HCLSIG BioRDF Subgroup/Meetings/2011/01-24 Conference Call

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Conference Details

  • Date of Call: Monday, January 24, 2011
  • Time of Call: 11:00 am Eastern Time, 4 pm UK, 5 pm CET
  • Dial-In #: +1.617.761.6200 (Cambridge, MA)

[Note: limited access to European dial in numbers below]

  • Dial-In #: +33.4.26.46.79.03 (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
  • Convener: M. Scott Marshall
  • Scribe: TBD

Participants

Scott, Katy Wolstencroft, Sudeshna Das, Philippe Rocca-Serra, Lena, Michael, Rob, Eric

Agenda

  • [Tentative - possibly postpone] Brief presentation: Towards 'Materials and Methods' for a computational experiment - Scott
  • Connecting microarray work in BioRDF and Scientific Discourse - Scott, Tim Clark, Sudeshna Das, Lena, Eric
  • Key steps: MAGE-TAB representation of gene lists - Michael Miller
  • Tasks, TODO items (bottom of page) - All

Minutes

24 Jan 2011

See also: IRC log

Attendees
Scott, Katy Wolstencroft, Sudeshna Das, Philippe Rocca-Serra, Lena, Michael, Rob, Eric
Present
+31.62.427.aaaa, [IPcaller], +1.617.768.aabb, +1.206.732.aacc, +1.832.386.aadd, EricP.a, EricP, +1.412.608.aaee, +1.832.386.aaff, +44.186.561.aagg
Regrets
Tim Clark
Chair
SV_MEETING_CHAIR
Scribe
Lena
Contents

Topics
Summary of Action Items
<scribe> new participant: Katie
<mscottm> Katy
<mscottm> Katy Wolstencroft
systems biology of micro-organisms
mscottm: metadata capture
... bioRDF work + computational experiments
<ericP> mscottm, could you paste the URL?
<michael> q
sudeshna: experimental context has most overlap
... most effort describing the experiment and factors
<mscottm> https://wiki.nbic.nl/index.php/2010_Symposium_on_Metadata_Capture
<mscottm> look there
<mscottm> differentially expressed genes vs. biological interpretation (pathways, disease change)
mscottm: idas - convert from mage-tab, etc, to RDF
<ericP> Lena: we used the @@a ontology for microarray normalization
<ericP> ... but for p-values and fold-change, i couldn't find existing statistical ontologies so i made up perls
<philippe> I think OBI has a few classes which could help
<philippe> p-value is definitely there
<ericP> mscottm: i've heard of a couple that were really basic
<philippe> and if things are missing, submissions should be made
rob_frost: genotype to phenotype aligment
mscottm: what type of RDF do we need for rob's example?
... beware of p-values without specifying the data analysis method
michael: genotype 2 phenotype usually captured as experimental factors
... mage-tab has a hard time handling multiple genelists
... but mage-ml would work
philippe: IS-A tab aligns with mage-tab
<ericP> weak!  (said referring to non-cvs approach to w3 note - not in response to what philippe said)
everybody "agreed" to edit the w3c note :-)

Summary of Action Items

  • ACTION: Scott to send invitation to edit
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