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RE: Answers to questions about BioPortal

From: Kashyap, Vipul <VKASHYAP1@PARTNERS.ORG>
Date: Wed, 17 Jan 2007 10:55:53 -0500
Message-ID: <2BF18EC866AF0448816CDB62ADF6538105EAF1BD@PHSXMB11.partners.org>
To: "Daniel Rubin" <rubin@med.stanford.edu>, <dirk.colaert@agfa.com>
Cc: "w3c semweb hcls" <public-semweb-lifesci@w3.org>
Daniel,

 

Thanks for the news. ICD and SNOMED are the two biggies used in healthcare and
this would a very useful services.

Hopefully, you have got an exhaustive set of "wish lists/requirements" from
various communities.

 

Was wondering if you are planning to make the requirements and/or spec open to
the public?

This would be valuable to both the HCLS and other W3C communities!

 

Best regards,

 

---Vipul

 

=======================================

Vipul Kashyap, Ph.D.

Senior Medical Informatician

Clinical Informatics R&D, Partners HealthCare System

Phone: (781)416-9254

Cell: (617)943-7120

http://www.partners.org/cird/AboutUs.asp?cBox=Staff&stAb=vik

 

To keep up you need the right answers; to get ahead you need the right questions

---John Browning and Spencer Reiss, Wired 6.04.95

________________________________

From: public-semweb-lifesci-request@w3.org
[mailto:public-semweb-lifesci-request@w3.org] On Behalf Of Daniel Rubin
Sent: Wednesday, January 17, 2007 10:26 AM
To: dirk.colaert@agfa.com
Cc: w3c semweb hcls; public-semweb-lifesci-request@w3.org
Subject: Re: Answers to questions about BioPortal

 

We will be adding terminologies such as ICD and SNOMED into BioPortal and
creating URIs for all terms in all terminologies/ontologies. Those URIs will
also probably contain the version info for the terminology so that new
terminology releases do not invalidate older URIs. Would that work from
everyone's perspective, or are there other requirements (for example, I could
imagine it would be nice is there were another layer that permitted people to
refer to a URI that pointed to the current version of a term, though it could be
quite a bit of work to provide that service).
Daniel


___



Daniel Rubin, MD, MS
Clinical Asst. Professor, Radiology
Research Scientist, Stanford Medical Informatics
Scientific Director, National Center of Biomedical Ontology
MSOB X-215
Stanford, CA 94305
650-725-5693


At 02:03 AM 1/17/2007, dirk.colaert@agfa.com wrote:

	I don't know if any commercial clinical system is rteally using URI's
right now, but I think this will come. If an URI is the ultiimate and unique way
of pointing to a resource then future systems should use URI's to 'codify'
diagnoses for example in stead of storing a local code in the data base.
Currently many systems store the combination of a coding system (ICD, SNOMED) +
the specific code + a locally deployed repository. However, conceptually this is
the same of pointing to the SNOMED or ICD URI in the SNOMED/URI ontology
residing at some site. 
	
	By the way also by using codesystem/code combinations you have the
versioning problem. "Code System" is also holding version info. 
	______________________________________
	Dr. Dirk Colaert MD
	Advanced Clinical Application Research Manager
	Agfa Healthcare               mobile: +32 497 470 871 
	
	
	Daniel Rubin <rubin@med.stanford.edu> 
	
	11/01/2007 04:43 

	To

	Dirk Colaert/AMIPU/AGFA@AGFA 

	cc

	"w3c semweb hcls" <public-semweb-lifesci@w3.org>,
public-semweb-lifesci-request@w3.org 

	Subject

	Re: Answers to questions about BioPortal 
	
	
	
	
	
	This is a very good.point; permanent URIs is a reasonable requirement we
will aim to provide. Though I am intrigued with your use case about clinical
systems referring to a URI. Are you aware of any commercial system that is
contemplating referring to entities on the semantic Web via URI? We'd certainly
be interested in catalyzing commercial efforts use these technologies
effectively, and it would be particularly nice if we could get these systems
using public knowledge sources such as terminologies instead of embedding them
in the code...
	BTW--if there are other requirements for BioPortal, it would be good to
elicit them now.
	Daniel
	
	At 11:53 PM 1/9/2007, dirk.colaert@agfa.com wrote:
	
	One comment on versioning issues (question2) . The matter is more
complex than the answer suggests. If a clinical system ever refers to a URI in
BioPortal this URI should stay forever. Even if a new version of the ontology is
deployed the original URI should still point to the old term or concept, even if
it is deprecated. So versioning is more than a development or collaboration
issue. I don't know wether the answer given to question 3 solves this. 
	
