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[ANN] News from the FlyWeb Project (Milestone 2)

From: Alistair Miles <alistair.miles@zoo.ox.ac.uk>
Date: Fri, 12 Dec 2008 16:41:58 +0000
To: public-semweb-lifesci@w3.org
Message-ID: <20081212164158.GA4185@skiathos>

Dear all,

This is an update from the FlyWeb Project team on our second milestone
release of cross-database search tools, data, web services and
software, exploring Web-based data integration for the Drosophila
research community.

Highlights in this release include:

* two new search applications at http://openflydata.org working across
  four genomic databases;

* a new RDF dataset on tissue-specific gene expression from flyatlas.org; 

* an updated RDF dataset from fly-ted.org with improved data quality
  and links to data from flybase.org;

* new and updated widgets in the FlyUI javascript library for FlyAtlas 
  and BDGP data;

* new quality-of-service features in SPARQLite, our experimental
  SPARQL protocol implementation based on Jena SDB/TDB

As always, we'd very much appreciate thoughts, suggestions, feedback,
re-use and bug reports. Please note that this is still work in
progress, and things may break, change, move or disappear without
notice.

All of the information in this email is also at:

* http://imageweb.zoo.ox.ac.uk/wiki/index.php/FlyWeb/MilestoneTwo

----
= OpenFlyData.org Cross-Database Search Tools =

The following *new* cross-database search applications are available at
http://openflydata.org ...

* http://openflydata.org/search/gene-expression -- search by gene
  across gene expression level data from flyatlas.org and images of in
  situ gene expression in D. melanogaster from fruitfly.org and
  fly-ted.org

* http://openflydata.org/search/flyatlas-by-gene -- search for
  tissue-specific gene expression level data from flyatlas.org by gene

The following application has been *updated* with new features and
improved data...

* http://openflydata.org/search/insitus -- search by gene across
  images of in situ gene expression in D. melanogaster from
  fruitfly.org and fly-ted.org; now with BDGP images grouped by
  developmental stage, and Fly-TED data corrected for links between in
  situ probes and genes

----
= Datasets & Web Services =

== FlyAtlas ==

A *new* RDF dataset made available in this release, derived from data
published by flyatlas.org. These data give you a quick answer to the
question: in which tissue(s) is my gene of interest expressed/enriched
in the adult fly?

We're behind flyatlas.org with this dataset, so don't yet have data on
5 recently added tissues.

RDF dumps: 
* FlyAtlas data: http://openflydata.org/dump/flyatlas_20080916 
* Affy D2 probe-to-gene links: http://openflydata.org/dump/flyatlas_probe2gene_20081203

SPARQL endpoint: 
* http://openflydata.org/query/flyatlas_20080916 (contains data from both dumps)

Ontologies (schemas):
* HTML: http://imageweb.zoo.ox.ac.uk/wiki/index.php/FlyAtlas/Schema
* OWL: http://openflydata.googlecode.com/svn/tags/flyatlas-FM2/FlyAtlas-Vocabulary.owl 

Data conversion utilities: 
* http://code.google.com/p/openflydata/source/browse/tags/flyatlas-FM2/ 

For more information on this dataset see: http://code.google.com/p/openflydata/wiki/Flyatlas 

== Fly-TED ==

This dataset derived from data published by www.fly-ted.org provides
metadata on images depicting in situ hybridisation in D. melanogaster
testes.
 
*Updated* in this release, now with correct linking between in situ
 probes and FlyBase genes.

RDF dump: http://openflydata.org/dump/flyted_20081203

SPARQL endpoint: http://openflydata.org/query/flyted_20081203

Ontology (schema):
* HTML: http://rodos.zoo.ox.ac.uk/ontologies/flyted-20081202/owldoc/
* OWL: http://rodos.zoo.ox.ac.uk/ontologies/flyted-20081202/flyted-schema.owl 

For more information on this dataset see: http://code.google.com/p/openflydata/wiki/Flyted 

== FlyBase ==

A subset of data from flybase.org, providing gene name disambiguation
data. No changes since previous announcement.

For more information on this dataset see: http://code.google.com/p/openflydata/wiki/Flybase

== BDGP ==

A subset of data from fruitfly.org, providing metadata on in situ
experiments in embryos. No changes since previous announcement.

For more information on this dataset see: http://code.google.com/p/openflydata/wiki/Bdgp

----
= Software =

== FlyUI Javascript UI Library ==

FlyUI is the library of javascript widgets used to build the
cross-database search tools deployed at openflydata.org.

Updated in this release with new applications, new features in the
BDGP image widget (images grouped by developmental stage), and a new
FlyAtlas widget.

* Anonymous SVN checkout: http://flyui.googlecode.com/svn/tags/flyui-20081210-FM2-RC4
* Browse source code: http://code.google.com/p/flyui/source/browse/ 

For more information on FlyUI see: http://code.google.com/p/flyui/ 

== SPARQLite ==

SPARQLite is the software we use to implement the SPARQL Web services
which provide data to the cross-database search tools, and which can
be used directly by other bioinformaticians.

Completely refactored in this release with a new test suite, and a new
query policy module allowing configurable SPARQL query
restrictions. Now also supports POST requests, and SELECT, ASK,
CONSTRUCT and DESCRIBE query forms.

* WAR download: http://sparqlite.googlecode.com/files/sparqlite-20081202-FM2-RC2.war
* Anonymous SVN checkout: http://sparqlite.googlecode.com/svn/tags/sparqlite-20081202-FM2-RC2
* Browse source code: http://code.google.com/p/sparqlite/source/browse/ 

For more information about SPARQLite, see: http://code.google.com/p/sparqlite/ 

----
= Note: SPARQL Endpoint Restrictions =

The following notes apply to all SPARQL endpoints mentioned
above and in previous announcements:

* All SPARQL query forms are now supported (ASK, SELECT, DESCRIBE,
  CONSTRUCT) via either GET or POST requests
* Only JSON format is supported for SELECT/ASK, only RDF/XML format is
  supported for DESCRIBE/CONSTRUCT
* All queries have a LIMIT ceiling, 500 for SELECT queries, 100 for
  CONSTRUCT queries, 20 for DESCRIBE
* Queries with variables in the predicate position of any triple
  pattern are disallowed (403)
* Queries with FILTER are disallowed (403)
* More than 5 requests in any 1 second from any source will results in
  a lockout period of 10 seconds (403)

Contact us if you need any of these restrictions lifted.

----
= Note: EC2 Platform =

As mentioned previously, openflydata.org is running on a small Amazon
EC2 instance, with RDF data in Jena TDB (0.6) stores located on an
attached EBS volume. If anyone is interested we'd be happy to make the
EC2 image and/or the EBS snapshots public.

---- 
No linked data yet, planned for future milestones but happy to
bring it forward if anyone wants it :)

Kind regards and best wishes,

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
Oxford
OX1 3PS
United Kingdom
Web: http://purl.org/net/aliman
Email: alistair.miles@zoo.ox.ac.uk
Tel: +44 (0)1865 281993
Received on Friday, 12 December 2008 16:42:33 GMT

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