Weird annotation assertion causes problems

[matentzn]

This annotation assertion in pco.owl causes some problems with ROBOT and profile validation:

<owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#created_by">
        <rdfs:isDefinedBy rdf:resource="http://www.geneontology.org/formats/oboinowl.owl"/>
    </owl:AnnotationProperty>

I think this is because http://www.geneontology.org/formats/oboInOwl#created_by is built-in vocabulary of the OBO spec and you should not put any annotations on it! Could you remove it? And make sure that its not added as part of your release?

[ramonawalls]

The only usages of this axiom in PCO that I can find are coming in from IAO, GO, PATO, and ENVO. Are you suggesting that we remove the annotations from those imports before we do a release? That does not seem right.

[ramonawalls]

Can you tell me where you are seeing the problem in FlyBase, @matentzn? Maybe we used that property once without realizing it.

[matentzn]

Oh I never saw this in FlyBase.. It just causes some issues with importing PCO into other ontologies! Maybe it is solved when you refresh the imports? I just checked IAO and PATO and they both do not have this axiom in their most recent releases!

[ramonawalls]

Hmm. I just made new imports about a month ago, and they are still there. It's not IAO we import, but the full file for IAO metadata. I just opened the latest release (http://purl.obolibrary.org/obo/iao/ontology-metadata.owl) and there are many uses of that property. Same with PATO. What are the two of us doing differently?

[ramonawalls]

Also, we've never gotten a ROBOT error about that annotation property, but maybe you have custom checks set up.

[matentzn]

Ok, so first thing:

This is a great mystery that I could not solve yet even after looking for a while. First of all: The annotation properties themselves are totally fine! Its the assertion

<rdfs:isDefinedBy rdf:resource="http://www.geneontology.org/formats/oboinowl.owl"/>

that is problematic. So instead of this (this is what it currently looks like):

<owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#created_by">
        <rdfs:isDefinedBy rdf:resource="http://www.geneontology.org/formats/oboinowl.owl"/>
    </owl:AnnotationProperty>

It should look like:

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

You can see here for an example how it should be.

So its really this rdf:isDefinedBy clause that is the problem, not the property itself (and unfortunately no ROBOT check will catch that).

Let me offer a hypothesis.
Before you migrated to ODK, you already had a few imports, especially go, ncbitaxon, envo and pato - the ones that have the problematic axiom. These seem to have not been refreshed by your new ODK setup (github says, they are more than 6 month old, while every other file you have is only 2 weeks old). Its this true? I also noticed that your ODK does not have ncbitaxon as a goal, so it will never be refreshed (hence the bad axiom will continue to linger. Do you thing I am thinking in the correct direction?

[ramonawalls]

Thanks for analyzing so carefully! You hypothesis is close. All of the imports are new, but I don't build them automatically with ODK. I use Robot, and then skip rebuilding them during release process. I do this to have more control over the import files, especially ENVO. I am working on integrating the import file builds into the releaseIn Robot, as I get better with make files. In Robot, I use the --annotate-with-source true option, which is what I think is adding that defined by annotation. I do want to include the defined by annotation for all the classes, and I don't currently know a way to remove it for just that property.

Let me play around with building the imports and see if I can get rid of it. If nothing else, I could remove it manually, although that is not ideal.

[matentzn]

Ahhh ok! This makes sense! Maybe avoid doing stuff manually.. I dont know whether --annotate-with-source is really worth it; You always have to remember that whatever stuff you add to your ontology, everyone downstream is adding as well - and maybe they dont want such annotations on all their classes - even if they are GO. This puts the burden on everyone else to remove such annotations again! Just my two cents.. I am pretty happy to hack around everything thrown my way, but maybe I am 1 of the 3 people in the world who like that.. :P Thanks for looking into it!

[ramonawalls]

Thanks again, Nico. I don't like to do anything manually either, but I don't use the defaults, and PCO is an old ontology - hard to script everything at this point. I suppose my hacking tolerance is quite a bit lower than yours! I just posted a question to obo discuss to try to figure out what the current consensus is on using defined by annotations with imports.

[ramonawalls]

Oops. Reopening until the issue is fixed.

[matentzn]

:P Oh god now you alerted the whole world to this issue.. Hahah. Ok... Lets I hope I leave the discussion with my head still attached!