Re: BioPortal

Let me emphasize that this is a pre-release version on the Web site.   
There will be lots of changes between now and February 1.

The system handles versioning very well, and you will be able to go  
back and review older versions in addition to the most current  
posting.  There is planned support for a variety of features that  
will be of particular interest, including alignment with other  
ontologies, support for additional metadata and annotations, and  
advanced visualization capabilities.

Mark


On Jan 9, 2007, at 8:02 AM, helen.chen@agfa.com wrote:

>
> Hi, Mark
>
> Thanks so much for your suggestion.
>
> Like Alan, I also registered as a user and had a very quick look at  
> the portal.  I agree with Alan's observation and his concern on the  
> copy right and the site's support for its availability and svn  
> services.
>
> I tried to submit a new ontology just to see how it works.  I  
> followed the 4 steps, and finally got an error "An unhandled  
> exception has occurred - Could not save metadata for ontology".  I  
> assume this is due to some temporary unavailability of this  
> service, or missing some information implicitly requested by the  
> submission process.
>
> I assume that I will be able to make some modifications to my  
> ontology or an updated version if needed.
>
> Kind regards.
>
> Helen
>
>
>
>
>
>
>
>
> Mark Musen <musen@stanford.edu>
> 01/09/2007 10:22 AM
>
> To
> Alan Ruttenberg <alanruttenberg@gmail.com>
> cc
> Helen Chen/AMPJB/AGFA@AGFA, "Eric Prud'hommeaux" <eric@w3.org>, w3c  
> semweb hcls <public-semweb-lifesci@w3.org>
> Subject
> Re: BioPortal
>
>
>
>
>
>
> On Jan 9, 2007, at 6:43 AM, Alan Ruttenberg wrote:
> > 1) 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 © 2005–2006, The Board of Trustees of
> > Leland Stanford Junior University. All rights reserved.", which I
> > would guess some would consider unacceptable.
>
> That certainly was not our intention, Alan, but I will take another
> look at our boilerplate.
>
>
> >
> > 2) 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.
>
> Good point.
>
>
> >
> > 3) Disclaimer: "... PROVIDED ON AN "AS IS" AND "AS AVAILABLE"
> > BASIS...". 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.
> >
>
> Point well taken.
>
>
> > 4) Use of ontologies: "Only the submitter of the ontology will be
> > able to modify it or submit new versions". 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.
> >
>
> We'll add this as a new requirement.  We need to be more clear about
> who "the submitter" is.
>
>
>
> > 5) 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?
> >
>
> Currently, BioPortal is meant to be used as a repository only.
> Future releases may have more support of broader development  
> activities.
>
> We are still in a pre-release mode until Feb 1, and these comments
> are extremely valuable to us.  As the workof the HCLS SIG is
> precisely the kind of activity that we have a mandate to support, we
> very much want to work with you to make our resource work for you.
> Your feedback has already been very helpful.
>
> Mark
>
>