bc2012 jyotiebi poster44ec82
TRANSCRIPT
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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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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Publication & Experiment
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Interaction
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Participant
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Feature
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Interactor
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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• 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
The Wellcome Trust Genome Campus
29
EMBL-EBI
Cairns Pavilion(shared)
Sanger InstituteSulston building
Data centre
Sanger labs / informatics
© John Freebury
New types of data
30
Genomes
Nucleotide sequence
Gene expression
Proteomes
Protein families, domains and motifs
Protein structure
Molecular interactions
Chemical entities
PathwaysSystems
Literature
Protein sequence