15:59:08 <RRSAgent> RRSAgent has joined #hcls
15:59:08 <RRSAgent> logging to http://www.w3.org/2009/12/07-hcls-irc
15:59:16 <kei> Zakim, this will be BioRDF
15:59:16 <Zakim> ok, kei; I see SW_HCLS(BioRDF)11:00AM scheduled to start in 1 minute
15:59:31 <kei> agenda+ introduction [Kei]
15:59:40 <mscottm> mscottm has joined #hcls
15:59:49 <kei> agenda+ magetab parsing [Lena, Jim, Michael, Helen]
16:00:10 <Zakim> SW_HCLS(BioRDF)11:00AM has now started
16:00:11 <kei> agenda+ provenance and workflow [Satya, Jun, Yolanda]
16:00:17 <Zakim> +ssahoo2
16:00:22 <kei> Zakim, take up next agendum
16:00:22 <Zakim> agendum 1. "introduction" taken up [from Kei]
16:01:02 <Zakim> +Kei_Cheung
16:01:05 <Zakim> -ssahoo2
16:01:06 <Zakim> +ssahoo2
16:01:20 <Zakim> + +1.510.381.aaaa
16:01:50 <Zakim> +mscottm
16:02:22 <mscottm> Zakim, who is here?
16:02:22 <Zakim> On the phone I see ssahoo2, Kei_Cheung, +1.510.381.aaaa, mscottm
16:02:23 <Zakim> On IRC I see mscottm, RRSAgent, Zakim, kei, matthias_samwald, ssahoo2, ericP
16:02:24 <matthias_samwald1> matthias_samwald1 has joined #hcls
16:03:14 <matthias_samwald1> dialing in
16:03:14 <mscottm> Zakim, aaaa is AllenHobbs
16:03:15 <Zakim> +AllenHobbs; got it
16:03:19 <LenaDeus> LenaDeus has joined #hcls
16:03:42 <Zakim> +??P21
16:04:05 <mscottm> Zakim, ??P21 is LenaDeus
16:04:05 <Zakim> +LenaDeus; got it
16:04:13 <Zakim> + +0012aabb
16:04:36 <matthias_samwald1> matthias_samwald1 has left #hcls
16:04:42 <matthias_samwald1> matthias_samwald1 has joined #hcls
16:05:18 <Zakim> +EricP
16:06:14 <mscottm> I can't hear Kei anymore..
16:06:20 <matthias_samwald1> i can
16:06:27 <mscottm> just came back!
16:06:54 <mscottm> strange..
16:07:17 <kei> ALan: Kaser Permanente attended F2F in Santa Clara
16:07:29 <kei> Software application in Health Care in general
16:07:38 <kei> follow up ...
16:08:18 <kei> clinical backgroup clinical psychology
16:08:30 <kei> clincian working with neurosurgeon
16:10:27 <LenaDeus> kei: we need to come up with a representation of the description of the experiment and associated raw data set in RDF
16:10:46 <LenaDeus> kei: looking at mage-tab format to convert to RDF structure
16:11:08 <LenaDeus> kei: there are many ways to convert in order to obtain the RDF
16:11:58 <mscottm> Lena: Limpopo is the name of a river
16:12:20 <LenaDeus> kei: mage-tab is a bundle of several tab delimited files
16:12:37 <LenaDeus> kei: idf stands for investigation description format
16:13:04 <LenaDeus> kei: sdrf is sample to data relationship format
16:13:47 <LenaDeus> kei: when generating gene list, different statistical tests are used
16:15:16 <ssahoo2> lena: IDF and SDRF files from array express using session number from authors of paper
16:15:49 <ssahoo2> lena: faced two issues in conversion of file data to RDF
16:16:16 <ssahoo2> lena: missing predicates to link entities extracted from the files
16:16:50 <ssahoo2> lena: created a list of predicates and will map these predicates to MGED ontology
16:17:46 <ssahoo2> lena: should the MAGE-ML structure be represented in RDF?
16:18:35 <ssahoo2> kei: need to include ontology terms for microarray data provenance
16:19:26 <ssahoo2> kei: Helen curated examples and identified relevant ontology terms
16:21:15 <ssahoo2> lena: easy to convert data in IDF SDRF files which are linked to MAGE-TAB 
16:22:17 <ssahoo2> kei: conversion should output RDF conforming to ontology terms 
16:22:27 <LenaDeus> kei: NCBO biomedicla annotator allows import free text to identify biological ontology terms
16:22:52 <ssahoo2> kei: tested with Bio-annotator to associate ontology terms to entities
16:23:27 <LenaDeus> scott: we should try to select the data that is interesting 
16:24:32 <LenaDeus> scott: take first the things that we can link to other types of data
16:24:40 <Zakim> -AllenHobbs
16:25:14 <LenaDeus> kei: we can maybe take a few examples and create the structure by hand
16:26:34 <LenaDeus> kei: mage-tab parsing can be fed back to the arrayexpress group
16:26:59 <LenaDeus> ssahoo2: we also need to create a schema and then convert to RDF
16:27:38 <LenaDeus> kei: we have 3 interesting examples that could demonstrate the use of much of the mage-tab content
16:29:11 <LenaDeus> matthias: programmed a prototype and integrated the ontology by NCBO for annotating and creating aTags
16:30:03 <LenaDeus> kei: based on the examples we have, we can look at the aTag approach and see how much we can annotate
16:30:23 <LenaDeus> kei: could aTag be complementary to a format like mage-tab?
