Bc2012 jyotiebi poster44ec82

Jyoti Khadake

Proteomic Services Team

IntAct editor - an effective Interaction curation tool.

Overview

• What is IntAct molecular interaction database

• What is a Molecular Interaction• Data Model• Standardized Schema and CV• Editor and management of entries

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What is IntAct?

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• IntAct is a database of molecular interaction• Capture interactions from literature• It is Manually Curated

• Is extensively cross-referenced • Provides tools to query, analyze and visualize

data• Open source and open access

What is a molecular interaction?

Physical interactions

• Types• Self• Binary: homomeric or heteromeric• N-nary complexes• Co-localisations• Enzymatic assays• Purified protein interactions

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Interaction details captured from literature

• Pubmed ID – Source of data

• The interactors

• Experimental conditions of interactions

• Type of interaction

• Properties of interactors

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Details of an interaction

Is it a duck or a rabbit?

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Interaction2

Interaction4

Interaction1

Interaction3

Publication

Experiment1

Experiment2

. Roles

. Features

. Preparations

Par

tici

pan

t

Data Model

Protein1

Protein2

Participant1

Participant2

Participant3

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How do databases store Interactions

www.ebi.ac.uk/ols for controlled vocabularies

How do we curate and manage data

• We use – The New Editor.

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Publication & Experiment

Publication View

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Experiment view

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Interaction

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Interaction View

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Participant

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Feature

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Participant View

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Interactor

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Interactor View

Master headline

“Lifecycle of an Interaction”

Publication(full text)

validator

IntAct Curation management

CVs

curator

Curation manual

.

reject

Super curator

In progress

p1

p2I

exp

Publishaccept

accept

Ready for recheckingche

ck

Author

reject

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Databases using Editor

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• IntAct editor is based on the PSI-MI schema v2.5

• This enables us to capture details of Interaction data

• Allows us to manage curation process

• It is used by various other databases.

Summary

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Proteom

ic Services T

eam

Pablo Dave

Thank you!

Questions?

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The five EMBL sites

The Wellcome Trust Genome Campus

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EMBL-EBI

Cairns Pavilion(shared)

Sanger InstituteSulston building

Data centre

Sanger labs / informatics

© John Freebury

New types of data

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Genomes

Nucleotide sequence

Gene expression

Proteomes

Protein families, domains and motifs

Protein structure

Molecular interactions

Chemical entities

PathwaysSystems

Literature

Protein sequence

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Format for storage and exchange –

PSI-MI XML 2.5

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Main objects - Experiment

Controlled by Ontologies

Literature references

Confidence measures

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Main objects - Participant

e.g. enzyme target

Interactor

e.g. bait, prey

Delivery methodexpression level…

Interactor used experimentally

Building of Complex