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[bioontology-support] Uploading new version of the ECGOntology to rectify issue of linking to Full ID

Trish Whetzel whetzel at stanford.edu
Fri Feb 13 12:40:24 PST 2009


Thanks for the heads up. It looks like the previous problem of adding
multiple rows to the metadata table did not occur. 

 

Trish

 

 

From: Stephen Granite [mailto:sgranite at jhu.edu] 
Sent: Friday, February 13, 2009 7:26 AM
To: 'Trish Whetzel'
Cc: bioontology-support at lists.stanford.edu
Subject: Uploading new version of the ECGOntology to rectify issue of
linking to Full ID

 

Trish,

 

  Just wanted to give you a heads up that I'm going to put an updated OWL
file in via the NCBO BioPortal.  I'll try to keep tabs on precisely what I
do in case the multiple insert issue arises again.  As a precursor, I am
using Mozilla Firefox 3.0.6 and I am using the Submit New Version interface.

 

Stephen J. Granite, MS, MBA

Director of Database and Software Development 

Center for Cardiovascular Bioinformatics and Modeling 

Institute for Computational Medicine 

The Johns Hopkins University 

3400 North Charles Street 

Computational Science and Engineering Building 312 

Baltimore, MD 21218-2686

phone: 410-516-8849

fax: 410-516-5294

 

From: Trish Whetzel [mailto:whetzel at stanford.edu] 
Sent: Wednesday, February 11, 2009 7:53 PM
To: 'Stephen Granite'
Subject: RE: Automated ontology term capture

 

PS - BioPortal recently added the ontology Full ID field to the term Display
tab. A consequence of this is that the full URI for terms is displayed and
therefore the location of the OWL file is expected to be at the location
specified in this URI. 

 

For example, for the term PositiveElectrode
(http://bioportal.bioontology.org/visualize/39175/PositiveElectrode), the
Full Id is
http://www.cvrgrid.org/ECGOntology1229347266968.owl#PositiveElectrode and
therefore the ECG ontology is expected to be at
http://www.cvrgrid.org/ECGOntology1229347266968.owl.

 

Trish

 

 

From: Trish Whetzel [mailto:whetzel at stanford.edu] 
Sent: Wednesday, February 11, 2009 3:17 PM
To: 'Stephen Granite'
Cc: 'Raimond Winslow'; 'pnambal1 at jhu.edu'
Subject: RE: Automated ontology term capture

 

Hi Stephen,

 

I'll check-in with Rebecca and her team on these questions and get back to
you. Also, I was wondering if you were planning to use the Notes feature in
BioPortal to collect comments on the ontology and if so had any questions on
the process to incorporate that information back into the ECG ontology. 

 

Trish

 

 

From: Stephen Granite [mailto:sgranite at jhu.edu] 
Sent: Wednesday, February 11, 2009 2:19 PM
To: whetzel at stanford.edu
Cc: 'Raimond Winslow'; pnambal1 at jhu.edu
Subject: Automated ontology term capture

 

Trish,

 

  Hello again.  In our ECG Ontology development, we commencing the
integration of NCBO REST Resources calls into a Java program to become more
familiar with term/definition retrieval from NCBO.

 

  While looking up information on the REST tools, we came across information
on Ontology Development and Information Extraction (ODIE).  This would be a
useful tool for us to extend the ontology we have developed so far.  I see
from the website that a demo version is available.  I'm in the process of
installing it.  I also see that v1.0 is to become available this fall.
Where is the next release with respect to the software development life
cycle?  Are individuals desired for beta testing and feedback?  If so, could
we be put in contact with the development team?  Thanks, in advance, for
your help.

 

Stephen J. Granite, MS, MBA

Director of Database and Software Development 

Center for Cardiovascular Bioinformatics and Modeling 

Institute for Computational Medicine 

The Johns Hopkins University 

3400 North Charles Street 

Computational Science and Engineering Building 312 

Baltimore, MD 21218-2686

phone: 410-516-8849

fax: 410-516-5294

 

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