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EBI is an Outstation of the European Molecular Biology Laboratory.

Master title

Molecular Interactions – the IntAct Database

Sandra Orchard

EMBL-EBI

18.04.23

2

1. Publicly available repository of molecular interactions (mainly PPIs) - >275K binary interactions taken from >5,000 publications (September 2011)

2. Data is standards-compliant and available via our website, for download at our ftp site or via PSICQUIC

3. Provide open-access versions of the software to allow installation of local IntAct nodes.

IntAct goals & achievements

http://www.ebi.ac.uk/intactftp://ftp.ebi.ac.uk/pub/databases/intactwww.ebi.ac.uk/Tools/webservices/psicquic/view/main.xhtml

Master headline

“Lifecycle of an Interaction”

Publication(full text)

Sanity Checks(nightly)

IntAct Curation

CVs

curator

report report

Curation manual

.

reject

Super curator

annotate

p1

p2I

exp

IMEx

MatrixDB Mint DIP

Public web site

FTP siteaccept

chec

k

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UniProt Knowledge Baseh

ttp

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ww

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org

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nip

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Interactions can be mapped to the canonical sequence…

.. to splice variants..

.. or to post-processed chains

Relationship with UniProtKB

Master headline

Protein sequence

Data filters

Other IMEx databases

High confidence PPIs

In place

Early 2012

Interaction curation

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Data model

• Support for detailed featuresi.e. definition of interacting interface

Interacting domains

Overlay of Ranges on sequence:

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How to deal with Complexes

• Some experimental protocol do generate complex data:Eg. Tandem affinity purification (TAP)

• One may want to convert these complexes into sets of binary interactions, 2 algorithms are available:

EBI is an Outstation of the European Molecular Biology Laboratory.

Performing and visualing a Simple Search

EBI WalthroughMay 2009EBI

Data, Standards and Tools

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IntAct – Home Pageh

ttp

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Performing a Simple Search

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Visualizing - networkView

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Extend and Visualise your Search

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Visualizing - Visualizing - networkViewnetworkView

Cytoscape Web

• Cytoscape Web - web-based network visualization tool• Modeled after Cytoscape – open-source, interactive,

customizable and easily integrated into web sites.• Contains none of the plugin architecture functionality of

Cytoscape

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Master headline

VisualizationVisualization

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Master headline

VisualizationVisualization

Ap

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Master headline

VisualizationVisualization

Ap

ply

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a b

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pp

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Master headline

VisualizationVisualization

Hig

hlig

hti

ng

netw

ork

pro

pert

ies…

Hig

hlig

hti

ng

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pro

pert

ies…

Master headline

VisualizationVisualization

Hig

hlig

hti

ng

netw

ork

pro

pert

ies…

Hig

hlig

hti

ng

netw

ork

pro

pert

ies…

Master headline

VisualizationVisualization

Hig

hlig

hti

ng

netw

ork

pro

pert

ies…

Hig

hlig

hti

ng

netw

ork

pro

pert

ies…

Master headline

VisualizationVisualization

Hig

hlig

hti

ng

netw

ork

pro

pert

ies…

Hig

hlig

hti

ng

netw

ork

pro

pert

ies…

Cytoscape Plugins

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EBI is an Outstation of the European Molecular Biology Laboratory.

Exploring a single interaction in more depth

Interaction detail

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Choice of UniProtKBor Dasty ViewDetails of

interaction

Detail of interaction

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UniProt Taxonomy PubMed

Expansionmethod

Details of interaction

Changing the tabular view

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Participant information

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Searc

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or

‘RA

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Searc

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‘RA

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Interaction detail

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Fir

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Details of interaction

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Viewing Interaction Details

Additionalinformation

Interaction Details

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IntAct – Home Page-Quick Search

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Advanced search: Fields

Filtering options

Add more filtering options

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Searching with MIQLFir

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searc

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rom

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om

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• Using the Molecular Interaction Query Language (MIQL), one can also build complex queries

• List of terms one can query on :

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Browsing – