We built a semantic web image repository called FlyTED to publish Drosophila gene expression images online and make them searchable. We used existing tools like Eprints to store metadata and images and made the metadata accessible through SPARQL. We then consumed the images and metadata in faceted browsers like Exhibit and jSpace to present them in more flexible user interfaces. This allows components like the metadata storage to potentially be replaced in the future with new tools.

1. Building a Semantic Web Image Repository for Biological Research Images Jun Zhao , Graham Klyne and David Shotton [email_address] Image Bioinformatics Research Group Department of Zoology University of Oxford, UK

2. FlyTED The Drosophila Testis Gene Expression Image Database Publish research data Use existing tools to build a biological image repository Browse-able and searchable by research biologists Accessible to wider communities, e.g. Semantic Web, Linked Data Loosely coupled software architecture maximises the opportunity of replacing or updating components used

3. Images “… so that people can come and see the images, and they will notice something special about the genes” --- Dr Helen White-Cooper ( Drosophila testis expert)

4. Where we started from In situ gene expression images of the ~1500 genes of the testis of Drosophila melanogaster >=1 image for each wild type gene Possibly, >=1 image for any of the 6 different mutant strains having defective sperm maturation Images stored in the file system Metadata in spreadsheets, but not expressed using controlled keywords No way to search for images Search through the hard disk whenever they need an image

5. The goal Publish Drosophila gene expression images to the Web Make them accessible and searchable to our biological researchers as well as third parties Quick, easy and cost-effective approach

6. EPrints 3.0 (http://eprints.org/software/) A digital repository software system Quick and easy to deploy Built-in user interface Programmatically data access Repository-specific protocol: OAI-PMH Support for domain-specific image metadata, e.g. Serpent Project http://archive.serpentproject.com/ A Piglet Squid from Serpent Project

7. Our gene expression images Gene name Strain name >1 Expression location Slide name Creation date ………… .

8. Adaptation of EPrints Basic structure cannot hold the domain metadata Customize underlying database: Add additional metadata fields in the database schema Keep both images and their metadata files as blobs Customize the user interface: CSS https://milos2.zoo.ox.ac.uk/svn/ImageWeb/FlyTED/Trunk/

15. Issues Difficult to query metadata programmatically Limited flexibility in the user interface

16. FlyTED on the Semantic Web Data become programmatically accessible: http://www.fly-ted.org/sparql Images can be used in more flexible UIs Semantic Web faceted browsers Exhibit from MIT SIMILE Javascripts, run in Web browsers http://simile.mit.edu/exhibit/ jSpace from clarkparsia Java Web Application http://clarkparsia.com/jspace/

17. Publish FlyTED on the Semantic Web Free-text metadata file OAI-PMH + Relational FlyTED Database N3 metadata Local Harvesting & Transformer script Jena RDF database Command-line Jena model loader Joseki SPARQL Endpoint JSON data HTTP-based Babel HTTP SPARQL jSpace Exhibit

18. FlyTED in Exhibit

20. Functionality Measurement Yes Yes Partial Yes Yes Yes Yes No Yes Partial No Yes Partial Yes Yes No No No

21. Performance Exhibit Exhibit jSpace jSpace

22. Summary We built an image repository, based on Eprints We used existing tools ( OAIHarvester2 API and Joseki ) to make metadata accessible through SPARQL We consumed these images using existing faceted browsers ( Exhibit and jSpace ) in order to present them in more flexible user interfaces Potentially, we can replace existing components with new tools, e.g. OAI2LOD , Joseki/SDB

23. To take home Publish your data Take a look at our “Exhibit” of FlyTED images http://www.fly-ted.org/exhibit/exhibit_flyted.html Play with and make a link to our SPARQL endpoint http://www.fly-ted.org/sparql VOID: Vocabulary of Interlinked Data

24. Since then More images Enrich the Fly Anatomy Ontology Link with others: the FlyWeb Project BDGP ( http://www.fruitfly.org/ ): Drosophila gene expression images in embryos FlyBase ( http://www.flybase.org/ ): Genomic Drosophila database Bio2RDF ( http://bio2rdf.org/ ): RDFized PubMed, Medline, UniProt, GO database, etc

25. Screen shot of FlyWeb

26. Acknowledgement David Shotton, Graham Klyne, and Alistair Miles Dr Helen White-Cooper and her research group JISC and BBSRC EPrints Southampton team HP Labs, SIMILE project (MIT), and Clark&Parsia

27. Thank you!