAO_import.owl"
+     xmlns:dc="http://purl.org/dc/elements/1.1/"
      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#"
@@ -191,6 +192,12 @@ We also have the outstanding issue of how to aim different definitions to differ
 
 
 
+    <!-- http://purl.org/dc/elements/1.1/creator -->
+
+    <owl:AnnotationProperty rdf:about="http://purl.org/dc/elements/1.1/creator"/>
+
+
+
     <!-- 
     ///////////////////////////////////////////////////////////////////////////////////////
     //
@@ -592,9 +599,27 @@ Request that IAO either clarify these or change definitions not to use them</rdf
         <rdfs:comment xml:lang="en">Revisit the term in Octorber 2020. Improve the defintion.</rdfs:comment>
         <rdfs:label xml:lang="en">publication</rdfs:label>
     </owl:Class>
+
+
+
+    <!-- http://purl.obolibrary.org/obo/IAO_0020000 -->
+
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0020000">
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000030"/>
+        <obo:IAO_0000111 xml:lang="en">identifier</obo:IAO_0000111>
+        <obo:IAO_0000115 xml:lang="en">An information content entity that is the outcome of a dubbing process and is used to refer to one instance of entity shared by a group of people to refer to that individual entity.</obo:IAO_0000115>
+        <obo:IAO_0000117 xml:lang="en">Justin Whorton</obo:IAO_0000117>
+        <obo:IAO_0000117 xml:lang="en">Mathias Brochhausen</obo:IAO_0000117>
+        <obo:IAO_0000118 xml:lang="en">proper name</obo:IAO_0000118>
+        <obo:IAO_0000233 xml:lang="en">https://github.com/information-artifact-ontology/IAO/issues/237</obo:IAO_0000233>
+        <obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/iao.owl"/>
+        <dc:creator>Mathias Brochhausen</dc:creator>
+        <rdfs:comment xml:lang="en">Sep 29, 2016: The current definition has been amended from the previous version: &quot;A proper name is an information content entity that is the outcome of a dubbing process and is used to refer to one instance of entity shared by a group of people to refer to that individual entity.&quot; to more accuratly reflect the necessary and sufficient condition on the class. (MB)</rdfs:comment>
+        <rdfs:label xml:lang="en">identifier</rdfs:label>
+    </owl:Class>
 </rdf:RDF>
 
 
 
-<!-- Generated by the OWL API (version 4.5.25) https://github.com/owlcs/owlapi -->
+<!-- Generated by the OWL API (version 4.5.26) https://github.com/owlcs/owlapi -->
 
diff --git a/src/modules/brand_name.owl b/src/modules/brand_name.owl
@@ -0,0 +1,141 @@
+<?xml version="1.0"?>
+<rdf:RDF xmlns="http://purl.obolibrary.org/obo/vo/dev/brand_name.owl#"
+     xml:base="http://purl.obolibrary.org/obo/vo/dev/brand_name.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/vo/dev/brand_name.owl"/>
+
+
+
+    <!-- 
+    ///////////////////////////////////////////////////////////////////////////////////////
+    //
+    // Annotation properties
+    //
+    ///////////////////////////////////////////////////////////////////////////////////////
+     -->
+
+
+
+
+    <!-- http://purl.obolibrary.org/obo/IAO_0000117 -->
+
+    <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000117"/>
+
+
+
+    <!-- 
+    ///////////////////////////////////////////////////////////////////////////////////////
+    //
+    // Classes
+    //
+    ///////////////////////////////////////////////////////////////////////////////////////
+     -->
+
+
+
+
+    <!-- http://purl.obolibrary.org/obo/VO_0015077 -->
+
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/VO_0015077"/>
+
+
+
+    <!-- 
+    ///////////////////////////////////////////////////////////////////////////////////////
+    //
+    // Individuals
+    //
+    ///////////////////////////////////////////////////////////////////////////////////////
+     -->
+
+
+
+
+    <!-- http://purl.obolibrary.org/obo/VO_0015341 -->
+
+    <owl:NamedIndividual rdf:about="http://purl.obolibrary.org/obo/VO_0015341">
+        <rdf:type rdf:resource="http://purl.obolibrary.org/obo/VO_0015077"/>
+        <obo:IAO_0000117>Jie Zheng</obo:IAO_0000117>
+        <rdfs:label>Vaqta</rdfs:label>
+    </owl:NamedIndividual>
+
+
+
+    <!-- http://purl.obolibrary.org/obo/VO_0015342 -->
+
+    <owl:NamedIndividual rdf:about="http://purl.obolibrary.org/obo/VO_0015342">
+        <rdf:type rdf:resource="http://purl.obolibrary.org/obo/VO_0015077"/>
+        <obo:IAO_0000117>Jie Zheng</obo:IAO_0000117>
+        <rdfs:label>Epaxal</rdfs:label>
+    </owl:NamedIndividual>
+
+
+
+    <!-- http://purl.obolibrary.org/obo/VO_0015343 -->
+
+    <owl:NamedIndividual rdf:about="http://purl.obolibrary.org/obo/VO_0015343">
+        <rdf:type rdf:resource="http://purl.obolibrary.org/obo/VO_0015077"/>
+        <obo:IAO_0000117>Jie Zheng</obo:IAO_0000117>
+        <rdfs:label>Havpur</rdfs:label>
+    </owl:NamedIndividual>
+
+
+
+    <!-- http://purl.obolibrary.org/obo/VO_0015344 -->
+
+    <owl:NamedIndividual rdf:about="http://purl.obolibrary.org/obo/VO_0015344">
+        <rdf:type rdf:resource="http://purl.obolibrary.org/obo/VO_0015077"/>
+        <obo:IAO_0000117>Jie Zheng</obo:IAO_0000117>
+        <rdfs:label>Havrix</rdfs:label>
+    </owl:NamedIndividual>
+
+
+
+    <!-- http://purl.obolibrary.org/obo/VO_0015345 -->
+
+    <owl:NamedIndividual rdf:about="http://purl.obolibrary.org/obo/VO_0015345">
+        <rdf:type rdf:resource="http://purl.obolibrary.org/obo/VO_0015077"/>
+        <obo:IAO_0000117>Jie Zheng</obo:IAO_0000117>
+        <rdfs:label>Vivaxim</rdfs:label>
+    </owl:NamedIndividual>
+
+
+
+    <!-- http://purl.obolibrary.org/obo/VO_0015346 -->
+
+    <owl:NamedIndividual rdf:about="http://purl.obolibrary.org/obo/VO_0015346">
+        <rdf:type rdf:resource="http://purl.obolibrary.org/obo/VO_0015077"/>
+        <obo:IAO_0000117>Jie Zheng</obo:IAO_0000117>
+        <rdfs:label>Hepatyrix</rdfs:label>
+    </owl:NamedIndividual>
+
+
+
+    <!-- http://purl.obolibrary.org/obo/VO_0015347 -->
+
+    <owl:NamedIndividual rdf:about="http://purl.obolibrary.org/obo/VO_0015347">
+        <rdf:type rdf:resource="http://purl.obolibrary.org/obo/VO_0015077"/>
+        <obo:IAO_0000117>Jie Zheng</obo:IAO_0000117>
+        <rdfs:label>ViATIM</rdfs:label>
+    </owl:NamedIndividual>
+
+
+
+    <!-- http://purl.obolibrary.org/obo/VO_0015348 -->
+
+    <owl:NamedIndividual rdf:about="http://purl.obolibrary.org/obo/VO_0015348">
+        <rdf:type rdf:resource="http://purl.obolibrary.org/obo/VO_0015077"/>
+        <obo:IAO_0000117>Jie Zheng</obo:IAO_0000117>
+        <rdfs:label>Hav Sorbat Ssw</rdfs:label>
+    </owl:NamedIndividual>
+</rdf:RDF>
+
+
+
+<!-- Generated by the OWL API (version 4.5.26) https://github.com/owlcs/owlapi -->
+
diff --git a/src/modules/individuals.owl b/src/modules/individuals.owl
@@ -81,6 +81,12 @@
 
