: Thursday, February 11, 2010 8:00 PM
To: Matthias Samwald
Cc: public-semweb-lifesci
Subject: Re: URIs for UMLS
May be a related question, for gene information, should be use entrez
gene id or umls id (cui)?
Cheers,
-Kei
Matthias Samwald wrote:
> Sorry for asking such a seemingly sim
May be a related question, for gene information, should be use entrez
gene id or umls id (cui)?
Cheers,
-Kei
Matthias Samwald wrote:
Sorry for asking such a seemingly simple question. Establishing URIs
for UMLS entities has now been discussed for years. What is the
current status of this de
> From: Eric Neumann [mailto:[EMAIL PROTECTED]
> To: Kwan, Kathy (NIH/NLM/NCBI) [E]
>
> Kathy,
>
> Yes, we are leaning towards a URL "http"
> identifier, thus requiring no additional urn (lsid)
> resolution mechanism.
Great! And as a reminder, if a resource owner al
Message-
From: Kwan, Kathy (NIH/NLM/NCBI) [E] [mailto:[EMAIL PROTECTED]
Sent: Thu 2/22/2007 6:18 PM
To: Eric Neumann
Cc: Kwan, Kathy (NIH/NLM/NCBI) [E]
Subject: RE: URIs for NCBI data
Hi Eric,
We had some intial discussions and plan to work on a stable/usable URL
scheme for our resources
I would like to add that I happen to think that Barry Smith's work on
mereotopology [1], the information flow framework [2] based on the work
of Barwise et al., and even the obscure works of Zippie Gonczarowski [3]
all warrant consideration in light of interest in the category-theoretic
appro
Oops - I forgot to add...
Again - in this area, I think the TMRM work Jack Park has mentioned
may turn out to be extremely useful. Several folks have already
begun to look for ways to bridge that formalism with RDF. He makes
some mention of this in early posts and had some additional ins
Another fantastic citation worth it's weight in gold and definitely
relevant to the long-term goal here of creating an algorithmic means
to express - and then operate on - biomedical knowledge! Many
thanks, Bob. I've already passed on your "hedging" reference to
several other colleagues
Hi Xiaoshu--
Xiaoshu Wang wrote:
Frank,
This isn't to deny the usefulness of being able to dereference a
URI and get something useful (or to be able to find the RDF or OWL
describing a vocabulary when you're trying to process statements
employing that vocabulary). I'm merely pointing out tha
I would suggest that both natural language *and* ontologies are views
of (possibly shallow) underlying knowledge. This knowledge is
difficult to characterize. It is also difficult to achieve agreement
on it within or across communities.
I find the following study sobering. Don't be misled by t
Here is a link to the message I sent out last year regarding handling
URNs in concatenated URL forms:
http://lists.w3.org/Archives/Public/public-semweb-lifesci/2005Apr/0010
This approach only works if it is explicitly agreed that URN's need to
be accompanied by a handler URL. As stated by ot
Hi All,
First, I'd like to recommend two articles I believe are very relevant
to this discussion and may help provide us a clearer sense of how to
proceed here:
1) X. Wang, Robert Gorlitsky, and Jonas S Almeida, From XML to RDF:
how semantic web technologies will change the design of 'o
Frank,
> This isn't to deny the usefulness of being able to
> dereference a URI and get something useful (or to be able to
> find the RDF or OWL describing a vocabulary when you're
> trying to process statements employing that vocabulary). I'm
> merely pointing out that RDF and OWL were del
A couple of comments:
1. The "processing model" of RDF isn't "ambiguous", it is
*unspecified*; that is, no processing model is specified, and that is
deliberate. RDF doesn't define if and when a URI should be
dereferenced from an RDF model because RDF doesn't assume URIs identify
things
Alan,
> > URI http://www.example.com/gene;
> >
> > You need to dereference the "gene" variable in order to
> understand it
> > and do something meaningful about it.
>
> That's one way. You can also publish a paper that describes
> it, get a bunch of people agree to use it the same way,
> sup
On Jun 19, 2006, at 9:49 AM, Xiaoshu Wang wrote:
URI http://www.example.com/gene;
You need to dereference the "gene" variable in order to understand
it and do
something meaningful about it.
That's one way. You can also publish a paper that describes it, get a
bunch of people agree to u
half Of William Bug
> Sent: Monday, June 19, 2006 8:20 AM
> To: John Madden
> Cc: Alan Ruttenberg; w3c semweb hcls
> Subject: Re: [rdf] Re: URIs
>
>
>
> I think this is an excellent reference to work from, when dealing
> with the issue of URIs in RDF generation &
Alan,
> Dereference, in that context, means something different than
> what I was using the term for.
> They mean that there has to be a definition of the subject
> and object in the OWL file or one of the imports.
>
> I was using it to mean, go to the network and do a geturl of
> the uri and
I think this is an excellent reference to work from, when dealing
with the issue of URIs in RDF generation & processing.
