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tidy oeo imports #4

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Dec 1, 2023
Merged

tidy oeo imports #4

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5707006
add comments for documentation to iao-w-hierarchy
stap-m Oct 30, 2023
4761427
add comments for documentation to omo-w-hierarchy
stap-m Nov 1, 2023
7e19b8d
move former shell script to archive
stap-m Nov 1, 2023
d04316a
add updated import script
stap-m Nov 1, 2023
6f35061
Update oeo-imports/iao/extract-iao-module.sh
stap-m Nov 1, 2023
3c401bd
Update oeo-imports/iao/extract-iao-module.sh
stap-m Nov 1, 2023
85d2676
Update oeo-imports/iao/extract-iao-module.sh
stap-m Nov 1, 2023
f6cd391
Update oeo-imports/iao/extract-iao-module.sh
stap-m Nov 1, 2023
f89b76b
Update oeo-imports/iao/extract-iao-module.sh
stap-m Nov 1, 2023
daa6a17
Add IAO Import File
h-spinde Nov 6, 2023
bce215f
add file from new script
h-spinde Nov 13, 2023
67362bd
update iao-w-hierarchy by iao class list from oeo issue #1700
stap-m Nov 22, 2023
934b598
add another relation to the import list
stap-m Nov 24, 2023
5d9c278
import additional classes
h-spinde Nov 27, 2023
f46d19f
fix wrong import
stap-m Nov 28, 2023
af7bae9
rerun script to add updated list of terms to the import
stap-m Nov 29, 2023
12efd4c
add file for import without hierarchy
stap-m Nov 30, 2023
b1cd5d4
update extraction script and run it to update iao-extracted
stap-m Nov 30, 2023
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22 changes: 22 additions & 0 deletions oeo-imports/iao/archive/extract-iao-module.sh
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# Note: For consistent results run with ROBOT v1.91 or higher
# Download the IAO release from 2022-11-07
curl -L https://raw.githubusercontent.com/information-artifact-ontology/IAO/v2022-11-07/iao.owl > iao-full-download.owl
# Extract the terms we want with hierarchy, This removes the domain of IAO_0000136
robot merge --input iao-full-download.owl extract --method MIREOT --lower-terms iao-w-hierarchy.txt --intermediates all --output iao-module-temp.owl
# Remove subclass axioms from BFO classes
robot remove --input iao-module-temp.owl --term BFO:0000001 --select "self descendants" --select "<http://purl.obolibrary.org/obo/BFO_*>" --axioms subclass --axioms annotation --signature true --exclude-term BFO:0000031 --preserve-structure false --output iao-module-temp.owl
# Extract domain of IAO_0000136
robot merge --input iao-full-download.owl filter --term http://purl.obolibrary.org/obo/IAO_0000136 --term rdfs:domain --term http://purl.obolibrary.org/obo/IAO_0000030 --select self --axioms all --signature false --output iao-extracted-domain.owl
# Extracted module
robot merge --input iao-module-temp.owl --input iao-extracted-domain.owl --output ../../ontology/imports/iao-extracted.owl
# Remove subproperty axioms
robot remove --input ../../ontology/imports/iao-extracted.owl --axioms subproperty --output ../../ontology/imports/iao-extracted.owl
# Annotates the output with a commentary to the origin of the content
robot annotate --input ../../ontology/imports/iao-extracted.owl --annotation rdfs:comment "This file contains externally imported content from the Information Artifact Ontology (IAO) for import into the Open Energy Ontology (OEO). It is automatically extracted using ROBOT." --output ../../ontology/imports/iao-extracted.owl
# Annotates each axiom with the ontology IRI, using prov:wasDerivedFrom
robot annotate --input ../../ontology/imports/iao-extracted.owl --annotate-derived-from true --annotate-defined-by true --output ../../ontology/imports/iao-extracted.owl
