Re: Answers to questions about BioPortal

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.