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Re: BioRDF Telcon

From: Marc-Alexandre Nolin <lotus@ieee.org>
Date: Tue, 19 Jun 2007 19:21:59 -0400
Message-ID: <d6a9bb0d0706191621g359766ddt47bd35481e469eda@mail.gmail.com>
To: "Jonathan Rees" <jonathan.rees@gmail.com>
Cc: public-semweb-lifesci@w3.org


In fact, it is not a complete new wiki on this discussions. In this
conversation, Kei Cheung give a URL about the Banff Manifesto. The
problem is, this document is not up to date anymore and since I'm not
aware of a functionalities for anybody to add comments on a Google
documents, we transfert it into a wiki. My email was a correction URL
about the URL given by Kei previously.

I can put a copy of it on the W3C wiki if you want, I don't see any
problem with this. I put it in my wiki because it is revelant to the
documentation of the Bio2RDF.org system wich use those rules to work
(We had to take decision about how we will normalize the URI we had or
else we would not have a working system by now). This wiki is the
documentation and the "how to use" the Bio2RDF.org system. Some people
at the HCLS workshop ask for it and it's why we are providing it (also
for us, because it help structure our work).

As for the comments you ask of me on the already existing document
about URI that you provide in you email:
I was at the informal discussion on URI in Banff animated by Eric N.
I'm all for a common decision about how to write URIs. In this
discussion (and also in the link you provide), I've seen that the
proposal to use Purl to get the caracteristics about how to write a
specific URI for a specific namespaces might be interesting, except
for the load we may put on the Purl server. In the end, the proposal
in the manifesto isn't really far from this, except that it is a
distributed way of doing this. Just a set of simple rule to apply and
the URI will connect. Purl could distributed the set of rule to write
every URI for specific namespaces. This way, a developer would go
there, read the rules, implement it in his system and  now his data
can connect with other program develop with those rules. The load on
Purl will be minimal, only developer and data manager will go there to
know the set of rules for URI for the data, not the millions of URI
request generated by every query on the life sciences space.
I'm for an HTTP resolvable URI, any browser or for that mather any
perl, ruby, Java script can resolve a HTTP link. I'm not convince yet
about the usefulness of pure LSID, it became useful if it is a use in
a URL like http://purl.org/urn:lsid:uniprot.org:uniprot:p26838 because
automatically I don't have to be stuck with a plugins in a specific
browser or using some LSID resolver on a server somewhere
Also, and not completely related to the current discussion, I've read
about going to concept in one of the pages you've link in your
precedent email. I also think we should go there for URI. As much has
we would like to call uniprot:p19367 a concept, it is still a database
number from the database uniprot. The real concept would be
protein:Hexokinase. This is what the searcher would be looking for.
The concept would then link to any database talking about it. For an
idea about this, look for Hexokinase in Wikipedia
http://en.wikipedia.org/wiki/Hexokinase , see in the right panel every
reference to other database talking about it, not just Uniprot. With
dbpedia http://dbpedia.org rdfizing Wikipedia, this could be very

Sorry for the long reply, but you ask for comments :)


2007/6/19, Jonathan Rees <jonathan.rees@gmail.com>:
> I hate to see the number of wikis used for this purpose multiply.
> There's already some discussion in the ESW wiki, e.g.
> http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/Tasks/URI_Best_Practices
> and http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/Tasks/URI_Best_Practices/Work_Plan,
> and in the neurocommons wiki,
> http://wiki.neurocommons.org/CommonNaming.
> Are you avoiding the ESW wiki because it's so slow? That was one of my
> reasons for using the neurocommons wiki for this job; I've regularly
> been seeing up to 60 seconds for basic operations such as 'edit' and
> 'save'. Eric P is looking into this. If it can't be fixed, I think
> we'll have to choose a different location.
> As for a "base of discussion", I think we already have too many of
> those. The trick is to relate new writings to old ones, or to update
> old ones to make them better, and that's what we need a wiki for.
> Before I comment on your "manifesto", may I ask if you have any
> comments on the URI practices work plan for which I requested
> feedback? Or is it your preference to set up a parallel effort?
> Jonathan
> On 6/19/07, Marc-Alexandre Nolin <lotus@ieee.org> wrote:
> >
> > Hi,
> >
> > About this Banff Manifesto, me and Francois Belleau wanted to give a
> > base of discussion with this text. The purpose of it, is to give some
> > simple rule where, when you followed them, URI will connect together
> > without having the added work to rewrite every URI before using them.
> >
> > For everybody to be able to place comment on it, the last version is
> > in a wiki at
> > http://bio2rdf.org/JSPWiki/Wiki.jsp?page=BanffManifesto
> >
> > In this same wiki, we are currently making a follow up of the article
> > we present in Banff and explaining every normalization and decision we
> > took about URI for our system to work. We welcome every comments.
> >
> > Marc-Alexandre Nolin
> >
> > 2007/6/18, Kei Cheung <kei.cheung@yale.edu>:
> > >
> > > Hi Jonathan et al.,
> > >
> > > Eric may add to it, but I just want to describe briefly what I know. At
> > > the Banff HCLS-DI Workshop
> > > (http://neuroweb.med.yale.edu/hcls/Welcome.htm), a number of authors had
> > > presented their work involving their own URI convention/format. As a
> > > result, there was a proposal called "Banff Manifesto"
> > > (http://docs.google.com/View?docid=ddm4nhwq_41cpz6kq). There was a
> > > follow-up meeting at Banff right after the HCLS demo that Eric and
> > > others might be able to tell people more about it (I wasn't at the
> > > follow-up meeting).
> > >
> > > Best,
> > >
> > > -Kei
> > >
> > > Jonathan Rees wrote:
> > > >
> > > >
> > > > On 6/11/07, *Eric Neumann* <eneumann@teranode.com
> > > > <mailto:eneumann@teranode.com>> wrote:
> > > >
> > > >
> > > >     +1 !
> > > >
> > > >     I've also added a reference to the Banff discussion on URI's. I
> > > >     plan to put this also on the agenda for the next HCLSIG TC (June 21).
> > > >
> > > >     -Eric
> > > >
> > > >
> > > >
> > > > Thanks, but for the benefit of those of us who weren't at this
> > > > dicussion in Banff, could you summarize what transpired, or  give a
> > > > link to minutes?
> > > >
> > >
> > >
> > >
> > >
> >
> >
Received on Tuesday, 19 June 2007 23:22:09 UTC

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