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conversely making a new idspace can also confuse (compare PR:P12345 vs UniProtKB:P12345)
ideally we would like upstream database to own the ontology representation, in practice this is likely to never happen, necessitating competing-cooperating alternative translations with no agreement on axioms
bioregistry conflates URLs for humans with semantic URIs
I propose that the bioregistry datamodel is extended to include inlined sub-records for ontology or KG translations of databases. These subrecords would have additional metadata to indicate the source (3rd party vs official vs quasi-official)
One case would be 3rd party ontology rendering with reminted prefixed IDs:
These renderings could even be first class entries as far as the bioregistry UI is concerned, e.g. obo$NCBITaxon (but obviously this wouldn't be used as a prefix)
Another would be 3rd part ontology renderings where the same prefixes and URL expansions are used:
rhea:
url: <official RHEA URL>renderings:
- provider: biopragmaticstype: ontologydocumentation: currently this includes all annotations but this is under discussion https://github.com/biopragmatics/pyobo/issues/170subset: COMPLETE
here there is no bespoke prefixmap so the standard RHEA ones would be used.
perhaps controversially:
uniprotkb:
url: <official uniprot URL>renderings:
- provider: prtype: ontologydocumentation: PRO classes at "species-gene" level generally use same local ID as uniprotkbsubset: OVERLAPbioregistry_entry: pr
here this would be a link between 2 existing overlapping bioregistry entries
This scheme could also be used for KG renderings of databases in formats that are more suited than OWL (e.g. kgx, rdfstar with owlstar semantics)
Note that in cases for entries that are "born" ontologies we would not curate this info, this would be considered a reflexive relation
The text was updated successfully, but these errors were encountered:
There is frequently a need to represent entities from a database as an ontology
See:
There are a lot of factors to condense here but some key points
I propose that the bioregistry datamodel is extended to include inlined sub-records for ontology or KG translations of databases. These subrecords would have additional metadata to indicate the source (3rd party vs official vs quasi-official)
One case would be 3rd party ontology rendering with reminted prefixed IDs:
These renderings could even be first class entries as far as the bioregistry UI is concerned, e.g.
obo$NCBITaxon
(but obviously this wouldn't be used as a prefix)Another would be 3rd part ontology renderings where the same prefixes and URL expansions are used:
here there is no bespoke prefixmap so the standard RHEA ones would be used.
perhaps controversially:
here this would be a link between 2 existing overlapping bioregistry entries
This scheme could also be used for KG renderings of databases in formats that are more suited than OWL (e.g. kgx, rdfstar with owlstar semantics)
Note that in cases for entries that are "born" ontologies we would not curate this info, this would be considered a reflexive relation
The text was updated successfully, but these errors were encountered: