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Re: Answers to questions about BioPortal

From: Tim Clark <twclark@nmr.mgh.harvard.edu>
Date: Wed, 10 Jan 2007 20:32:21 -0500
Message-Id: <D4BF8F27-9148-4982-AB13-4AD77F87684A@nmr.mgh.harvard.edu>
Cc: dirk.colaert@agfa.com, rubin@med.stanford.edu, "w3c semweb hcls" <public-semweb-lifesci@w3.org>, public-semweb-lifesci-request@w3.org
To: Mark Wilkinson <markw@illuminae.com>

LSID not dirty. LSID nice.  :-)


On WednesdayJan 10, 2007, at 11:19 AM, Mark Wilkinson wrote:

> Hmmmm... sounds like a job for LSID's...  oops! Said a dirty  
> word!  ;-)
> Cheers all!
> M
> On Tue, 09 Jan 2007 23:53:49 -0800, <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 Thursday, 11 January 2007 01:38:56 UTC

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