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