pombase/chobo

Try to merge part_of from go-basic.obo and ro-chado.obo

Opened this issue · 4 comments

kimrutherford commented

There are two Typedef for part_of that have different IDs so Chobo stores two cvterms. Try to merge them.

go-basic.obo:

[Typedef]
id: part_of
name: part of
namespace: external
xref: BFO:0000050
is_transitive: true

ro-chado.obo:

[Typedef]
id: BFO:0000050
name: part_of
def: "a core relation that holds between a part and its whole" []
is_transitive: true
is_a: RO:0002131 ! overlaps
inverse_of: BFO:0000051 ! has part
ValWood commented

I think @dosumis was talking about integrating these soon...?

kimrutherford commented

I think @dosumis was talking about integrating these soon...?

That would be great.

If the two stanzas had an id: or alt_id: in common Chobo would happily merge them.

dosumis commented

Hmmm - They are the same. This is just an OBO<->OWL issue.

In the roundtrip

OBO
id: part_of
xref: BFO:0000050

=> OWL:

http://purl.obolibrary.org.obo/BFO_0000050
short_hand: part_of

@cmungall - should ro-chado still be OBO-ish, surely better to be using owl short_form or OBO equivalent everywhere now. I guess in chado this would be DB:BFO, ACC:0000050

cmungall commented

Hmm, I would opt for using a prefixed ID in all places. That would remove the need for chobo and other consumers to perform the xref hack.

Can follow up here:
oborel/obo-relations#68