Broken xref annotation property

[matentzn]

The current EXO release contains a broken annotation property that causes issues with old loading pipelines:

<owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#http://www.geneontology.org/formats/oboInOWL#xref"/>

This should be:

<owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#xref"/>

Would you be able to fix that and make a new release?

[matentzn]

Correction, the correct annotation property IRI would be:

http://www.geneontology.org/formats/oboInOwl#hasDbXref

So make sure that neither once of the two

• http://www.geneontology.org/formats/oboInOwl#http://www.geneontology.org/formats/oboInOWL#xref
• http://www.geneontology.org/formats/oboInOwl#xref

is used.. Thanks!

[cjgrondin]

Ok, I'll look into it. Thanks

[diatomsRcool]

@cjgrondin what is the status of this?

[cjgrondin]

I can not find an annotation with http://www.geneontology.org/formats/oboInOwl#http://www.geneontology.org/formats/oboInOWL#xref in the code at all (under which term is the annotation property?), though it looks like http://www.geneontology.org/formats/oboInOwl#xref appears in ExO 83 times in various contexts for different terms. Can you please be more specific with the issue? Is the broken link every time an annotation property value specifies the IRI http://www.geneontology.org/formats/oboInOwl#xref, and the IRI should now be http://www.geneontology.org/formats/oboInOwl#hasDbXref? Thanks.

[matentzn]

Hey @cjgrondin

I reworked exo.obo to make it OBO compliant; see here: https://github.com/CTDbase/exposure-ontology/pull/14

This will fix this here issue and some other; I tried to explain everything in detail in the pull request. If you need help, clarifications or assurances, I am happy to help!

[cjgrondin]

Thanks Nico, Can you tell me which tool/software you are using to produce the obo compliant file? I want to investigate the details of why there are differences in the formatting of certain annotations (and whether it's a software or version issue).

[matentzn]

To be honest, I mostly use text-editors and ROBOT - I am not an ontology curator, I am an ontology engineer with @dosumis and @cmungall and @jamesoverton and I basically make sure ontologies are logically consistent and are formally correct (and OBO compliant).

The problem with ExO was, that it was indeed legal obo (so you could open it in whatever software), i.e it was not broken in the super strict syntax-parse sense of the word. My assumption is that your issues stem from a weird older version of Protege. OBOEdit or Protege 5.5 should not cause these serialization problems!

My preferred environment is Protege 5.5, but OBO Edit is still in use so.. No problem, I think. What do you use?

[cjgrondin]

I did not create the original ontology, but I believe I used Protege 4.0 to add terms back in 2017. I have since downloaded protege 5.5, which should hopefully be compliant to add new terms.

~~~~~~~~~Cynthia J. Grondin, PhDBiocuratorComparative Toxicogenomics Databasehttp://ctdbase.org http://ctdbase.org

On Thu, Sep 10, 2020 at 10:10 AM Nico Matentzoglu notifications@github.com wrote:

To be honest, I mostly use text-editors and ROBOT - I am not an ontology curator, I am an ontology engineer with @dosumis https://github.com/dosumis and @cmungall https://github.com/cmungall and @jamesoverton https://github.com/jamesoverton and I basically make sure ontologies are logically consistent and are formally correct (and OBO compliant).

The problem with ExO was, that it was indeed legal obo (so you could open it in whatever software), i.e it was not broken in the super strict syntax-parse sense of the word. My assumption is that your issues stem from a weird older version of Protege. OBOEdit or Protege 5.5 should not cause these serialization problems!

My preferred environment is Protege 5.5, but OBO Edit is still in use so.. No problem, I think. What do you use?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/CTDbase/exposure-ontology/issues/11#issuecomment-690315108, or unsubscribe https://github.com/notifications/unsubscribe-auth/AFK5XAJWOVDOCL6W3W5YRN3SFDM5BANCNFSM4KTA7ZRQ .

[matentzn]

Sounds great! If you need help merging the pull request, or any further help, I am happy to be of assistance :)

[cjgrondin]

Thanks for your help. Before merging the pull request, I'd like to understand the syntax differences between the current ExO and new version and figure out why it is not compliant. For the 'maternal' term id: ExO: 0000159 that I added last month, I added the annotations in Protege 5.5 and saved it in obo format, then uploaded to Github. This also looks like the old syntax. If I add new terms in Protege 5.5, I'm concerned the same syntax errors will occur. What did you use to update all of the syntax? Thanks

[matentzn]

So I used a text editor to update the syntax (it would take a month or more to manually do all this) and then used Protege 5.5 to verify that everything was correct; if it helps you, we can have quick Zoom call tomorrow and I will describe everything in more detail :)

[matentzn]

I think the syntax error will go away now if you use Protege, because when you select some entity (relation, annotation property) in Protege, it will now only give you the correct ones to chose from! If you use Protege 5.5 you will be fine.

As this is Github, you can also just merge it and make a test; if you dont like it, you can still roll back to the old version! Or call me to sort it out!

[cjgrondin]

Ok, I merged it and will roll back if we encounter any issues. Thanks

[matentzn]

Great! :) I am here to help!