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Re: [BioRDF] All about the LSID URI/URN

From: Eric Neumann <eneumann@teranode.com>
Date: Sun, 30 Jul 2006 14:07:04 -0400
To: "public-semweb-lifesci hcls" <public-semweb-lifesci@w3.org>
Message-ID: <8B57BC2C-0380-40B6-AD92-AEF365B3B571@teranode.com>

I am very pleased to see the enthusiastic discussion wrt LSIDs/URIs.  
I am also encouraged by the sense of urgency many of you are feeling,  
since I think this is a very important set of issues that need to be  
addressed AND resolved, in order for any advancement of a scientific  
research web to succeed. Indeed, Resource Identification is one of  
HCLS's stated objectives [1]. But to be clear, I do not see it as a  
confrontation of one form over the other, and even would hope to see  
(if possible) a coexistence that is both functional AND does not lead  
to confusion.

I would like to ensure everyone, that the upcoming BioRDF call--  
though a critical step for framing the relevant issues-- will not be  
the definitive discussion of LSID's/URI's. This can only happen when  
all the necessary issues are fully presented and discussed by the  
engaged community. That being said, it is our intent to have that  
definitive discussion at the next planned F2F meeting Oct 3-4 in  
Amsterdam, and I strongly recommend that all parties who view this  
issue as being important should plan to attend the F2F meeting.

 From what I have been able to gather from the discussions so far,  
there is still incomplete clarity on several points, and these will  
require more work over the coming months. I list here a few, not to  
force the conf call's agenda, but merely as a guide to keep in the  
back of our minds:

1. When are/must URI's (be) resolvable ?
2. What are the best transport mechanisms for different kinds/volumes  
of data ?
3. What best practice(s) does this community need around incomplete  
data graphs ?
4. Would global indexing of all references to a URI in annotations  
and other predicates be necessary ?
5. Will life sciences require a large amount of metadata caching per  
URI in order to support semantc web use in general ?
6. How important is knowing type of a URI before de-referencing it ?
7. WRT the semantic web, is there a clear distinction between  
Metadata and Data (as it relates to the LSID specs of mutability) ?
8. Is there a fundamental difference between data-record of Gene, and  
an agreed unique Gene symbol standard (e.g., Unigene), and how should  
the two be related ?
9. Can healthcare and life sciences work with semantic web data as  
large, flat graphs, or do we need to support hypotheses and local  
curations as reified graphs (ala NamedGraphs or something similar) ?
10. When we begin to develop, publish, and apply rules to bio-chem or  
medical objects, will the rules require stable identifiers, and will  
the rules be considered part of the URI graph ?

There is still a lot of work to be done, but my hope is that we will  
have some form of deliverable on best practices down before the end  
of 2006. I plan to be on monday's call as well...

cheers,
Eric

[1] - http://www.w3.org/2001/sw/hcls/charter#Scope , Guidelines and  
Best Practices for Resource Identification


Eric Neumann, PhD
co-chair, W3C Healthcare and Life Sciences,
and Senior Director Product Strategy
Teranode Corporation
83 South King Street, Suite 800
Seattle, WA 98104
+1 (781)856-9132
www.teranode.com

--- kc28 <kei.cheung@yale.edu> wrote:

Hi All,

I second Tim's suggestions. This is a really community effort to move
this important SW component forward.

Best,

-Kei

Tim Clark wrote:

