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[bioontology-support] [BioPortal] Feedback from Chai

Michael Vladimir Dorf mdorf at stanford.edu
Mon Apr 20 18:21:43 PDT 2020


Hi Chai,

Thank you for contacting us. I am not exactly sure how I can help except to point out that we display the hierarchy of the classes based on the subClassOf relationship. The details of each class presented in our user interface display ALL available properties of the class. You can view the same data using our REST API, and you can see, the two views are identical. For example:

https://bioportal.bioontology.org/ontologies/FMA/?p=classes&conceptid=http%3A%2F%2Fpurl.org%2Fsig%2Font%2Ffma%2Ffma293882<https://bioportal.bioontology.org/ontologies/FMA/?p=classes&conceptid=http://purl.org/sig/ont/fma/fma293882>

AND

http://data.bioontology.org/ontologies/FMA/classes/http%3A%2F%2Fpurl.org%2Fsig%2Font%2Ffma%2Ffma293882?no_links=true&no_context=true&display=prefLabel,synonym,definition,properties,submission<http://data.bioontology.org/ontologies/FMA/classes/http://purl.org/sig/ont/fma/fma293882?no_links=true&no_context=true&display=prefLabel,synonym,definition,properties,submission>

You’ll need to append your BioPortal API key to the latter example for it to display properly.

You can also try using the FMA Visualization tool to see if that presentation gives you a better idea of the relationships between FMA classes:

http://bioportal.bioontology.org/ontologies/FMA/?p=classes&conceptid=http%3A%2F%2Fpurl.org%2Fsig%2Font%2Ffma%2Ffma293882#visualization<http://bioportal.bioontology.org/ontologies/FMA/?p=classes&conceptid=http://purl.org/sig/ont/fma/fma293882#visualization>

Just note that there’s currently a known issue in BioPortal where the visualizations don’t work over HTTPS, so please make sure to use “http://“ instead of “https://“ when viewing that tab.

Do you have specific examples of classes in FMA, whose relationships are missing from BioPortal?

Thanks,

Michael


On Apr 19, 2020, at 9:50 PM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: Chai

Email: humanitiesclinic at gmail.com<mailto:humanitiesclinic at gmail.com>

Location: http%3A%2F%2Fbioportal.bioontology.org<http://2Fbioportal.bioontology.org>%2F

Feedback:

Dear Person-in-Charge

My question pertains to the Foundational Model of Anatomy. As from the original website for the FMA, there are (1) spatial (2) part-of/contains relationship data available between classes in the FMA. However, I cannot seem to find these on your website. Can you advise where I can access such data?

Regards,
Chai

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