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Re: Parkinson's Disease use-case

From: Eric Miller <em@w3.org>
Date: Mon, 13 Mar 2006 08:47:19 -0500
Message-Id: <861F2888-C9A5-4D6B-BC86-B5252AEA0DA2@w3.org>
Cc: Eric Neumann <eneumann@alum.mit.edu>, public-semweb-lifesci@w3.org
To: Brian Osborne <osborne1@optonline.net>


On Mar 10, 2006, at 2:57 PM, Brian Osborne wrote:

> Eric M.,
>
> I'm looking at the Piggy Bank scrapers at
> http://potlach.org/2005/10/scrapers/, I think we want to create an
> additional one that uses the results of an NCBI eutils query, the  
> PubMed one
> is not well suited for the "Gene Neural related gene data" and  
> "Protein
> Neural related protein data" tasks.

As is, no. but the original idea was to extract subject, gene, and  
protien information associated with each article. the scraper is set  
up to do this (in the sense of spidering off the document page and  
calling off to other constructed URIs), but I haven't filled in the  
blanks yet.

> I can provide the field-to-field mapping, XML to Uniprot RDF, and I  
> believe
> I know what the eutils query is. Shall we proceed with this or did  
> you have
> something else in mind?

Go for it! :) I can then update the scraper then to reflect your  
results, use your namespaces, etc. so we can have at least 2  
independent implementations of this.

pls use the wiki to keep track of this work so others can follow along.

--e


>
> Brian O.
>
>
>
> On 3/8/06 9:08 AM, "Eric Miller" <em@w3.org> wrote:
>
>>
>>
>> On Mar 6, 2006, at 2:36 PM, Eric Neumann wrote:
>>
>>>
>>> I have added a Parkinson's Disease (PD) information aggregation use-
>>> case on the wiki site:
>>>
>>> http://esw.w3.org/topic/ParkinsonsDisease
>>>
>>> Currently it has disease related information on implicated genes,
>>> causes, treatments, inheritance, and pathways. It eventually is to
>>> serve as a resource for one possible scientific scenario that
>>> effectively utilizes RDF structured data (and eventually
>>> ontologies) in support of neuroscience research.
>>
>> Excellent example! Use cases like this are extremely helpful in
>> putting the various tasks in an important context. In particular,
>> I've related the Parkinsons use case to the following Task...
>>
>> Create RDF to describe entries in NCBI database
>> - http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/Tasks/
>> Gene_Neural_related_gene_data
>>
>> I'd appreciates thoughts on additional tasks that would be useful in
>> addressing this use case.
>>
>> Note: I recommend that tasks list people who are interested in
>> working on the particular problem.
>>
>>> Additional scientific scenarios are very much welcomed!
>>
>> agreed!
>>
>> --
>> eric miller                              http://www.w3.org/people/em/
>> semantic web activity lead               http://www.w3.org/2001/sw/
>> w3c world wide web consortium            http://www.w3.org/
>>
>>
>>
>
>
Received on Monday, 13 March 2006 13:47:27 UTC

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