 > Hi All,
 >
 > I think Susie is performing a valuable service which we all respect
 > and which may help to advance the discussion.  HOWEVER...
 >
 > ...  I STRONGLY RECOMMEND that no-one consider the Bio-RDF call
Monday
 > as anything else than a very preliminary discussion FOR INITIAL
 > EDUCATIONAL PURPOSES ONLY, which needs to be followed up by much more
 > in-depth and authoritative discussions on LSID and other identifier
 > schemes.
 >
 > I am certain that Susie never intended the Monday call to be anything
 > else than that, i.e. a preliminary educational discussion.
 >
 > I recommend that we in HCLS work, after the conclusion of ISMB, to
 > prepare a more inclusive and authoritative discussion on this topic,
 > with all the key players involved.  We ought to aim to leverage ALL
 > the good work people have done in this area, LSID in
 > particular.  Discussions on this topic that do not include - in a
 > well-organized way - some of the key contributors to the practice of
 > bioinformatics and semantic web,  have to be considered
 > non-authoritative and therefore not a basis for making important
 > decisions.
 >
 > Again, I am very sure Susie would share this opinion.  This is just a
 > caution to people around the W3C but from outside bioinformatics --
 > who may not realize how much serious work on distributed identifiers
 > has been done by people who cannot participate in Monday's call --
and
 > whom we very much need to consult.
 >
 > Best
 >
 > Tim
 >
 >
------------------------------------------------------------------------ 
------
 > Tim Clark
 >
 > Director of Research Programs
 > Harvard University Initiative in Innovative Computing
 > 60 Oxford Street, Cambridge, MA 02138
 > http://iic.harvard.edu
 >
------------------------------------------------------------------------ 
------
 >
 >
 >
 > On SaturdayJul 29, 2006, at 9:25 AM, William Bug wrote:
 >
 >> Hi All,
 >>
 >> I would also give a strong DITTO to the leadership Susie is
providing
 >> on this extremely important issue.  Getting clarification on the
pros
 >> & cons is essential to catalyzing broader adoption of SWTech.
 >>
 >> I would also add I'm extremely grateful to ALL the experts who've
 >> been presenting clear arguments and information related to this
 >> issue.  It's all been extremely valuable.  Susie is working very
hard
 >> to collate this information and provide this as a resource to the
 >> community.  As Alan mentioned, this will remain an ongoing and
 >> critical debate, and it will be of value to us all to help provide a
 >> clearing house for documentation related to to this issue on the
 >> BioRDF Wiki pages.
 >>
 >> The group of people listening in on this debate here on this list
are
 >> a self-selected population of technically astute folks with
 >> implementation of SWTech on their minds - and probably on their
 >> immediate list of TODOs, if not already on their list of previous
 >> achievements.  Most will be very knowledgeable of the general
 >> technical issues and will be likely to dig into the details
presented
 >> on both sides of the argument.   I have found all the details
 >> extremely illuminating - especially the thorough background and
 >> references provided by Sean and the specifics given regarding the
 >> debates the TAG has had on this issue.
 >>
 >> I think I can assure Carole no one here would be likely to take the
 >> achievements of those who've implemented LSID-based systems - and
ARK
 >> and the others - lightly - or those who might, would be doing
 >> themselves and the communities they represent a great disservice.
 >>
 >> I look forward to Monday and the follow-up discussions both on the
 >> list, in future TCons, and on the HCLSIG-BioRDF Wiki.
 >>
 >> Cheers,
 >> Bill
 >>
 >>
 >>
 >> On Jul 29, 2006, at 8:09 AM, jbarkley@nistgov
 >> <mailto:jbarkley@nist.gov> wrote:
 >>
 >>>
 >>>
 >>>> (who very much appreciates Susie's efforts to
 >>>> coordinate)
 >>>
 >>>
 >>> Ditto on that!
 >>>
 >>> jb
 >>>
 >>>
 >>>
 >>> Quoting Alan Ruttenberg <alanruttenberg@gmail.com
 >>> <mailto:alanruttenberg@gmail.com>>:
 >>>
 >>>>
 >>>> Susie shouldn't take any blame for this - The meeting is
 >>>> one in a
 >>>> series, is well announced, and would certainly have been
 >>>> rescheduled
 >>>> if, like,  anyone with an interest had bothered to
 >>>> request it with
 >>>> adequate advance notice.
 >>>>
 >>>> There's nothing particularly special about this meeting.
 >>>> If others with
 >>>> interest in the subject want a further meeting to discuss
 >>>> things then
 >>>> we should do that.
 >>>>
 >>>> Regards,
 >>>> Alan
 >>>>
 >>>> (who very much appreciates Susie's efforts to
 >>>> coordinate)
 >>>>
 >>>> On Jul 28, 2006, at 2:24 PM, Carole Goble wrote:
 >>>>
 >>>>> By the way I have already lodged an objection to Susie
 >>>>
 >>>> that to have
 >>>>
 >>>>> such a telecon when many people who actually, like, use
 >>>>
 >>>> the stuff for,
 >>>>
 >>>>> like, real are at ISMB2006 in Brazil and will not be
 >>>>
 >>>> able to
 >>>>
 >>>>> participate. Like Doh!
 >>>>>
 >>>>> Carole
 >>>>
 >>>>
 >>>>
 >>>>
 >>>
 >>>
 >>>
 >>
 >> Bill Bug
 >> Senior Research Analyst/Ontological Engineer
 >>
 >> Laboratory for Bioimaging  & Anatomical Informatics
 >> www.neuroterrain.org
 >> Department of Neurobiology & Anatomy
 >> Drexel University College of Medicine
 >> 2900 Queen Lane
 >> Philadelphia, PA    19129
 >> 215 991 8430 (ph)
 >> 610 457 0443 (mobile)
 >> 215 843 9367 (fax)
 >>
 >>
 >> Please Note: I now have a new email - William.Bug@DrexelMed.edu
 >> <mailto:William.Bug@DrexelMed.edu>
 >>
 >>
 >>
 >>
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 >>
 >



Eric Neumann, PhD
co-chair, W3C Healthcare and Life Sciences,
and Senior Director Product Strategy
Teranode Corporation
83 South King Street, Suite 800
Seattle, WA 98104
+1 (781)856-9132
www.teranode.com
Received on Sunday, 30 July 2006 18:07:22 GMT

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