Merge pull request #1706 from obi-ontology/administration_1703

Template for 'administration of substance in vivo' terms

Makefile

@@ -101,7 +101,8 @@ src/ontology/modules/%.owl: src/ontology/templates/%.tsv | build/robot.jar
 
 # Update all modules.
 # NOTE: GNU Make will compare timestamps to see which updates are required.
-MODULE_NAMES := assays\
+MODULE_NAMES := administration\
+ assays\
  biopsy\
  biobank-specimens\
  organizations\

src/ontology/OntoFox_inputs/HP_input.txt

@@ -7,11 +7,13 @@ HP
 
 [Low level source term URIs]
 http://purl.obolibrary.org/obo/HP_0000855
+http://purl.obolibrary.org/obo/HP_0002664 #neoplasm
 
 [Top level source term URIs and target direct superclass URIs]
 http://purl.obolibrary.org/obo/HP_0000855
 subClassOf http://purl.obolibrary.org/obo/BFO_0000016
-
+http://purl.obolibrary.org/obo/HP_0002664 #neoplasm
+subClassOf http://purl.obolibrary.org/obo/UBERON_0000465
 
 [Source term retrieval setting]
 includeNoIntermediates

src/ontology/OntoFox_inputs/Uberon_input.txt

@@ -130,6 +130,14 @@ http://purl.obolibrary.org/obo/UBERON_0013757 # capillary blood
 http://purl.obolibrary.org/obo/UBERON_0036149
 http://purl.obolibrary.org/obo/UBERON_3000016 # anterior nasal wall
 http://purl.obolibrary.org/obo/UBERON_8470000 # placental blood
+http://purl.obolibrary.org/obo/UBERON_0001811 # conjunctiva
+http://purl.obolibrary.org/obo/UBERON_0000305 # amnion
+http://purl.obolibrary.org/obo/UBERON_0001637 # artery
+http://purl.obolibrary.org/obo/UBERON_0001893 # telencephalon
+http://purl.obolibrary.org/obo/UBERON_0003128 # cranium
+http://purl.obolibrary.org/obo/UBERON_0001003 # skin epidermis
+http://purl.obolibrary.org/obo/UBERON_0002465 # lymphoid system
+http://purl.obolibrary.org/obo/UBERON_0001530 # common carotid artery plus branches
 
 [Top level source term URIs and target direct superclass URIs]
 http://purl.obolibrary.org/obo/UBERON_0000465 # material anatomical entity

src/ontology/OntoFox_outputs/HP_imports.owl

@@ -77,6 +77,24 @@
         <obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/hp.owl"/>
         <rdfs:label>Insulin resistance</rdfs:label>
     </owl:Class>
+
+
+
+    <!-- http://purl.obolibrary.org/obo/HP_0002664 -->
+
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/HP_0002664">
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/UBERON_0000465"/>
+        <obo:IAO_0000111>Neoplasm</obo:IAO_0000111>
+        <obo:IAO_0000115>An organ or organ-system abnormality that consists of uncontrolled autonomous cell-proliferation which can occur in any part of the body as a benign or malignant neoplasm (tumor).</obo:IAO_0000115>
+        <obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/hp.owl"/>
+        <rdfs:label>Neoplasm</rdfs:label>
+    </owl:Class>
+
+
+
+    <!-- http://purl.obolibrary.org/obo/UBERON_0000465 -->
+
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0000465"/>
 </rdf:RDF>
 
 

src/ontology/OntoFox_outputs/Uberon_imports.owl

@@ -191,6 +191,19 @@
 
 
 
+    <!-- http://purl.obolibrary.org/obo/UBERON_0000305 -->
+
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0000305">
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000040"/>
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/UBERON_0000465"/>
+        <obo:IAO_0000111>amnion</obo:IAO_0000111>
+        <obo:IAO_0000115>The thin innermost layer of the extraembryonic membranes that contains the amniotic fluid; the membrane forms a closed sac in which the embryo and later, the fetus, is suspended and protected.</obo:IAO_0000115>
+        <obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/uberon.owl"/>
+        <rdfs:label>amnion</rdfs:label>
+    </owl:Class>
+
+
+
     <!-- http://purl.obolibrary.org/obo/UBERON_0000310 -->
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0000310">
@@ -448,6 +461,19 @@
 
 
 
+    <!-- http://purl.obolibrary.org/obo/UBERON_0001003 -->
+
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0001003">
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/UBERON_0000465"/>
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/UBERON_0000483"/>
+        <obo:IAO_0000111>skin epidermis</obo:IAO_0000111>
+        <obo:IAO_0000115>The outer epithelial layer of the skin that is superficial to the dermis.</obo:IAO_0000115>
+        <obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/uberon.owl"/>
+        <rdfs:label>skin epidermis</rdfs:label>
+    </owl:Class>
+
+
+
     <!-- http://purl.obolibrary.org/obo/UBERON_0001004 -->
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0001004">
@@ -705,6 +731,18 @@
 
 
 
+    <!-- http://purl.obolibrary.org/obo/UBERON_0001530 -->
+
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0001530">
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/UBERON_0001637"/>
+        <obo:IAO_0000111>common carotid artery plus branches</obo:IAO_0000111>
+        <obo:IAO_0000115>A bilaterally paired branched artery that originates from the aortic arches and divides into and includes as parts the internal and external carotid arteries[cjm].</obo:IAO_0000115>
+        <obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/uberon.owl"/>
+        <rdfs:label>common carotid artery plus branches</rdfs:label>
+    </owl:Class>
+
+
+
     <!-- http://purl.obolibrary.org/obo/UBERON_0001555 -->
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0001555">
@@ -771,6 +809,7 @@
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0001621">
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000040"/>
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/UBERON_0000465"/>
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/UBERON_0001637"/>
         <obo:IAO_0000111>coronary artery</obo:IAO_0000111>
         <obo:IAO_0000115>An artery that supplies the myocardium.</obo:IAO_0000115>
         <obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/uberon.owl"/>
@@ -779,6 +818,19 @@
 
