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

Hi Dietrich,

Many people on this list would be curious about the contents of a
tutorial on "Linked Data / Ontologies / Semantic resources". I can
think of several who would be interested.. The relevance of the EBI
work to HCLS has already been demonstrated by your and James Malone's
engagement* with the BioRDF task force.

It would be great if you could put a link to the slides on the EBI web
page for your tutorial and send the link to the list.

Cheers,
Scott

* as well as: Helen Parkinson, Tomasz Adamusiak, Christoph
Grabmeuller, Camille Laibe, Nicolas Le Novere, and others from EBI.

On Thu, Sep 29, 2011 at 10:08 AM, RebholzSchuhmann
<d.rebholz.schuhmann@gmail.com> wrote:
> 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 08:38:45 UTC