Re: Answers to questions about BioPortal

Hi,

Are we talking about versioning at a very high granularity level (e.g., 
a URI that points to an entire ontology)? Should we also consider 
versioning at finer granularity levels such as the levels of concepts or 
terms and their relationships within an ontology? Some of these 
concepts, terms and their relationships may evolve over time. We many 
need a versioning scheme for these. I think some of these finer 
granularity versioning examples can be found in the UMLS (Unified 
Medical Language System). At the instance level, we may need versioning 
as well. Also, the semantics of versioning may be unclear sometimes. For 
example, two different SNPs (Single Necleotide Polymorphisms) that were 
submitted to dbSNP may refer to the same location in the genome. Do we 
say they are two different versions of the same SNP? There may not be a 
standard notion/definition of versioning for biomedical entities.

Just my two-cent thought,

-Kei

 Alan Ruttenberg wrote:

>
> I guess  what I'm trolling for is some more careful description of  
> the desired behavior. Some examples would be helpful, etc.
> My feeling is the technical management of how to arrange a uri/lsid  
> is much easier than specifying and agreeing upon what the versioning  
> behavior should be.
>
> For instance, BioPAX took the strategy of using a different namespace  
> for each of its versions. That cleanly separates which version you  
> are referring to. Too cleanly - people who want to integrate data  
> from the two versions now need to think too hard about how to do that.
>
> -Alan
>
> On Jan 10, 2007, at 12:23 PM, Chimezie Ogbuji wrote:
>
>>
>> Well, (not to open up a can of worms) ontology versioning can be  
>> handled as a mechanism 'built-in' to the protocol (as is the case  
>> with LSID) or via an HTTP resolution service (such as PURL).  I'm  
>> more familiar with the latter scenario than the former.  Assuming  
>> you have a static PURL address for the ontology you can specify  
>> which version the request is redirected to.
>>
>> This is similar to the way W3C spec URLs work (from what I gather).  
>> There is usually a 'latest' link (which is always static) which  
>> redirects the a location specific to the current 'version'.  I  think 
>> this is a good model to follow for managing ontology  locations (per 
>> version).
>>
>>
>> On Wed, 10 Jan 2007, 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.
>>>
>>>
>>>
>>>
>>> -- 
>>> Using Opera's revolutionary e-mail client: http://www.opera.com/mail/
>>>
>>
>> Chimezie Ogbuji
>> Lead Systems Analyst
>> Thoracic and Cardiovascular Surgery
>> Cleveland Clinic Foundation
>> 9500 Euclid Avenue/ W26
>> Cleveland, Ohio 44195
>> Office: (216)444-8593
>> ogbujic@ccf.org
>>
>
>

Received on Thursday, 11 January 2007 02:21:37 UTC