biolink
what is the correct Biolink category for CNV and large deletion variants?
Is your feature request related to a problem? Please describe.
The October 2022 QotM revealed confusion related to CAids, in general, and CAID:CA358802, in particular. It was noted that CAID:CA358802 is a valid Biolink prefix. Additionally, it was noted that CAids work well when applied to genomic deletions / CNVs, but not for large deletions or CNVs, in which case, Translator does not offer another acceptable solution.
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@sierra-moxon @mbrush : I did not attend the QotM call during which this issue was raised, so I may not be capturing the complete issue. I believe Colleen X. raised the issue and Chris B. responded, so they may be able to provide additional information. I'm also not entirely sure if this is a Biolink issue, so please feel free to point me to another repo. Thanks!
Talking with a couple of people offline, I refined the request to this set of issues:
It's often unclear how IDs should be formatted
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CLINVAR:1333833 or ClinVarVariant:1333833?
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[x] remove ClinVarVariant prefix https://github.com/biolink/biolink-model/pull/1129/files
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DBSNP:rs869320661 or something different (dbSNP, remove the "rs")?
Prefix registry entries exist in all three flavors for dbsnp - good software exists to help normalize prefixes: https://github.com/biopragmatics/bioregistry
In general, we want to follow the prefix guidelines established by Biolink. Biolink uses DBSNP to prefix this identifier, and we can use the tools above to normalize the prefixes as necessary. If Biolink is missing a prefix (in the id_prefixes section of an entity, please open a ticket and we will get it in.
- CAID:CA358802 or remove the "CA" part?
CA is part of the local identifier for this resource, do not remove it. also of use: https://github.com/biopragmatics/bioregistry/issues/647
- Is the biolink-model prefix ORPHANET or ORPHA:2131?
- [x] update the prefix in Biolink to 'orphanet' to follow bioregistry designation. https://github.com/biolink/biolink-model/pull/1128
