HCLSIG/LODD/Meetings/2010-03-03 Conference Call

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Conference Details

  • Date of Call: Wednesday March 3, 2010
  • Time of Call: 11:00am Eastern Daylight Time (EDT), 16:00 British Summer Time (BST), 17:00 Central European Time (CET)
  • 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 W3C IRC page for details, or see Web IRC)
  • Duration: ~1h
  • Convener: Susie

Agenda

Minutes

Attendees: Michel, Oktie, Egon, Elgar, Bosse

Apologies: Scott, Kei

<michel> Data updates

<michel> Egon: installed virtuoso, placed on more powerful server

<michel> Egon: for ChEMBL data

<michel> Egon: can't easily link due to lack of smiles/inchi matching (?)

<michel> Egon: sources don't always have the proper stereochemistry

<michel> Egon: so might link through rdfs:seeAlso vs owl:sameAs

<michel> Egon: data needs curation

<michel> Oktie: please add link on the Wiki to ChEMBL

<michel> http://esw.w3.org/topic/HCLSIG/LODD/Data

<michel> http://bio2rdf.semanticscience.org:8012/describe/?url=http://bio2rdf.org/ndc_listing:224571

<egonw> ChEMBL rdf node available at: http://rdf.farmbio.uu.se/chembl/snorql/

<egonw> and SPARQL end point at: http://rdf.farmbio.uu.se/chembl/sparql/

<michel> http://chem2bio2rdf.org/

<michel> http://scimaps.org/flat/meeting/100304/

<OktieH> http://linkeddata.cs.toronto.edu/linkedfda

<michel> oktie: have a look at the data and comment on the quality of the data

<michel> oktie: re:linkage - need to work with anja

<michel> topic: inclusion/exclusion criterion

<michel> to follow up

<michel> topic: mapping of experimental data to RDF

<sstephen> http://esw.w3.org/topic/HCLSIG/LODD/Mapping_Experimental_Data

<michel> susie: multidimensional - many attributes

  • egonw added ChEMBL to the wiki page

<michel> susie: mappings to RDF look to map data so that it reflects real world

<michel> susie: how does the multidimensional data reflect the real world

<michel> susie: does it make sense to change the schema of the relational data

<michel> e.g. entity - quality - value

<michel> bosse: did susie do something while at lily

<michel> susie: not so much, but now are mapping alzheimers data to RDF

<michel> susie: using ontologies to annotate the data

<michel> susie: discussing challenges with releasing UK gov data - how to do this

<michel> susie: multi-dimensional vs multi-attribute

<michel> susie: attribute as information about

<michel> egon: thinks of experimental data as multi-dimensional - numeric

<michel> egon: metabolomics data; lc/gc-ms to proteomics/sequence data; make statistical models from this data

<michel> susie: need to specify e.g. 3 data sources, how to best represent

<michel> susie: optimal in terms of bringing data together across many different data sources

<michel> susie: how to map and link

<michel> susie: be ideally positioned to query

<michel> susie: to answer a specific question, or to pull data of interest; use that data of interest to then do some kind of data mining

<egonw> the project I worked on then: http://metware.org/

<michel> michel: exactly agree - i) answer specific question, ii) obtain all the information about something, iii) collect data for further analysis

<michel> susie: identify datasets of interest

<michel> topic: outreach

<michel> egon: ACS workshop march 28 deadline

<michel> michel: TMO paper to bioontologies

<michel> susie: future of collaboration in science workshop many submissions

  • egonw is looking at the ACS database, but does not see any submissions at all... I think I need to ask about permissions :(