Use the Database

Browse the Database

Users can browse FlyTED by gene name, strain name or gene expression location.

Browse by Gene Name

For example, the Browse by Gene Name view groups all the FlyTED images according to the gene names associated with the images, and construct a Web page listing the 817 gene names currently in our database, in alphabetical order. Each name links to one of 817 Web pages in which thumbnails of all images recorded for that gene name are displayed, ordered by strain name, each annotated with a caption containing its gene and strain name. This allows users to compare the images relating to a single gene side by side in a single page.

Hovering the mouse over the centre of a thumbnail gives a pop-up box containing a description of the staining pattern. On selecting an individual image record, the user can view both the full-size image (by clicking on the thumbnail) and a detailed information page containing an intermediate-sized image, descriptive metadata about the image (by clicking on the image caption) and a link to the FlyBase database.

Similar presentation of images is given in the other three FlyTED browse views:

Browse by CG Number view that groups images by the CG number of gene which the images hybridized the transcript of;
Browse by Strain Name view that groups images by the strain of fly from which the images were acquired;
Browse by Expression Location view that groups images by the pattern of gene expression revealed in the images. Because our images are annotated using controlled terms from the extended Fly Anatomy Ontology, users can browse images using the hierarchical structure of the ontology.

Home Page

On the FlyTED Home Page, in addition to a general description of the database and a few exemplar images, users can also find links to pages providing details of the dataset and the database, to other Drosophila resources such as FlyBase, and to further relevant information. The footer on all pages of the database displays the copyright and terms of use statements.

Search interfaces

We provide both a simple search interface and an advanced search interface to permit users to make specific queries across the database content.

The simple search interface allows querying for images by synonyms of a gene, including the gene name given by FlyTED biologists and the CG number and FlyBase gene id retrieved from the FlyBase. Queries using multiple gene names can be achieved by separating the names with commas.

The advanced search interface supports more complex queries, allowing users to search across multiple gene names, and/or strain names, and/or gene expression locations. The image results are presented as a tiled array of captioned thumbnails, allowing users to compare them side by side. Again, enlarged images can be viewed by clicking on the thumbnail images, and metadata can be displayed by clicking on the captions.

Programmatic Access to the Database

In addition to the conventional Web interfaces permitting human access to the FlyTED database, the FlyTED images themselves can be programmatically obtained by HTTP get requests to relevant URIs, and the FlyTED image metadata (including the relevant URIs) can be programmatically access in three ways.

Direct download of the database content

The metadata content of the FlyTED database can be downloaded in its entirety as an sql-dump file, obtainable from our SVN repository (http://purl.org/net/flyted-db/archives/). A new versioned sql-dump file is published each time the database is updated with new data.

Use of OAI-PMH

EPrints has intrinsic support for the OAI-PMH protocol (Open Archives Initiative Protocol for Metadata Harvesting; http://www.openarchives.org/OAI/openarchivesprotocol.html), an HTTP protocol developed by the Open Archives Initiative for harvesting the metadata descriptions of resources in digital archives. Its limitations are that it works only for the simple Dublin Core (DC; http://dublincore.org/) metadata items intrinsic to EPrints, such as dc:creationDate, dc:creator, etc., and it cannot expose the domain-specific metadata that we have added for our images. Furthermore, it is unable to support queries of images based on their metadata values, and so cannot be used for programmatic searches. However, this protocol enables us to expose our DC metadata to the digital repository community. The OAI-PMH URL of our repository is http://www.fly-ted.org/cgi/oai2.

Use of SPARQL

The FlyTED Database can be querying programmatically using SPARQL, the W3C-recommended Semantic Web standard RDF query language and protocol. RDF is a knowledge representation language for describing Web resources using triples, in the form: subject, predicate and object. By using URIs (Uniform Resource Identifiers; http://en.wikipedia.org/wiki/Uniform_Resource_Identifier) in the triples, RDF enables assertions about Web resources to be linked together, and thus enables the building of a Web of Data, the Semantic Web.

To make all our image metadata programmatically accessible to and queryable by other applications, we have deployed a SPARQL endpoint (http://semanticweb.org/wiki/SPARQL_endpoint) over FlyTED (http://openflydata.org/query/flyted). Using this, applications can use SPARQL queries to search our images by domain-specific metadata values. The SPARQL query results are returned in RDF, which enables them to be linked into the wider Semantic Web of data. Furthermore, publication of our FlyTED metadata through the SPARQL endpoint enables our images to be presented to users in alternative Semantic Web-enabled faceted browsers, which are more flexible than the built-in EPrints user interface. More detail of our work in this area can be found in Zhao, J., Klyne, G. and Shotton, D. (2008) Building a Semantic Web image repository for biological research images. Proceedings of the European Semantic Web Conference, 5021: 154-169.