About the Database

The FlyTED Database has been developed by Jun Zhao of the Image Bioinformatics Research Group in the Department of Zoology at the University of Oxford, with funding from the UK's BBSRC.

Database construction

To create an image database with a minimum of development effort, we adapted the EPrints open source repository software system (http://eprints.org/software/), widely used within the digital library community for publishing and archiving digital text-based documents. We were encouraged in this choice because EPrints had previously been successfully used to establish an image database of marine organisms, the SERPENT Image and Video Database (http://archive.serpentproject.com/). EPrints is a Perl-based application powered by an Apache HTTP server, with an underlying MySQL relational database. It has the advantage of having a built-in user interface that is relatively easy to customize by editing the EPrints configuration files and its CSS style sheet.

We modified the underlying EPrints relational database schema to accommodate certain important domain-specific metadata terms - gene names, strain name and expression pattern - needed for browsing and searching the images. We also modified the EPrints configuration file to permit different browse views over our image data to be presented in a Web browser interface, based on these metadata properties.

Database population

Population of the FlyTED Database with our biological research images and their metadata involved the following steps:

We pre-processed the original Excel metadata spreadsheets into a set of text files, one for each image, containing on separate lines the domain-specific metadata terms described above.
Bulk ingest of the images and their metadata files into EPrints was then accomplished using a customised Perl script, which:

stored selected metadata terms in the EPrints relational database, to permit subsequent search and browse activities over them; and
stored each image and its complete metadata file as binary objects within the EPrints database for later reuse.

The scripts for populating the FlyTED Database can be found in our SVN repository (http://purl.org/NET/flyted-db/source/).

Download Data Archives

MySQL dump of the core metadata of the current and previous release of the Fly-TED repository can be downloaded from our SubVersion Repository.

Contact Information

Any correspondence concerning the FlyTED Database should be sent to jun.zhao@zoo.ox.ac.uk.

About the Repository software

FlyTED is powered by EPrints 3, which was developed by the School of Electronics and Computer Science at the University of Southampton. FlyTED is currently running on GNU EPrints / revision: EPrints 3.0.3 (Sage) [Born on 2007-12-05]. It is freely available at http://software.eprints.org/. More EPrints information and software credits here.

Technologies employed and supported:

Supports: Open Archives Initiative Protocol for Metadata Harvesting, Valid XHTML, Valid CSS.