From ImageWeb

This page describes the second milestone release of all resources under development in the FlyWeb project.

Contents 1 OpenFlyData.org Cross-Database Search Tools 2 Datasets & Web Services 2.1 FlyBase (D. melanogaster genes) 2.2 BDGP (in situ images) 2.3 FlyAtlas 2.4 Fly-TED 3 Software 3.1 FlyUI Javascript UI Library 3.2 SPARQLite

OpenFlyData.org Cross-Database Search Tools

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

• search/gene-expression :: search across gene expression level data and images of in situ gene expression in D. melanogaster
• search/insitus :: compare images of in situ gene expression in D. melanogaster testes and embryos
• search/flyatlas-by-gene :: search by gene for expression level data

Datasets & Web Services

The following datasets are made available in this release...

FlyBase (D. melanogaster genes)

• RDF dump: http://openflydata.org/dump/flybase_genenames_20081017
• SPARQL endpoint: http://openflydata.org/query/flybase_genenames_20081017
• Ontologies (schemas):
  • Chado:
    • HTML: http://rodos.zoo.ox.ac.uk/ontologies/chado-20081017-1/schema-content/owldoc/
    • OWL: http://rodos.zoo.ox.ac.uk/ontologies/chado-20081017-1/schema-content/chado-schema.owl
  • FlyBase Synonym Types:
    • HTML: http://rodos.zoo.ox.ac.uk/ontologies/flybase-20081008/synonym-types-content/owldoc/
    • OWL: http://rodos.zoo.ox.ac.uk/ontologies/flybase-20081008/synonym-types-content/flybase-syntypes.owl
  • OpenFlyData FlyBase Utilities:
    • HTML: http://rodos.zoo.ox.ac.uk/ontologies/openflydata-20081008/flybase-utils-content/owldoc/
    • OWL: http://rodos.zoo.ox.ac.uk/ontologies/openflydata-20081008/flybase-utils-content/openflydata-flybase-utils.owl
• Data conversion utilities: http://code.google.com/p/openflydata/source/browse/tags/flybase-FM1/

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

BDGP (in situ images)

• RDF dump: http://openflydata.org/dump/bdgp_images_20081030
• SPARQL endpoint: http://openflydata.org/query/bdgp_images_20081030
• Ontology (schema):
  • HTML: http://rodos.zoo.ox.ac.uk/ontologies/bdgp-20081016/owldoc/
  • OWL: http://rodos.zoo.ox.ac.uk/ontologies/bdgp-20081016/bdgp-schema.owl
• Data conversion utilities: http://code.google.com/p/openflydata/source/browse/tags/bdgp-FM2/

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

FlyAtlas

• RDF dumps:
  • FlyAtlas affy data: http://openflydata.org/dump/flyatlas_20080916
  • Affy probe-to-gene links: http://openflydata.org/dump/flyatlas_probe2gene_20081203
• SPARQL endpoint: http://openflydata.org/query/flyatlas_20080916 (contains 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

• 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

Software

FlyUI Javascript UI Library

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

• 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.

• 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/