- From: Alistair Miles <alistair.miles@zoo.ox.ac.uk>
- Date: Fri, 12 Dec 2008 16:44:25 +0000
- To: public-lod@w3.org
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 16:45:00 UTC