W3C home > Mailing lists > Public > public-semweb-lifesci@w3.org > January 2007

Re: Answers to questions about BioPortal

From: Mark Wilkinson <markw@illuminae.com>
Date: Wed, 10 Jan 2007 08:19:15 -0800
To: dirk.colaert@agfa.com, rubin@med.stanford.edu
Cc: "w3c semweb hcls" <public-semweb-lifesci@w3.org>, public-semweb-lifesci-request@w3.org
Message-ID: <op.tlx4ydp8nbznux@mini>

Hmmmm... sounds like a job for LSID's...  oops! Said a dirty word!  ;-)

Cheers all!


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 Wednesday, 10 January 2007 16:19:25 UTC

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