16:06:00 <RRSAgent> RRSAgent has joined #hcls
16:06:00 <RRSAgent> logging to http://www.w3.org/2009/11/23-hcls-irc
16:06:12 <mscottm> Zakim, who is here?
16:06:12 <Zakim> On the phone I see +1.410.720.aaaa, YolandaG, +1.414.456.aabb, Kei_Cheung, +1.937.775.aacc, ??P18, ??P20, [IPcaller], ??P21
16:06:13 <ericP> meeting: BioRDF
16:06:15 <Zakim> On IRC I see RRSAgent, mscottm, ssahoo2, YolandaGil, Zakim, jun, rfrost, kei, curoli, Simon, Joshua, matthias_samwald, ericP
16:06:22 <ericP> RRSAgent, please draft minutes
16:06:22 <RRSAgent> I have made the request to generate http://www.w3.org/2009/11/23-hcls-minutes.html ericP
16:06:29 <ericP> RRSAgent, please make log world-readable
16:06:48 <rfrost> Yolanda Gil introduction: chairing W3C provenance interest group
16:07:03 <ericP> Zakim, please dial ericP-office
16:07:03 <Zakim> ok, ericP; the call is being made
16:07:05 <Zakim> +EricP
16:07:33 <rfrost> Yolanda: talked about semantic workflows
16:08:16 <rfrost> Christain Fritz intro: postdoc with Yolanda at USC, working on semantic workflows
16:09:00 <Zakim> +[IPcaller.a]
16:09:20 <YolandaGil> The site of the W3C Provenance Group I mentioned is http://www.w3.org/2005/Incubator/prov/wiki
16:09:26 <curoli> zakim, IPcaller.a is Oliver
16:09:26 <Zakim> +Oliver; got it
16:09:33 <mscottm> Welcome Yolanda, Christian, and Simon!
16:09:46 <rfrost> Simon Twiger, U. of Wisconsin, intro: interested in integrated semantic web technologies into rat database they maintain
16:10:10 <Simon> Its the Medical College of Wisconsin, not actually part of the U.Wisconsin system :)
16:10:34 <mscottm> Simon: also one of NCBO's Research Application collaborations
16:10:55 <YolandaGil> YolandaGil has joined #HCLS
16:11:43 <rfrost> Agenda item 1: how to represent microarray data in RDF/OWL and use this representation to support query federation over the web
16:12:54 <rfrost> query federation paper identified provenance and workflow as future directions; would like to explore microarray use cases in these areas
16:13:11 <kei> http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/QueryFederation2?action=AttachFile&do=get&target=Microarray_Use_Case.pdf
16:13:37 <jun> jun has joined #hcls
16:14:33 <jun> can anyone pls post the link to the irc again? I lost my irc when kei posted the link. thanks
16:15:50 <rfrost> kei: linked doc contains description of example neuroscience microarray experiment
16:16:50 <Joshua> http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/QueryFederation2?action=AttachFile&do=get&target=Microarray_Use_Case.pdf
16:18:51 <rfrost> kei: experiment compared gene expression profiles for multiple classes of patients to evaluate the relationship between NFT and Alzheimer's
16:21:50 <rfrost> kei: has been collaborating with another researcher at Yale to propose a structured digital abstract  (not specifically RDF)
16:23:22 <rfrost> kei: 3 main elements of the structured digital abstract: 1) translation table listing all biological entities (e.g. genes, protiens) in article (maps human names to db identifiers)   
16:24:06 <rfrost> kei: 2) list of main results described as a simple ontology
16:24:54 <rfrost> kei: 3) standard evidence codes for how how the results were obtained
16:25:04 <Simon> FEBS info on SDA: http://www.febsletters.org/content/sda_summary
16:25:22 <rfrost> kei: has been evaluated on pilot basis
16:26:58 <rfrost> kei: Question: can we do something similar for microarray data?
16:27:17 <Simon> FEBS special issue with SDAs: http://www.sciencedirect.com/science/issue/4938-2008-994179991-684107
16:28:10 <rfrost> kei: import the gene lists into public database (gene omnibus, etc.)
