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Create GALLONT.md #2541
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,32 @@ | ||
| --- | ||
| layout: ontology_detail | ||
| id: gallont | ||
| title: "Plant Gall Ontology" | ||
| contact: | ||
| email: [email protected] | ||
| github: adeans | ||
| label: Andy Deans | ||
| orcid: 0000-0002-2119-4663 | ||
| dependencies: | ||
| - id: pato | ||
| - id: po | ||
| - id: ro | ||
| - id: flopo | ||
| - id: caro | ||
| - id: obi | ||
| - id: poro | ||
| - id: ncbitaxon | ||
| description: Ontology of plant gall phenotypes. Plant galls are novel plant structures, generated by plants in response to biotic stressors. This ontology is used to annotate gall phenotypes (e.g., their colors, textures, sizes, locations on the plant) in a semantic way, in order to facilitate discoveries about the genetic and physiologic mechanisms responsible for such phenotypes. The ontology can also be used as a controlled vocabulary for natural language descriptions of plant galls. | ||
| domain: phenotype | ||
| homepage: https://github.com/adeans/gallont/tree/main | ||
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||
| license: | ||
| url: https://creativecommons.org/publicdomain/zero/1.0/ | ||
| label: CC0 1.0 | ||
| preferredPrefix: GALLONT | ||
| products: | ||
| - id: gallont.owl | ||
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| - id: gallont.obo | ||
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| repository: https://github.com/adeans/gallont | ||
| tracker: https://github.com/adeans/gallont/issues | ||
| activity_status: active | ||
| --- | ||
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Strange homepage link. Did you consider using the ODK documentation feature to generate a proper documentation page like https://pato-ontology.github.io/pato/?
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(not a requirement)
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Oh yah. That would be preferable. I must've missed it in the ODK package. Is there documentation somewhere that would walk me through it? Somewhere in here? https://ontology-development-kit.readthedocs.io/en/latest/
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You add this to the ODK config:
https://github.com/obophenotype/human-phenotype-ontology/blob/53c4e0dcf3337e223c9afcd29dfb18e7ed372e7a/src/ontology/hp-odk.yaml#L182
then run update_repo twice
then set up your github pages like this:
Sorry for not having better docs on this :D
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Ok, I think I am close. Where do I "run update_repo twice"?
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https://oboacademy.github.io/obook/howto/odk-update/
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Thanks, @matentzn. I made progress (I think), but I get two QC errors now:
Are these easy?
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The second seems to be a bug.
Lets start with the first https://github.com/adeans/gallont/actions/runs/8266804229/job/22615690174
This is a QC check that reflects the OBO foundries decision to fade out the dc elements namespace in favour of dc terms. So in your ontology, you need to replace all occurrences of the old dc elements namespace with dcterms.
The second can be circumvented by manually deleting this row:
https://github.com/adeans/gallont/blob/37daf2a543720392d16afb28b9031d0af6d8a796/mkdocs.yaml#L8
I would apprciate if you could make a bug report in the ODK repo though, as this needs to be fixed urgently.. :)