Implement basic COB alignment check in new ODK ROBOT plugin #1175
Comments
Yeah, sounds good. Modulo one thing: I would prefer such a validation pipeline not to be tied specifically to COB. Instead, I would rather have it take any “upper ontology” as argument (COB or something else), and check that all base IRIs are subclasses of at least one class of that upper ontology. This is for the sake of people who use the ODK to maintain ontologies that are not part of the OBO Foundry (we know there are some, though they are likely a minority) and who might not be interested in COB alignment. |
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(COB support can still be hardcoded in such a plugin for convenience, for example with a |
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@matentzn Assigning myself for now. Happy to step back if you want to use this feature request to train someone in how to write a ROBOT command. |
Even better! Agreed.
I'd rather you tell me - I have someone, but I was going to let them do this only if you said you were not interested; the reason is that for you or me, this issue will take a fraction of the time it would take someone that has never seen the OWL API before :D |
OK, I’ll do it then. (Am I jumping at an opportunity to write some code because I’d rather do that than migrate curation data from one database to another? You have no proof.) |
We add a new option in the 'robot_report' section called 'upper_ontology'. If set, it should be the (resolvable) IRI of an upper ontology (such as http://purl.obolibrary.org/obo/cob.owl). When set, a a new report is added to the list of ROBOT report, one that tests whether all classes of the ontology are classified under one of the classes of the upper ontology. The new report uses the same parameters as the standard ROBOT reports regarding the file to perform the check on ('report_on') and whether the check should be limited to classes within the project's namespaces or not ('use_base_iris'). See #1175
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Experimental ROBOT command is here. Tentative exploitation in a ODK pipeline is in my current experimental PR about an ODK plugin. (I have tested the ROBOT command; I have not tested the ODK pipeline yet, it might very well contain a stupid Jinja2 mistake.) |
... And indeed it seems it does. I’ll look into that later. |
As per request (see INCATools/ontology-development-kit#1175), when producing a report, it should only list the *top-level* unaligned classes, not their descendants.
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This is super cool, THANKS! |
@gouttegd is adding an ODK specific ROBOT plugin in #1174;
The next big phase in OBO Foundry is to roll out COB widely. I would like to request the following pipeline:
odk:validate-cob(I don't yet what parameters are needed).The pipeline:
I can see that functionality moving to ROBOT eventually, but I would like to try it first here.
@gouttegd I might have someone that would be interested to help us implementing stuff like this, but I am not sure if it is worth the learning curve; do you agree with this issue here in general? Not sure how familiar you are with COB and OBO Foundry, maybe you need some more context?
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