introduction

<matthias_samwald1> dialing in

<mscottm> I can't hear Kei anymore..

<matthias_samwald1> i can

<mscottm> just came back!

<mscottm> strange..

<kei> ALan: Kaser Permanente attended F2F in Santa Clara

<kei> Software application in Health Care in general

<kei> follow up ...

<kei> clinical backgroup clinical psychology

<kei> clincian working with neurosurgeon

kei: we need to come up with a representation of the description of the experiment and associated raw data set in RDF
... looking at mage-tab format to convert to RDF structure
... there are many ways to convert in order to obtain the RDF

<mscottm> Lena: Limpopo is the name of a river

kei: mage-tab is a bundle of several tab delimited files
... idf stands for investigation description format
... sdrf is sample to data relationship format
... when generating gene list, different statistical tests are used

<ssahoo2> lena: IDF and SDRF files from array express using session number from authors of paper

<ssahoo2> lena: faced two issues in conversion of file data to RDF

<ssahoo2> lena: missing predicates to link entities extracted from the files

<ssahoo2> lena: created a list of predicates and will map these predicates to MGED ontology

<ssahoo2> lena: should the MAGE-ML structure be represented in RDF?

<ssahoo2> kei: need to include ontology terms for microarray data provenance

<ssahoo2> kei: Helen curated examples and identified relevant ontology terms

<ssahoo2> lena: easy to convert data in IDF SDRF files which are linked to MAGE-TAB

<ssahoo2> kei: conversion should output RDF conforming to ontology terms

kei: NCBO biomedicla annotator allows import free text to identify biological ontology terms

<ssahoo2> kei: tested with Bio-annotator to associate ontology terms to entities

scott: we should try to select the data that is interesting
... take first the things that we can link to other types of data

kei: we can maybe take a few examples and create the structure by hand
... mage-tab parsing can be fed back to the arrayexpress group

ssahoo2: we also need to create a schema and then convert to RDF

kei: we have 3 interesting examples that could demonstrate the use of much of the mage-tab content

matthias: programmed a prototype and integrated the ontology by NCBO for annotating and creating aTags

kei: based on the examples we have, we can look at the aTag approach and see how much we can annotate
... could aTag be complementary to a format like mage-tab?

<mscottm> agree

<ssahoo2> +1 matthias

ssahoo2: using NCBO to look for all existing ontologies

kei: although there is a lot of redundancy, which terms should be used frmo which ontolgy

satya: we usually look for the text description to understand which fits best

<ssahoo2> lena: map entity to mulitple ontology terms

kei: shared names ontology can be used to map to many ontologies

satya: ncbo has mappings to other ontologies that we could use

scott: gene lists are in the scope of shared names
... find a neutral source of URI to identify concepts
... if we have a gene list, it would be good to bring it to the shareed names comitee

kei: something like the neuroscience ontology (NIFSTD) should be used
... mged has done a good job in annotating experimental details

<mscottm> +1 on using NIFSTD

kei: we should only use semi-automatic mage-tab parsing to generate rdf output to assess the target ontology structure

scott: how to process a list?

kei: if the paper includes a few hundred expressions genes, these com in the format of text files

matthias: it can maybe be broken down into smaller lists

scott: is there an alterantive to use rdf:Bag for the gene list?

matthias: instead, we could repeat properties

<kei> rdf representation of a gene list

kei: as 'gene list', do we mean the list of gene IDs or some expression values associated and reported in the experiment?

satya: we should probably leave room to allow for numeric expression values

<kei> http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/MicroarrayExperimentContext

satya: we can describe the attributes of the experimental set - these are all provenance about the gene list
... we should pick and chose what is the provenance information that is relevant
... right now we have a list of terms, but a problem is the predicates that link the terms together

kei: how to apply the gene lists to the shared names?

scott: add the use case to the wiki of shared names
... ncbo is also involved in shared names

<kei> scott: express gene lists using shared names

I have to leave... can someone take over scribbing, please? :)

<ssahoo2> I will scribe lena

<matthias_samwald1> i have to leave now as well! -- bye.

tks!

bye everybody!

<kei> thanks, Lena

<ssahoo2> scott: shared names will reference other sources that describe the given gene, for example Entrez gene

<ssahoo2> ACTION: item to add gene list to shared names [recorded in http://www.w3.org/2009/12/07-hcls-minutes.html#action01]

<ssahoo2> ACTION: item to add additional terms to microarray experiment context wiki: http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/MicroarrayExperimentContext [recorded in http://www.w3.org/2009/12/07-hcls-minutes.html#action02]

<ssahoo2> kei: next meeting on 23rd Dec

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Got date from IRC log name: 07 Dec 2009
Guessing minutes URL: http://www.w3.org/2009/12/07-hcls-minutes.html
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