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

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

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

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)

“… 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)

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

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

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

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

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

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/

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

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/

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/

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

Difficult to query metadata programmatically

Limited flexibility in the user interface

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/

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/

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

FlyTED in Exhibit

Functionality Measurement Yes Yes Partial Yes Yes Yes Yes No Yes Partial No Yes Partial Yes Yes No No No

Performance Exhibit Exhibit jSpace jSpace

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

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

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

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

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

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

Screen shot of FlyWeb

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

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

Thank you!