16:28:41 <rfrost> kei: leverage GO for representing the gene list
16:29:07 <ericP> q+
16:29:17 <rfrost> kei: also need to capture the context (the biological condition, the brain region); need to capture this contextual information as part of the gene list
16:33:41 <ssahoo2> Provenance related Experiment Context: http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/QueryFederation2?action=AttachFile&do=get&target=NeuroscienceMicroarrayConsortium_ProvenanceTerms.txt
16:34:05 <rfrost> kei: this use case can help guide work on representing microarray data in RDF
16:34:07 <ssahoo2> http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/MicroarrayProvenanceUseCase
16:34:48 <ericP> ack me
16:35:58 <rfrost> ericp: NLP over the document will give you the set of keywords but won't give relationships between the keywords
16:36:41 <rfrost> kei: can use text mining to generate initial set of gene names but still need manual curation
16:37:50 <rfrost> kei: authors need to be convinced to enter gene lists in a standard format; it is currently up to the author whether to make it available
16:39:14 <rfrost> q+
16:40:34 <rfrost> ericp: our work is how to map the SDA into a semantic web representation
16:41:00 <rfrost> ericp: are the identifiers URLs?
16:41:54 <rfrost> ericp: if not URLs, need to provide some additional scheme/context information that can eliminate identifier ambiguity
16:42:37 <mscottm> q+
16:42:48 <rfrost> ericp: are folks open to creating SDA info in RDF from the start?
16:43:12 <rfrost> kei: the key is having an easy interface/tools to create the metadata
16:44:28 <rfrost> mscottm: who are the folks that will be creating the SDA data?
16:45:11 <rfrost> kei: Mark Goldstein at Yale
16:48:02 <curoli> q+
16:48:25 <rfrost> kei: need to convince Mark and others to use sem web technology
16:48:45 <rfrost> rfrost: are all resources used in results ontology defined in translation table?
16:48:48 <rfrost> kei: yes
16:49:20 <rfrost> rfrost: what is the target expressiveness of the ontology?
16:49:51 <rfrost> kei: simple set of relations based on results reported in papers
16:51:05 <mscottm> http://www.ebi.ac.uk/gxa/qrs?gprop_0=&gval_0=&fexp_0=UP_DOWN&fact_0=&specie_0=&fval_0=brain&view=hm
16:51:20 <YolandaGil> q+
16:51:33 <rfrost> mscottm: explore ways of representing gene list data in RDF
16:51:40 <mscottm> http://compbio.dfci.harvard.edu/genesigdb/
16:52:14 <rfrost> q-
16:52:31 <rfrost> kei: explore bridge between paper and gene atlas
16:53:14 <mscottm> ack me
16:53:50 <rfrost> ?: role of biopax?
16:53:52 <matthias_samwald> (need to leave now,  bye)
16:54:03 <mscottm> bye Matthias
16:54:21 <Zakim> -??P21
16:55:05 <rfrost> kei: you could eventually incorporate gene list representation into biopax
16:55:20 <curoli> q-
16:58:09 <rfrost> Yolanda/Kei: use of genespring to generate results, how to reproduce results if not using that software package
17:00:12 <rfrost> Yolanda/Kei/Scott: providing workflow information and annotated data sufficient to reproduce results as well as apply methodology to other experiments
17:01:53 <rfrost> Yolanda/Kei/Scott: semantic annotation/description of workflow would enable the retrieval of data relevant to that workflow (i.e. data that could be used to populate that workflow for a different experimental scenario)
17:02:59 <YolandaGil> q-
17:03:13 <rfrost> Scott: two data sources relevant to gene lists: genesigdb, gene expression atlas
17:04:06 <rfrost> scott: Helen indicated that we can get RDF data returned from gxa
17:05:42 <rfrost> rfrost: what would RDF look like from gxa?
17:06:12 <rfrost> rfrost: just URLs/linked data or RDF that references an ontology?
