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

From: Alistair Miles <alistair.miles@zoo.ox.ac.uk>
Date: Tue, 12 May 2009 10:57:51 +0100
To: public-semweb-lifesci@w3.org
Message-ID: <20090512095751.GF8738@skiathos>
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

* Retrieval of literature references from FlyBase added to

* 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

= 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

For full details of the FlyBase Milestone 3 release, see:

== BDGP (mRNA in situ images) ==

No change from FlyWeb Milestone Two (FM2).

For more information on this dataset see:

== FlyAtlas ==

No change from FlyWeb Milestone Two (FM2).

For more information on this dataset see:

== Fly-TED ==

No change from FlyWeb Milestone Two (FM2).

For more information on this dataset see:

= Software =

== FlyUI ==

FlyUI (http://flyui.googlecode.com/) is the library of JavaScript
widgets used to build the cross-database search tools deployed at

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):

* JavaScript bundled download of FlyUI libraries (doesn't include

* 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:

* Anonymous SVN checkout:

* Browse source code:

For more information about SPARQLite, see:

= Presentations =


= 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 Miles
Senior Computing Officer
Image Bioinformatics Research Group
Department of Zoology
The Tinbergen Building
University of Oxford
South Parks Road
United Kingdom
Web: http://purl.org/net/aliman
Email: alistair.miles@zoo.ox.ac.uk
Tel: +44 (0)1865 281993
Received on Tuesday, 12 May 2009 09:58:29 UTC

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