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monarch-initiative / mondo

Mondo Disease Ontology
http://obofoundry.org/ontology/mondo
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Obsoletion TSV Release file has links to non-mondo sites? #5713

Closed larrybabb closed 1 year ago

larrybabb commented 1 year ago

The mondo_obsoletioncandidates.tsv file that is provided with each release has 5 columns: mondo_id, label, comment, issue, obsoletion_date. For the most part the "issue" column provides a link to the mondo github issue that is the source for the reason for obsoletion. However sometimes, a NIH rarediseases.info site is referenced.

It would be very helpful if the issue value was always the MONDO issue that was the source behind the obsoletion. For example in the Dec 01.2022 release the record

mondo_id | label | comment | issue | obsoletion_date
MONDO:0008952 | cerebrofaciothoracic dysplasia | This will be obsoleted in the 2023-02-01   release. The term ... | https://rarediseases.info.nih.gov/diseases/1210/cerebro-facio-thoracic-dysplasia | 2/1/23

Seems to have been produced from the mondo issue #5619. It seems like it would be more consistent and logical to provide the mondo issue link under the issue column.

Is this intentional or a bug? If it is a bug, can we get an estimate on when it might be corrected.

matentzn commented 1 year ago

Thanks for reporting this @larrybabb - this was a consequence of a move to use a different annotation property during curation, and failure to update our reporting pipeline, which is all done in #5715, including QC to guard against future mistakes.