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Re: BioPortal

From: <helen.chen@agfa.com>
Date: Tue, 9 Jan 2007 11:02:03 -0500
To: musen@stanford.edu
Cc: Alan Ruttenberg <alanruttenberg@gmail.com>, "Eric Prud'hommeaux" <eric@w3.org>, w3c semweb hcls <public-semweb-lifesci@w3.org>
Message-ID: <OF3FBE3467.0034CB07-ON8525725E.00568AB6-8525725E.005817B6@agfa.com>
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.



Mark Musen <musen@stanford.edu> 
01/09/2007 10:22 AM

Alan Ruttenberg <alanruttenberg@gmail.com>
Helen Chen/AMPJB/AGFA@AGFA, "Eric Prud'hommeaux" <eric@w3.org>, w3c semweb 
hcls <public-semweb-lifesci@w3.org>
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.

Received on Tuesday, 9 January 2007 16:02:38 UTC

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