# Annotate with new ontology information
robot annotate --input ../../ontology/imports/iao-extracted.owl --ontology-iri http://openenergy-platform.org/ontology/oeo/imports/iao-extracted.owl --version-iri http://openenergy-platform.org/ontology/oeo/dev/imports/iao-extracted.owl --output ../../ontology/imports/iao-extracted.owl
rm iao-full-download.owl
rm iao-extracted-domain.owl
rm iao-module-temp.owl
24 changes: 8 additions & 16 deletions oeo-imports/iao/extract-iao-module.sh
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# Note: For consistent results run with ROBOT v1.91 or higher
# Download the IAO release from 2022-11-07
curl -L https://raw.githubusercontent.com/information-artifact-ontology/IAO/v2022-11-07/iao.owl > iao-full-download.owl
# Extract the terms we want with hierarchy, This removes the domain of IAO_0000136
robot merge --input iao-full-download.owl extract --method MIREOT --lower-terms iao-w-hierarchy.txt --intermediates all --output iao-module-temp.owl
# Remove subclass axioms from BFO classes
robot remove --input iao-module-temp.owl --term BFO:0000001 --select "self descendants" --select "<http://purl.obolibrary.org/obo/BFO_*>" --axioms subclass --axioms annotation --signature true --exclude-term BFO:0000031 --preserve-structure false --output iao-module-temp.owl
# Extract domain of IAO_0000136
robot merge --input iao-full-download.owl filter --term http://purl.obolibrary.org/obo/IAO_0000136 --term rdfs:domain --term http://purl.obolibrary.org/obo/IAO_0000030 --select self --axioms all --signature false --output iao-extracted-domain.owl
# Extracted module
robot merge --input iao-module-temp.owl --input iao-extracted-domain.owl --output ../../ontology/imports/iao-extracted.owl
# Remove subproperty axioms
robot remove --input ../../ontology/imports/iao-extracted.owl --axioms subproperty --output ../../ontology/imports/iao-extracted.owl
# Annotates the output with a commentary to the origin of the content
robot annotate --input ../../ontology/imports/iao-extracted.owl --annotation rdfs:comment "This file contains externally imported content from the Information Artifact Ontology (IAO) for import into the Open Energy Ontology (OEO). It is automatically extracted using ROBOT." --output ../../ontology/imports/iao-extracted.owl
# Extract the terms we want with hierarchy until the upper term "informatio content entity" (IAO_0000030).
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# Warning: This removes the domain of IAO_0000136 -- tbd in oeo-import-edits
# Classification: tbd in oeo-import-edits
robot merge --input C:/Users/stappel/Documents/Ontologies/test_oeo_imports/iao-full-download.owl extract --method MIREOT --lower-terms C:/Users/stappel/Documents/Ontologies/test_oeo_imports/iao-w-hierarchy.txt --intermediates all --upper-term http://purl.obolibrary.org/obo/IAO_0000030 --output C:/Users/stappel/Documents/Ontologies/test_oeo_imports/iao-extracted.owl
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# Annotates the output module with a commentary to the origin of the content
robot annotate --input C:/Users/stappel/Documents/Ontologies/test_oeo_imports/iao-extracted.owl --annotation rdfs:comment "This file contains externally imported content from the Information Artifact Ontology (IAO) for import into the Open Energy Ontology (OEO). It is automatically extracted using ROBOT." --output C:/Users/stappel/Documents/Ontologies/test_oeo_imports/iao-extracted.owl
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# Annotates each axiom with the ontology IRI, using prov:wasDerivedFrom
robot annotate --input ../../ontology/imports/iao-extracted.owl --annotate-derived-from true --annotate-defined-by true --output ../../ontology/imports/iao-extracted.owl
