HCLSIG/Meetings/2009-08-06 Conference Call

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Conference Details

  • Date of Call: Thursday August 6, 2009
  • 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: Scott
  • Scribe: Scott

Agenda

Minutes

Attendees: Anja, Christi, Bosse, Julia, Kei, Matthias, Michel, Scott, Tim

Scott: Updates from task forces

Kei (BioRDF update): Collaboration with LODD task force, looking at how to link TCM data with drug data

<matthias_samwald> TCMGeneDIT

Kei: have converted CT.gov, TCM, TCMGeneDIT, to RDF ... Contacted Huajun Chen who agreed to give a presentation on TCM ontology work on Aug. 17 ... The microarray data federation use case is an extension of the receptor use case ... Looked at some example data and accompanying MAGE data to see how we can use it to link semantically related microarray experiments in the neuroscience context. ... Often people list a number of differentially expressed genes. The idea is to narrow down the list to genes relevant to certain disease conditions. ... Helen Parkinson of EBI recently expressed interest in collaborating in the microarray work of BioRDF. ... Looking forward to explore ways to connect data in ArrayExpress and gene expression atlas, with the microarray use case and possibly with the Scientific Discourse task force, where they have some experience with microarray data. ... MAGEML is in XML and we can look at how to convert it into RDF (extracting the semantics).

Scott: Do you mean things like extracting triples from ontological markup in MAGEML (such as with GRDDL)?

Kei: Yes.

Anja (LODD update): We've published a number of datasets as RDF (see URL's).

<AnjaJentzsch> DrugBank: http://www4.wiwiss.fu-berlin.de/drugbank/

<AnjaJentzsch> DailyMed: http://www4.wiwiss.fu-berlin.de/dailymed/

<AnjaJentzsch> Diseasome: http://www4.wiwiss.fu-berlin.de/diseasome/

<AnjaJentzsch> Clinical Trials: http://linkedct.org/

<AnjaJentzsch> RDF-TCM: http://code.google.com/p/junsbriefcase/wiki/TGDdataset

<AnjaJentzsch> Sider: http://www4.wiwiss.fu-berlin.de/sider/

<AnjaJentzsch> STITCH: http://www4.wiwiss.fu-berlin.de/stitch/

<AnjaJentzsch> Interlinking of the LODD Data Sets:

<AnjaJentzsch> 2009-07_lodd_interlinking_by_type.png

<AnjaJentzsch> LOD Cloud:

<AnjaJentzsch> lod-datasets_2009-07-14_colored.png

Anja: Have been mapping the schemas mostly by OWL equivalences and updating about once a month. ... There are about 1.5 million triples and links to external sources. ... Jun Zhao is working on linking in TCM data. Looking for hubs of genes that are related to diseases. Are converting sets of useful scientific questions to SPARQL queries. Submitting an entry to the Triplification Challenge: http://triplify.org/Challenge/2009 tomorrow.

<AnjaJentzsch> Silk: http://www4.wiwiss.fu-berlin.de/bizer/silk/

<AnjaJentzsch> Alternative Medicine Use Case:

<AnjaJentzsch> http://esw.w3.org/topic/HCLSIG/AlternativeMedicineUseCase/

<AnjaJentzsch> Application for finding information on herbs: http://www.open-biomed.org.uk/

<AnjaJentzsch> Top Questions: http://esw.w3.org/topic/HCLSIG/LODD/Questions

Anja: Matthias, would you tell a little about your work with aTags?

Matthias: Manually curated data related to TCM as aTags, turning statements found in articles into RDF triples.

Scott (question for Anja): How do you deal with aligning the different names across the different RDF data sets?

Anja: We maintain lists of schema mappings.

<matthias_samwald> SILK, yes.

Anja: We use SILK mapping language with rule sets, that allows one to define thresholds for mappings.

Scott: Is the mapping the main bottleneck for LODD?

<AnjaJentzsch> Maintaining Links Between Changing Linked Data Sources: http://www4.wiwiss.fu-berlin.de/bizer/silk/wodlmp/

Anja: Yes, but there are some other challenges such as data cleaning and once you've written the mapping rules, you usually don't need to adjust them too much.

<michel> ICBO - in Buffalo

<christi> Link to roles: http://esw.w3.org/topic/HCLSIG/PharmaOntology/Roles

Christi (TMO update): The PharmaOntology/Roles URL (above) lists some of the ontologies and interesting entities. ... Had some good contacts and info from DILS Manchester and ICBO in Buffalo.

Tim (Scientific Discourse update): Hoping to have a closing discussion on the SWAN/SIOC documents on the 14th. ... Looking forward to exploring some new ideas with David Shotton in a future call.

Scott (AOB): There will be a SWAT4LS (Semantic Web Applications and Tools for the Life Sciences) workshop in Amsterdam on Nov. 20. Relevant to HCLS participants.