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TRANSCRIPT
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