	______________________________________
	Dr. Dirk Colaert MD
	Advanced Clinical Application Research Manager
	Agfa Healthcare               mobile: +32 497 470 871 
	
	
	Daniel Rubin <rubin@med.stanford.edu> 
	Sent by: public-semweb-lifesci-request@w3.org 
	
	10/01/2007 01:46 

	
	To

	
	"w3c semweb hcls" <public-semweb-lifesci@w3.org> 

	
	cc
	Subject

	
	Answers to questions about BioPortal 
	
	
	
	
	
	Dear HCLSIG users,
	
	We have received a number of questions/comments from you for our
BioPortal sneak preview. Please continue to provide comments/suggestions as this
will help us to ensure BioPortal meets the community needs. We have collected
the following recent feedback from several different members of this list, and
would like to summarize our responses to them below to clarify some of the
recent questions:
	
	1. Looking at the interface, it is not clear to me how best to reference
an element of the ontologies there-- is there a URI mechanism that can be used
directly by outside researchers? How does
	this relate to the DOID # (i.e., namespaces)?
	
	Yes, a URI mechanism will be made available soon. Ontologies will have
their own namespaces defined by the authors, or if none is provided, we will
create one based on our bioontology.org namespace.
	
	2. Also, can you provide more details on how the BioPortal will provide
versioning? Last I understood, there were no SVN capabilities with the BioPortal
- has that changed or did I misunderstand the set-up?
	
	It is important to understand that BioPortal is a Web application that
accesses an ontology library, and that it is not a content management system
(such as cvs and subversion). BioPortal stores the released versions of
ontologies and indexes their content.  For ontology development, the authors use
their preferred local systems (local cvs, svn, sourceforge, or gforge). When
they create a new version that is ready to be released publicly, it is submitted
directly to BioPortal by the author. In some cases, we may be able to set up URL
pull into BioPortal on a regular basis.
	
	3. Will there be a general way to identify deprecated terms in the
ontologies posted in BioPortal, how does LexGrid handle this information?
	
	Yes, and LexGrid provides this functionality. 
	
	4. Are you [Mark Musen] the person to request updates of information
currently displayed on the site?
	
	You can contact Daniel Rubin.
	
	5. The terms of service says: "Except as expressly prohibited on the
Site, you are permitted to view, copy, print and distribute publications and
documents within this Site, subject to your agreement that:... You will display
the below copyright notice and other proprietary notices on every copy you make"
I read this as saying that anything submitted to the repository would be
copyright "Copyright (c) 2005-2006, The Board of
	Trustees of Leland Stanford Junior University. All rights reserved.",
which I would guess some would consider unacceptable.
	
	This is not the intended interpretation and we will change the wording
of the terms.
	
	6. Termination of Use: "You agree that The National Center for
Biomedical Ontology may, in its sole discretion, at any time terminate your
access to the Site and any account(s) you may have in connection
	with the Site. Access to the Site may be monitored by The National
Center for Biomedical Ontology."  This is scary. There ought to be explicit
cause for termination, otherwise people might be reluctant to entrust their work
to the site.
	
	We will modify the terms to declare the conditions that would be a cause
for termination.
	
	7. Disclaimer: "... PROVIDED ON AN "AS IS" AND "AS AVAILABLE" BASIS...
".  (B The W3C has taken steps to ensure that access to the files hosted at the
W3C domain will be maintained under a variety of circumstances, using mirrors,
externals services, etc. It would be desirable that similar actions be taken by
the NCBO, and some mention of them included in the terms of service,
particularly if URIs in the bioontology.org namespace are to be used.
	
	NCBO sites are hosted by Stanford Information Technology Services, the
same people who host the Stanford Hospital clinical database and Highwire Press.
We anticipate having reliable availability of the services we provide.
	
	8. Use of ontologies: "Only the submitter of the ontology will be able
to modify it or submit new versions".  B In a project such as ours that is group
oriented, it is likely that individuals will come and go. I think there needs to
be some notion of group access so that we aren't vulnerable to a key individual
becoming unavailable.
	
	Yes, we are planning on adding group access.
	
	9. It wasn't clear to me whether there was developer support e.g. svn
access. I don't know whether Helen et. all had in mind using such services at
W3C, but such access is certainly part of the development cycle of projects such
as ours. Is the model that ontology developers use external sites for this and
only submit relatively stable versions of the ontology to the BioPortal?
	
	Correct. The model is that ontology developers use external resources
such as sourceforge or their own local cvs for internal development, and they
submit stable release versions of their ontologies to the BioPortal. 
	
	
	-BiPortal Team. 





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Received on Wednesday, 17 January 2007 15:57:51 UTC

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