1. Master headline RDFizing the EBI Gene Expression Atlas James Malone, Electra Tapanari malone@ebi.ac.uk

2. Master headline -Initial motivation is explorative -Can we ask new questions? -Do we get new answers? -Can we integrate this data with other related data? -Is there a sufficient user community to justify an RDF Atlas resource? Motivation

3. Master headline SESL Project -Semantic Enrichment of Scientific Literature Working Group -Includes EBI (Dietrich Rebholz) and Pistoia Alliance -Pilot project in 2010 looking at Developing knowledge brokering standards for semantic integration of gene to Type II diabetes data using Gene Expression Atlas, OMIM, UniProt literature

4. Master headline Gene Expression: Archive to Atlas AE/GEO acquire >250,000 Assays >10,000 experiments Re-annotate & summarize ATLAS ArrayExpress Curation

5. Master headline12/9/20155 Experimental Factor Ontology We consume parts of reference ontologies from domain Construct new classes and relations to answer our use cases Aim is reuse of existing resources, shared frameworks and mapping of equivalencies where they exist EFO Disease Ontology Anatomy Reference Ontology Ontology Biomedical Investigations Chemical Entities of Biological Interest (ChEBI) Various Species Anatomy Ontologies Relation Ontology Text mining

6. Master headline Gene Expression Atlas @ www.ebi.ac.uk/gxa Query for Cell adhesion genes in all ‘organism parts’ ‘View on EFO’ Ontologically Modeling Sample Variables in Gene Expression Data malone@ebi.ac.uk

7. Master headline Input XML

8. Master headline Mapping XML Results to RDF (1) Id here is an ENSEMBL Gene ID, e.g. RUNX1 (ENSG00000159216) Gene to related transcripts, sequence and gene functions Also EFO ontology classes in RDF form (shown is label to IRI triple)

9. Master headline Mapping XML Results to RDF (2) Connecting gene and ontology id together with experimental metrics

10. Master headline Mapping XML Results to RDF (3) Connecting gene with experimental metadata

11. Master headline Relationship Issues EFO attempts to follow OBO Foundry guidance and uses the OBO Relation Ontology OBI model is more complex, e.g. the relation between sample and measure is indirect* Relationship between some of entities is still not well represented across community, even protein product to gene (see my post to OBO list) is_about relation is very generic and largely meaningless We will use RO where possible, subclass RO otherwise and continue to monitor OBO *see Brinkman et al, (2010) Modeling biomedical experimental processes with OBI, JBMS, 1(Suppl 1):S7

12. Master headline Display of query results in Gene Expression Atlas DB Already: 1) JSON format 2) XML format Plus now: 3) RDF format

13. Master headline Java codeRDF triples XML doc XML result doc from Atlas INPUT PROCESS OUTPUT XML doc with triple patterns RDF pipeline Pipeline for generating the RDF given the XML input note this works with any XML code

14. Master headline Triple Pattern specification

15. Master headline Example RDF

16. Master headline Blank Node Connections First row (n1_0 )  7 triples

17. Master headline Is there a community that warrants directing resources towards this? Can we answer new questions? Can we integrate with other data sources? Can we consolidate complex, non-interoperable ontologies? EFO represents a view on this but is a scoped, pragmatic choice – will this indeed always be the case? Discussion

18. Master headline Acknowledgements Electra Tapanari (intern that did bulk of implementation) Dietrich Rebholz-Schumann (funding internship) Christoph Grabmuller Misha Kapushesky Helen Parkinson Contact me James Malone: malone@ebi.ac.uk