As I have always seen it (this is admittedly a the view of an RDF
naif), DOIs and LSIDs both seek to fulfill the role one would expect
to be played by URIs in the STM l
[Nicolas Novere comments on part of a recent proposal for BioPAX to
be presented tomorrow: http://mumble.net/~alanr/cshl/URICV.htm]
On Jun 19, 2006, at 5:45 AM, Nicolas Le Novere wrote:
Regarding this problem, we should team-up because we already did
it. We bumped into the same problems for
It's probably worth noting (for the purpose of this thread) that there is
a recently created ESW Wiki on the mechanics / best practices of Dereferencing URIs:
http://esw.w3.org/topic/DereferenceURI
Chimezie Ogbuji
Lead Systems Analyst
Thoracic and Cardiovascular Surgery
Cleveland Clinic Found
I would just want to chime in and endorse what others have said -
that this is an EXTREMELY important issue to provide some clarity on
for the community.
Many folks in neuroinformatics, for instance, are interested in
knowing more about the practical issues involved in moving toward an
Alan,
I find myself continually groping for the requirements. Could you
provide a specific example of what you want to do with the URI in RDF,
i.e. a specific piece of RDF with a specific gene? It might help us to
frame the discussion (if you still have time!).
It seems like what we'd all l
Dereference, in that context, means something different than what I
was using the term for.
They mean that there has to be a definition of the subject and object
in the OWL file or one of the imports.
I was using it to mean, go to the network and do a geturl of the uri
and do something wi
Hi, Alan,
This is an important topic and I think it should be an action item in one of
our task groups.
This is my two cents about the topic.
> 1) The relationship between the use of a URI in a
> representation and what it dereferences to, if anything. The
> possibilities seem to be:
>
>
hi alan,
> On the matter of what a URI dereferences to, I think it is more
> important to get the names in place quickly.
I agree. I think we are all ready to start on the demo. Nonetheless, getting
the names in place quickly does not mean they cannot dereference. According
to:
http://www.w3.org
Alan et al,
Wow, great topic. I'll need to get my thoughts together on this.
Meanwhile, operationally what a uri "means" is clearly related to the
question of its (non)persistence. I recently found a wonderful
historical review of this topic from the point of view of a library
scientist.
[It was on this list: http://lists.w3.org/Archives/Public/public-
semweb-lifesci/2006Jun/0149]
-Alan'
On Jun 18, 2006, at 12:20 PM, John Madden wrote:
I can't locate the beginning of this thread. Did the discussion
start on another list?
Thanks.
John
On Jun 17, 2006, at 1708, Eric Neuman
I can't locate the beginning of this thread. Did the discussion start
on another list?
Thanks.
John
On Jun 17, 2006, at 1708, Eric Neumann wrote:
This is a very useful and important discussion thread, and I would
like to see others on the list to contribute their thoughts/
concerns as
Eric Neumann <[EMAIL PROTECTED]> wrote on
06/17/2006 12:33:25 PM:
> May I ask all the contributors to include HTML links to any acronyms
> they reference (e.g., NAPTR)? This will make it easier for the rest
of
> us to catch up quickly, and to eventually collect the approaches out
> there into
This is a very useful and important discussion thread, and I would like
to see others on the list to contribute their thoughts/concerns as
well.
May I ask all the contributors to include HTML links to any acronyms
they reference (e.g., NAPTR)? This will make it easier for the rest of
us to
MW>
MW> I believe this SRV-redirection behaviour is part of the LSID spec,
and
MW> we use it for all of the BioMOBY LSIDs...
MW>
It also uses NAPTR's as described in IETF RFC's 3401->3405
to traverse the URN namespace, allowing the dereferencing process to bridge
the gap that separates authorit
On Fri, 2006-06-16 at 10:41 -0400, Alan Ruttenberg wrote:
> something, but as far as I can see, the only authority related to
> namespaces in URLs is the DNS, and while there is the SRV field which
> might be used to direct someone to information about the namespace, I
> don't know whether
Hi Tony,
Thanks for the clarification. I took a closer look at the spec and have
come comments:
- Normalization. Upon review of rfc 2396, prompted by reading the
normalization rules, it strikes me that all of these are problematic
because they require scheme dependent logic for comparin
Hi Alan,
AR> b) The URI is used primarily as
a name. Insofar as we want use
AR> names, it is important there be some stable URIs. Of course it
AR> doesn't hurt if the URI becomes dereferenceable at some point, and
it
AR> would even be nice,
AR> d) Any URL we use needs to be
able to
Hi Alan:
Just to clarify one point re INFO. You say:
>a) The identifier is not intended to be dereferencable. In that
> case the info: scheme was suggested for the form of the uri, as that
> is explicitly not dereferenceable.
This is not actually quite true - but represents an earlier posit
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