Re: [ANN] News from the FlyWeb Project

''We'd like to develop credible, robust and genuinely useful tools for the 
Drosophila research community; and  to provide data and services of value to 
bioinformaticians and
Semantic Web / Life Science developers.''

Drosophila melanogaster, a friut fly with joint legs and segmented body of 
chitin is becoming a celebrity of modern life science. Alistair, with all 
respects to your enthusiasm, there may be up to 4 m insect species, do we 
really need such many research communities?  Then I wish the medfly, sorry, 
Ceratitis capitata research community to be organized, to study carefully 
why this Mediterranian fly sometimes bothers me here while sunbathing. May 
be, to drop a hint that his relative's inheritance mechanisms is a major 
model in today's genetics and that all human genetics can be reduced to the 
fruit fly genetics?

Azamat Abdoullaev

----- Original Message ----- 
From: "Alistair Miles" <alistair.miles@zoo.ox.ac.uk>
To: <semantic-web@w3.org>
Sent: Wednesday, November 05, 2008 6:41 PM
Subject: [ANN] News from the FlyWeb Project


>
> Dear all,
>
> This is a summary of work so far by the FlyWeb Project team. We're
> exploring integration of life science data in support of Drosophila
> (fruit fly) functional genomics. We'd like to develop credible, robust
> and genuinely useful tools for the Drosophila research community; and
> to provide data and services of value to bioinformaticians and
> Semantic Web / Life Science developers.
>
> This is the first time we've announced our work more widely, and we'd
> very much appreciate thoughts, suggestions, feedback, re-use and
> testing of the applications, services, software and data described
> below. Please note however that this is work in progress, and things
> may break, change, move or disappear without notice.
>
>
> = 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 Drosophila Testis
> Gene 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 used in the search application above 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
>
> The endpoints are implemented using our own Java SPARQL protocol
> implementation (SPARQLite, see below) backed by Jena TDB 0.6
> stores. The endpoints run inside Tomcat 5.5 behind Apache 2.2 via
> mod_jk, on a small EC2 instance, with TDB storing data on an attached
> EBS volume.
>
>
> = Software Downloads & Source Code =
>
> * 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. FlyUI is built on YAHOO's javascript user
> interface library (YUI).
>
> * 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 a subset 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 a subset 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
>
>
> = Future Developments =
>
> We're currently working on improving the user interface to the BDGP
> data (grouping and ordering images by developmental stage) and on
> integrated expression level data from FlyAtlas.
>
> Other suggestions for future developments are warmly welcomed.
>
>
> = Acknowledgments =
>
> Thanks especially to Helen White-Cooper and Andy Seaborne for all
> their help.
>
> The FlyWeb Project is funded by the UK Joint Information Systems
> Committee (JISC).
>
>
> = Further Information =
>
> The FlyWeb project website is at:
>
> http://imageweb.zoo.ox.ac.uk/wiki/index.php/FlyWeb_project
>
> Graham will be presenting this work at the UK SWIG meeting next week.
>
> Or send us an email :)
>
> 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
>

Received on Wednesday, 5 November 2008 20:41:14 UTC