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[bioontology-support] [BioPortal] Feedback from jimmccusker

McCusker, James Patrick mccusj2 at rpi.edu
Tue May 23 18:51:50 PDT 2017


Thanks, I can fix that quickly. Those are supposed to be reified definition objects that allow for additional statements about a class. Not so much punning as annotations.

Jim

On May 23, 2017, at 8:28 PM, Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>> wrote:

Hello Jim,


On May 23, 2017, at 8:04 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:


When I uploaded the CHEAR ontology, Bioportal ignored the import closure. Is this because the imported ontology hasn't been uploaded to Bioportal?



It looks like there were three separate ontology files submitted to BioPortal.  The first one parsed successfully, but I don’t see any import statements in that file.

The next two files submitted do have import statements, but BioPortal failed to successfully parse either of those files.

I started doing some troubleshooting using your latest (3rd) submission.  The parsing step is failing due to some object property assertions (using the “is described by” object property) that appear to have invalid individual names as the value.  The object property assertion involves the following seven individuals:

AmericanIndianOrAlaskanNative
Asian
BlackOrAfricanAmerican
HispanicOrLatino
NativeHawaiianOrOtherPacificIslander
NonHispanicOrLatino
White

I opened your ontology in the Protege Desktop ontology editor so that I could generate a screen shot of the particular issue I’m referring to:


<Screenshot 2017-05-23 17.01.45.png>



In the screen shot above, I had selected the AmericanIndianOrAlaskanNative individual, then selected the “is described by” object property, then clicked the Edit button to bring up the dialog shown in the top layer.  The parser reports that “_:genid7189” is an invalid value.  The same error is show for the seven individuals I listed above.

In the ontology source file, this is the snippet of the declaration of that individual:

    <owl:NamedIndividual rdf:about="http://hadatac.org/ont/chear/AmericanIndianOrAlaskanNative">
        <sio:isDescribedBy>
            <rdf:Description rdf:nodeID="_:genid130">
                <rdf:type rdf:resource="http://semanticscience.org/resource/Definition"/>
                <prov:wasAttributedTo rdf:resource="http://hadatac.org/kb/chear#PER-Jeanette-Stingone"/>
                <prov:wasQuotedFrom rdf:resource="https://www.whitehouse.gov/sites/default/files/omb/assets/information_and_regulatory_affairs/re_app-a-update.pdf"/>
                <sio:hasValue>A person having origins in any of the original peoples of North, Central, or South America, and who maintains tribal affiliations or community attachment.</sio:hasValue>
            </rdf:Description>
        </sio:isDescribedBy>
        <skos:definition>A person having origins in any of the original peoples of North, Central, or South America, and who maintains tribal affiliations or community attachment.</skos:definition>
    </owl:NamedIndividual>

I believe it’s the blank node identifier (rdf:nodeID for rdf:Description) that is creating problems for the parsers.

Are you able to give us any information about the process you used to generate this OWL file?

I’ve create an issue in our tracker for your ontology where you can follow our progress:

https://github.com/ncbo/bioportal-project/issues/24

Kind regards,
Jennifer



Jim McCusker, Ph.D.
mccusj2 at rpi.edu<mailto:mccusj2 at rpi.edu>
http://tw.rpi.edu/web/person/JamesMcCusker
Director, Data Operations
Tetherless World Constellation
Department of Computer Science
Rensselaer Polytechnic Institute


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