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Re: [ANN] News from the FlyWeb Project (Milestone FM3)

From: Kingsley Idehen <kidehen@openlinksw.com>
Date: Tue, 12 May 2009 07:16:22 -0400
Message-ID: <4A095A86.6000701@openlinksw.com>
To: Alistair Miles <alistair.miles@zoo.ox.ac.uk>
CC: public-lod@w3.org
Alistair Miles wrote:
> Dear all,
>
> This is an update from the FlyWeb Project (http://flyweb.info) on our
> third milestone release (FM3) of cross-database search applications,
> web services and software, exploring Web-based data integration for
> Drosophila functional genomics.
>
> Highlights in this milestone include:
>
> * Two new gene expression data search applications:
>   http://openflydata.org/search/gene-batch-expression and
>   http://openflydata.org/search/by-expression-profile
>
> * Retrieval of literature references from FlyBase added to
>   http://openflydata.org/search/gene-expression
>
> * Significantly expanded conversion of FlyBase (FB2009_02) to RDF,
>   covering all Chado modules except companalysis.
>
> * New release of SPARQLite SPARQL protocol implementation, including
>   support for TDB named graph datasets, ARQ query language, and LARQ
>   (Lucene + ARQ) integration.
>
> We are nearing the end of the project, so this may be the last
> milestone release we are able to make. Nevertheless, we'd still very
> much appreciate thoughts, suggestions, feedback and bug reports. All
> of the services and resources described here will persist as described
> at least until May 2010.
>
> All of the information in this email is also at:
>
> * http://imageweb.zoo.ox.ac.uk/wiki/index.php/FlyWeb/MilestoneThree
>
> ----
> = openflydata.org Cross-Database Search Tools =
>
> The following search applications are deployed at
> http://openflydata.org in this release...
>
> * (updated) http://openflydata.org/search/gene-expression :: find &
>   compare microarray data from FlyAtlas, in situ images from BDGP and
>   Fly-TED, and literature references from Flybase, for a single
>   D. melanogaster gene
>
> * (new) http://openflydata.org/search/gene-batch-expression :: find &
>   compare microarray data from FlyAtlas, in situ images from BDGP and
>   Fly-TED, and literature references from Flybase, for a batch of one
>   or more D. melanogaster genes
>
> * (new) http://openflydata.org/search/by-expression-profile :: search
>   for genes matching a tissue expression profile (e.g. up in testes,
>   down in all other tissues)
>
> The applications at http://openflydata.org/search/insitus (compare
> images of in situ gene expression in D. melanogaster testes and
> embryos) and http://openflydata.org/search/flyatlas-by-gene (search by
> gene for expression level data) are both still available also -- these
> are variants on the http://openflydata.org/search/gene-expression
> application.
>
> = Datasets & Web Services =
>
> The following datasets are made available in this release.
>
> == FlyBase (FB2009_02) ==
>
> A relatively complete conversion of the FlyBase Chado database
> (version FB2009_02) was completed in this milestone. A public SPARQL
> endpoint is available, in addition to RDF dump downloads, D2RQ maps,
> and a first complete release of the Chado-in-OWL ontology
> (http://purl.org/net/chado/schema/).
>
> For full details of the FlyBase Milestone 3 release, see:
> http://code.google.com/p/openflydata/wiki/FlyBaseMilestone3
>
> == BDGP (mRNA in situ images) ==
>
> No change from FlyWeb Milestone Two (FM2).
>
> For more information on this dataset see:
> http://code.google.com/p/openflydata/wiki/Bdgp
>
> == FlyAtlas ==
>
> No change from FlyWeb Milestone Two (FM2).
>
> For more information on this dataset see:
> http://code.google.com/p/openflydata/wiki/Flyatlas
>
> == Fly-TED ==
>
> No change from FlyWeb Milestone Two (FM2).
>
> For more information on this dataset see:
> http://code.google.com/p/openflydata/wiki/Flyted
>
> = Software =
>
> == FlyUI ==
>
> FlyUI (http://flyui.googlecode.com/) is the library of JavaScript
> widgets used to build the cross-database search tools deployed at
> http://openflydata.org.
>
> This release includes a new widget for FlyBase references, and new
> widgets and applications to enable the search by gene batch and search
> by tissue expression profile applications.
>
> * Anonymous SVN checkout (whole eclipse project):
>   http://flyui.googlecode.com/svn/tags/flyui-20090414-FM3-RC2
>
> * JavaScript bundled download of FlyUI libraries (doesn't include
>   applications):
>   http://flyui.googlecode.com/files/flyui-all-min-20090414-FM3-RC2.js
>
> * Browse source code: http://code.google.com/p/flyui/source/browse/
>
> For more information on FlyUI see: http://flyui.googlecode.com/
>
> == SPARQLite ==
>
> SPARQLite (http://sparqlite.googlecode.com/) is an implementation of
> the SPARQL Protocol, using Jena TDB as the underlying RDF storage and
> query engine.
>
> SPARQLite version 0.4 includes an upgrade to TDB 0.7.2, support for
> TDB named graph datasets, support for the ARQ query language, and
> support for LARQ (Lucene + ARQ) integration.
>
> * WAR download:
>   http://sparqlite.googlecode.com/files/sparqlite-20090226-0.4-alpha4.war
>
> * Anonymous SVN checkout:
>   http://sparqlite.googlecode.com/svn/tags/sparqlite-20090226-0.4-alpha4
>
> * Browse source code:
>   http://code.google.com/p/sparqlite/source/browse/
>
> For more information about SPARQLite, see:
> http://sparqlite.googlecode.com/
>
> ----
> = Presentations =
>
> http://openflydata.org/about/flyweb-20090506-oerc.pdf
> http://openflydata.org/about/flyweb-20090506-jisc-demo.pdf
> http://openflydata.org/about/flyweb-20090423-oxford.pdf
> http://openflydata.org/about/flyweb-20090325-ogn.pdf
> http://openflydata.org/about/flyweb-20090126-cambridge.pdf
> http://openflydata.org/about/flyweb-20090121-london.pdf
> http://openflydata.org/about/flyweb-20081113-HCLS-call.ppt
> http://openflydata.org/about/flyweb-20081111-gk-swig-uk.pdf
>
> ----
> = Known Issues =
>
> * URI design for the FlyBase dataset has changed from FM2. This
>   includes URIs for gene features. Other datasets that use gene
>   feature URIs have not yet been updated to reflect this change. This
>   includes the FlyAtlas and FlyTED datasets, which still use gene
>   feature URIs from FlyBase FM2, so links between these datasets based
>   on gene feature URIs are currently broken.
>
> ----
>
> Kind regards,
>
> Alistair Miles
> Jun Zhao
> Graham Klyne
> David Shotton
>
>   
Alistair,

Great stuff!

btw - has the RDF dumps page on ESW Wiki [1] been updated?

Links:

1. http://esw.w3.org/topic/DataSetRDFDumps


-- 


Regards,

Kingsley Idehen	      Weblog: http://www.openlinksw.com/blog/~kidehen
President & CEO 
OpenLink Software     Web: http://www.openlinksw.com
Received on Tuesday, 12 May 2009 11:17:03 UTC

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