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[bioontology-support] [BioPortal] Feedback from Ranjana Srivastava

Srivastava, Ranjana [USA] srivastava_ranjana at bah.com
Wed Apr 18 11:21:04 PDT 2012


Hi Trish,

I checked the terminology on the Bioportal site (http://bioportal.bioontology.org/ontologies/47234/?p=terms&conceptid=Ontology1310048037%3ANICHD_Pediatric_Terminology ).


·         Each term has a prefix (Ontology1310048037) which is not needed.

·         On the previous version (1.0) we had the following annotation properties displayed:

o   Definition

o   NCI Id

o   NCI PT

o   Synonym

But on the current version (the one you recreated on the Production instance of BioPortal), the owl file when opened in Protégé only shows the following in the Data Properties tab.

o   Definition

o   NCI Id

o   NCI PT
Two properties are missing. Synonym and NICHD Definition.
But on the class tab, all annotation properties are displayed.


>>What property is used to display the preferred name of terms? This metadata is not specified in BioPortal for this ontology.   Also, the Full Id for terms [1] does not seem to exist.

·         It seems the owl file which was uploaded (both version 1.0 and 1.1)does not include Preferred Name and Full ID properties. Is it possible that BioPortal assigned those or am I missing something here? Do you suggest I include these in the owl file?

Thanks
Ranjana Srivastava

Booz | Allen | Hamilton
________________________________
Ranjana Srivastava, Ph.D.
Lead Associate,
One Preserve Parkway, Rm.2080
Rockville, MD 20852
Tel +1 (301) 838-3813
Mobile +1 (240) 483-3879
srivastava_ranjana at bah.com

From: Trish Whetzel [mailto:whetzel at stanford.edu]
Sent: Sunday, April 15, 2012 10:34 AM
To: Srivastava, Ranjana [USA]
Cc: support at bioontology.org Support
Subject: Re: [bioontology-support] [BioPortal] Feedback from Ranjana Srivastava

Using the "Submit New Version" option and uploading the RDF/XML file resulted in the proper display of the root nodes of the ontology in BioPortal as compared to the display in Protege 4.1. I've recreated these steps on the Production instance of BioPortal. Can you review this new version to confirm it looks ok?

What property is used to display the preferred name of terms? This metadata is not specified in BioPortal for this ontology.  Also, the Full Id for terms [1] does not seem to exist.

Trish

[1] http://www.owl-ontologies.com/Ontology1310048037.owl<http://www.owl-ontologies.com/Ontology1310048037.owl#Anatomic_Structure_or_System>


On Apr 15, 2012, at 12:10 AM, Trish Whetzel wrote:


Hi Ranjana,

Did you upload these other versions as new versions of the Pediatric Terminology on the production BioPortal site? I've downloaded the 1.1 version and saved this as RDF/XML in Protege 4.1 and uploaded to the staging server to investigate further.

Trish


On Apr 10, 2012, at 3:18 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:



Name: Ranjana Srivastava

Email: srivastava_ranjana at bah.com<mailto:srivastava_ranjana at bah.com>

Location: http://bioportal.bioontology.org/ontologies/1640

Comment:
I submitted a new version of the ontology on 3/25/12. I do not see it correctly on the browser(shows just one class owl: DataProperty). The ontology was saved as RDF/XML.
Next, I edited the version I had uploaded earlier (1.0) and saved as rdf/XML and re-uploaded to BioPortal.
None of these methods worked.
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Trish Whetzel, PhD
Outreach Coordinator
The National Center for Biomedical Ontology
Ph: 650-721-2378
http://www.bioontology.org

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