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[bioontology-support] Feedback Parasite Experiment ontology

Trish Whetzel whetzel at stanford.edu
Mon Aug 3 14:41:13 PDT 2009


Hi Satya, 

 

I have uploaded the file that you sent and can take care of removing the 2
previous versions. 

 

Trish

 

 

From: Satya Sahoo [mailto:satya_sanket at hotmail.com] 
Sent: Monday, August 03, 2009 2:15 PM
To: whetzel at stanford.edu
Subject: RE: [bioontology-support] Feedback Parasite Experiment ontology

 

Hi Trish,
You are correct, we made a mistake, "cell_culture_agent" is a instance value
of a deleted class. 

I am not sure why an instance value with "rdf:Description" element tag was
interpreted by both Protege 3.4.1 (Build 537) and BioPortal as a class -
which uses "owl:Class" element tag. I checked this using the new Protege 4.0
(build 113), it did not show "cell_culture_agent" as a class.

How do we delete the two "versions" of the Parasite Experiment ontology
(Ontology Id:1335) currently listed on BioPortal? Once these incorrect files
are deleted, we can upload the correct OWL file. 

I have also attached the correct OWL file for Parasite Experiment ontology
with this mail.

Thank you for your help in resolving this issue.

With Best Regards,
Satya

> CC: support at bioontology.org
> From: whetzel at stanford.edu
> To: satyasahoo at ieee.org
> Subject: Re: [bioontology-support] Feedback
> Date: Mon, 3 Aug 2009 09:54:28 -0700
> 
> Hi Satya,
> 
> In the OWL file, the information that I see for this term is:
> <rdf:Description rdf:ID="cell_culture_agent">
> <rdfs:comment rdf:datatype="http://www.w3.org/2001/ 
> XMLSchema#string"
> >A cell_culture_agent is and machine, instrument, or device that 
> is responsible for maintaining samples.</rdfs:comment>
> </rdf:Description>
> 
> Is this intended to be a class? In Protege 3.4.1 (Build 537), the 
> first level of the hierarchy is displayed as in BioPortal.
> 
> Trish
> 
> 
> On Jul 27, 2009, at 2:01 PM, admin at bioontology.org wrote:
> 
> > Name : satya sahoo
> >
> > Email : satyasahoo at ieee.org
> >
> > Comment:
> > Parasite Experiment Ontology
> >
> > We submitted the parasite experiment ontology to NCBO today 
> > (07/27/09). We uploaded the OWL file 
> > (ParasiteExperimentOntology.owl) as part of the submission process.
> >
> > We noticed that "Visualize" tool is not parsing the file correctly - 
> > the concept "cell_culture_agent" is displayed as a top-level class 
> > along with "process", "data", and "agent".
> >
> > This is incorrect and does not match with the concept hierarchy 
> > displayed in Protege-OWL editor, version 3.3.1 (Build 430), which 
> > correctly lists "process", "data" and "agent" as the three top level 
> > concepts.
> >
> > We tried to replace the OWL file by re-uploading the file, but it is 
> > now listed as "new version" of the ontology. Hence, please clarify/ 
> > help:
> > 1. Why the "Visualize" shows the incorrect concept hierarchy?
> > 2. How to delete the one of the two ontology versions?
> >
> > Thank you.
> >
> > With Regards,
> > Satya
> > _______________________________________________
> > bioontology-support mailing list
> > bioontology-support at lists.stanford.edu
> > https://mailman.stanford.edu/mailman/listinfo/bioontology-support
> 

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