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FYI there's a PyOBO export of Rhea in the OBO format available at https://github.com/biopragmatics/obo-db-ingest/tree/main/export/rhea/122
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# Re-implementing the N2T ARK Resolver | Biopragmatics
Archival Resource Keys (ARKs) are flavor of persistent identifiers like DOIs, URNs, and Handles that have the benefit of being free, flexible wi…
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See https://github.com/biopragmatics/obo-db-ingest
It would be quite easy to add these as builds, and distribute the sqlite on s3.
Advantages:
- easy to query in OAK (though some methods and…
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(lmk if you prefer these in pyobo vs here)
The correct ID to use for grouping class is something like "EC:1.1.1.-", not "EC:1.1.1"
See:
https://github.com/biopragmatics/bioregistry/issues/681
…
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As pointed out here: https://github.com/biopragmatics/bioregistry/issues/527
The OLS PURLs for COs use a http + www scheme e.g. https://www.ebi.ac.uk/ols/ontologies/co_325/terms?iri=http%3A%2F%2Fww…
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I just skimmed https://arxiv.org/abs/2404.03044 and have two suggestions:
1. might be worth mentioning the overlaps with the Intelligent Task ontology https://bioregistry.io/registry/ito
2. we pre…
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# You Should Use a Private Email on Publications | Biopragmatics
While we were recently preparing to submit a manuscript, the lead author said they looked at my last few papers and noticed I always u…
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The NCBI taxonomy database is a database, not an ontology. As such that automatic translation includes various things that are not ideal from an ontology modeling perspective
If we were to make the…
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# Connecting Preprints to Peer-reviewed Articles on Wikidata | Biopragmatics
After the BioCypher preprint went up on the arXiv, I checked in on the missing co-author items list on the Scholia page th…
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