Use-case detail

Eric et al.,

Working on writing up some use cases. Chembank is a nice compound database
for demonstration purposes since it associates some fraction of its
compounds with MeSH Diseases terms (
http://chembank.broad.harvard.edu/chemistry/search/input/ontology.htm), it
refers to this ontology as Therapeutic Indication. They also use GO
Biological Process.

A year or so ago you could could access its pages by GET, now it looks like
it's doing a POST - is this a problem for our programmers? No description of
any API, as far as I can see.


Brian O.


On 3/13/06 8:47 AM, "Eric Miller" <em@w3.org> wrote:

> 
> 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 Wednesday, 15 March 2006 17:51:02 UTC