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Cleanup re: Biolink categories #100

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Dec 3, 2024
Merged

Cleanup re: Biolink categories #100

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a65e7e0
Remove material related to adding Biolink categories
caufieldjh Dec 3, 2024
40561b2
Clean up metadata
caufieldjh Dec 3, 2024
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41 changes: 20 additions & 21 deletions src/metadata/README.md
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Metadata files for the OBO Library
# Metadata files for the OBO Library

* [phenio.yml](phenio.yml)
* Determines how your purl.obolibrary.org/obo/phenio/ redirects will be handled
* Go here: https://github.com/OBOFoundry/purl.obolibrary.org/tree/master/config
* Click [New File](https://github.com/OBOFoundry/purl.obolibrary.org/new/master/config)
* Paste in the contents of [phenio.yml](phenio.yml)
* Click "Commit new file"
* IMPORTANT: remember to make a pull request
* An OBO admin will merge your Pull Request *providing it meets the requirements of the OBO library*
* [phenio.md](phenio.md)
* Determines how your metadata is shown on OBO Library, OLS and AberOWL
* Go here: https://github.com/OBOFoundry/OBOFoundry.github.io/tree/master/ontology
* Click [New File](https://github.com/OBOFoundry/OBOFoundry.github.io/new/master/ontology)
* Paste in the contents of [phenio.md](phenio.md)
* Click "Commit new file"
* IMPORTANT: remember to make a pull request
* An OBO admin will merge your Pull Request *providing it meets the requirements of the OBO library*

For more background see:
- [phenio.yml](phenio.yml)
- Determines how your purl.obolibrary.org/obo/phenio/ redirects will be handled
- Go here: https://github.com/OBOFoundry/purl.obolibrary.org/tree/master/config
- Click [New File](https://github.com/OBOFoundry/purl.obolibrary.org/new/master/config)
- Paste in the contents of [phenio.yml](phenio.yml)
- Click "Commit new file"
- IMPORTANT: remember to make a pull request
- An OBO admin will merge your Pull Request _providing it meets the requirements of the OBO library_
- [phenio.md](phenio.md)
- Determines how your metadata is shown on OBO Library, OLS and AberOWL
- Go here: https://github.com/OBOFoundry/OBOFoundry.github.io/tree/master/ontology
- Click [New File](https://github.com/OBOFoundry/OBOFoundry.github.io/new/master/ontology)
- Paste in the contents of [phenio.md](phenio.md)
- Click "Commit new file"
- IMPORTANT: remember to make a pull request
- An OBO admin will merge your Pull Request _providing it meets the requirements of the OBO library_

* http://obofoundry.org/
* http://obofoundry.org/faq/how-do-i-edit-metadata.html
For more background see:

- http://obofoundry.org/
- http://obofoundry.org/faq/how-do-i-edit-metadata.html
4 changes: 1 addition & 3 deletions src/metadata/phenio.md
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Expand Up @@ -60,6 +60,4 @@ license:
activity_status: active
---

Enter a detailed description of your ontology here. You can use arbitrary markdown and HTML.
You can also embed images too.

PHENIO
25 changes: 12 additions & 13 deletions src/metadata/phenio.yml
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Expand Up @@ -4,24 +4,23 @@ idspace: PHENIO
base_url: /obo/phenio

products:
- phenio.owl: https://raw.githubusercontent.com/monarch-initiative/phenio/main/phenio.owl
- phenio.obo: https://raw.githubusercontent.com/monarch-initiative/phenio/main/phenio.obo
- phenio.owl: https://raw.githubusercontent.com/monarch-initiative/phenio/main/phenio.owl
- phenio.obo: https://raw.githubusercontent.com/monarch-initiative/phenio/main/phenio.obo

term_browser: ontobee
example_terms:
- PHENIO_0000000
- PHENIO_0000000

entries:
- prefix: /releases/
replacement: https://raw.githubusercontent.com/monarch-initiative/phenio/v

