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[bioontology-support] Radlex display

Jennifer Leigh Vendetti vendetti at stanford.edu
Fri Nov 18 13:49:32 PST 2016


Hello Beverly,


On Nov 18, 2016, at 11:56 AM, Collins, Beverly <Beverly.Collins at uphs.upenn.edu<mailto:Beverly.Collins at uphs.upenn.edu>> wrote:

We just posted a new version of Radlex (version 3.14) to Bioportal, and it seems to be having some issues.
It is coming out as a hodgepodge of terms and numerical identifiers (RID’s, called “label” on Bioportal).  Hard to see what the distinction is, since e.g. RID28573 and 28579 are showing RID’s while RID28574 (jugular foramina, which was created temporally in between these) is showing the term.


Derrick Lottich reported this yesterday on the support list (full thread here: [1]).  I wasn’t seeing this behavior, in retrospect because I was probably looking at a cached version of the ontology.  I cleared all of BioPortal’s caches and I was able to observe what you describe.  I looked at the submission properties for version 3.14 (accessible to ontology administrators via the “Edit submission information” link).  I found errors in the designation of desired properties for preferred name, definition, and synonym.  They were all missing a ‘#’ sign in the IRI.  For example, the desired preferred name property had been entered as:

http://www.radlex.org/RID/Preferred_name

… when instead it should have been:

http://www.radlex.org/RID/#Preferred_name

I also corrected the synonym and definition properties.  After doing so, I re-parsed your ontology and BioPortal is now using the value of the Preferred_name property to display your ontology entities:


[cid:AD198B1D-2C0F-488C-8997-BC00656D2C46 at stanford.edu]





  The RID seems to have been put into the “Preferred Name” slot for some and not others.  I’m guessing that is a slot created by Bioportal, because there is another slot called “Preferred_name” (with an underscore) that has the right term in it, I think.


BioPortal is a read-only application and will never add properties or other entities to uploaded ontologies.  The “Preferred Name” row in the Details table simply indicates to end-users the text that we are using to display that particular ontology entity throughout BioPortal.  If an end-user doesn’t specify a property to use for the preferred name at the time of submitting an ontology, the application will default to the value of the http://www.w3.org/2004/02/skos/core#prefLabel property.  There’s a bit more to the algorithm of choosing a preferred display name if SKOS prefLabel is absent, but it’s probably not worth going into on the support list at the moment.


Any idea what went wrong here and how to fix it?

In the future if you’d like to double-check that you’re entering the correct IRI for preferred name, synonym, and definition properties, a helpful thing to do could be to open your ontology in the Protege ontology editing tool, and verify what you see there with what you enter in BioPortal.  BioPortal and Protege generally use the same software under the hood for parsing ontologies.  Here’s a screen shot for your reference of RadLex 3.14 in Protege with the Preferred_name datatype property selected in the bottom left:


[cid:EBDEDC53-8997-4FB8-A2C7-BC2E7440A42A at stanford.edu]


You can either hover your mouse over the property to see the full IRI as a tooltip, or you can check the top of the right-hand pane, which displays the full IRI.

Kind regards,
Jennifer

[1] http://ncbo-support.2288202.n4.nabble.com/bioontology-support-BioPortal-Feedback-from-Derrick-Lottich-td4655143.html


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