W3C home > Mailing lists > Public > public-semweb-lifesci@w3.org > May 2009

Re: BioRDF Telcon - Provenance related information

From: Kei Cheung <kei.cheung@yale.edu>
Date: Thu, 14 May 2009 10:52:46 -0400
To: Satya Sahoo <sahoo.2@wright.edu>
Cc: HCLS <public-semweb-lifesci@w3.org>
Message-id: <4A0C303E.8000804@yale.edu>
Thanks for sharing the information, Satya.

Your group's work on workflow provenance seems to be quite synergistic 
with what the BioRDF and Scientific Discourse task forces are doing and 
could potentially facilitate task force intersection.

To provide a neuroscience context, below is an example from the NIH 
neuroscience microarray consortium:

http://np2.tgen.org/np2/viewProject.do?action=viewProject&projectId=176167

It describes a drosophila (fruit fly) microarray experiment that uses 
gene expression profiling to study how the genes involved in circadian 
rhythm regulation affect long-term memory/learning. As described in the 
project, such a neuroscience microarray study is relevant to drug 
addiction research and Alzheimer's disease research. The project 
description has sections such as hypothesis and experimental procedure 
and design, which may contain relevant provenance information.

Cheers,

-Kei

Satya Sahoo wrote:
> Hi all,
> This is pursuant to our provenance-related discussion during the 
> telecon earlier today. As part of our collaborative RO1 with the 
> national center for biomedical ontologies (NCBO) called "Tcruzi SPSE" 
> (http://wiki.knoesis.org/index.php/Trykipedia), we have developed an 
> upper-level reference ontology for provenance called "provenir" 
> modeled in OWL-DL.
>  
> Provenir was developed using the OBO Foundry principles (and has been 
> recently submitted to the OBO foundry for review), details are at: 
> http://wiki.knoesis.org/index.php/Provenir_Ontology. We have extended 
> Provenir ontology to create a Parasite Experiment ontology 
> (http://wiki.knoesis.org/index.php/Parasite_Experiment_ontology) for 
> provenance of transcriptome and gene knockout data.
>  
> As Kei mentioned, we have proposed to organize a workshop at ISWC 2009 
> on the role of Semantic Web in provenance management (keynote by Dr. 
> Carole Goble, if the workshop proposal is accepted). Further details 
> are at: http://wiki.knoesis.org/index.php/SWPM-2009.
>  
> A couple of references discussing our work in detail:
> 1. Semantic Provenance for eScience - 
> http://knoesis.wright.edu/library/resource.php?id=00310. This paper 
> gives a broad overview of our approach with an use case from the 
> glycobiology domain
> 2. An Algebra and RDF Query Engine for Provenance - 
> http://knoesis.wright.edu/library/resource.php?id=00706. This paper 
> discusses the technical details of a Provenir ontology-based algebra 
> we have proposed for provenance and an implementation of a provenance 
> query engine over Oracle10g RDF store
>  
> I will be happy to discuss further details of our work in future telecons.
>  
> Cheers,
> Satya Sahoo
> http://knoesis.wright.edu/researchers/satya
>
> ----- Original Message -----
> From: Kei Cheung <kei.cheung@yale.edu>
> Date: Monday, May 11, 2009 1:38 pm
> Subject: Re: BioRDF Telcon
> To: HCLS <public-semweb-lifesci@w3.org>
>
> > The minutes for today's BioRDF minutes are available at:
> >
> > http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/Meetings/2009-05-
> > 11_Conference_Call
> > Thanks to Rob for scribing.
> >
> > Cheers,
> >
> > -Kei
> >
> > Kei Cheung wrote:
> > > This is a reminder that the next BioRDF teleconf. will be held
> > at 11
> > > am EDT (5 pm CET) on Monday, May 11 (see details below).
> > >
> > > Cheers,
> > >
> > > -Kei
> > >
> > > == Conference Details ==
> > > * Date of Call: Monday May 11, 2009
> > > * Time of Call: 11:00 am Eastern Time
> > > * Dial-In #: +1.617.761.6200 (Cambridge, MA)
> > > * Dial-In #: +33.4.89.06.34.99 (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
> > > [http://www.w3.org/Project/IRC/ W3C IRC page] for details, or
> > see
> > > [http://cgi.w3.org/member-bin/irc/irc.cgi Web IRC])
> > > * Duration: ~1 hour
> > > * Frequency: bi-weekly
> > > * Convener: Kei Cheung
> > >
> > > == Agenda ==
> > > * Roll call and introduction (Kei)
> > > * HCLS F2F BioRDF update and follow-up (All)
> > > * Finalize revisions of the BMC Bioinformatics paper (All)
> > >
> >
> >
> >
Received on Thursday, 14 May 2009 14:53:34 GMT

This archive was generated by hypermail 2.3.1 : Tuesday, 26 March 2013 18:00:55 GMT