FlyWeb/MilestoneThree

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This page describes the third milestone release (FM3) of all resources under development in the FlyWeb project.

FM3 Highlights

  • Two new Drosophila gene expression data search applications deployed at openflydata.org: search by gene batch, and search by tissue expression profile.
  • Retrieval of literature references from FlyBase added to openflydata.org search by gene application.
  • Significantly expanded conversion of FlyBase (FB2009_02) to RDF, covering all Chado modules except companalysis.
  • New release of SPARQLite, including support for TDB named graph datasets, ARQ query language, and LARQ (Lucene + ARQ) integration.

Contents

openflydata.org Cross-Database Search Tools

The following search tools are deployed at openflydata.org in this release...

  • 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
  • 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
  • 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 search/insitus (compare images of in situ gene expression in D. melanogaster testes and embryos) and search/flyatlas-by-gene (search by gene for expression level data) are both still available also -- these are variants on the 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.

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 FM2.

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

FlyAtlas

No change from FM2.

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

Fly-TED

No change from FM2.

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

Software

FlyUI

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

For more information on FlyUI see: http://flyui.googlecode.com/

SPARQLite

SPARQLite 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.

For more information about SPARQLite, see: http://sparqlite.googlecode.com/

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 been updated in this milestone. 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.
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