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.
- Answers to questions about BioPortal Daniel Rubin
- Re: Answers to questions about BioPortal dirk . colaert
- Re: Answers to questions about BioPortal Mark Wilkinson
- Re: Answers to questions about BioPortal Chimezie Ogbuji
- Re: Answers to questions about BioPorta... Alan Ruttenberg
- Re: Answers to questions about Bio... kc28
- Re: Answers to questions about... Trish Whetzel
- RE: Answers to questions a... Kashyap, Vipul
- RE: Answers to questions a... Nigam Haresh Shah
- Versioning vs Temporal mod... Kashyap, Vipul
- Re: Versioning vs Temporal... Chimezie Ogbuji