HCLSIG/LODD/Meetings/2010-03-03 Conference Call
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
- Data updates - All
- FDA terms - Oktie & colleague
- Mapping experimental data - Susie
- Outreach (TCM, Bio-Ontologies SIG, W3C LOD Track, ACS) - All
- AOB
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 :(