Add xrefs curated in Biomappings #2950
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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. |
See issue pointed out by Damien: obophenotype/uberon#2950 (comment)
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Btw, what should I make of the QC failing? It appears the feedback is the process is being killed |
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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. |
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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. |
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I think this will require 1) a new ODK release INCATools/ontology-development-kit#925 and 2) updating UBERON's ODK config |
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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
changed the title
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@gouttegd, shouldn't this PR constantly fail because of the property issue in the OBO format? |
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@anitacaron I don’t think so. Last QC checks passed fine. The problem with this kind of syntax: is that it currently yields bogus IRIs (such as It’s only when the property IRI contains a |
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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.
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.
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.
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