C-SHALS

<kei> scribenick Matthias

kei: agenda will start with don's demo of his iPhone app

<Donald_Doherty> Download slides from:

<Donald_Doherty> http://www.actionpotential.com/SemanticWb_beta2_1.pdf

kei: then we will go on to the microarray use-case and discussion of cross-task activities

<kei> http://www.actionpotential.com/SemanticWb_beta2_1.pdf

introduction

TOPIC -- Don's iPhone Application

don: slides are at http://www.actionpotential.com/SemanticWb_beta2_1.pdf
... if you go to iTunes and donwload the "SemanticWb" application, you can choose between SPARQL endpoints
... i will be using the Neurocommons endpoint
... i will show version 2.1, which will soon be available
... you have to run the application on the iPhone / iPod Touch / iPad, you cannot run it through iTunes directly
... you can do a lot with a central server where you aggregate everything, but what could i do with accessing SPARQL endpoints?
... you cannot do complex calculations or reasoning on an iPhone
... to start, you type in something interesting.
... autocomplete turned out to be too slow
... MeSH terminology is integrated into the system
... search gives you MeSH results
... you can navigate to proteins (e.g., amyloid beta)
... from there to articles

<sudeshna> Hi! Ti asked me to join the call - can you please send a pointer to the presenatation?

don: associated genes [slide 10]

http://www.actionpotential.com/SemanticWb_beta2_1.pdf

that is the link, sudeshna

<sudeshna> Thanks!

scribe: association of genes, gene products...

don: ... summary of information about a protein, acess to UniProt website, structure data
... structure data and images can be browsed
... including 3d views

<mscottm> <applause>

don: the newest version will be available on iTunes in 1-2 weeks

kei: this is interesting and impressive, gives people a feel of what can be done on an iPhone.
... have you thought about adding links to podcasts etc.?

don: not yet, but great idea

kei: other ideas: scientific newsfeeds? using the iPhone during meetings and conferences?

don: yes, quickly looking up something during meetings is important

<mscottm> scott: It would be nice to add a tab that integrates the BioRDF microarray use case in a generic way.

but i'm back.

<mscottm> thanks for coming back :)

<mscottm> ..Specific idea (if possible?): add a 'data tab' next to the existing tabs that allows you see gene lists from specific microarray data sets within the context of Alzheimer's Disease.

who is talking? i can take over scribing again.

<mscottm> Michael Miller

michael: bioconductor could be useful in this context

<mscottm> Michael: mentioned that Misha Kapushesky demo'd a cloud application of BioConductor at an MGED meeting

kei: don, can you create a wiki page for the iPhone app?

don: yes, i will do that.

scott: if you could annotate / aTag you own relation and add it to the HCLS or Concept Web Alliance knowledge base (protein a has something to do with protein b etc.), this could be valuable
... the idea behind the Concept Wiki, for example, is to find people that have made similar research statements like you

<kei> http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/MicroarrayExperimentContext

TOPIC -- Microarray use-case

kei: if you scroll down on http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/MicroarrayExperimentContext you find a long list of provenance terms
... i used the NCBO Biomedical Annotator on Pubmed abstracts and experiment texts to identify terms
... we also identify some provenance ontologies -- Provenir, MGED, NIF etc.
... gene lists represent a nice use-case for provenance information
... gene lists are not treated as a standard submission for microarray databases, we could work with MGED to make this part of the standard submission process (in addition to raw data)

scott: people know that there is a need for disclosing gene lists, this would be a good extension for MAGE-TAB, but there is also a policy decision if MGED requires the disposition of this data
... decisions on this might be made during the next MGED meeting.

michael: one of the things about MGED, which started out as a grass-roots organization: people are enthusiastic, but realization can be tricky.
... gene lists are disclosed, but mostly as supplemental data in a non-machine-readable way.
... not everything in the paper is useful, even though authors might claim so.

kei: if MGED or MIAME could define a very simple standard/spreadsheet/template, this would already be a small step forward.

michael: it is not a MIAME issue, MIAME does not state a format

sudeshna: MIAME gives you the essential elements, but not more
... having an entry mask where people enter text and generate RDF this way, this could be useful
... tim clark was talking to carole goble, linking SWAN to MyExperiment ontology, linking to SWAN claims

kei: with named graphs you could capture some of the provenance information
... based on your experience, maybe we could come up with a way to represent provenance

<mscottm> Scott: Chris Stoeckert (current MGED board president) suggested the basic requirements for gene list disclosure to be: probe ID (could be a list as multiple probes are often combined and averaged), Gene symbol (could be optional), plus the protocol and parameters used for generating the gene list.

kei: to have something concrete to suggest to MGED
... maybe even a standard Excel format for entry

michael: kei, that is exactly what i was thinking

kei: this would facilitate the cross-task work between BioRDF and Scientific Discourse

<mscottm> Her name is Aedin.

<ssahoo2> I have been contact with Tim Clark regarding a provenance use case from scientific discouse community - I will get back in touch with him

scott: last week in boston, kei, tim, I and some other people noted that provenance work was done is several task forces.

<ericP> jun, i believe you can type "ack me" to be immediately unmuted -- less typing

<jun> great tip, thanks

kei: to make this synergistic, it would be crucial to move this project forward and to make a real impact on the communities
... i just came back from an NSF workshop (about visualisation)
... the Concept Web Alliance and the VIVO community could also be potentially synergistic
... some people at this workshop were aware of our work
... people confuse BioRDF and Bio2RDF. want to know about overlap etc.
... I chatted with Michel, we should try to clarify

rob: there is another group that is comparable to VIVO called eagle-i, less focusing on people, but on research resources, consortium made up of 9 institutions, headed by harvard.

<jun> http://esw.w3.org/topic/HCLS/WWW2010/Workshop

<rfrost> currently collaborating with VIVO, NIF, OBI and BRO groups on ontology dev

kei: we will meet again in two weeks

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