22 Mar 2010

See also: IRC log


matthias_samwald, Don_Doherty, Kei_Cheung, +1.506.648.aaaa, +1.937.775.aabb


<Donald_Doherty> Restricted conference?

<AlexPassant> cannot join on phone neither

me neither

I pinged Eric, to see whether he could help

<ericP> working on it

I could join in on 42572

<ericP> go with 42572

<ericP> ok, 42572

<ericP> i don't know what will happen with term

<ericP> but you all can probably work it out

<mscottm> I can't make TERM today John will need to know the magic incantation.

<david_newman> Hi All

look at the wiki page

<kei> http://esw.w3.org/HCLSIG/SWANSIOC/Actions/SWANmyExpArray


<david_newman> I can't seem to join the concall as it says its restricted

try 42572

<david_newman> ok I will try that

ScribNick: jun

<mscottm> https://docs.google.com/viewer?url=http://esw.w3.org/images/a/ac/SWAN-myExp-MGED_Sketch_v3-1%252B2.pdf

Sudeshna: integrate different ontologies, SWAN and myExperiemnt ontology, etc
... introduce a layer of "study" to link SWAN and myExperiment ontology
... a study has data acquistion, using some assay in the lab, etc.
... data acquistion has replicates

scott: plan to work together with EFO ontology from EBI?

Sudeshna: no research on that yet

Kei: the key is to identify overlaps between different experiment ontologies, coordinate and interact with other people

Action to Sudeshna: investigate how to align with other ontologies

<trackbot> Sorry... I don't know anything about this channel

Sudeshna: we identify how MGED can interact with SWAN and other ontolgoies
... how the gene list objects from biordf task can fit with MGED ontology
... can link a claim with a data

Kei: gene lists are actually kind of evidence, part of the hypothesis

david: the OBI investigation ontology precedes the MGEN ontology?

satya: MGED is part of the OBI now


Action to satya: check our ontologies align with the OBI ontologies

<trackbot> Sorry... I don't know anything about this channel

Sudeshna: would like to have some examples to test this model

Kei: the microarray study from BioRDF might fit it. and we also find some terms to capture the exeriments, and we looked at other ontologies from the neuro. science domain
... we haven't gone into a lot of details at the workflow level
... we need some one who really understands the computational part of the experiment, in order to capture this part of the metadata

David: I have looked at some workflow ontologies

Sudeshna: can we still use that ontology to describe processes that are not web services?

David: a process from the myExperiment ontology could be a web service or a script

<david_newman> myExperiment's workflow components ontology - http://rdf.myexperiment.org/ontologies/components

<egonw> like a Taverna activity?

Kei: we have someone working on the provenance of experiments and we need someone to pick up Lena's work of modelling gene lists

Action to Jun, Satya, and Kei: create an RDF graph to describe the microarray experiment from bioRDF using these ontologies

<trackbot> Sorry... I don't know anything about this channel

<david_newman> @egonw Currently no RDF is being generated for the components of non-taverna workflows but the ontology is intended to be extensible

Action to Paolo: create an OWL for the file at https://docs.google.com/viewer?url=http://esw.w3.org/images/a/ac/SWAN-myExp-MGED_Sketch_v3-1%252B2.pdf

<trackbot> Sorry... I don't know anything about this channel

introduction to the group

trackbot, end telcon

<egonw> david_newman: yeah, I wish I had a bit more time to look at the myexperiment onto

<egonw> been using the RDF/onto in Bioclipse to search and download Bioclipse Scripts

<egonw> david_newman: also recently started uploading SPARQL queries, after talking with Kathy in November at SWAT4LS

<david_newman> @egonw Sorry just in transit there. I have to admit there isn't much documentation for the components ontology yet. There is a autogenerated spec document at http://rdf.myexperiment.org/generic/spec?ontology=41

<egonw> one thing that comes to mind: a XMPPProcessor

<egonw> love to see that :)

<david_newman> @egonw If you want to talk about this further I think I have you as a skype contact

<david_newman> The intention is to allow for specification of other types of processor

<egonw> tomorrow the main XMPP IO-Data developer is here in our group... I'll see if I can write up some OWL for the processor...

<egonw> will email if so

<egonw> btw, why is there no SOAPProcessor? or is all SOAP nowadays via WSDL? Perhaps even T2 requires that (practically)?

<david_newman> If you some example of the XMPPProcessor as they are represented in the workflow markup I should be able to incorporate them fairly quickly

<david_newman> I'll talk to you in skype as I think this channel will be in use

<egonw> indeed :)

<matthias_samwald> matthias is here as well, i cannot really talk at the moment (shared office)

<kei> chris baker introduction

<kei> semantic web ontologies in canada

<kei> worked with kei on the sw book.

<kei> moved to singapore to work on text mining (dengue fever)

<kei> lipid ontology

<kei> visual query access

<kei> axioms and classes for the lipid ontology

<kei> based on function lipid groups

<kei> reflect structures of lipid molecules

<kei> semantic web services

<kei> mark up lipid related abstracts

<kei> semantic assistant framework

<kei> semantic assistant

<kei> described through wsdl

<kei> standard person location etc

Summary of Action Items

[End of minutes]

Minutes formatted by David Booth's scribe.perl version 1.135 (CVS log)
$Date: 2010/03/22 16:48:24 $

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Default Present: matthias_samwald, Don_Doherty, Kei_Cheung, +1.506.648.aaaa, +1.937.775.aabb
Present: matthias_samwald Don_Doherty Kei_Cheung +1.506.648.aaaa +1.937.775.aabb

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<dbooth> Chair: dbooth

Got date from IRC log name: 22 Mar 2010
Guessing minutes URL: http://www.w3.org/2010/03/22-hcls-minutes.html
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