Re: Answers to questions about BioPortal

I added this requirement (URI for most current version) to the wiki  
since it is essential for the operation of the software we use. Be  
nice to have the chaining between versions as well.

-S

On Jan 17, 2007, at 7:26 AM, Daniel Rubin wrote:

> 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.