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15:55:08 <kei> Zakim, this will be BioRDF
15:55:08 <Zakim> ok, kei; I see SW_HCLS(BioRDF)11:00AM scheduled to start in 5 minutes
15:55:35 <kei> agenda+ introduction [Kei]
15:55:44 <kei> agenda+ BioRDF breakout update [Kei]
15:55:57 <kei> agenda+ Follow-up [All]
15:56:06 <kei> Zakim, take up next agendum
15:56:06 <Zakim> agendum 1. "introduction" taken up [from Kei]
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15:59:59 <Zakim> SW_HCLS(BioRDF)11:00AM has now started
16:00:06 <Zakim> +Kei_Cheung
16:00:09 <Zakim> + +1.410.720.aaaa
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16:02:02 <Zakim> +??P6
16:02:28 <matthias_samwald> zakim, ??P6 is matthias_samwald
16:02:30 <Zakim> +matthias_samwald; got it
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16:03:38 <Zakim> +andy
16:04:10 <Zakim> + +1.617.324.aabb
16:04:45 <oshani> Zakim, +1.617.324.aabb is me
16:04:45 <Zakim> +oshani; got it
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16:05:17 <mscottm> Zakim, who is here?
16:05:17 <Zakim> On the phone I see Kei_Cheung, +1.410.720.aaaa, matthias_samwald, andy, oshani (muted)
16:05:19 <Zakim> On IRC I see mscottm, oshani, matthias_samwald, Joshua, RRSAgent, Zakim, kei, jerven, Cloud, ericP
16:05:56 <mscottm> Zakim, +1.410.720.aaaa is Joshua
16:05:56 <Zakim> +Joshua; got it
16:06:52 <mscottm> Zakim, who is here?
16:06:52 <Zakim> On the phone I see Kei_Cheung, Joshua, matthias_samwald, andy, oshani (muted)
16:06:54 <Zakim> On IRC I see mscottm, oshani, matthias_samwald, Joshua, RRSAgent, Zakim, kei, jerven, Cloud, ericP
16:07:47 <kei> scribenick Matthias
16:07:51 <Zakim> +??P10
16:08:00 <matthias_samwald> scribenick matthias_samwald
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16:09:59 <kei> http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/QueryFederation2?action=AttachFile&do=get&target=BioRDF+Breakout+Update.pdf 
16:10:21 <matthias_samwald> kei: The presentation is available as a PDF
16:11:05 <matthias_samwald> Joshua: my name is joshua philips. work at semantic bits. worked for caBIG (infrastructure etc.)
16:11:20 <matthias_samwald> ... Currently I am trainig that community in Semantic Web technology
16:12:02 <oshani> There are 2 of us: Oshani and Rachel, and we are working on this project: http://code.google.com/p/querymed
16:12:14 <matthias_samwald> oshani: hi, i am Oshani Seneviratne.
16:12:44 <matthias_samwald> ... we are involved in a small project (sparql queries, user interface for physicians).
16:13:03 <matthias_samwald> kei: thanks for your introductions.
16:14:24 <matthias_samwald> ... at the BioRDF breakout last week in Santa Clara we had 20 participants.
16:14:43 <matthias_samwald> ... we had two main parts. first presentations, then discussions.
16:15:36 <matthias_samwald> ... presentation by me (kei) about microarray work
16:15:48 <matthias_samwald> ... work on expanding query federation demo with microarray dat
16:17:39 <matthias_samwald> ... MIAME standard -- what is the minimum information to practically annotate microarray data.
16:18:09 <matthias_samwald> ... MAGE-TAB is a new standard for capturing such data, Michael Miller gave a presentation.
16:19:24 <Zakim> -matthias_samwald
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16:19:35 <ericP> oops
16:19:40 <matthias_samwald> ... Matthias Samwald gave a presentation on aTags
16:21:19 <Zakim> +??P0
16:21:33 <Zakim> +Prateek
16:21:57 <mscottm> Zakim, who is here?
16:21:57 <Zakim> On the phone I see Kei_Cheung, Joshua, andy, oshani (muted), ??P10, ??P0, Prateek
16:21:59 <Zakim> On IRC I see matthias_samwald, LenaDeus, mscottm, oshani, Joshua, RRSAgent, Zakim, kei, jerven, Cloud, ericP
16:22:50 <matthias_samwald> matthias_samwald has joined #hcls
16:22:52 <matthias_samwald> Kei: slide number 3: we talked about possible RDF structures for representing microarray data
16:23:10 <matthias_samwald> ... we also invited the SPARQL group to discuss extensions to SPARQL
16:24:23 <matthias_samwald> ... other points of discussion: tools and visualization (how to integrate heterogeneous tools)
16:24:34 <Zakim> +EricP
16:26:24 <matthias_samwald> ... integration of databases and literature
16:27:17 <matthias_samwald> ... microarray data needs to be integrated with pathway data etc
16:28:50 <matthias_samwald> ... we have started an interaction with the NCBO
16:28:59 <matthias_samwald> ... they helped us use some of their tools
16:31:00 <Zakim> -oshani
16:31:06 <matthias_samwald> bye!
16:31:41 <matthias_samwald> kei: we have huge amounts of raw data in native format that can be read by certain types of tools for processing
16:32:26 <matthias_samwald> ... we discussed how much of it needs to be converted to RDF. we agreed that not everything needs to be converted to RDF, because it would be too huge
16:33:44 <matthias_samwald> ... gene lists (e.g. which genes are affected in a certain experiment) usually consist of several hundreds of genes of interest.
16:34:20 <matthias_samwald> ... what genes are upregulated in a certain neurological condition? and other questions. these data should be comparable between experiments.
