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Switch to use uPheno base and import phenotype ontologies separately #94

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Switch to use uPheno base and import phenotype ontologies separately #94

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7436bd8
Switch to use uPheno base and import phenotype ontologies separately
matentzn Nov 18, 2024
5fed463
Update phenio-odk.yaml
matentzn Nov 19, 2024
b7569bf
Update phenio-odk.yaml
matentzn Nov 20, 2024
8d54f6d
Removing unnecessary namespaces from final phenio.owl
matentzn Nov 20, 2024
4e7a5cc
Stripping the edit file of all things but metadata
matentzn Nov 20, 2024
e43b533
Add CL and Uberon mappings
matentzn Nov 23, 2024
7c09490
Remove import from git index
matentzn Nov 23, 2024
6e0a853
Update ODK config and related files
matentzn Nov 23, 2024
78b71f6
Create file for ROBOT renames
matentzn Nov 23, 2024
77c9a1f
Added MAXO component
matentzn Nov 23, 2024
14ab476
Add MAXO to ODK config
matentzn Nov 23, 2024
ab0c270
MISC refactor phenio.Makefile
matentzn Nov 23, 2024
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1 change: 1 addition & 0 deletions .gitignore
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Expand Up @@ -50,3 +50,4 @@ src/ontology/debug.log
src/ontology/phenio-relation-graph.tar.gz
src/ontology/phenio-relation-graph.tsv
src/ontology/phenio-test.owl
src/ontology/imports/merged_import.owl
60 changes: 35 additions & 25 deletions docs/odk-workflows/RepositoryFileStructure.md
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Expand Up @@ -16,23 +16,25 @@ These are the current imports in PHENIO

| Import | URL | Type |
| ------ | --- | ---- |
| chebi | http://purl.obolibrary.org/obo/chebi.owl | None |
| monochrom | https://raw.githubusercontent.com/monarch-initiative/monochrom/refs/heads/master/chr-base.owl | None |
| ncbigene | http://purl.obolibrary.org/obo/mondo/imports/merged_import.owl | None |
| hgnc | http://purl.obolibrary.org/obo/mondo/imports/merged_import.owl | None |
| so | http://purl.obolibrary.org/obo/so.owl | None |
| bspo | http://purl.obolibrary.org/obo/bspo.owl | None |
| wbls | http://purl.obolibrary.org/obo/wbls.owl | None |
| zfs | http://purl.obolibrary.org/obo/zfa.owl | None |
| fbdv | http://purl.obolibrary.org/obo/fbdv.owl | None |
| chebi | https://raw.githubusercontent.com/obophenotype/chebi_obo_slim/main/chebi_slim.owl | None |
| pr | https://raw.githubusercontent.com/obophenotype/pro_obo_slim/master/pr_slim.owl | None |
| eco | http://purl.obolibrary.org/obo/eco.owl | None |
| bfo | http://purl.obolibrary.org/obo/bfo.owl | None |
| ro | http://purl.obolibrary.org/obo/ro.owl | None |
| ncbitaxon-taxslim | http://purl.obolibrary.org/obo/ncbitaxon/subsets/taxslim.owl | None |
| oba | http://purl.obolibrary.org/obo/oba.owl | None |
| pato | http://purl.obolibrary.org/obo/pato.owl | None |
| uberon-bridge-to-emapa | http://purl.obolibrary.org/obo/uberon/bridge/uberon-bridge-to-emapa.owl | None |
| uberon-bridge-to-zfa | http://purl.obolibrary.org/obo/uberon/bridge/uberon-bridge-to-zfa.owl | None |
| uberon-bridge-to-ma | http://purl.obolibrary.org/obo/uberon/bridge/uberon-bridge-to-ma.owl | None |
| uberon-bridge-to-wbbt | http://purl.obolibrary.org/obo/uberon/bridge/uberon-bridge-to-wbbt.owl | None |
| uberon-bridge-to-fbbt | http://purl.obolibrary.org/obo/uberon/bridge/uberon-bridge-to-fbbt.owl | None |
| uberon-bridge-to-fma | http://purl.obolibrary.org/obo/uberon/bridge/uberon-bridge-to-fma.owl | None |
| cl-bridge-to-emapa | http://purl.obolibrary.org/obo/uberon/bridge/cl-bridge-to-emapa.owl | None |
| cl-bridge-to-ma | http://purl.obolibrary.org/obo/uberon/bridge/cl-bridge-to-ma.owl | None |
| cl-bridge-to-fma | http://purl.obolibrary.org/obo/uberon/bridge/cl-bridge-to-fma.owl | None |
| cl-bridge-to-wbbt | http://purl.obolibrary.org/obo/uberon/bridge/cl-bridge-to-wbbt.owl | None |
| cl-bridge-to-fbbt | http://purl.obolibrary.org/obo/uberon/bridge/cl-bridge-to-fbbt.owl | None |
| cl-bridge-to-zfa | http://purl.obolibrary.org/obo/uberon/bridge/cl-bridge-to-zfa.owl | None |
| mpath | http://purl.obolibrary.org/obo/mpath.owl | None |
| nbo | http://purl.obolibrary.org/obo/nbo.owl | None |
| upheno-bridge | https://raw.githubusercontent.com/obophenotype/upheno-dev/refs/heads/master/src/ontology/components/upheno-bridge.owl | None |
| upheno-alignments | https://raw.githubusercontent.com/obophenotype/upheno-dev/refs/heads/master/src/ontology/components/upheno-alignments.owl | None |

