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Handling integrated biological data using Python, Jupyter, and InterMine

Yo Yehudi

Kevin Herald Reierskog

July 4 2019

bit.ly/intermine-gcc2019

@intermineorg

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What is InterMine

bit.ly/intermine-gcc2019

@intermineorg

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Who Uses InterMine?

WormMine

FlyMine

ZebrafshMine

YeastMine

RatMine

MouseMine

PeanutMine

XenMine

LegumeMine

ne

HumanMine

modMine

TargetMine

PhytoMine

HymenopteraMine

ChickpeaMine

SynbioMine

SoyMine

CowpeaMine

PeanutMine

MedicMine

PlanMine

WheatMine

BovineMine

BovineMine

ThaleMine

bit.ly/intermine-gcc2019

@intermineorg

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http://registry.intermine.org/

bit.ly/intermine-gcc2019

@intermineorg

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Data

EXPRESSION

GENE ONTOLOGY

GENES

PROTEINS

RNA-seq

REGULATORY

SNPs

VARIANTS

INTERACTIONS

UTRs

EXONS

TRANSCRIPTS

GWAS

PATHWAYS

PHENOTYPES

MICROARRAY

ALLELES

DISEASE

ORTHOLOGUES

Protein Domains

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Why use InterMine?

  • Query across several data sources at once
  • Data formatting issues resolved
  • Identifier resolution system
  • Collate information about items and sets
  • Common platform to many organisms and type of data

bit.ly/intermine-gcc2019

@intermineorg

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Using InterMine

Search

Report Pages

Template Queries

List Analysis & Enrichment

Build Queries

bit.ly/intermine-gcc2019

@intermineorg

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Using InterMine

Search + report pages

(What’s your favourite human gene?)

Live Demo - follow along at humanmine.org

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Using InterMine

Search

Report Pages

Template Queries

List Analysis & Enrichment

Build Queries

bit.ly/intermine-gcc2019

@intermineorg

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Using InterMine

Templates & lists:

(What’s another favourite human gene?)

Live Demo - follow along at humanmine.org

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Using InterMine

Search

Report Pages

Template Queries

List Analysis & Enrichment

Build Queries

bit.ly/intermine-gcc2019

@intermineorg