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14:59:29 <kei> Zakim, this will be BioRDF
14:59:29 <Zakim> ok, kei; I see SW_HCLS(BioRDF)11:00AM scheduled to start in 1 minute
15:00:42 <kei> agenda + introduction [Kei]
15:00:59 <kei> agenda+ tcm data [Jun, Kei]
15:01:07 <Zakim> SW_HCLS(BioRDF)11:00AM has now started
15:01:08 <kei> agenda+ microarray [All]
15:01:14 <Zakim> +??P3
15:01:15 <kei> Zakim, take up next agendum
15:01:15 <Zakim> agendum 1. "introduction" taken up [from Kei]
15:02:43 <Zakim> +Kei_Cheung
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15:03:49 <Zakim> +??P7
15:04:01 <apaschke> Zakim, ??P7 is me
15:04:01 <Zakim> +apaschke; got it
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15:08:00 <Zakim> +Prateek
15:09:14 <LenaDeus> Kei: TCM dataset update
15:09:32 <ericP> hye all
15:09:48 <LenaDeus> Kei: Jun has updated the dataset, will update a new version into KB
15:09:58 <LenaDeus> (hi Eric :-) )
15:11:51 <LenaDeus> Kei: August 17th, presentation by Chen 
15:13:16 <LenaDeus> Kei: Moving to the Microarray Use Case
15:13:48 <apaschke> http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/QueryFederation2
15:13:50 <LenaDeus> http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/QueryFederation2
15:14:59 <LenaDeus> Kei: Contacted the neuroscience consortium, focusing on microarray experiments
15:16:03 <LenaDeus> Kei: EBI hosts public microarray repository; US hosts the GEO;
15:16:29 <LenaDeus> Most of the publish data in the neuroscience microarray consoroitum have been deposited in GEO 
15:17:04 <LenaDeus> 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
15:17:54 <LenaDeus> http://np2.ctrl.ucla.edu/np2/viewProject.do?action=viewProject&projectId=433773
15:18:01 <LenaDeus> Alzheimer disease patients
15:18:53 <LenaDeus> this paper compares the gene expersssion profiles between normal individual and alzheimer disease patients, especially those patients with tangled cells
15:19:29 <LenaDeus> sattya has identified some experimental type of provenance
15:19:40 <LenaDeus> the paper also provides additional datasets
15:20:17 <LenaDeus> the datasets represents different experimental conditions and a small subset of genes has been found with over/under expressed genes
15:21:01 <LenaDeus> it would be interesting to find additional datasets on neural cell, namely pyramidal neurons
15:21:44 <LenaDeus> another level of integration would be to find comparable experiments
15:22:02 <LenaDeus> where a gene list could be extracted and common genes between the two datasets to be found
15:22:47 <LenaDeus> rules that make biological sense could be devised
15:23:13 <LenaDeus> the gene annotations could be potentially integrated with gene ID and also the samples
15:24:02 <LenaDeus> 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
15:24:45 <LenaDeus> the microarray consortium, in addition to providing XML also provides MAGE-ML, a standardized XML format, proposed by the MGED
15:25:25 <LenaDeus> over time, the Committee also proposes MAGE-Tab, a reduced version of MAGE-ML
15:26:07 <LenaDeus> (although the consoritia only provides the MAGE-ML)
15:26:56 <LenaDeus> there is acollection of ontologies we could tap into,for example gene ontology, SWAN and NIFSTD for neurology
15:28:41 <Zakim> +EricP
15:28:46 <LenaDeus> 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
15:29:14 <LenaDeus> satya: there are many tools to convert realtional databases to RDF
15:30:03 <apaschke> there are tools which consider the XML schema for the transformation to RDF and tools which do not consider the schema
15:30:08 <LenaDeus> satya: there is very fine level control of the data that converted to RDF in existing tools
15:36:59 <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
15:37:18 <LenaDeus> can  we convert a SPARQL query into an XML query much the same way that we do it for SQL?
15:38:21 <LenaDeus> RDAL: from an XML schema, an XSLT is generated, which is the GRDDLS transform
15:39:24 <LenaDeus> the most interesting scenario would be the dinamyc mapping from SPARQL to XML
15:40:42 <LenaDeus> what would be the best practice/recommendation for such a task?
15:41:32 <LenaDeus> Adrian: if the schema could be converted into an ontology, it would easily integrate with other ontologies, such as GO
15:41:57 <LenaDeus> how to represent the provenance information?
15:45:25 <LenaDeus> http://bioportal.bioontology.org/visualize/38801
15:45:37 <LenaDeus> (MGED ontology)
15:48:43 <LenaDeus> it would be good also to find interesting rules 
15:50:09 <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
15:51:56 <Zakim> -Prateek
15:51:58 <Zakim> -apaschke
15:52:00 <Zakim> -Kei_Cheung
15:52:01 <Zakim> -??P3
15:52:03 <Zakim> -EricP
15:52:04 <Zakim> SW_HCLS(BioRDF)11:00AM has ended
15:52:05 <Zakim> Attendees were Kei_Cheung, apaschke, Prateek, EricP
15:52:11 <ericP> RRSAgent, please draft minutes
15:52:11 <RRSAgent> I have made the request to generate http://www.w3.org/2009/07/20-hcls-minutes.html ericP
15:52:20 <ericP> RRSAgent, please make log world-visible
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