HCLSIG BioRDF Subgroup/Meetings/2009-08-17 Conference Call

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Conference Details

  • Date of Call: Monday August 17, 2009
  • Time of Call: 11:00 am Eastern Time
  • 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)
  • Duration: ~1 hour
  • Frequency: bi-weekly
  • Convener: Kei Cheung
  • Scribe: Kei Cheung


Kei Cheung, Eric Prud'hommeaux, Lena Deus, Satya Sahoo, Scott Marshall, Jun Zhao, Rob Frost


  • Roll call (Kei)
  • TCM update (Jun)
  • Microarray use case discussion (All)


<kei> Kei: tcm update

<kei> The date of Huajun’s talk was changed to Sept 28 at 10 am EDT

<kei> DILS 09 update (collaboration between BioRDF and LODD)

<kei> Jun will post a url for the updated verison

<zhaoj> http://www4.wiwiss.fu-berlin.de/lodd/DILS2009_Poster.pdf

<kei> Nature preceding (http://precedings.nature.com/) for poster dissemination?

<kei> Jun: poster presented the poster at DILS 09 about one month ago

<kei> Jun: other people used similar technologies like linked data

<kei> Jun: feedback: how to maintain update? how to link between different datasets and how these links are maintained?

<kei> Jun: A German group’s building warehouse for drug data ...

<kei> Jun: a group at Univ. of Manchester developing TCM ontology

<zhaoj> Goran Nenadic

<kei> Jun: Maybe in Oct after Huajun’s talk we can invite Goran to give a talk

<kei> Scott: Allister Miles? flybase or flyweb

<zhaoj> OpenFlyDAta

<kei> Jun: contact Jun and/or Allister for further information

<zhaoj> FlyAtlas

<kei> Kei: what types of data contained in OpenFlyData?

<kei> Jun: some microarray data

<kei> Jun: may be relevant to the microarray use case

<LenaDeus> Kei: Helen Parkinson is developing a gene expression atlas at EBI

<LenaDeus> Kei: Helen is interested in giving the gene expression project a neuroscience focus

<LenaDeus> Kei: Helen is willing to curate some examples for our use case development

<LenaDeus> Kei gave Helen a few microarray examples from the neuroscience microarray consortium

<LenaDeus> Kei: helen has started interaction with neurolex

<LenaDeus>It may be possible that Helen may integrate their neuro atlas curation with MAGE-ML

<kei> Kei: Eric: suggested sending group email with different prefixes (e.g.< BioRDF)

<kei> Scott: how to coordinate our efforts with neurolex and ebi

<LenaDeus> kei: what's the best practice for microarray annotation?

<LenaDeus> kei: mage-rdf?

<LenaDeus> kei: would MAGE-RDF be an xml-based annotation or we need to invent a completely new rdf or owl format for that?

<mscottm> http://www.ebi.ac.uk/microarray/General/Positions/student.html

<kei> scott: what kind of important semantics are needed for comparing microarray experiments?

<kei> scott: suggested establishing a sparql endpoint at EBI

<LenaDeus> scott: when we know more about what the interesting semantic are in array express, it may be interesting to set up a sparql endpoint directly to their database

<LenaDeus> scott: that would be a good way of "rdf-izing" on the fly

<LenaDeus> kei: mage-tab is an alternative to XML that might be easier to handle

<LenaDeus> rob: is helen manually annotaing the experiments using terms from neurolex?

<LenaDeus> kei: yes I think, especially we are still in the early stage of the annotation

<LenaDeus> kei: the annotation is still a moving target

<kei> rob: how to annotate data in a larger scale.

<kei> scott: conversion of magetab into rdf

<kei> kei: VOID may be helpful

<kei> grant people who are interested in editing the group wiki page

<eric> those who are interested can enter their ids

<LenaDeus> helenadeus

<ssahoo2> ssahoo

<ericP> http://esw.w3.org/topic/ESWEditorsGroup#preview

<mscottm> <ArrayDesign_assnref>

<mscottm> <PhysicalArrayDesign_ref identifier="Affymetrix.com::PhysicalArrayDesign.HG-U133_Plus_2"/>

<mscottm> </ArrayDesign_assnref>

<LenaDeus> jun: GO annotation may also be useful to annotate the datasets

<LenaDeus> kei: pathway information could also be valuable

<kei> scott: Andrew Gibson converted GO into SKOS

<mscottm> kei: just responded to Albert (editor) BMC Bioinformatics special issue with only a few minor issues. Any others?

<ericP> would like to add a sentence and a link to (sourceforge) download a demo/tool.