Document strategy for genes in CL

obophenotype / cell-ontology

An ontology of cell types

https://obophenotype.github.io/cell-ontology/

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Document strategy for genes in CL #952

Open cmungall opened 3 years ago

cmungall commented 3 years ago

Pertains to #901

[ ] form of ensembl URIs. The slash form is more canonical ie https://identifiers.org/ensembl/ENSMUSG00000019772 not https://identifiers.org/ensembl:ENSMUSG00000019772. Also in prefix commons and GO we are using http not https as our usage predated https switch
[ ] coordinate with PRO axiomatization. PRO uses HGNC + MOD IDs
[ ] implement a strategy for TCs. E.g. put TCs on genes, and add a property chain. Or a simply sparql construct inference
[ ] coordinate with an overall OBO strategy for database entities. See my slides
[ ] write dosdps - even for subClassOf patterns
[ ] general documentation

dosumis commented 3 years ago

form of ensembl URIs. The slash form is more canonical ie https://identifiers.org/ensembl/ENSMUSG00000019772 not https://identifiers.org/ensembl:ENSMUSG00000019772. Also in prefix commons and GO we are using http not https as our usage predated https switch.

Looks like http://identifiers.org/ensembl/ENSMUSG00000019772 resolves, so happy to switch.

dosumis commented 3 years ago

CC @shawntanzk

dosumis commented 3 years ago

Decision:

Switch to from Ensembl to using Pro and Uniprot (via pro) for defining CL terms. (Sorry Shawn).
- e.g. https://www.ebi.ac.uk/ols/ontologies/pr/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FPR_000013502&viewMode=PreferredRoots&siblings=false
Also make sure property chains are present to => species inference from PRO. (@dosumis to check)

Note - we will continue to use ENSEMBL on BDS region specific terms for now, but these will not be merged into CL yet.

shawntanzk commented 3 years ago

Happy to change it, just a couple of things: 1) do we want to change the label to whats on Pro and put the current name as a synonym (similar to Pro) - (eg for Pvalb: parvalbumin alpha, synonym: PVALB) or leave the label as it is and add the Pro name as synonym? 2) Should I put the Ensembl ID as a xref annotation? (seems like it might be useful)

dosumis commented 3 years ago

do we want to change the label to whats on Pro and put the current name as a synonym (similar to Pro)

Please retain the current label, as this is what biologists expect, and use PRO label and synonyms to derive synonyms for CL terms.

Also - please make sure to research the terms used carefully. The species specific terms are derived from uniprot. There's a link to uniprot here:

https://www.ebi.ac.uk/ols/ontologies/pr/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FPR_P32848&viewMode=PreferredRoots&siblings=false

Also note - the ID is derived from uniprot: PR:P32848 -> P32848

Uniprot has an ID mapping service that is useful for going from ensembl IDs to uniprot IDs which might be useful for mapping: https://www.uniprot.org/uploadlists/