- prefix: /releases/
replacement: https://raw.githubusercontent.com/monarch-initiative/phenio/v
- prefix: /tracker/
replacement: https://github.com/monarch-initiative/phenio/issues

- prefix: /tracker/
replacement: https://github.com/monarch-initiative/phenio/issues
- prefix: /about/
replacement: http://www.ontobee.org/ontology/PHENIO?iri=http://purl.obolibrary.org/obo/

- prefix: /about/
replacement: http://www.ontobee.org/ontology/PHENIO?iri=http://purl.obolibrary.org/obo/

## generic fall-through, serve direct from github by default
- prefix: /
replacement: https://raw.githubusercontent.com/monarch-initiative/phenio/main/
## generic fall-through, serve direct from github by default
- prefix: /
replacement: https://raw.githubusercontent.com/monarch-initiative/phenio/main/
14,564 changes: 0 additions & 14,564 deletions src/ontology/bl-model.ttl
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92 changes: 92 additions & 0 deletions src/ontology/doc1.txt
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<owl:Class rdf:about="http://purl.obolibrary.org/obo/HP_0000002">
<owl:equivalentClass>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<owl:someValuesFrom>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/PATO_0000119"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000052"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/UBERON_0000468"/>
</owl:Restriction>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0002573"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/PATO_0000460"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
</owl:equivalentClass>
<owl:equivalentClass>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<owl:someValuesFrom>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/PATO_0000119"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000052"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/UBERON_0000468"/>
</owl:Restriction>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0002573"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/PATO_0000460"/>
</owl:Restriction>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/UPHENO_9000005"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/UPHENO_HP"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
</owl:equivalentClass>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/HP_0001507"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/UPHENO_0081424"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<owl:someValuesFrom>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/PATO_0000119"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000052"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/UBERON_0000468"/>
</owl:Restriction>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0002573"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/PATO_0000460"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<owl:someValuesFrom>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/PATO_0000119"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000052"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/UBERON_0000468"/>
</owl:Restriction>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0002573"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/PATO_0000460"/>
</owl:Restriction>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/UPHENO_9000005"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/UPHENO_HP"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
</owl:Class>
94 changes: 94 additions & 0 deletions src/ontology/doc2.txt
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<!-- http://purl.obolibrary.org/obo/HP_0000002 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/HP_0000002">
<owl:equivalentClass>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<owl:someValuesFrom>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/PATO_0000119"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000052"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/UBERON_0000468"/>
</owl:Restriction>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0002573"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/PATO_0000460"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
</owl:equivalentClass>
<owl:equivalentClass>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<owl:someValuesFrom>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/PATO_0000119"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000052"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/UBERON_0000468"/>
</owl:Restriction>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0002573"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/PATO_0000460"/>
</owl:Restriction>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/UPHENO_9000005"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/UPHENO_HP"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
</owl:equivalentClass>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/HP_0001507"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/UPHENO_0081424"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<owl:someValuesFrom>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/PATO_0000119"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000052"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/UBERON_0000468"/>
</owl:Restriction>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0002573"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/PATO_0000460"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<owl:someValuesFrom>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/PATO_0000119"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000052"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/UBERON_0000468"/>
</owl:Restriction>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0002573"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/PATO_0000460"/>
</owl:Restriction>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/UPHENO_9000005"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/UPHENO_HP"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
</owl:Class>
2 changes: 0 additions & 2 deletions src/ontology/phenio.Makefile
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# similar process including subq reconstruction

# Constants
BLMODEL = bl-model.ttl
BLMODEL_URL = "https://w3id.org/biolink/biolink-model.owl.ttl"
MINIMAL_PATH= $(TMPDIR)/$(ONT)-min.owl
OT_MEMO= 50G
OWLTOOLS= OWLTOOLS_MEMORY=$(OT_MEMO) owltools --no-logging
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26 changes: 0 additions & 26 deletions src/sparql/bl-categories.ru
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