introduction

<kei> scribenick Matthias

scribenick matthias_samwald

<kei> http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/QueryFederation2?action=AttachFile&do=get&target=BioRDF+Breakout+Update.pdf

kei: The presentation is available as a PDF

Joshua: my name is joshua philips. work at semantic bits. worked for caBIG (infrastructure etc.)
... Currently I am trainig that community in Semantic Web technology

<oshani> There are 2 of us: Oshani and Rachel, and we are working on this project: http://code.google.com/p/querymed

oshani: hi, i am Oshani Seneviratne.
... we are involved in a small project (sparql queries, user interface for physicians).

kei: thanks for your introductions.
... at the BioRDF breakout last week in Santa Clara we had 20 participants.
... we had two main parts. first presentations, then discussions.
... presentation by me (kei) about microarray work
... work on expanding query federation demo with microarray dat
... MIAME standard -- what is the minimum information to practically annotate microarray data.
... MAGE-TAB is a new standard for capturing such data, Michael Miller gave a presentation.

<ericP> oops

kei: Matthias Samwald gave a presentation on aTags
... slide number 3: we talked about possible RDF structures for representing microarray data
... we also invited the SPARQL group to discuss extensions to SPARQL
... other points of discussion: tools and visualization (how to integrate heterogeneous tools)
... integration of databases and literature
... microarray data needs to be integrated with pathway data etc
... we have started an interaction with the NCBO
... they helped us use some of their tools

bye!

kei: we have huge amounts of raw data in native format that can be read by certain types of tools for processing
... 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
... gene lists (e.g. which genes are affected in a certain experiment) usually consist of several hundreds of genes of interest.
... what genes are upregulated in a certain neurological condition? and other questions. these data should be comparable between experiments.
... annotation should also capture which algorithm was used
... based on the algorithm, users can decide whether two datasets are comparable or not

<mscottm> NIFSTD

kei: the NIFSTD is a terminology/OWL ontology developed for the neuroscience information framework (NIF).
... it is available in BioPortal.

<mscottm> Experimental Factors = CFO = Experimental Factors Ontology

kei: when data is expressed in linked data format, metadata / provenance need to be represented as well. vOID is interesting in this regard.
... aTags is an interesting approach for representing both structured and unstructured/text data in a single format.
... query federation: we used the hierarchical query feature to get all brain regions located within a larger brain region, enabling query expansion
... aggregate functions could be useful for statistical analysis of data.
... provenance and workflowas are important. projects include taverna and biomoby.
... data analysis projects: bioconductor (based on R), matlab
... how could we get software vendors interested in use-case?
... how can grid and cloud computing be incorporated in use-case?

eric: we need to find out how we interact with caBIG.

kei: looking at slide 6... the Genepattern application has been used by caBIG, i think

joshua: Genepattern has been exposed as a service
... there is some opportunity to express these data with OWL / NCI Thesaurus

<Joshua> https://cabig-kc.nci.nih.gov/Molecular/KC/index.php/GenePattern_caGrid

kei: database-literature integration: gene lists could be a low-hanging fruit
... we need to confirm whether MAGE-TAB contains gene lists or not
... we could look into adding that
... aTags could be used to represent gene lists found in literature etc.
... for numeric data, maybe aTags is not designed for that, need to look into generic linked data representation
... we started collaboration with EBI
... during breakout Nigam showed us the NCBO annotator

(eric takes over scribing)

scribe: scientific discourse / hypothesis represntation should also be integrated

<ericP> scribenic: ericP

<ericP> [slide 10]

<ericP> kei: ADNI is disease-related MRI data

<ericP> ... could connect disease and data

<ericP> ... drug and model data (systems biology)

<ericP> ... LoDD has a rich collection of drug data

<ericP> [slide 11: Translational use case]

<ericP> kei: would be interesting to integrate microarray data with phenotype data

<ericP> [slide 12: acks]

follow up

<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

<ericP> ... we'll know what we need to model, and maybe we can even get some of that model from CaBIG

<ericP> ... can see if there's redundancy between CaBIG and e.g. CFO

<kei> structure of rdf -- how to relate cabig

<mscottm> Experimental Factors Ontology

<ericP> Joshua: could start by (before next call) sending out a set of models which are important in this space

<ericP> ... lots of models

<kei> ACTION: item to joshua can give use cases on catissue, caarray, etc [recorded in http://www.w3.org/2009/11/09-hcls-minutes.html#action01]

<ericP> ... molecular workspace within CaBIG has lots of use cases

<ericP> mscottm: should see what we can use from TMO

<kei> TMO -- what components can be reused

<ericP> ... or what requirements we can bring to them

<ericP> ... do they have hooks to experiments or tissues?

<ericP> http://www.w3.org/2009/Talks/1103-hclsalign-egp/#%2813%29

<ericP> kei: genes can link TMO, SWAN, etc.

<mscottm> Hmm. That was mscottm actually.

This is scribe.perl Revision: 1.135  of Date: 2009/03/02 03:52:20  
Check for newer version at http://dev.w3.org/cvsweb/~checkout~/2002/scribe/

Guessing input format: RRSAgent_Text_Format (score 1.00)

Succeeded: s/EFO/CFO/
No ScribeNick specified.  Guessing ScribeNick: matthias_samwald
Inferring Scribes: matthias_samwald
Default Present: Kei_Cheung, matthias_samwald, andy, oshani, Joshua, Prateek, EricP
Present: Kei_Cheung matthias_samwald andy oshani Joshua Prateek EricP

WARNING: No meeting title found!
You should specify the meeting title like this:
<dbooth> Meeting: Weekly Baking Club Meeting


WARNING: No meeting chair found!
You should specify the meeting chair like this:
<dbooth> Chair: dbooth

Got date from IRC log name: 09 Nov 2009
Guessing minutes URL: http://www.w3.org/2009/11/09-hcls-minutes.html
People with action items: item