## Components
Components, in contrast to imports, are considered full members of the ontology. This means that any axiom in a component is also included in the ontology base - which means it is considered _native_ to the ontology. While this sounds complicated, consider this: conceptually, no component should be part of more than one ontology. If that seems to be the case, we are most likely talking about an import. Components are often not needed for ontologies, but there are some use cases:
Expand All @@ -45,17 +47,25 @@ These are the components in PHENIO

| Filename | URL |
| -------- | --- |
| bfo.owl | http://purl.obolibrary.org/obo/bfo.owl |
| emapa.owl | http://purl.obolibrary.org/obo/emapa.owl |
| fbbt.owl | http://purl.obolibrary.org/obo/fbbt.owl |
| go.owl | http://purl.obolibrary.org/obo/go.owl |
| hsapdv.owl | http://purl.obolibrary.org/obo/hsapdv.owl |
| mondo.owl | http://purl.obolibrary.org/obo/mondo.owl |
| mpath.owl | http://purl.obolibrary.org/obo/mpath.owl |
| nbo.owl | http://purl.obolibrary.org/obo/nbo.owl |
| ro.owl | http://purl.obolibrary.org/obo/ro.owl |
| uberon.owl | http://purl.obolibrary.org/obo/uberon.owl |
| upheno.owl | https://github.com/obophenotype/upheno-dev/releases/latest/download/upheno.owl |
| go.owl | http://purl.obolibrary.org/obo/go/go-base.owl |
| mondo.owl | http://purl.obolibrary.org/obo/mondo/mondo-base.owl |
| maxo.owl | http://purl.obolibrary.org/obo/maxo/maxo-base.owl |
| upheno.owl | https://github.com/obophenotype/upheno-dev/releases/latest/download/upheno-base.owl |
| oba.owl | http://purl.obolibrary.org/obo/oba/oba-base.owl |
| hp.owl | http://purl.obolibrary.org/obo/hp/hp-base.owl |
| fypo.owl | http://purl.obolibrary.org/obo/fypo/fypo-base.owl |
| zp.owl | http://purl.obolibrary.org/obo/zp/zp-base.owl |
| xpo.owl | http://purl.obolibrary.org/obo/xpo/xpo-base.owl |
| mp.owl | http://purl.obolibrary.org/obo/mp/mp-base.owl |
| wbphenotype.owl | http://purl.obolibrary.org/obo/wbphenotype/wbphenotype-base.owl |
| ddpheno.owl | http://purl.obolibrary.org/obo/ddpheno/ddpheno-base.owl |
| dpo.owl | http://purl.obolibrary.org/obo/dpo/dpo-base.owl |
| uberon.owl | http://purl.obolibrary.org/obo/uberon/uberon-base.owl |
| cl.owl | http://purl.obolibrary.org/obo/cl/cl-base.owl |
| ddanat.owl | http://purl.obolibrary.org/obo/ddanat.owl |
| wbbt.owl | http://purl.obolibrary.org/obo/wbbt.owl |
| fbbt.owl | http://purl.obolibrary.org/obo/fbbt.owl |
| zfa.owl | http://purl.obolibrary.org/obo/zfa.owl |
| xao.owl | http://purl.obolibrary.org/obo/xao.owl |
| emapa.owl | http://purl.obolibrary.org/obo/emapa.owl |
| hsapdv.owl | http://purl.obolibrary.org/obo/hsapdv.owl |
6 changes: 6 additions & 0 deletions src/mappings/README.md
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# SSSOM mapping directory

Do not overwrite, contents will be generated automatically.



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