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[bioontology-support] OWL Ontology

Michael Dorf mdorf at stanford.edu
Fri May 10 13:59:44 PDT 2019


Hi Juliusz,

Thanks for getting back to us. Before I proceed with my specific comments on your ontology, please note that the BioPortal support is mainly focused on issues related to using the BioPortal system as well as the BioPortal REST APIs. For questions related to ontology development, I would suggest posting your query on the Protege support list [1], which tends to be monitored by a larger community of ontology experts.  My background is in software development, so I’m not very good at recommending ways of defining your ontology structure.

That said, I’ve compared the class in your ontology that you were referring to, “Maxillary sinus”, with a couple of classes from other UMLS ontologies that define the properties “notation” and “cui”. The difference appears to be in the namespace that is used for the “notation”:


Your class:
http://data.bioontology.org/ontologies/ICD-O-3-T/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FCDN-O-3-T%2FC31.0?display=all<http://data.bioontology.org/ontologies/ICD-O-3-T/classes/http://purl.bioontology.org/ontology/CDN-O-3-T/C31.0?display=all>

http://purl.bioontology.org/ontology/CDN-O-3-T/notation": [

  *   "C001"

]

SNOMEDCT:
http://data.bioontology.org/ontologies/SNOMEDCT/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSNOMEDCT%2F410607006?display=all<http://data.bioontology.org/ontologies/SNOMEDCT/classes/http://purl.bioontology.org/ontology/SNOMEDCT/410607006?display=all>

http://www.w3.org/2004/02/skos/core#notation": [

  *   "410607006"

]

ICD10:
http://data.bioontology.org/ontologies/ICD10/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FICD10%2FK70-K77.9?display=all<http://data.bioontology.org/ontologies/ICD10/classes/http://purl.bioontology.org/ontology/ICD10/K70-K77.9?display=all>

http://www.w3.org/2004/02/skos/core#notation": [

  *   "K70-K77.9”

]

Try using the namespace http://www.w3.org/2004/02/skos/core for your “notation” property. Once in place, we should be able to recognize it and process it correctly for our search index.

As far as the property “cui”, it doesn’t appear to exist in any of the classes that you referred to in your ontology, so I can’t comment on whether it’s defined properly.

Thanks,

Michael

[1] https://protege.stanford.edu/support.php


On May 10, 2019, at 1:26 AM, filipowj at tchpc.tcd.ie<mailto:filipowj at tchpc.tcd.ie> wrote:

Hi Michael,

Many thanks for your email.
I'm sorry for confusion there I used TESTJF for testing and tried uploading different versions.
Please take a look at my correct ontology: ICD-O-3-T and screenshots attached

I've added notation through the annotations to class Lip and it's visible in the description but via API call
it is attached to properties and not to an actual attribute?

In an essence I'm not sure how to add attributes: notation and cui.

I appreciate your help.

Juliusz Filipowski

May 9, 2019 10:45 PM, "Michael Dorf" <mdorf at stanford.edu<mailto:mdorf at stanford.edu?to=%22Michael%20Dorf%22%20%3Cmdorf at stanford.edu%3E>> wrote:
Hi Juliusz,
Thank you for contacting us. The ontology TESTJF that your call below is referring to isn’t the same as the one you are referring to in your screenshots. TESTJF contains only two classes and none of the annotations that you mentioned (see screenshots). Is it possible that you uploaded a wrong ontology?
Michael
<PastedGraphic-1.png>
<PastedGraphic-2.png>


On May 9, 2019, at 4:29 AM, filipowj at tchpc.tcd.ie<mailto:filipowj at tchpc.tcd.ie> wrote:
Hi there,

I work for Trinity College Dublin and looking to submit new ontology to the BioPortal.
I'm also fairly new to OWL standard and having issue with parsing the data in BioPortal.
I'd like to add `notation` or `cui` as they are used in REDCap as dropdown value.
So I add them as annotation to the class in protege.
Once .owl file is submitted to BioPortal I can see them as new properties on Details Section
but when I use API Get call they're not visible like they were never parsed.

Here is the call:
http://data.bioontology.org/search?q=%22Tumor%22&ontologies=TESTJF&include=prefLabel,notation,cui&suggest=false&display_links=false&display_context=false&format=json&apikey=myKey<http://data.bioontology.org/search?q=%22Tumor%22&ontologies=TESTJF&include=prefLabel,notation,cui&suggest=false&display_links=false&display_context=false&format=json&apikey=ce36656e-7615-400a-ac5c-2f1ea4b39908>

cui and notation are included but there are not showing up.

My ontology is created with Protege, please find attached the screenshots.
I'd appreciate your suggestions.

Best Regards,
Juliusz Filipowski



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