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Re: URIs for NCBI data

From: William Bug <William.Bug@DrexelMed.edu>
Date: Mon, 26 Feb 2007 12:09:21 -0500
Message-Id: <652CE189-6B58-42E9-9CB4-B4D99CF7858E@DrexelMed.edu>
Cc: W3C HCLSIG hcls <public-semweb-lifesci@w3.org>, Olivier Bodenreider <olivier@nlm.nih.gov>
To: "Eric Neumann" <eneumann@teranode.com>
This is great.  Thanks, EricN.

Do we know if the tentative consideration Olivier had mentioned a  
while back they were giving to doing this with the UMLS Semantic  
Network would be a part of this effort?

Cheers,
Bill

On Feb 26, 2007, at 9:56 AM, Eric Neumann wrote:

>
> FYI...
>
> -----Original Message-----
> From: Kwan, Kathy (NIH/NLM/NCBI) [E] [mailto:kwan@ncbi.nlm.nih.gov]
> 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.  When it is done, outside people could use
> them to as URI to point to our resources.   I'll keep you posted as  
> the
> project gets closer to production.
>
> Thank you for your interest in NCBI resources.
>
> Kathy
>
>
>
>
> ________________________________
>
>         From: Eric Neumann [mailto:eneumann@teranode.com]
>         Sent: Saturday, February 17, 2007 12:40 PM
>         To: Kwan, Kathy (NIH/NLM/NCBI) [E]
>         Subject: RE: URIs for NCBI data
>
>
>
>         Kathy,
>
>         Yes, we are leaning towards a URL "http" identifier, thus
> requiring no additional urn (lsid) resolution mechanism.
>
>         Regarding the use of #, it is usually used to describe "the
> entity" (on the right side) within a RDF doc (or database). This is  
> not
> a necessity, since a slash can always be used instead, and the request
> re-routed to a database.
>
>         Something like
> http://www.ncbi.nlm.nih.gov/2006/entrez/<DATABASE_GOES_HERE>/ 
> <IDENTIFIER
> _GOES_HERE>  would work fine!
>
>         Eric
>
>         -----Original Message-----
>         From: Kwan, Kathy (NIH/NLM/NCBI) [E]
> [mailto:kwan@ncbi.nlm.nih.gov]
>         Sent: Fri 2/16/2007 4:36 PM
>         To: Eric Neumann
>         Cc: Kwan, Kathy (NIH/NLM/NCBI) [E]
>         Subject: RE: URIs for NCBI data
>
>         Hi Eric,
>
>         Hi Eric,
>
>         Just a couple of questions, is the URI that your group
> considering
>         mainly URL, right?  If yes, is there a reason behind it?
>
>         Also, is the example that you gave:
>
> http://www.ncbi.nlm.nih.gov/2006/entrez/ 
> <DATABASE_GOES_HERE>#<IDENTIFIER
>         _GOES_HERE
>         arbituary, or there is a reason behind using "#" to separate
> database
>         and identifier?
>
>         TIA,
>
>         Kathy
>
>         -----Original Message-----
>         From: Eric Neumann [mailto:eneumann@teranode.com]
>         Sent: Monday, January 29, 2007 1:29 PM
>         To: Kwan, Kathy (NIH/NLM/NCBI) [E]
>         Subject: URIs for NCBI data
>
>
>         Kathy,
>
>         Last year HCLSIG had a discussion on how best to define  
> URIs for
> life
>         science data that would work with current data providers.
> Discussion
>         have progressed, and more notes have been created regarding
> authority
>         web identifiers for life science data entities (e.g.,
> entrez-gene, etc).
>         Here's one such note describing how to define asn used  
> metadata:
>         http://www.w3.org/2001/tag/doc/metaDataInURI-31.html
>
>         I am not sure if you are still interested in this topic,  
> but our
>         upcoming demos hope to capitalize on URI's for data from  
> centers
> such as
>         NCBI. To this end it would be useful to try and see if a
> straightforward
>         and easy to maintain URI scheme could be considered by  
> NCBI, so
> that we
>         would not have to create 'dummy' URIs for Entrez that might
> accumulate
>         lots of links and annotations.
>
>         Basically, we would only need to agree on a stable space  
> for the
> data in
>         consideration (e.g.,
>
> http://www.ncbi.nlm.nih.gov/2006/entrez/ 
> <DATABASE_GOES_HERE>#<IDENTIFIER
>         _GOES_HERE>)-- it would not need to resolve to anything (like
> RDF or
>         XML) at this point.
>
>         If you have questions or need more information, I'd be  
> happy to
> help
>         out, or even organize a discussion with interested HCLSIG
> members.
>
>         best,
>         Eric
>
>         Eric Neumann, PhD
>         co-chair, W3C Healthcare and Life Sciences
>         +1 (781)856-9132
>
>
>
>
>
>

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
Received on Monday, 26 February 2007 17:09:42 GMT

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