17:06:46 <Zakim> -Oliver
17:07:04 <rfrost> scott: would be RDF references ontology
17:08:40 <rfrost> scott/yolanda/kei: to do: look at application of workflow systems to microarray analysis
17:08:50 <ssahoo2> q+
17:09:31 <rfrost> scott: experimental factor ontology (http://www.ebi.ac.uk/efo/)
17:11:22 <rfrost> kei: try to create a workflow process for generating the gene list?
17:12:04 <rfrost> scott: given analytical challenge, may be better to start with the gene list and look at workflows that start with the gene list
17:12:39 <rfrost> yolanda: want to focus on a workflow were the use of semantics have a clear goal
17:14:09 <rfrost> yolanda/satya: example: provenance of the microarray data, represented in RDF, would impact the execution of the workflow
17:15:55 <rfrost> yolanda: provenance would include information about how the microarray data was obtained (equipment, data processing steps, etc.)
17:17:03 <Joshua> Joshua has left #hcls
17:17:15 <Zakim> - +1.410.720.aaaa
17:17:20 <rfrost> satya: provenance data could reference OBI terms
17:17:23 <ssahoo2> q -
17:17:29 <ssahoo2> q-
17:18:19 <rfrost> scott: some of this provenance data will already be in the MAGE files
17:18:38 <rfrost> scott: type of analysis may not be included
17:18:45 <ericP> RRSAgent, please disconnect ericP 
17:18:45 <RRSAgent> I'm logging. I don't understand 'please disconnect ericP ', ericP.  Try /msg RRSAgent help
17:18:57 <ericP> zakim, please disconnect ericP 
17:18:57 <Zakim> EricP is being disconnected
17:18:58 <Zakim> -EricP
17:19:14 <ericP> RRSAgent, please dafte minutes
17:19:14 <RRSAgent> I'm logging. I don't understand 'please dafte minutes', ericP.  Try /msg RRSAgent help
17:19:21 <ericP> RRSAgent, please draft minutes
17:19:21 <RRSAgent> I have made the request to generate http://www.w3.org/2009/11/23-hcls-minutes.html ericP
17:20:30 <rfrost> jun: good to review existing data files (MAGE) and evaluate to what extent necessary provenance data is contained and, if not, what ontologies define these concepts
17:20:53 <rfrost> kei: can start that process via a wiki page
17:22:14 <rfrost> scott: another idea for application of workflows: visualization of data related to differentially expressed genes
17:23:34 <rfrost> jun: should combine provenance data with domain-specific annotations 
17:24:07 <rfrost> satya: will create wiki page with set of experimental contexts for evaluation
17:24:55 <Zakim> - +1.414.456.aabb
17:24:57 <Zakim> - +1.937.775.aacc
17:24:57 <Zakim> -YolandaG
17:24:58 <ssahoo2> quit
17:24:58 <Zakim> -??P18
17:25:01 <Zakim> -Kei_Cheung
17:25:03 <Zakim> -??P20
17:25:16 <Simon> quit
17:25:26 <mscottm> ericP - you still on?
17:25:39 <Simon> Simon has left #hcls
17:25:51 <Zakim> -[IPcaller]
17:25:52 <Zakim> SW_HCLS(BioRDF)11:00AM has ended
17:25:54 <Zakim> Attendees were +1.410.720.aaaa, YolandaG, +1.414.456.aabb, Kei_Cheung, +1.937.775.aacc, [IPcaller], EricP, Oliver
17:26:20 <mscottm> RRSAgent, please draft minutes
17:26:20 <RRSAgent> I have made the request to generate http://www.w3.org/2009/11/23-hcls-minutes.html mscottm
17:26:27 <mscottm> RRSAgent, please make log world-visible
19:04:43 <egonw> egonw has joined #hcls
19:33:57 <Zakim> Zakim has left #hcls
19:57:40 <ericP_> ericP_ has joined #hcls
20:26:42 <mscottm> mscottm has joined #hcls