See also: IRC log
<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
<kei> http://esw.w3.org/HCLSIG/SWANSIOC/Actions/SWANmyExpArray
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
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
ack
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
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
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/skupe/skype/ No ScribeNick specified. Guessing ScribeNick: jun Inferring Scribes: jun WARNING: Replacing list of attendees. Old list: +0186528aaaa +1.506.648.aabb New list: +1.404.778.aaaa +0186528aabb WARNING: Replacing list of attendees. Old list: +1.404.778.aaaa +0186528aabb New list: +03539149aaaa Kei_Cheung Don_Doherty AlexPassant +1.404.778.aacc jun +1.937.775.aadd +03539149aaee +1.506.648.aaff Luc +1.763.463.aagg matthias_samwald WARNING: Replacing list of attendees. Old list: +03539149aaaa Kei_Cheung Don_Doherty AlexPassant +1.404.778.aacc jun +1.937.775.aadd +03539149aaee +1.506.648.aaff Luc +1.763.463.aagg matthias_samwald New list: +1.506.648.aaaa 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 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: 22 Mar 2010 Guessing minutes URL: http://www.w3.org/2010/03/22-hcls-minutes.html People with action items: WARNING: Input appears to use implicit continuation lines. You may need the "-implicitContinuations" option.[End of scribe.perl diagnostic output]