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Data Integration Model for Re-use of Biological Data

Julie Sullivan

InterMine as a data sharing platform

1. How InterMine enables data sharing

2. A specific example of data sharing

Who is InterMine?

● Started in 2003

● Department of Genetics

● Gos Micklem’s Lab

What is InterMine?● Data warehouse

● Open source

● Biological data

What is InterMine? cont’d● Import data

○ Core data model

○ Sophisticated data integration system

● Webapp

○ Analysis tools

○ Advanced search

● API

InterMine

FUNCTION

PHENOTYPES

PROTEIN DOMAINS EXPRESSION

INTERACTIONSGENES

PROTEINS

DISEASE

ORTHOLOGUES GWAS

ALLELES

SEQUENCE VARIANTS

GENE ONTOLOGY

PATHWAYS

REGULATION

How InterMine Enables Data Sharing and Re-use● Makes data available (and useful) to public● FAIR data principles*

○ Findable■ Identifiers■ Searchable

○ Accessible■ Public API■ Perl / Python .. , JSON / XML ..

○ Interoperable■ Ontologies

○ Re-usable■ Provenance

*Wilkinson, M. D. et al. The FAIR Guiding Principles for scientific data management and stewardship. Sci. Data3:160018 doi: 10.1038/sdata.2016.18 (2016).

InterMine as a data sharing platform

1. How we (InterMine) enable data sharing

2. A specific example of data sharing

Normal Cell Tumor Cell

BRCA1/2PARP

BRCA1/2PARP

BRCA1/2PARP

Normal Cell Tumor Cell

BRCA1/2PARP

PARP Inhibitor+

BRCA1/2PARP

Normal Cell Tumor Cell

BRCA1/2PARP

PARP Inhibitor+

BRCA1/2PARP

BRCA1/2PARP

BRCA1/2PARP

Normal Cell Tumor Cell

BRCA1/2PARP

PARP Inhibitor+

BRCA1/2PARP

BRCA1/2PARP

YeastMine1. http://yeastmine.yeastgenome.org

2. SGD

a. Saccharomyces Genome Database

b. Stanford

c. Mike Cherry’s lab

2. Yeast data

a. Interactions loaded from BioGRID, an interactions database

We will analyse 173 tumor suppressor genes from Vanderbilt's TSGene Database

Tumour Suppressor Genes

Equivalent Yeast Genes

HOMOLOGUES

Tumour Suppressor Genes

Equivalent Yeast Genes

HOMOLOGUES

SYNTHETIC

LETHAL

Interactors (yeast)

Tumour Suppressor Genes

Equivalent Yeast Genes

HOMOLOGUES

SYNTHETIC

LETHAL

Interactors (yeast)

HOMOLOGUES

Equivalent Human Genes

Tumour Suppressor Genes

Equivalent Yeast Genes

HOMOLOGUES

SYNTHETIC

LETHAL

Interactors (yeast)

HOMOLOGUES

Equivalent Human Genes

SYNTHETIC

LETHAL (POTENTIAL)

Human ATR and POLD1 potentially share a synthetic lethal interaction.

Human ATR and POLD1 potentially share a synthetic lethal interaction.

There is evidence that ATR-POLD1 have a synthetic lethal interaction

Oncotarget. 2016 Feb 9;7(6):7080-95. doi: 10.18632/oncotarget.6857.

A synthetic lethal screen identifies ATR-inhibition as a novel therapeutic approach for POLD1-deficient cancers.Hocke S1, Guo Y1, Job A2, Orth M3, Ziesch A1, Lauber K3, De Toni EN1, Gress TM2, Herbst A1, Göke B1, Gallmeier E1,2.

The Future - InterMine in the cloudPlanning for a “InterMine in the Cloud”

Upload data file and deploy an InterMine for your data

Federated search tools