HCLSIG/LODD/Meetings/2010-02-03 Conference Call

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Conference Details

  • Date of Call: Wednesday February 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 - Anja, Jun, Matthias, Egon
  • Mapping to drugs/intervention - Oktie
  • Mapping experimental data - All
  • Outreach (TCM, Bio-Ontologies SIG, ACS, AMIA) - All
  • AOB

Minutes

Attendees: Matthias, Kei, Oktie, Joanne, Egon, Jun

  • Data Updates
  • <OktieH> http://linkeddata.cs.toronto.edu/linkedfda
  • <Susie> Oktie: Linked FDA data is already ready
  • <Susie> Oktie: Can talk about it more during the next call
  • <Susie> Susie: Having your colleague present sounds good
  • <Susie> Egon: Egon did a schema walk through on ChEMBL
  • <Susie> Egon: Looking at protein classification scheme
  • <Susie> Egon: Struggling to make it available in a useful way
  • <Susie> Egon: Looking at indexing schemes
  • <Susie> Egon: Lots of data
  • <Susie> Egon: Activities is over 1GB in RDF/XML, over 2GB in total
  • <egonw> Egon: chembl sparql end point: http://pele.farmbio.uu.se/chembl/sparql/
  • <jun> This might be helpful for you:

http://www.openlinksw.com/dataspace/dav/wiki/Main/VirtBulkRDFLoaderExampleMultiple

  • <jun> Egon: I have loaded more than 1GB RDF triples to Virtuoso
  • <Susie> Egon: Interesting as links proteins to assays
  • <egonw> Egon: ChEMBL links: protein, assay, activity, molecule
  • <egonw> Egon: and all to DOIs
  • <Susie> Matthias: Matthias has written to data providers
  • <Susie> Matthias: But they didn't reply and provide access to data
  • <Susie> Matthias: So rather short of data relating to chinese data
  • <Susie> Matthias: Nice data sources exist but are not available to integrate
  • <Susie> Matthias: Focus paper on structured data, mined data and TCM
  • <egonw> jun: I have been looking at this page for the indexing: http://docs.openlinksw.com/virtuoso/rdfperformancetuning.html#rdfperfgeneraldbpedia
  • <Susie> Matthias: Although there isn't new data to add to the collection, thinking about how to combine in the best
  • <Susie> Matthias: Very interested in how best to present the data
  • <Susie> Kei: wonder if papers provide supplementary dat asets that you can use
  • <Susie> Matthias: Old school, so no supplementary data
  • <Susie> Kei: Wikipedia/DBpedia has broad classification of herbs that could be useful
  • <Susie> Kei: Another source that could be useful for inferring could be the NCI taxonomy
  • <Susie> Matthias: Plan to focus on small set of plant species that appear promising
  • <Susie> Matthias: Present aggregated way so that the researcher can look at the data and make inferences in their mind
  • <Susie> Matthias: Goal is for researchers to get insights more quickly by looking at the aggregated paper rather than by reading the papers
  • <matthias_samwald> http://less.aksw.org/browse
  • <Susie> Matthias: Looked at this templating language, where looking at simple views from linked data or results from sparql query
  • <Susie> Matthias: Looks nice but might be too limited for our purposes
  • <matthias_samwald> http://sig.ma/
  • <Susie> Matthias: Also looked at Sigma
  • <Susie> Matthias: It allows nicely formatted mashup of data for a certain query
  • <egonw> matthias_samwald: looks interesting...
  • <matthias_samwald> http://samwald.info/antidepressant-effects-of-magnolia-officinalis-aggregated-linked-data/
  • <egonw> matthias_samwald: is it free, or open source?
  • <Susie> Matthias: Contains data from Jun's TCM data set and DBpedia
  • <Susie> Matthias: Limited for our use case
  • <Susie> Matthias: As want to view data that spans many triples at once
  • <Susie> Matthias: While Sigma more focused on showing a particular triple
  • <Susie> Matthias: So not always helpful
  • Mapping Experimental Data
  • <Susie> Susie: Approach for understanding best approaches for mapping linked data
  • <Susie> Susie: Create a doc with questions
  • <Susie> Susie: And then begin to fill in with solutions
  • <Susie> Susie: Can then discuss what would make best practices
  • <jluciano> Joanne: who decides what the answer is? Is there more than one answer (for different interperations of the data)?
  • <Susie> Susie: ADNI is an example of such data
  • <Susie> Susie Contains information about patients, cognitive scores, brain scans, CSF data, etc.
  • <Susie> Susie: What are best practices for mapping data about a patient, on a particular visit, having an MRI, that is of 1.5T, where hippocampal volume is measured, and a number derived using a particular image analysis approach
  • Outreach
  • <Susie> Matthias: TCM Paper
  • <Susie> Matthias: Deadline extended to mid-Feb
  • <Susie> Matthias: Going to Japan this w/e for the biohackathon
  • <Susie> Matthias: So time becomes limited
  • <egonw> Egon: cool :) heard good stories about that meeting
  • <Susie> Matthias: Aiming to get it finished this w/e
  • <Susie> BioOntologies SIG
  • <Susie> http://sites.google.com/site/bioontologies/
  • <Susie> Susie: Deadline is April 16.
  • <Susie> Egon: CFP for the linked data workshop at ACS went out
  • <egonw> http://chem-bla-ics.blogspot.com/2010/01/semantic-chemistry-with-resource.html
  • <Susie> Egon: March 28 deadline for submissions
  • <Susie> Egon: May be half or full day depending on numbers of submissions
  • <Susie> Egon: Meeting is in August in Boston
  • <Susie> Egon: Looking for anything related to chemistry
  • <Susie> Egon: ACS covers biochemistry under chemistry too
  • <Susie> Egon: Have a student working on substructure mining
  • <Susie> Egon: Just ChEMBL isn't enough for a paper
  • <Susie> Egon: Just need to submit an abstract for consideration for a talk
  • <Susie> Talks may be written up as papers for publication in a journal
  • <Susie> Protein structures or small molecules will need to be a focus
  • <egonw> Egon: let me stress, I'd love to see a HCLS submission... but being organized, someone else need to bootstrap that
  • <egonw> Egon: umm... but being organizeR..
  • <egonw> Egon: for ACS :)