HCLSIG BioRDF Subgroup/Meetings/2009-08-17 Conference Call
- 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 #: +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: ~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
<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
<kei> Jun: contact Jun and/or Allister for further information
<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?
<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
<mscottm> <PhysicalArrayDesign_ref identifier="Affymetrix.com::PhysicalArrayDesign.HG-U133_Plus_2"/>
<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.