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Re: Good news from the EBI Semantic Web Industry Workshop and LODD members

From: RebholzSchuhmann <d.rebholz.schuhmann@gmail.com>
Date: Thu, 26 May 2011 08:08:51 +0100
Message-ID: <4DDDFC83.7040100@gmail.com>
To: LeeH <leeharland@gmail.com>
CC: Erick Antezana <erick.antezana@gmail.com>, "M. Scott Marshall" <mscottmarshall@gmail.com>, HCLS <public-semweb-lifesci@w3.org>

this looks pretty comprehensive.

Below is the list of speakers:

    * *M. Scott Marshall* (The W3C consortium). Where is the W3C now and
      what should happen next?
    * *Phil Brooks* (Eli Lilly), Semantic Web for Health Care and Life
      Sciences <http://videolectures.net/iswc08_prudhommeaux_swhcls/>
    * *Lee Harland *(Pfizer) Industry needs
    * *Derek Scuffell *(Syngenta) Opportunities and minimum requirements
      for industry
    * *Phil Ashworth *(UCB) Industrial Strength Architectures for life
      sciences, including considerations for federated search.
    * *Don Jennings* (Eli Lilly) Experience of TopBraid, Integrating
      semantic access to data within Lilly and building linked data maps
    * *Laurent Alquier* (J&J) Intranet data integration using Semantic
    * *Nicolas Le Novère* (EMBL-EBI), the Importance of Semantics to
      Systems Biology
    * *Dietrich Rebholz-Schuhmann* (EMBL-EBI) Practical experiences from
      the SESL (Semantic Enhancement of the Scientific Literature) project.
    * *Jerven Bolleman* (SIB) Quality control using sparql and UniProt rdf
    * *Jeremy Frey* (U. Southampton) Practical applications of semantic
      web technology in Chemistry.
    * *Dean Allemang* Examples of best practice from industry
    * *Michel Dumontier* (Carleton University) Bio2RDF
    * *Matthias Samwald,* (Medical University of Vienna), title TBC

=> 50 Attendees sounds right.
=> There has been some room for break-out sessions and the definition of 
business needs / challenges
=> The workshop serves as one source of input to define the EBI's stand 
on Semantic Web technology (past, present, future)
=> The IP workshop was followed by a two-day tutorial on Linked Data / 
Ontologies / Semantic resources (Slides will be available soon)

Concerning Scott's email: there are a couple of resources (Triple 
Stores) under development at the EBI, which are or will be available as 
public resources and which distribute data of different kinds:
* SPARQL endpoints (UniProt, SESL, possibly ChEMBL)
* Triple Stores for download:
*** UniProt
*** SESL: Diabetes driven data integration, incl. ArrayExpress, UniProt, 
publisher data, in preparation
*** CALBC: several 100k Medline abstracts with a large number of 
annotations, genes/proteins, diseases, chemical entities, species, all 
about immunology

Stay tuned,

On 25/05/2011 11:57, LeeH wrote:
> I didnt see these questions get answered so...
> - The workshop was organised by me (Lee Harland, Pfizer), Derek 
> Scuffle (Syngenta), Dominc Clark & Nicolas Le Novere.
> - There were about 50 people there, mostly industry and some invited 
> speakers & some EBI
> - For those who dont know it, the EBI industry programme is a 
> subscription-based group that provides a mechanism for life science 
> industry to work directly with the EBI on strategy and addressing 
> needs. The workshop was part of a large series of workshops we run on 
> many different topics relevant to industry (google ebi industry 
> programme for more info). The aim of this was to allow industry to 
> chat about its experience with SW in an informal setting, away from 
> the pressure of big conferences, and to explore areas of collaboration 
> with the EBI
> - There were no biotech representatives there; the EBI also runs an 
> SME forum which provides a similar mechanism for EBI & biotech to get 
> together. I dont know much more than this, but if interested Dominic 
> Clark is your man.
> - Access to the presentations. I was going to speak to dominic about 
> this next week. Generally presentations are stored in a secure 
> website, which allows presenters (especially from companies) to be 
> sure their materials are not generally distributed. However, i think 
> many presenters whould be OK with this, so we will see what we can do...
> - Finally, is this related to the Pistoia alliance.... The direct 
> answer is no. The EBI industry programme is a completely separate 
> entity and this was purely based on that. However, a significant 
> number of folks who are active in Pistoia (such as me) have also 
> worked long term with the EBI. the EBI is also a member of Pistoia 
> too. So, i think the best thing to say is that "there are great 
> connections between the 2 groups". Also the EBI is the lead on the 
> Pistoia SESL project (semantic enrichement of the scientific 
> literature - more details are available to those interested), so there 
> are firm connections between ebi & pistoia in the semantic area
> I think that answers all the questions I've seen.... Happy to talk to 
> anyone about thoughts/opportunities etc. Within Pistoia we're actively 
> discussing where the semantic web fits, to that end there's an 
> interesting meeting coming up
> http://www.pistoiaalliance.org/2011-Events/6-june-2011-pistoia-alliance-technical-committee-open-teleconference-and-webinar.html
> Lee
> On 25 May 2011 09:17, Erick Antezana <erick.antezana@gmail.com 
> <mailto:erick.antezana@gmail.com>> wrote:
>     are the presentations/program somewhere available?
>     was there any representative of a biotech company attending such
>     workshop?
>     is it somehow related to the Pistoia Alliance?
>     cheers,
>     Erick
>     On 25 May 2011 00:56, M. Scott Marshall <mscottmarshall@gmail.com
>     <mailto:mscottmarshall@gmail.com>> wrote:
>     > Last week, Michel Dumontier, Matthias Samwald and I were invited to
>     > speak at the EBI Semantic Web Industry Workshop. We each gave some
>     > HCLS perspectives and heard many other very interesting talks from
>     > industry representatives. Phil Brooks (Johnson & Johnson) gave an
>     > excellent tutorial. TopBraid Composer was widely touted. A few
>     > encouraging news items: Nicolas Le Novere told us that MIRIAM
>     > identifiers will go to URIs (from URNs) and Jerven Bolleman told us
>     > that Uniprot is getting a SPARQL endpoint for their RDF. There was a
>     > strong pharma presence at the workshop.
>     >
>     > Also, on the LODD front:
>     >
>     > * Oktie Hassanzadeh has created a linkedct (linked version of
>     > clinicaltrials.gov <http://clinicaltrials.gov/>) that is updated
>     nightly
>     > * Anja Jentzsch is working on an update of several Berlin-hosted
>     LODD data sets
>     > * Egon Willighagen is updating the downloadable RDF version of
>     ChEMBL
>     > to version 9
>     >
>     > Cheers,
>     > Scott
>     >
>     > --
>     > M. Scott Marshall, W3C HCLS IG co-chair, http://www.w3.org/blog/hcls
>     > http://staff.science.uva.nl/~marshall
>     <http://staff.science.uva.nl/%7Emarshall>
>     >
>     >

Dietrich Rebholz-Schuhmann, MD, PhD - Research Group Leader
EBI, Wellcome Trust Genome Campus, Hinxton CB10 1SD (UK)
  - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
TM support:www.ebi.ac.uk/Rebholz-svr | tm-support@ebi.ac.uk
Received on Thursday, 26 May 2011 07:09:35 UTC

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