HCLSIG/Meetings/2009-12-03 Conference Call

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Conference Details

  • Date of Call: Thursday December 3, 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 #: + (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), Quick Start: Use mibbit for IRC access.
  • Duration: ~1h
  • Convener: Scott, Susie
  • Scribe: TBD



Kei: (BioRDF) Looking at metadata especially in MAGE-TAB format. The metadata can be used to help users make sense of their data during analysis and link it together. ... there is a lot of microarray out there that could be integrated with Gene Ontology, pathways, and so forth.

Scott: I am very excited about these new developments bringing us closer to life scientists and their data.

Kei: Yes, there is a lot of promise and it will be interesting to see how this settles out.

Colin: I heard mention of MGED ontology. People at EBI are using EFO (Experimental Factor Ontology). Is Helen Parkinson involved in any of the work that you've just mentioned?

Kei: Yes, Helen has helped to look at ontological annotations of some microarray data sets, together with Maryann Martone to clean up neurological annotations for some ArrayExpress data sets.

Colin: It sounds like you're involving the microarray people from EBI, which is good.

Scott: Yes, we've been in contact with several people in the Brazma group as well as some in Helen's group such as Misha Kapushesky.

<egonw> sorry, I missed the last LODD call

<egonw> so cannot give update on that

Eric: (COI): Group just presented at the recent AMIA, still interest in access control

<egonw> LODD minutes of 11/25: http://esw.w3.org/topic/HCLSIG/LODD/Meetings/2009-11-25_Conference_Call

<colin> http://code.google.com/p/translationalmedicineontology

<colin> journal of biomedical informatics

Colin (TMO): We've actually started testing our ontology with use cases and using LODD data. Submitted to Journal of Biomedical Informatics

Colin: <describes sections of submitted paper>

Scott: What was the easiest and the hardest part of the work?

Colin: There was a variety of people with different angles and backgrounds which made it occasionally challenging to define requirements.

Scott: So, it seems that ontology was the hardest. ... What was the easiest? LODD testing?

Colin: Yes.

Scott: Where to now?

Colin: Soon..

Elgar: We have just scratched the surface. Will probably make some revisions when we are farther along.

Scott: Talked about recent EU FP7 grant proposal involving several from HCLS IG. Any other grant opportunities?

Kei: I've been thinking about submitting a proposal to NCBO as an R01 partner (biological application) for SenseLab. ... I'm hoping that such new grants will help to fund my W3 membership.

Scott: Can R01 grants involve foreign (EU) partners?

<egonw> but it helps to have US PIs...

<egonw> and since multiple PI NIH grant apps are still rare and new... a single US PI is prefered

<egonw> and liked the meeting *very* *much*


<egonw> my SWAT4LS presentation is available at: http://chem-bla-ics.blogspot.com/2009/11/swat4ls-linking-open-drug-data-to.html


<ericP> http://www.w3.org/2009/Talks/1203-rdb2rdf-egp/

<egonw> nico's blog with coverage of swat4ls: http://semanticscience.wordpress.com/

<egonw> ha, slidy :)

<egonw> mscottm: thanx!