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16:34:39 <matthias_samwald> ... annotation should also capture which algorithm was used
16:35:09 <matthias_samwald> ... based on the algorithm, users can decide whether two datasets are comparable or not
16:35:23 <mscottm> NIFSTD
16:35:55 <matthias_samwald> ... the NIFSTD is a terminology/OWL ontology developed for the neuroscience information framework (NIF). 
16:36:03 <matthias_samwald> ... it is available in BioPortal.
16:37:46 <mscottm> Experimental Factors = EFO = Experimental Factors Ontology
16:38:59 <matthias_samwald> ... when data is expressed in linked data format, metadata / provenance need to be represented as well. vOID is interesting in this regard.
16:39:24 <matthias_samwald> ... aTags is an interesting approach for representing both structured and unstructured/text data in a single format.
16:40:06 <matthias_samwald> ... query federation: we used the hierarchical query feature to get all brain regions located within a larger brain region, enabling query expansion
16:40:22 <matthias_samwald> ... aggregate functions could be useful for statistical analysis of data.
16:41:52 <matthias_samwald> ... provenance and workflowas are important. projects include taverna and biomoby.
16:42:19 <matthias_samwald> ... data analysis projects: bioconductor (based on R), matlab
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16:43:29 <matthias_samwald> ... how could we get software vendors interested in use-case?
16:43:55 <matthias_samwald> ... how can grid and cloud computing be incorporated in use-case?
16:44:34 <matthias_samwald> eric: we need to find out how we interact with caBIG.
16:45:06 <matthias_samwald> kei: looking at slide 6... the Genepattern application has been used by caBIG, i think
16:45:24 <matthias_samwald> joshua: Genepattern has been exposed as a service
16:46:02 <matthias_samwald> ... there is some opportunity to express these data with OWL / NCI Thesaurus
16:47:03 <Joshua> https://cabig-kc.nci.nih.gov/Molecular/KC/index.php/GenePattern_caGrid
16:47:25 <matthias_samwald> kei: database-literature integration: gene lists could be a low-hanging fruit
16:47:52 <matthias_samwald> ... we need to confirm whether MAGE-TAB contains gene lists or not
16:48:05 <matthias_samwald> ... we could look into adding that
16:48:50 <matthias_samwald> ... aTags could be used to represent gene lists found in literature etc.
16:50:06 <matthias_samwald> ... for numeric data, maybe aTags is not designed for that, need to look into generic linked data representation
16:50:36 <matthias_samwald> ... we started collaboration with EBI
16:51:28 <matthias_samwald> ... during breakout Nigam showed us the NCBO annotator
16:53:45 <matthias_samwald> (eric takes over scribing)
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16:54:09 <matthias_samwald> ... scientific discourse / hypothesis represntation should also be integrated
16:54:12 <ericP> scribenic: ericP
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16:54:44 <ericP> [slide 10]
16:55:14 <ericP> kei: ADNI is disease-related MRI data
16:55:21 <ericP> ... could connect disease and data
16:55:44 <ericP> ... drug and model data (systems biology)
16:55:45 <Zakim> -??P0
16:55:59 <ericP> ... LoDD has a rich collection of drug data
16:56:18 <ericP> [slide 11: Translational use case]
16:56:48 <ericP> kei: would be interesting to integrate microarray data with phenotype data
16:56:58 <ericP> [slide 12: acks]
16:58:07 <ericP> topic: follow up
16:58:56 <ericP> mscottm: re: struturing RDF, if we can do it with a use case in hand, we have a better chance of understaing CaBIG tools and models
16:59:20 <ericP> ... we'll know what we need to model, and maybe we can even get some of that model from CaBIG
16:59:39 <ericP> ... can see if there's redundancy between CaBIG and e.g. CFO
16:59:51 <mscottm> s/EFO/CFO/
16:59:51 <kei> structure of rdf -- how to relate cabig
17:00:02 <mscottm> Experimental Factors Ontology
17:00:20 <ericP> Joshua: could start by (before next call) sending out a set of models which are important in this space
17:00:36 <ericP> ... lots of models
17:00:37 <kei> action item: joshua can give use cases on catissue, caarray, etc
17:00:50 <ericP> ... molecular workspace within CaBIG has lots of use cases
17:00:58 <Zakim> -Joshua
17:01:04 <Joshua> Joshua has left #hcls
17:01:17 <ericP> mscottm: should see what we can use from TMO
17:01:21 <kei> TMO -- what components can be reused
17:01:36 <ericP> ... or what requirements we can bring to them
17:01:51 <ericP> ... do they have hooks to experiments or tissues?
17:03:16 <ericP> http://www.w3.org/2009/Talks/1103-hclsalign-egp/#%2813%29
17:04:18 <ericP> kei: genes can link TMO, SWAN, etc.
17:05:08 <Zakim> -andy
17:05:22 <mscottm> Hmm. That was mscottm actually.
17:05:22 <Zakim> -EricP
17:05:23 <Zakim> -Prateek
17:05:25 <Zakim> -??P10
17:05:28 <Zakim> -Kei_Cheung
17:05:30 <Zakim> SW_HCLS(BioRDF)11:00AM has ended
17:05:31 <Zakim> Attendees were Kei_Cheung, matthias_samwald, andy, oshani, Joshua, Prateek, EricP
17:05:37 <ericP> RRSAgent, please draft minutes
17:05:37 <RRSAgent> I have made the request to generate http://www.w3.org/2009/11/09-hcls-minutes.html ericP
17:05:46 <ericP> RRSAgent, please make log world-visible
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