Permalinks for annotations

obophenotype / human-phenotype-ontology

Ontology for the description of human clinical features

http://obophenotype.github.io/human-phenotype-ontology/

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Permalinks for annotations #7183

Closed eric-czech closed 2 years ago

eric-czech commented 2 years ago

Hi @pnrobinson, is there a way to get permalinks to annotations files at https://hpo.jax.org/app/download/annotation that are fixed to specific HPO releases (much like the tags available for the obo/owl files in this repo)?

Thanks!

pnrobinson commented 2 years ago

This is a good suggestion. We are in the process of updating our curation/release pipeline. @drseb @matentzn is there an interim solution for @eric-czech ? The jenkins server is no longer easily accessible.

matentzn commented 2 years ago

There are three possible solutions:

Attach the annotation files to the release. My preference, problem solved. Its easy, there are no relevant file size limits.
Check-in annotation files into the HPO repo on GitHub, problem solved again (no further again needed, the OBO system will give them resolvable version IRIs)
Manually curate the version PURLS to the HPO annotation files in the OBO metadata registry. This would require an additional 5 minutes of work for @drseb for each release, but many ontologies do it.

Up to @drseb - functionally all are the same, but 3 has a serious downside in that it redirects to an none-repo (a CI pipeline, i.e. https://ci.monarchinitiative.org/view/hpo/job/hpo.annotations.current/lastSuccessfulBuild/artifact/rare-diseases/current/phenotype.hpoa) currently, which can disappear very very easily. I would strongly suggest 1.

drseb commented 2 years ago

I think 1) sounds good. What do you think @pnrobinson ?

pnrobinson commented 2 years ago

I agree, I think users would most appreciate 1).

matentzn commented 2 years ago

@drseb

Action items:

[x] Edit latest release by dropping all relevant HPOA files (phenotypes, genes, whatever they may be) into the section named Attach binaries by dropping them here or selecting them. When uploaded, click "update release".
[ ] Change your release procedure documentation to add the following: "When creating a GitHub release, drag and drop all relevant HPOA files into the section named Attach binaries by dropping them here or selecting them before running 'update release'."
[x] Ping me to update the hp PURL systems to recognise PURLs for the files.

pnrobinson commented 2 years ago

@drseb @matentzn can we move forward with this?

matentzn commented 2 years ago

@pnrobinson this is just @drseb todo - he when running the next release ne needs to do the 3 todo things above. Maybe share it in slack with him as I am not sure if he reads github messages frequently!

matentzn commented 2 years ago

We are very close to this now:

https://github.com/OBOFoundry/purl.obolibrary.org/pull/825

Before closing, please make sure that @drseb has updated the documentation and checked the remaining task box in the comment above.

matentzn commented 2 years ago

Note that this only introduces versioned HPOA files from the current release onwards - past release will not have HPOA version IRIs attached with them!

matentzn commented 2 years ago

From today, we provide versioned PURLs to our HPOA annotation files, for example:

http://purl.obolibrary.org/obo/hp/releases/hpoa/2022-02-14/genes_to_phenotype.txt

Finally! :) This can be closed once @drseb has documented how to maintain this in the release instructions.

pnrobinson commented 2 years ago

@matentzn @drseb I am not sure where the release instructions are? Can we close this?

matentzn commented 2 years ago

I will work on this on Tuesday, but no need to keep it open!