- From: Alistair Miles <alistair.miles@zoo.ox.ac.uk>
- Date: Tue, 12 May 2009 10:50:12 +0100
- To: semantic-web@w3.org
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 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 _______________________________________________ BioImage mailing list BioImage@mail.ontonet.org http://lists.ontonet.org/mailman/listinfo/bioimage ----- End forwarded message ----- -- 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 Tuesday, 12 May 2009 09:50:51 UTC