BioRDF26Mar07Minutes

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BioRDF Conference Call
26 March 2007
Attendees: Susie Stephens, Vipul Kashyap, Eric Neumann, Eric Prud'hommeaux, Scott Marshall, June Kinoshita, Jonathan Reese, Alan Ruttenberg, Matthia Samwald, Elizabeth Wu (Scribe)

Susie put together a word document outlining the demo
Vipul: Is it on the wiki?
Susie will post on wiki after getting feedback
ericP posted http://www.w3.org/2007/03/entrez-gene/ mapping of Entrez-Gene data to RDF
ericP posted http://www.w3.org/2007/03/entrez-gene/snapshots/ examples of mapping of Entrez-Gene data to RDF
ericP posted http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=homologene
AlanR says look at TP63
ACTION:: For Alan, deadline for Entrez Gene example is April 10th
EricN: Alan, are you using any of Olivier's work with Entrez?
ACTION: Alan - mapping phenotype data, RGD, pathway association, and GO, April 10th for an update
Alan has access to Olivier's data, files is too big for demo, model much more tied to XML/ANS model, prefer to have "slimmer" version
Alan will follow up wtih Olivier since current form is difficult to work with
BAM dataset in good shape, Don Doherty looking at final modeling
mapping SenseLab to RDF/OWL - Kei is still working on, Matthias will be working with Kei after April 1st
Alzgene - Michael Heuer is working on
ACTION: Jonathan Rees to make a MeSH / PubMed association
Images - GeneSTAT, Allen Brain Map, CCDB
Antibodies - Alan almost finish
ACTION: SWAN hypotheses - June and Gwen - three hypotheses related to use case
SWAN first release of annotation tool last Friday
ACTION: June will check if end of March is a reasonable deadline
EricN suggested to incorporate PubChem into the demo
EricN - some compounds are used as therapeutic agents, some are experimental, one could associate compounds with targets
Susie asked if EricN would be willing to look at PubChem
ACTION: EricN will report back April 10th
keep it simple for now - therapeutic agents
Susie will post info on wiki by end of today, asking for feedback from group
two deadlines - end of March, April 10th
will try to schedule another informal F2F gathering on April 10th afternoon before semantic web group gathering that evening.
JonathanR: not demo related: I will tell folks on HCLS list today about availability of neurocommons text mining alpha
EricN posted: http://simile.mit.edu/exhibit/
EricN posted: http://simile.mit.edu/wiki/Exhibit/Getting_Started_Tutorial
EricN posted: converting RDF to json: http://simile.mit.edu/babel/
Susie asked group to look at exhibit this week, perhaps schedule a demo during F2F
AlanR: useful to imagine a question and display from Exhibit
EricN: first thing to ask - which databases are available for a certain disease?
AlanR: question needs to be useful
SusieS: could have multiple users in the demo
SusieS: need to follow up on the story line for the demo in F2F
Vipul: So, is prefuse a graph visualization tool?
SusieS: how to run the demo - on a local laptop? on web? a video?
SusieS: in favor on web or local laptop, backup video or screenshots
mscottm: 1+ on screenshots, movie backups
ericP: q+ to promote multi-laptop deployment
JonathanR: in theory, one could configure a local proxy (apache) to serve up most pages, thus avoid screen shots
SusieS: need a box, what are options? W3C? HP? IBM? welcome thoughts
EricP: looking at hosting at W3C, but ran into challenges
EricP: prefers demo on laptop, able to show others after presentation
EricP: could also mirror demo on web
AlanR: one possibility to build on virtual machines
Discussion on what machines to use for demo:
ACTION:Vipul will follow up HP for donation
ACTION:Susie will follow up with IBM
ACTION:EricN will follow up with Apple
What kind of boxes?
AlanR: box can run databases, fast disk access, decent memory, can run RedHat preferrably
SusieS: needs to know conference room set up, can we have two screen projections?
ACTION:ericP to ask ISWC folks about dueling projectors
SusieS: demo need to show both technical and scientific components
JuneK: use case is amiable to late person to understand the biology
EricN: pharma folks will be in the meeting
SusieS: should describe the challenges for life science information retrieval
Vipul: how semantic web could do faster, better, etc, compare to other technology
ACTION:SusieS: will put on wiki the important points to discuss on demo