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Re: BioRDF call -- update about aTags, text extraction

From: Kei Cheung <kei.cheung@yale.edu>
Date: Mon, 08 Jun 2009 10:35:33 -0400
To: Matthias Samwald <samwald@gmx.at>
Cc: HCLS <public-semweb-lifesci@w3.org>
Message-id: <4A2D21B5.5030807@yale.edu>
Thanks for the update, Matthias.

Cheers,

-Kei

Matthias Samwald wrote:
> I cannot join the call today, so let me summarize recent progress here:
>
> *Extending the Science Commons Text Annotation Service with support 
> for additional entities and aTag output format*
> aTags can now be generated automatically from Pubmed abstracts and 
> result sets of Pubmed queries. I extended the Science Commons Text 
> annotation service (http://whatizit.neurocommons.org) service, which 
> uses the 'Whatizit' entity recogntion web service [1] provided by the 
> Rebholz group at EBI. These extensions are NOT available on the public 
> website yet (sorry), but I will make them available online in the next 
> 2-3 days.
>  
> Sentences in Pubmed abstracts that contain one or more named entities 
> are annotated with embedded RDFa, following the aTag convention. You 
> can use this service to create RDF/OWL statements based on Pubmed. Of 
> course, entities are identified with URIs from OBO and "linked data" 
> resources. This can be a simple entry point for creating RDF/OWL 
> information for arbitrary Pubmed queries.
>  
> Currently, the service recognizes entities from Gene Ontology, ChEBI, 
> some smaller OBO ontologies, Uniprot and NCBI Taxonomy. Potentially it 
> could also link to Drug Bank and to a disease ontology, but this is 
> made a bit difficult because of the types of identifiers returned by 
> the original EBI web service. For example, the EBI service uses the 
> secondary DrugBank identifiers to identify drugs, while the Linked 
> Data version of DrugBank [2] uses the primary DrugBank identifiers to 
> create URIs for database records -- therefore, I cannot currently use 
> the EBI service to easily generate annotations with DrugBank URIs. I 
> will look into solving this issue.  Furthermore, I will also update 
> the service when new URI schemes are available (new OBO URIs; URIs 
> minted by the Shared Names initiative). Support for caching is also on 
> my todo list.
>  
> *Ligand-receptor interaction data now available in aTag format*
> ** 
> I have created a conversion of (part of) the PDSK Ki database of 
> ligand-receptor interactions into aTag format. It uses identifiers 
> from NeuronDB and ChEBI for tagging. Another version that uses DBpedia 
> identifiers is planned.
>  
> Ligand-receptor interaction aTags, collected in a single HTML file, 
> you can extract the RDF with a RDFa/GRDDL parser of your choice:
> http://hcls.deri.org/atag/data/kidb_atags.html
>  
> RDF in Turtle format, extacted from this HTML page:
> http://hcls.deri.org/atag/data/kidb_atags_jun_2009.ttl
>  
> The Ki value is a measure of how strong ligand and receptor interact, 
> smaller numbers mean stronger interaction.
>  
> Further information:
> http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/aTags/datasets
>  
> *HCLS KB at DERI*
> We got a new server for the HCLS KB at DERI (with 6 separate hard 
> drives, which should improve query performance considerably). I will 
> also upgrade the HCLS KB from Virtuoso 5 to Virtuoso 6, which should 
> also bring performance improvements. The only problem at the moment 
> is finding the time to do the server migration...
>  
> Cheers,
> Matthias Samwald
>  
> [1] http://www.ebi.ac.uk/webservices/whatizit/
> [2] http://www4.wiwiss.fu-berlin.de/drugbank/
>  
>  
>  
>
>
>
> --------------------------------------------------
> From: "Kei Cheung" <kei.cheung@yale.edu>
> Sent: Saturday, June 06, 2009 1:48 AM
> To: "HCLS" <public-semweb-lifesci@w3.org>
> Subject: BioRDF call
>
> > This is a reminder that the next BioRDF teleconf. will be held at 11 am
> > EDT (5 pm CET) on Monday, June 8 (see details below).
> >
> > Cheers,
> >
> > -Kei
> >
> > == Conference Details ==
> > * Date of Call: Monday June 8, 2009
> > * Time of Call: 11:00 am Eastern Time
> > * Dial-In #: +1.617.761.6200 (Cambridge, MA)
> > * Dial-In #: +33.4.89.06.34.99 (Nice, France)
> > * Dial-In #: +44.117.370.6152 (Bristol, UK)
> > * Participant Access Code: 4257 ("HCLS")
> > * IRC Channel: irc.w3.org port 6665 channel #hcls (see
> > [http://www.w3.org/Project/IRC/ W3C IRC page] for details, or see
> > [http://cgi.w3.org/member-bin/irc/irc.cgi Web IRC])
> > * Duration: ~1 hour
> > * Frequency: bi-weekly
> > * Convener: Kei Cheung
> >
> > == Agenda ==
> > * Provenance/workflow presentation (Satya)
> > * HCLS KB update (Matthias, Adrian)
> > * Image data (Rob)
> > * SPARQL control access (Eric, Helena)
> > * Shared name -- pathway use case (Eric, Scott, Helena)
> > * AIDA (Scott)
> > * TCM data (Jun)
> > * aTag (Matthias)
> >
Received on Monday, 8 June 2009 14:36:12 GMT

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