RE: Use-case detail

Thanks Brian,

I didn't see a 'browse the ontology/db' function. Do you
know if there is one?  I'd like to poke around a bit.

Joanne

> -----Original Message-----
> From: public-semweb-lifesci-request@w3.org 
> [mailto:public-semweb-lifesci-request@w3.org] On Behalf Of 
> Brian Osborne
> Sent: Wednesday, March 15, 2006 12:50 PM
> To: Eric Miller
> Cc: Eric Neumann; public-semweb-lifesci@w3.org
> Subject: 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/ontol
> ogy.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 18:03:12 UTC