Adding 'type' to definition references

[beckyjackson]

Options for property to use with eco codes:

• MI:0353 (cross-reference type)
• dc:type (type)
• rdfs:comment (comment)
• IAO:0000232 (curator note)

I went with dc:type for this first pass, but this can always be changed. The definition of cross-reference type (MI:0353) is a little to restrictive in my opinion, because then you wouldn't want to include the 'curator inference' part (just say the type is dictionary, encyclopedia, etc...)

Right now, the reference types are annotations on the DbXref annotations. This is only possible with ROBOT templates right now, so new references would need to be added via templates as follows:

ID	Definition	Xref	Xref Type
ID	A IAO:0000115	>A oboInOwl:hasDbXref	>>AI dc11:type
DOID:ex1	Some definition	url:http://example.com	curator inference from dictionary
DOID:ex1	Some definition	PMID:123456	curator inference from journal publication

Then running template followed by repair -merge-axiom-annotations true to merge axiom annotations:

robot template \
  --input doid-edit.owl \
  --merge-before \
  --collapse-import-closure false \
  --template template.csv \
repair \
  --merge-axiom-annotations true \
  --output new-doid-edit.owl

The alternative is to have the reference types alongside the DbXrefs, but that may get confusing with multiple references:

[lschriml]

Hello @sbello -- want to check with you that adding this annotation on the references' database cross reference will not cause a problem for the AGR ??

Thank you,
Lynn

[lschriml]

@beckyjackson -- Hello Becky,
Looks good to me, just need to confirm this will not cause any AGR/MOD conflicts with @sbello.
If it will be OK with those groups, then I will merge the branches.

Cheers,
Lynn

[sbello]

@beckyjackson Will this additional information make it into the doid.obo or doid-merged.obo files? If this does not make it into the OBO files then I can be confident this won't cause issues for the MODs. If this ends up in the OBO files I will need to check with the SEs.

[lschriml]

Hello Sue, please check with the SEs. Cheers, Lynn

…

On Tue, Sep 10, 2019 at 10:30 AM Sue Bello ***@***.***> wrote: @beckyjackson <https://github.com/beckyjackson> Will this additional information make it into the doid.obo or doid-merged.obo files? If this does not make it into the OBO files then I can be confident this won't cause issues for the MODs. If this ends up in the OBO files I will need to check with the SEs. — You are receiving this because your review was requested. Reply to this email directly, view it on GitHub <#748?email_source=notifications&email_token=ABBB4DJI734I2ICMZOTVGG3QI6VQ5A5CNFSM4ISXGT62YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD6LJOYQ#issuecomment-529962850>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ABBB4DNL6RO6CRA4MT6NRZDQI6VQ5ANCNFSM4ISXGT6Q> .

-- Lynn M. Schriml, Ph.D. Associate Professor Institute for Genome Sciences University of Maryland School of Medicine Department of Epidemiology and Public Health 670 W. Baltimore St., HSFIII, Room 3061 Baltimore, MD 21201 P: 410-706-6776 | F: 410-706-6756 lschriml@som.umaryland.edu

[sbello]

@lschriml will do

[sbello]

@beckyjackson Will I need to change the ROBOT template once this is implemented? If so where do I find the new template?

[sierra-moxon]

Thanks for the heads up @beckyjackson @lschriml @sbello :) - would it be possible to post an excerpt from the resulting obo file? (I'm a SE at Alliance and ZFIN).

[lschriml]

Yes, we can update the file internally, produce the usual set of files for a release, and before releasing, share with you the set of resulting files. Cheers, Lynn

…

On Tue, Sep 10, 2019 at 11:05 AM Sierra Moxon ***@***.***> wrote: Thanks for the heads up @beckyjackson <https://github.com/beckyjackson> @lschriml <https://github.com/lschriml> :) - would it be possible to post an excerpt from the resulting obo file? (I'm a SE at Alliance and ZFIN). — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#748?email_source=notifications&email_token=ABBB4DP3CAGXWM2VEJM6G73QI6ZT3A5CNFSM4ISXGT62YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD6LNT6Q#issuecomment-529979898>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ABBB4DOKUFYWHJF755MCR33QI6ZT3ANCNFSM4ISXGT6Q> .

-- Lynn M. Schriml, Ph.D. Associate Professor Institute for Genome Sciences University of Maryland School of Medicine Department of Epidemiology and Public Health 670 W. Baltimore St., HSFIII, Room 3061 Baltimore, MD 21201 P: 410-706-6776 | F: 410-706-6756 lschriml@som.umaryland.edu

[beckyjackson]

@sierra-moxon - The resulting OBO file will not include these type references, so it will look exactly the same.

@sbello - The ROBOT template will be slightly different for new terms, as there will be one additional column for these immediately to the right of the definition source (xref) column.

[sierra-moxon]

@beckyjackson -ok great! thanks. We're planning to prototype moving to the obo-JSON copy of this ontology (when its available, etc...), but at that point, we can certainly adjust to a type column addition. For now, if no changes to obo, we're good. :)

[sbello]

As the changes won't show up in the OBO files this should not cause any problems for the Alliance or the MODs

[beckyjackson]

This PR is failing due to too many messages being printed by ROBOT. I'm looking into this issue now, but it does not have anything to do with the changes made in this PR.