16:30:40 <mscottm> agree
16:30:50 <ssahoo2> +1 matthias
16:32:09 <LenaDeus> ssahoo2: using NCBO to look for all existing ontologies
16:32:54 <LenaDeus> kei: although there is a lot of redundancy, which terms should be used frmo which ontolgy
16:33:13 <LenaDeus> satya: we usually look for the text description to understand which fits best
16:34:38 <ssahoo2> lena: map entity to mulitple ontology terms
16:35:04 <LenaDeus> kei: shared names ontology can be used to map to many ontologies
16:36:24 <LenaDeus> satya: ncbo has mappings to other ontologies that we could use
16:36:46 <LenaDeus> scott: gene lists are in the scope of shared names
16:37:03 <LenaDeus> scott: find a neutral source of URI to identify concepts
16:37:53 <LenaDeus> scott: if we have a gene list, it would be good to bring it to the shareed names comitee
16:39:02 <LenaDeus> kei: something like the neuroscience ontology (NIFSTD) should be used
16:40:34 <LenaDeus> kei: mged has done a good job in annotating experimental details
16:40:35 <mscottm> +1 on using NIFSTD
16:42:29 <LenaDeus> kei: we should only use semi-automatic mage-tab parsing to generate rdf output to assess the target ontology structure
16:43:43 <LenaDeus> scott: how to process  a list?
16:44:07 <LenaDeus> kei: if the paper includes a few hundred expressions genes, these com in the format of text files
16:44:36 <LenaDeus> matthias :it can maybe be broken down into smaller lists
16:45:11 <LenaDeus> scott: is there an alterantive to use rdf:Bag for the gene list?
16:45:43 <LenaDeus> matthias: instead, we could repeat properties
16:45:47 <kei> rdf representation of a gene list
16:46:26 <LenaDeus> kei: as 'gene list', do we mean the list of gene IDs or some expression values associated and reported in the experiment?
16:47:25 <LenaDeus> satya: we should probably leave room to allow for numeric expression values
16:48:12 <kei> http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/MicroarrayExperimentContext
16:48:18 <LenaDeus> satya: we can describe the attributes of the experimental set - these are all provenance about the gene list
16:49:09 <LenaDeus> satya: we should pick and chose what is the provenance information that is relevant
16:51:06 <LenaDeus> satya: right now we have a list of terms, but a problem is the predicates that link the terms together
16:51:54 <LenaDeus> kei: how to apply the gene lists to the shared names?
16:52:27 <LenaDeus> scott: add the use case to the wiki of shared names
16:52:59 <LenaDeus> scott: ncbo is also involved in shared names
16:54:13 <kei> scott: express gene lists using shared names
16:54:59 <LenaDeus> I have to leave... can someone take over scribbing, please? :)
16:55:13 <ssahoo2> I will scribe lena
16:55:14 <matthias_samwald1> i have to leave now as well! -- bye.
16:55:17 <LenaDeus> tks!
16:55:25 <LenaDeus> bye everybody!
16:55:32 <kei> thanks, Lena
16:55:33 <Zakim> -LenaDeus
16:55:41 <Zakim> - +0012aabb
16:55:56 <ssahoo2> scott: shared names will reference other sources that describe the given gene, for example Entrez gene
16:56:59 <ssahoo2> action item: add gene list to shared names
16:57:47 <ssahoo2> action item: add additional terms to microarray experiment context wiki:  http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/MicroarrayExperimentContext
16:58:21 <ssahoo2> kei: next meeting on 23rd Dec
16:59:07 <ericP> RRSAgent, please draft minutes
16:59:07 <RRSAgent> I have made the request to generate http://www.w3.org/2009/12/07-hcls-minutes.html ericP
16:59:15 <ericP> RRSAgent, please make log world-visible
16:59:20 <Zakim> -ssahoo2
16:59:25 <Zakim> -mscottm
16:59:37 <mscottm> RRSAgent, please draft minutes
16:59:37 <RRSAgent> I have made the request to generate http://www.w3.org/2009/12/07-hcls-minutes.html mscottm
16:59:43 <mscottm> RRSAgent, please make log world-visible
17:13:45 <Zakim> -Kei_Cheung
17:18:45 <Zakim> disconnecting the lone participant, EricP, in SW_HCLS(BioRDF)11:00AM
17:18:48 <Zakim> SW_HCLS(BioRDF)11:00AM has ended
17:18:49 <Zakim> Attendees were ssahoo2, Kei_Cheung, +1.510.381.aaaa, mscottm, AllenHobbs, LenaDeus, +0012aabb, EricP
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