W3C

- DRAFT -

SV_MEETING_TITLE

20 Jul 2009

See also: IRC log

Attendees

Present
Kei_Cheung, apaschke, Prateek, EricP
Regrets
Chair
SV_MEETING_CHAIR
Scribe
LenaDeus

Contents


 

 

introduction

Kei: TCM dataset update

<ericP> hye all

Kei: Jun has updated the dataset, will update a new version into KB

(hi Eric :-) )

Kei: August 17th, presentation by Chen
... Moving to the Microarray Use Case

<apaschke> http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/QueryFederation2

http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/QueryFederation2

Kei: Contacted the neuroscience consortium, focusing on microarray experiments
... EBI hosts public microarray repository; US hosts the GEO;

Most of the publish data in the neuroscience microarray consoroitum have been deposited in GEO

the website of the consoritum provides annotation on each of the microarray experiments, but the public repository does not have a lot of microarray annotation

http://np2.ctrl.ucla.edu/np2/viewProject.do?action=viewProject&projectId=433773

Alzheimer disease patients

this paper compares the gene expersssion profiles between normal individual and alzheimer disease patients, especially those patients with tangled cells

sattya has identified some experimental type of provenance

the paper also provides additional datasets

the datasets represents different experimental conditions and a small subset of genes has been found with over/under expressed genes

it would be interesting to find additional datasets on neural cell, namely pyramidal neurons

another level of integration would be to find comparable experiments

where a gene list could be extracted and common genes between the two datasets to be found

rules that make biological sense could be devised

the gene annotations could be potentially integrated with gene ID and also the samples

it would be interesting to compara gene annotation between experiments in order to create rules on certain genes that are over-expressed across the experiments

the microarray consortium, in addition to providing XML also provides MAGE-ML, a standardized XML format, proposed by the MGED

over time, the Committee also proposes MAGE-Tab, a reduced version of MAGE-ML

(although the consoritia only provides the MAGE-ML)

there is acollection of ontologies we could tap into,for example gene ontology, SWAN and NIFSTD for neurology

one option of converting this data to RDF would be to automatically convert the MAGE-ML into RDF using a general XML-to-RDF converter

satya: there are many tools to convert realtional databases to RDF

<apaschke> there are tools which consider the XML schema for the transformation to RDF and tools which do not consider the schema

satya: there is very fine level control of the data that converted to RDF in existing tools

<apaschke> we should also take a look at the XSD schema; maybe we also want to translate the XSD into a ontology for the XML microarry data into RDF data

can we convert a SPARQL query into an XML query much the same way that we do it for SQL?

RDAL: from an XML schema, an XSLT is generated, which is the GRDDLS transform

the most interesting scenario would be the dinamyc mapping from SPARQL to XML

what would be the best practice/recommendation for such a task?

Adrian: if the schema could be converted into an ontology, it would easily integrate with other ontologies, such as GO

how to represent the provenance information?

http://bioportal.bioontology.org/visualize/38801

(MGED ontology)

it would be good also to find interesting rules

<apaschke> using that microarray data can be intersting to use it in the RuleResponder use case, e.g. finding experts for Alzheimer disease http://ibis.in.tum.de/projects/paw/docs/ResponderHCLS_slides.pdf

Summary of Action Items

[End of minutes]

Minutes formatted by David Booth's scribe.perl version 1.135 (CVS log)
$Date: 2009/07/20 15:52:16 $

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No ScribeNick specified.  Guessing ScribeNick: LenaDeus
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Default Present: Kei_Cheung, apaschke, Prateek, EricP
Present: Kei_Cheung apaschke Prateek EricP

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<dbooth> Meeting: Weekly Baking Club Meeting


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<dbooth> Chair: dbooth

Got date from IRC log name: 20 Jul 2009
Guessing minutes URL: http://www.w3.org/2009/07/20-hcls-minutes.html
People with action items: 

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