robot annotate --input C:/Users/stappel/Documents/Ontologies/test_oeo_imports/iao-extracted.owl --annotate-derived-from true --annotate-defined-by true --output C:/Users/stappel/Documents/Ontologies/test_oeo_imports/iao-extracted.owl
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# Annotate with new ontology information
robot annotate --input ../../ontology/imports/iao-extracted.owl --ontology-iri http://openenergy-platform.org/ontology/oeo/imports/iao-extracted.owl --version-iri http://openenergy-platform.org/ontology/oeo/dev/imports/iao-extracted.owl --output ../../ontology/imports/iao-extracted.owl
robot annotate --input C:/Users/stappel/Documents/Ontologies/test_oeo_imports/iao-extracted.owl --ontology-iri http://openenergy-platform.org/ontology/oeo/imports/iao-extracted.owl --version-iri http://openenergy-platform.org/ontology/oeo/dev/imports/iao-extracted.owl --output C:/Users/stappel/Documents/Ontologies/test_oeo_imports/iao-extracted.owl
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rm iao-full-download.owl
rm iao-extracted-domain.owl
rm iao-module-temp.owl
30 changes: 16 additions & 14 deletions oeo-imports/iao/iao-w-hierarchy.txt
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http://purl.obolibrary.org/obo/IAO_0000136
http://purl.obolibrary.org/obo/IAO_0000010
http://purl.obolibrary.org/obo/IAO_0000025
http://purl.obolibrary.org/obo/IAO_0000028
http://purl.obolibrary.org/obo/IAO_0000030
http://purl.obolibrary.org/obo/IAO_0000033
http://purl.obolibrary.org/obo/IAO_0000064
http://purl.obolibrary.org/obo/IAO_0000088
http://purl.obolibrary.org/obo/IAO_0000100
http://purl.obolibrary.org/obo/IAO_0000104
http://purl.obolibrary.org/obo/IAO_0000300
http://purl.obolibrary.org/obo/IAO_0000310
http://purl.obolibrary.org/obo/IAO_0000590
http://purl.obolibrary.org/obo/IAO_0000233
http://purl.obolibrary.org/obo/IAO_0000136 # is about
http://purl.obolibrary.org/obo/IAO_0000010 # software
http://purl.obolibrary.org/obo/IAO_0000025 # programming language
http://purl.obolibrary.org/obo/IAO_0000028 # symbol
http://purl.obolibrary.org/obo/IAO_0000030 # information content entity
http://purl.obolibrary.org/obo/IAO_0000033 # directive information entity
http://purl.obolibrary.org/obo/IAO_0000064 # algorithm
http://purl.obolibrary.org/obo/IAO_0000088 # report
http://purl.obolibrary.org/obo/IAO_0000100 # data set
http://purl.obolibrary.org/obo/IAO_0000104 # plan specification
http://purl.obolibrary.org/obo/IAO_0000300 # textual entity
http://purl.obolibrary.org/obo/IAO_0000310 # document
http://purl.obolibrary.org/obo/IAO_0000590 # written name
http://purl.obolibrary.org/obo/IAO_0000233 # term tracker item

http://purl.obolibrary.org/obo/IAO_0006011 # may be identical to
14 changes: 7 additions & 7 deletions oeo-imports/omo/omo-w-hierarchy.txt
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http://purl.obolibrary.org/obo/IAO_0000027
http://purl.obolibrary.org/obo/IAO_0000112
http://purl.obolibrary.org/obo/IAO_0000115
http://purl.obolibrary.org/obo/IAO_0000116
http://purl.obolibrary.org/obo/IAO_0000118
http://purl.obolibrary.org/obo/IAO_0000119
http://purl.obolibrary.org/obo/IAO_0006011
http://purl.obolibrary.org/obo/IAO_0000027 # data item
http://purl.obolibrary.org/obo/IAO_0000112 # example of usage
http://purl.obolibrary.org/obo/IAO_0000115 # definition
http://purl.obolibrary.org/obo/IAO_0000116 # editor note
http://purl.obolibrary.org/obo/IAO_0000118 # alternative label
http://purl.obolibrary.org/obo/IAO_0000119 # definition source
http://purl.obolibrary.org/obo/IAO_0006011 # may be identical to