HCLSIG BioRDF Subgroup/Meetings/2010/01-25 Conference Call

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Conference Details

  • Date of Call: Monday January 25, 2010
  • Time of Call: 11:00 am Eastern Time
  • Dial-In #: +1.617.761.6200 (Cambridge, MA)
  • Dial-In #: + (Nice, France)
  • Dial-In #: +44.117.370.6152 (Bristol, UK)
  • Participant Access Code: 4257 ("HCLS")
  • IRC Channel: irc.w3.org port 6665 channel #HCLS (see W3C IRC page for details, or see Web IRC), Quick Start: Use http://www.mibbit.com/chat/?server=irc.w3.org:6665&channel=%23hcls for IRC access.
  • Duration: ~1 hour
  • Frequency: bi-weekly
  • Convener: Kei Cheung
  • Scribe: Kei Cheung


Matt Cherian, Kei Cheung, Helena Deus, Don Doherty, Eric Prud'hommeaux, Matthias Samwald, Scott Marshall



  • Introduction [Kei]
  • Microarray use case -- exploring the RDF structure [All]
  • Applicatios/demos [All]


<ericP> use cases for rdb2rdf:

<ericP> COI

<ericP> 7tm

<ericP> gene lists

<ericP> mscottm: many gene lists are not machine readable

<ericP> tabular structure can come from excel ericP welcome mcherian

<mcherian> thank you

<mcherian> does the telecon usually start at 1000 EST or 1100 EST?

<LenaDeus> kei: eric suggests using RDB to SPARQL query structure

<kei> matt: 2nd year grad. student at mit

<kei> matt: next to w3c office

<ericP> topic: RDF structure for gene lists

<kei> eric, can you scribe for Lena

<ericP> LenaDeus: considering annotating the gene lists from the mircoarray use case

<ericP> kei: you have an example of links to a specific gene card

<ericP> ... can we make that link broader, so folks can link other sources?

<ericP> ericP: depends on operational semantics

<ericP> ericP: is this typically in a spreadsheet?

<mscottm> no

<mscottm> http://sharedname.org/page/Use_Cases#Health_Care_and_Life_Sciences_Interest_Group

<mscottm> Scott: We need to provide a gene list to Shared Na

<mscottm> .. Shared Names so that SN can arrive at an agreement about how the URI's will look

<kei> http://public.tgen.org/tgen.org/supplementarydata/neurogenomics/supplementarydata/dunckley_etal/U133_plus_2.0_AD.xls

<LenaDeus> scott: shared names - given a gene list, which names we should use?

<LenaDeus> scott: how to approach the "/" vs "#" issue?

<LenaDeus> eric: motivation from both sides;

<mscottm> ericP: Another issue is that the slashes proposed by Shared Names are syntactically incompatible with the hash (#) approach

<LenaDeus> eric: shared names uses an "architecturally pure" approach

<LenaDeus> scott: how much data using hash vs dash?

<LenaDeus> eric: what are the relative costs of the two? the trade-off needs to be determined so that we can take a stand

<mscottm> http://www.ncbi.nlm.nih.gov/sites/entrez?Db=gene&Cmd=ShowDetailView&TermToSearch=261729

<LenaDeus> http://www.ncbi.nlm.nih.gov/gene/261729

<LenaDeus> eric: a variety of gene identifier that may be used (and that's the goal of shared names)

<LenaDeus> ericP: how to handle RDB to RDF mapping?

<LenaDeus> kei: mapping using the schema

<LenaDeus> kei: graph mapping rather than identifier mapping;

<LenaDeus> eric: is there a use case to use the federation of this with other data structure?

<LenaDeus> scott: taken a set of gene and looking at its function, the expression value may not mean much

<LenaDeus> kei: in some cases we want to look at over expressed genes, other cases we may want to compare the expression values

<LenaDeus> scott: the favorite gene approach - if a certain gene is know n to be involved in a phenomena, then it can be included in multiple studies

<LenaDeus> kei: next steps - start with the gene lists; learn how to convert it from excel to rdf

<LenaDeus> kei: how to demo?

<ericP> LenaDeus: two ideas for linking gene lists to experiements:

<ericP> ... .. simply say <experiementX> :generated <gene list Y> .

<ericP> ... .. include process (workflow) which led to the gene list

<LenaDeus> don: iphone application; were certain genes from the gene list already known to be involved in problematic pathways

<mscottm> Checkout: http://www.biomedcentral.com/1471-2105/10/S2/S3

<LenaDeus> scott: Rubin paper presents mapping genes to neurological regions

<LenaDeus> scott: mapping it eventually to an mri scanning would be useful to understand the process

<LenaDeus> mscottm: how to link with them

<ericP> how about links to myexperiment?

<mscottm> ACTION: Scott will contact Rubin et al to explore possible overlap

<mscottm> have to go to TERM call - bye!

<LenaDeus> action items: kei to add the spreadsheet gene lists; LenaDeus to create the gene list rdf structure and share it through a wiki page; consult with Satya and Jun how to connect it to experiment description (provenir) and see what metadata needs to be captured at the experiment level.