FlyWeb/MilestoneOne

From ImageWeb

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

Contents 1 Search Applications 2 RDF Data 3 Data Services 4 Software 5 Ontologies/Schemas 6 RDF Data Conversion Utilities

Search Applications

http://openflydata.org/search/insitus

This application allows you to search for images of in situ RNA hybridisation experiments, depicting expression of specific genes in different organs (testes and embryos). It is a mashup of data from the Berkeley Drosophila Genome Project (BDGP) and the Fly Testis Expression Database (Fly-TED). It also uses data from FlyBase to disambiguate gene name synonyms.

It's a pure AJAX application using SPARQL to access data from each of the three sources on the fly (pardon the pun :).

RDF Data

The following RDF data are available for bulk download:

• http://openflydata.org/dump/flybase (latest)
• http://openflydata.org/dump/flybase_genenames_20081017 (snapshot)

data on D. melanogaster gene identifiers, symbols and synonyms, derived from flybase.org; approx 8 million triples; gzipped n-triples

• http://openflydata.org/dump/bdgp (latest)
• http://openflydata.org/dump/bdgp_images_20081030 (snapshot)

metadata on images of embryo in situ gene expression experiments, derived from fruitfly.org; approx 1 million triples; gzipped n-triples

• http://openflydata.org/dump/flyted (latest)
• http://openflydata.org/dump/flyted_20080626 (snapshot)

metadata on images testis in situ gene expression experiments, derived from www.fly-ted.org; approx 30,000 triples; gzipped turtle

Data Services

The following SPARQL endpoints are available for queries over the above data. See also limitations below.

• http://openflydata.org/query/flybase (latest)
• http://openflydata.org/query/flybase_genenames_20081017 (snapshot)

• http://openflydata.org/query/bdgp (latest)
• http://openflydata.org/query/bdgp_images_20081030 (snapshot)

• http://openflydata.org/query/flyted (latest)
• http://openflydata.org/query/flyted_20080626 (snapshot)

Limitations: only GET requests are supported; only SELECT and ASK queries are supported; only JSON results format is supported (request must specify output=json); SELECT queries are limited to max 500 results; no more than 5 requests per second from any one origin

Software

• FlyUI http://flyui.googlecode.com

This is a library of composable javascript widgets, providing a user-interface to above data. These widgets are used to build the search application above.

• SPARQLite http://sparqlite.googlecode.com

This is an experimental and incomplete implementation of the SPARQL protocol, designed to work with Jena TDB or SDB stores. We're using this as a platform to explore a number of quality of service issues that SPARQL raises.

Ontologies/Schemas

The following OWL schemas are used in the above data:

• CHADO OWL Schema http://purl.org/net/chado/schema/

This is an OWL representation of the CHADO relational schema used by FlyBase (see http://gmod.org/wiki/Schema).

• FlyBase OWL Synonym Types http://purl.org/net/flybase/synonym-types/

This is a micro-ontology, representing the FlyBase synonym type vocabulary.

• BDGP OWL Schema http://purl.org/net/bdgp/schema/

This is an OWL representation of the BDGP relational schema.

• FlyTED OWL Schemas

These are under revision, to be published shortly.

RDF Data Conversion Utilities

The following utilities were developed to obtain the RDF data described above:

• CHADO/FlyBase D2RQ Map http://code.google.com/p/openflydata/source/browse/trunk/flybase/genenames/d2r-flybase-genenames.ttl

This provides a mapping from the CHADO/FlyBase relational schema to the CHADO/FlyBase OWL ontologies, for basic D. melanogaster gene (feature) data (identifiers, symbols, synonyms, species).

• BDGP D2RQ Map http://code.google.com/p/openflydata/source/browse/trunk/bdgp/imagemapping/d2r-bdgp-insituimages.ttl

This maps the BDGP relational schema to OWL/RDF.

See also: http://openflydata.googlecode.com