- From: Brian Osborne <osborne1@optonline.net>
- Date: Wed, 15 Mar 2006 13:12:03 -0500
- To: jluciano@predmed.com, public-semweb-lifesci@w3.org
Joanne, Yes. Select "by function" from the Find Small Molecules menu on the left. Select your ontology, then click on the tiny little magnifying glass icon next to the Term field. Brian O. On 3/15/06 1:02 PM, "Joanne Luciano" <jluciano@predmed.com> wrote: > > 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 18:12:39 UTC