Policy around using COB identifiers vs other OBO Ontology identifiers

[ddooley]

Should I assume that if I see a COB term and its COB id that originates from another OBO ontology term, that in adopting COB in an ontology, I can/should switch to the COB id? I understand that the SSSOM mapping file must indicate equivalency between the two.

And is this true too of properties? For example "is specified input of" is COB_0000027, and SSSOM file makes equivalency to OBI_0000295. I was puzzled because I thought COB would still stay away from minting common properties, instead leaving that to RO's domain.

[matentzn]

It's a good question to ask at the COB seminar today! I think we should align to the mapped ids and not the COB ids, but I may not see the whole picture here.

[wdduncan]

There's a COB seminar today!? I had no idea.

On Wed, Jan 25, 2023 at 6:15 AM Nico Matentzoglu @.***> wrote:

It's a good question to ask at the COB seminar today! I think we should align to the mapped ids and not the COB ids, but I may not see the whole picture here.

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[matentzn]

Went out to obo discuss yesterday by James! And also on slack.

[jamesaoverton]

Chris is presenting on COB today at noon Eastern as part of the 2023 Ontology Summit, which I am co-organizing: https://ontologforum.org/index.php/ConferenceCall_2023_01_25. I've done my best to advertise this on OBO Discuss, OBO Tools, and Slack over the past month, but I hate advertising things and I may not have done a good job.

[wdduncan]

Thanks @jamesaoverton ! You've done a great job getting the word out about the 2023 Ontology Summit. I just didn't make the connection that COB was part of the summit today. Sorry for my confusion.

Unfortunately, I can't make it today. My dance card is full.

[jamesaoverton]

Ok. A recording of the session should be available at that link promptly. If it isn't let me know and I'll sort it out.

[kaiiam]

I plan to ask the question at today's seminar.

[jamesaoverton]

Here is a link to the bridge document: http://obofoundry.org/COB/obo-bridge/.

[kaiiam]

Summary of @cmungall's answer from today's workshop:

This is more a less a bug in the process. They plan on swapping out COB object properties for the original RO object properties. Chris said they would fix this in a new release, so we can just use the original OPs.

So perhaps this ticket can now serve as a request to fix the OP release process to use the original RO terms not the COB prefixes.

Much obliged!

[matentzn]

I think this is simply a bug in sssom toolkit: https://github.com/mapping-commons/sssom-py/issues/339