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[bioontology-support] BioPortal Preferred Name Issue

Michael Dorf mdorf at stanford.edu
Tue Mar 27 15:17:33 PDT 2018


Hi Michael and Derrick,

I’ve reparsed the ontology, and the tree now appears correctly. A quick check revealed that the Preferred Name property was not set correctly in the ontology metadata. The property was set to:

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

However, if you look at a sample of the ontology classes, it appears that the actual pref label is held in the property with this URI:

http://www.owl-ontologies.com/Ontology1521559847.owl#Preferred_name

The property http://www.radlex.org/RID/#Preferred_name does not appear to exist, so our code did a fallback to the default, http://www.w3.org/2004/02/skos/core#prefLabel, which holds the ID (RIDXX). Here is a sample of the classes that demonstrates the issue:

http://data.bioontology.org/ontologies/RADLEX/classes/http%3A%2F%2Fwww.owl-ontologies.com%2FOntology1521559847.owl%23RID1/children?include=prefLabel,synonym,properties<http://data.bioontology.org/ontologies/RADLEX/classes/http://www.owl-ontologies.com/Ontology1521559847.owl#RID1/children?include=prefLabel,synonym,properties>

Please contact us if you experience further problems.

Thanks,

Michael



----------------------------------------------------
Michael Dorf
Chief Software Architect
The National Center for Biomedical Ontology
Stanford Biomedical Informatics Research
mdorf at stanford.edu<mailto:mdorf at stanford.edu>
O: 650-723-0357
M: 650-995-4374
----------------------------------------------------

On Mar 27, 2018, at 6:08 AM, Michael Crabtree <mcrabtree at rsna.org<mailto:mcrabtree at rsna.org>> wrote:

Hi John,

We’re still experiencing issues after resubmitting the OWL files.  We’re still seeing the RID’s instead of the preferred names in the tree.

Thanks,
Michael

From: John Graybeal [mailto:jgraybeal at stanford.edu]
Sent: Saturday, March 24, 2018 4:59 PM
To: Derrick Lottich <dlottich at rsna.org<mailto:dlottich at rsna.org>>
Cc: support at bioontology.org<mailto:support at bioontology.org>; kcwang at gmail.com<mailto:kcwang at gmail.com>; Michael Crabtree <mcrabtree at rsna.org<mailto:mcrabtree at rsna.org>>
Subject: Re: [bioontology-support] BioPortal Preferred Name Issue

Derrick,

With apologies, can I request you re-try your submission now?  We had some recent problems with the system, and while normally we would try to take care of things for you, most of us are out of the office this entire week.

We will have someone monitoring the list, so if the problem occurs on your resubmission also, please respond accordingly.

Thanks very much.

John

On Mar 21, 2018, at 8:18 PM, Derrick Lottich <dlottich at rsna.org<mailto:dlottich at rsna.org>> wrote:

Hello BioPortal Support Team,

Could you possibly help us with some issues with our RADLEX ontology on bioportal?  We submitted a new version yesterday and noticed all the class names in the tree are the ID field and not the Preferred Name.  Attached is a screen shot of what we are experiencing.

Much appreciated,
Derrick

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========================
John Graybeal
Technical Program Manager
Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal
Stanford Center for Biomedical Informatics Research
650-736-1632

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