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Template for 'administration of substance in vivo' terms #1706

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merged 15 commits into from
Nov 30, 2023
Merged

Template for 'administration of substance in vivo' terms #1706

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bd2b203
Update Uberon_imports.owl
sebastianduesing May 30, 2023
5580657
Adding Uberon terms
sebastianduesing May 30, 2023
5cba548
Added anatomy terms and scratching process term.
sebastianduesing May 30, 2023
64e40f3
Adding administration template
sebastianduesing Jun 1, 2023
95e4256
Simplifying axioms as discussed
sebastianduesing Jun 12, 2023
52401a1
Importing HP:'neoplasm'
sebastianduesing Jul 5, 2023
5c10c1e
Adding intratumoral administration term for IEDB
sebastianduesing Jul 5, 2023
49745bd
Merge branch 'master' into administration_1703
jamesaoverton Jul 10, 2023
2c2e9fa
Moving some terms from obi-edit into administration.tsv
sebastianduesing Jul 20, 2023
20c1aad
Moving more terms from obi-edit to administration.tsv
sebastianduesing Jul 25, 2023
3c22e78
Add column for objective
sebastianduesing Oct 16, 2023
af24d7e
Merge branch 'master' of https://github.com/obi-ontology/obi into adm…
sebastianduesing Nov 7, 2023
480b578
Updating obi.owl to merge changes from master
sebastianduesing Nov 7, 2023
e809a75
Adds disease-related objectives
sebastianduesing Nov 9, 2023
21039d0
Merge branch 'master' into administration_1703
jamesaoverton Nov 30, 2023
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3 changes: 2 additions & 1 deletion Makefile
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Expand Up @@ -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\
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4 changes: 3 additions & 1 deletion src/ontology/OntoFox_inputs/HP_input.txt
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Expand Up @@ -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
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8 changes: 8 additions & 0 deletions src/ontology/OntoFox_inputs/Uberon_input.txt
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Expand Up @@ -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
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18 changes: 18 additions & 0 deletions src/ontology/OntoFox_outputs/HP_imports.owl
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Expand Up @@ -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>


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102 changes: 102 additions & 0 deletions src/ontology/OntoFox_outputs/Uberon_imports.owl
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Expand Up @@ -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">
Expand Down Expand Up @@ -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">
Expand Down Expand Up @@ -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">
Expand Down Expand Up @@ -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"/>
Expand All @@ -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">
Expand Down Expand Up @@ -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">
Expand Down Expand Up @@ -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">
Expand Down Expand Up @@ -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">
Expand Down Expand Up @@ -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">
Expand Down Expand Up @@ -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"/>
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1 change: 1 addition & 0 deletions src/ontology/catalog-v001.xml
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Expand Up @@ -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"/>
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