See also: IRC log
Yolanda Gil introduction: chairing W3C provenance interest group
Yolanda: talked about semantic workflows
Christain Fritz intro: postdoc with Yolanda at USC, working on semantic workflows
<YolandaGil> The site of the W3C Provenance Group I mentioned is http://www.w3.org/2005/Incubator/prov/wiki
<mscottm> Welcome Yolanda, Christian, and Simon!
Simon Twiger, U. of Wisconsin, intro: interested in integrated semantic web technologies into rat database they maintain
<Simon> Its the Medical College of Wisconsin, not actually part of the U.Wisconsin system :)
<mscottm> Simon: also one of NCBO's Research Application collaborations
Agenda item 1: how to represent microarray data in RDF/OWL and use this representation to support query federation over the web
query federation paper identified provenance and workflow as future directions; would like to explore microarray use cases in these areas
<jun> can anyone pls post the link to the irc again? I lost my irc when kei posted the link. thanks
kei: linked doc contains description of example neuroscience microarray experiment
kei: experiment compared gene
expression profiles for multiple classes of patients to
evaluate the relationship between NFT and Alzheimer's
... has been collaborating with another researcher at Yale to
propose a structured digital abstract (not specifically
RDF)
... 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)
... 2) list of main results described as a simple
ontology
... 3) standard evidence codes for how how the results were
obtained
<Simon> FEBS info on SDA: http://www.febsletters.org/content/sda_summary
kei: has been evaluated on pilot
basis
... Question: can we do something similar for microarray
data?
<Simon> FEBS special issue with SDAs: http://www.sciencedirect.com/science/issue/4938-2008-994179991-684107
kei: import the gene lists into
public database (gene omnibus, etc.)
... leverage GO for representing the gene list
... also need to capture the context (the biological condition,
the brain region); need to capture this contextual information
as part of the gene list
<ssahoo2> Provenance related Experiment Context: http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/QueryFederation2?action=AttachFile&do=get&target=NeuroscienceMicroarrayConsortium_ProvenanceTerms.txt
kei: this use case can help guide work on representing microarray data in RDF
<ssahoo2> http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/MicroarrayProvenanceUseCase
ericp: NLP over the document will give you the set of keywords but won't give relationships between the keywords
kei: can use text mining to
generate initial set of gene names but still need manual
curation
... 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
ericp: our work is how to map the
SDA into a semantic web representation
... are the identifiers URLs?
... if not URLs, need to provide some additional scheme/context
information that can eliminate identifier ambiguity
... are folks open to creating SDA info in RDF from the
start?
kei: the key is having an easy interface/tools to create the metadata
mscottm: who are the folks that will be creating the SDA data?
kei: Mark Goldstein at Yale
... need to convince Mark and others to use sem web
technology
rfrost: are all resources used in results ontology defined in translation table?
kei: yes
rfrost: what is the target expressiveness of the ontology?
kei: simple set of relations based on results reported in papers
<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
mscottm: explore ways of representing gene list data in RDF
<mscottm> http://compbio.dfci.harvard.edu/genesigdb/
kei: explore bridge between paper and gene atlas
?: role of biopax?
<matthias_samwald> (need to leave now, bye)
<mscottm> bye Matthias
kei: you could eventually incorporate gene list representation into biopax
Yolanda/Kei: use of genespring to generate results, how to reproduce results if not using that software package
Yolanda/Kei/Scott: providing workflow information and annotated data sufficient to reproduce results as well as apply methodology to other experiments
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)
Scott: two data sources relevant
to gene lists: genesigdb, gene expression atlas
... Helen indicated that we can get RDF data returned from
gxa
rfrost: what would RDF look like
from gxa?
... just URLs/linked data or RDF that references an
ontology?
scott: would be RDF references ontology
scott/yolanda/kei: to do: look at application of workflow systems to microarray analysis
scott: experimental factor ontology (http://www.ebi.ac.uk/efo/)
kei: try to create a workflow process for generating the gene list?
scott: given analytical challenge, may be better to start with the gene list and look at workflows that start with the gene list
yolanda: want to focus on a workflow were the use of semantics have a clear goal
yolanda/satya: example: provenance of the microarray data, represented in RDF, would impact the execution of the workflow
yolanda: provenance would include information about how the microarray data was obtained (equipment, data processing steps, etc.)
satya: provenance data could reference OBI terms
scott: some of this provenance
data will already be in the MAGE files
... type of analysis may not be included
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
kei: can start that process via a wiki page
scott: another idea for application of workflows: visualization of data related to differentially expressed genes
jun: should combine provenance data with domain-specific annotations
satya: will create wiki page with set of experimental contexts for evaluation
<ssahoo2> quit
<Simon> quit
<mscottm> ericP - you still on?
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