HCLSIG BioRDF Subgroup/Meetings/2010/08-02 Conference Call

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Conference Details

  • Date of Call: Monday, August 2, 2010
  • Time of Call: 11:00 am Eastern Time (5 pm CET)
  • Dial-In #: +1.617.761.6200 (Cambridge, MA)
  • Dial-In #: + (Nice, France)
  • Dial-In #: +44.203.318.0479 (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 http://www.mibbit.com/chat/?server=irc.w3.org:6665&channel=%23hcls for IRC access.
  • Duration: ~1 hour
  • Frequency: bi-weekly
  • Convener: Kei
  • Scribe: Kei


Kei Cheung, Lena Deus, Matthias Samwald, Jun Zhao



kei: possible paper submission

Kei: http://wiki.knoesis.org/index.php/SWPM-2010

jun: paper submission deadline is Aug 27

kei: format and size of paper?

jun: 6 page IEEE format

jun: demo paper and short papers -- 2 pages.

jun: perhaps we can get one-week extension at the most

kei: the group is interested in submitting a regular paper

lena: http://ibl.mdanderson.org/~mhdeus/sparql_federation/endpoint2.php

lena: Lena shows an example of sparql query (what genes are expressed in a given region)

kei: it may be interesting to also show genes that are upregulated in one sample while being down regulated in another sample

kei: other types of data that can be integrated with gene expression data include pathways, diseases, drugs, etc

mathias: it’s possible to include lodd data sets

matthias: stitch data (accessible through d2r) -- protein -- drug --molecules

matthias: there is a SPARQL endpoint for STITCH at Berlin: http://www4.wiwiss.fu-berlin.de/stitch/

kei: atag could be added to the paper

jun: the open provenance model: http://code.google.com/p/opmv/

kei: provenance information could be captured based on standard models

jun: identify some sentences that are related to provenance

kei: initial list of authors (not ordered yet): lena, jun, scott, kei, michael, satya, matthias

lena: will send out an email about the paper

matthias: we should identify people responsible for writing different sections

kei: let’s meet on a weekly basis until the end of this month.