 
 
+    <!-- http://purl.obolibrary.org/obo/UBERON_0001637 -->
+
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0001637">
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000040"/>
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/UBERON_0000465"/>
+        <obo:IAO_0000111>artery</obo:IAO_0000111>
+        <obo:IAO_0000115>An epithelial tube or tree of tibes that transports blood away from the heart[modified from AEO definition].</obo:IAO_0000115>
+        <obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/uberon.owl"/>
+        <rdfs:label>artery</rdfs:label>
+    </owl:Class>
+
+
+
     <!-- http://purl.obolibrary.org/obo/UBERON_0001638 -->
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0001638">
@@ -840,6 +892,18 @@
 
 
 
+    <!-- http://purl.obolibrary.org/obo/UBERON_0001811 -->
+
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0001811">
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/UBERON_0000465"/>
+        <obo:IAO_0000111>conjunctiva</obo:IAO_0000111>
+        <obo:IAO_0000115>The mucous membrane that lines the inner surface of the eyelids and the front of the eyeball.</obo:IAO_0000115>
+        <obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/uberon.owl"/>
+        <rdfs:label>conjunctiva</rdfs:label>
+    </owl:Class>
+
+
+
     <!-- http://purl.obolibrary.org/obo/UBERON_0001826 -->
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0001826">
@@ -902,6 +966,19 @@
 
 
 
+    <!-- http://purl.obolibrary.org/obo/UBERON_0001893 -->
+
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0001893">
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/UBERON_0000465"/>
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/UBERON_0000481"/>
+        <obo:IAO_0000111>telencephalon</obo:IAO_0000111>
+        <obo:IAO_0000115>Part of the forebrain consisting of paired olfactory bulbs and cerebral hemispheres.</obo:IAO_0000115>
+        <obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/uberon.owl"/>
+        <rdfs:label>telencephalon</rdfs:label>
+    </owl:Class>
+
+
+
     <!-- http://purl.obolibrary.org/obo/UBERON_0001913 -->
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0001913">
@@ -1216,6 +1293,18 @@
 
 
 
+    <!-- http://purl.obolibrary.org/obo/UBERON_0002465 -->
+
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0002465">
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/UBERON_0000465"/>
+        <obo:IAO_0000111>lymphoid system</obo:IAO_0000111>
+        <obo:IAO_0000115>The lymphatic system in vertebrates is a network of conduits that carry a clear fluid called lymph. It also includes the lymphoid tissue through which the lymph travels. Lymphoid tissue is found in many organs, particularly the lymph nodes, and in the lymphoid follicles associated with the digestive system such as the tonsils. The system also includes all the structures dedicated to the circulation and production of lymphocytes, which includes the spleen, thymus, bone marrow and the lymphoid tissue associated with the digestive system[WP].</obo:IAO_0000115>
+        <obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/uberon.owl"/>
+        <rdfs:label>lymphoid system</rdfs:label>
+    </owl:Class>
+
+
+
     <!-- http://purl.obolibrary.org/obo/UBERON_0002469 -->
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0002469">
@@ -1266,6 +1355,18 @@
 
 
 
+    <!-- http://purl.obolibrary.org/obo/UBERON_0003128 -->
+
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0003128">
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/UBERON_0000465"/>
+        <obo:IAO_0000111>cranium</obo:IAO_0000111>
+        <obo:IAO_0000115>Upper portion of the skull that excludes the mandible (when present in the organism).</obo:IAO_0000115>
+        <obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/uberon.owl"/>
+        <rdfs:label>cranium</rdfs:label>
+    </owl:Class>
+
+
+
     <!-- http://purl.obolibrary.org/obo/UBERON_0003688 -->
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0003688">
@@ -1418,6 +1519,7 @@
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0007610">
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000040"/>
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/UBERON_0000465"/>
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/UBERON_0001637"/>
         <obo:IAO_0000111>tibial artery</obo:IAO_0000111>
         <obo:IAO_0000115>The anterior and posterior arteries created at the bifurcation of the popliteal artery. The anterior tibial artery begins at the lower border of the popliteus muscle and lies along the tibia at the distal part of the leg to surface superficially anterior to the ankle joint. Its branches are distributed throughout the leg, ankle, and pes. The posterior tibial artery begins at the lower border of the popliteus muscle, lies behind the tibia in the lower part of its course, and is found situated between the medial malleolus and the medial process of the calcaneal tuberosity. Its branches are distributed throughout the leg and foot.</obo:IAO_0000115>
         <obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/uberon.owl"/>

src/ontology/catalog-v001.xml

@@ -23,6 +23,7 @@
     <uri name="http://purl.obolibrary.org/obo/obi/dev/import/UO_imports.owl" uri="OntoFox_outputs/UO_imports.owl"/>
     <uri name="http://purl.obolibrary.org/obo/obi/dev/import/UO_instance_imports.owl" uri="OntoFox_outputs/UO_instance_imports.owl"/>
     <uri name="http://purl.obolibrary.org/obo/obi/dev/import/VO_imports.owl" uri="OntoFox_outputs/VO_imports.owl"/>
+    <uri name="http://purl.obolibrary.org/obo/obi/dev/modules/administration.owl" uri="modules/administration.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"/>