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.che...@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)
> >
>
>
>