 
 
+    <!-- http://purl.obolibrary.org/obo/VO_0015076 -->
+
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/VO_0015076"/>
+
+
+
     <!-- 
     ///////////////////////////////////////////////////////////////////////////////////////
     //
@@ -1801,6 +1807,46 @@ http://www.hoovers.com/company-information/cs/company-profile.advent_srl.aebb99e
         <obo:IAO_0000119>https://www.syneoshealth.com</obo:IAO_0000119>
         <rdfs:label>Syneos Health</rdfs:label>
     </owl:NamedIndividual>
+
+
+
+    <!-- http://purl.obolibrary.org/obo/VO_0015078 -->
+
+    <owl:NamedIndividual rdf:about="http://purl.obolibrary.org/obo/VO_0015078">
+        <rdf:type rdf:resource="http://purl.obolibrary.org/obo/VO_0015076"/>
+        <obo:IAO_0000117>Jie Zheng</obo:IAO_0000117>
+        <rdfs:label>Box of 1</rdfs:label>
+    </owl:NamedIndividual>
+
+
+
+    <!-- http://purl.obolibrary.org/obo/VO_0015079 -->
+
+    <owl:NamedIndividual rdf:about="http://purl.obolibrary.org/obo/VO_0015079">
+        <rdf:type rdf:resource="http://purl.obolibrary.org/obo/VO_0015076"/>
+        <obo:IAO_0000117>Jie Zheng</obo:IAO_0000117>
+        <rdfs:label>Box of 10</rdfs:label>
+    </owl:NamedIndividual>
+
+
+
+    <!-- http://purl.obolibrary.org/obo/VO_0015082 -->
+
+    <owl:NamedIndividual rdf:about="http://purl.obolibrary.org/obo/VO_0015082">
+        <rdf:type rdf:resource="http://purl.obolibrary.org/obo/VO_0015076"/>
+        <obo:IAO_0000117>Jie Zheng</obo:IAO_0000117>
+        <rdfs:label>Box of 20</rdfs:label>
+    </owl:NamedIndividual>
+
+
+
+    <!-- http://purl.obolibrary.org/obo/VO_0015083 -->
+
+    <owl:NamedIndividual rdf:about="http://purl.obolibrary.org/obo/VO_0015083">
+        <rdf:type rdf:resource="http://purl.obolibrary.org/obo/VO_0015076"/>
+        <obo:IAO_0000117>Jie Zheng</obo:IAO_0000117>
+        <rdfs:label>Box of 50</rdfs:label>
+    </owl:NamedIndividual>
 </rdf:RDF>