Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Add xrefs curated in Biomappings #2950

Merged
merged 6 commits into from
Oct 24, 2023
Merged

Add xrefs curated in Biomappings #2950

merged 6 commits into from
Oct 24, 2023

Conversation

cthoyt
Copy link
Contributor

@cthoyt cthoyt commented Jul 4, 2023 •
edited
Loading

This PR adds 54 xrefs to BTO terms and one to a MeSH term that have been curated in Biomappings. It also annotates the contributor. This diff was generated programatically from tools in Biomappings.

Blocked by:

@github-actions
Copy link

github-actions bot commented Aug 4, 2023

This PR has not seen any activity in the past month; if nobody comments or reviews it in the next week, the PR creator will be allowed to proceed with merging without explicit approval, should they wish to do so.

gouttegd
gouttegd requested changes Aug 21, 2023
View reviewed changes
Copy link
Collaborator

@gouttegd gouttegd left a comment •
edited
Loading

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Sorry for the late negative review, but we can’t accept that contribution in its current state. Please see inline comment.

src/ontology/uberon-edit.obo Show resolved Hide resolved
cthoyt added a commit to biopragmatics/biomappings that referenced this pull request Aug 23, 2023
@cthoyt
Fix ORCID formatting
7d60d79 
See issue pointed out by Damien: obophenotype/uberon#2950 (comment)
@cthoyt cthoyt mentioned this pull request Aug 23, 2023
Closed
@cthoyt
Copy link
Contributor Author

cthoyt commented Aug 23, 2023

Btw, what should I make of the QC failing? It appears the feedback is the process is being killed

@gouttegd
Copy link
Collaborator

Not sure what’s going on with the QC. It was killed because OWLTools ran out of memory, I don’t think this has anything to do with your PR. I did run the test suite on your branch on my local machine and it passed fine.

@gouttegd gouttegd added the blocked blocked by another issue label Aug 23, 2023
@github-actions
Copy link

This PR has not seen any activity in the past month; if nobody comments or reviews it in the next week, the PR creator will be allowed to proceed with merging without explicit approval, should they wish to do so.

@cthoyt cthoyt requested a review from anitacaron as a code owner September 23, 2023 08:01
@cthoyt
Copy link
Contributor Author

cthoyt commented Sep 23, 2023

I think this will require 1) a new ODK release INCATools/ontology-development-kit#925 and 2) updating UBERON's ODK config

@gouttegd
Copy link
Collaborator

Yes for ①, no for ②. No need for a ODK config update for a point release like 1.4.3. :) All that will be required is to update the QC workflow to use the latest ODK release.

@cthoyt cthoyt changed the title Add 55 xrefs curated in Biomappings Add xrefs curated in Biomappings Sep 23, 2023
@gouttegd gouttegd mentioned this pull request Sep 23, 2023
Closed
@anitacaron
Copy link
Collaborator

anitacaron commented Sep 25, 2023 •
edited
Loading

@gouttegd, shouldn't this PR constantly fail because of the property issue in the OBO format?

@gouttegd
Copy link
Collaborator

@anitacaron I don’t think so. Last QC checks passed fine.

The problem with this kind of syntax:

{http://purl.org/dc/terms/contributor="https://orcid.org/0000-0003-4423-4370"}

is that it currently yields bogus IRIs (such as http://www.geneontology.org/formats/oboInOwl#http://purl.org/dc/terms/contributor), and that’s why we are waiting for the next ODK, but such bogus IRIs should not, by themselves, causing the QC checks to fail.

It’s only when the property IRI contains a # character that there is a real problem, for example with http://www.w3.org/2000/01/rdf-schema#seeAlso. Because then the bogus IRI contains two # characters (http://www.geneontology.org/formats/oboInOwl#http://www.w3.org/2000/01/rdf-schema#seeAlso), and that’s something the RDF/XML parser doesn’t like at all. But the present PR does not use any such property.

@anitacaron anitacaron requested a review from gouttegd October 23, 2023 14:06
gouttegd
gouttegd approved these changes Oct 23, 2023
View reviewed changes
Copy link
Collaborator

@gouttegd gouttegd left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

As discussed with @cthoyt on Slack, in the future the plan is for Uberon to automatically import Biomappings-provided mappings by exploiting the Biomappings SSSOM export.

Most of the machinery to do that will be added with #3061, but since it is not ready yet, no objection to adding the xrefs directly in the -edit file for now. I’ll remove them when we’ll switch to the SSSOM import.

@anitacaron anitacaron merged commit 2494303 into obophenotype:master Oct 24, 2023
2 checks passed
@cthoyt cthoyt deleted the add-bto-xrefs branch October 24, 2023 09:11
gouttegd added a commit that referenced this pull request Dec 6, 2023
@gouttegd
Revert "Add xrefs curated in Biomappings (#2950)"
cf56ae9 
This reverts commit 2494303. That
commit manually introduced Biomappings-provided cross-references
directly in the -edit file, but we are now importing those
cross-references automatically using the Biomappings SSSOM set.
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@gouttegd gouttegd gouttegd approved these changes

@anitacaron anitacaron Awaiting requested review from anitacaron

Assignees
No one assigned
Labels
blocked blocked by another issue mapping
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.
3 participants
@cthoyt @gouttegd @anitacaron