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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, 29 Sep 2011 09:08:50 +0100
Message-ID: <4E842792.1020908@gmail.com>
To: Erick Antezana <erick.antezana@gmail.com>
CC: "M. Scott Marshall" <mscottmarshall@gmail.com>, HCLS <public-semweb-lifesci@w3.org>
Hi Erick,

not sure who else is interested in them. I will send them in a separate 
email.

     -drs-

> Hi Rebholz,
>
> are the slides you mentioned already available? if so, where can I find them?
>
> thanks,
> Erick
>
> On 26 May 2011 09:08, RebholzSchuhmann<d.rebholz.schuhmann@gmail.com>  wrote:
>> Hi,
>>
>> 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
>> (Tutorial)
>> 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 MediaWiki
>> 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,
>>      -drs-
>>
>>
>>
>> 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>  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>  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) 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
>>>
>>>
>>
>>
>>
>> --
>> 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, 29 September 2011 08:09:45 UTC

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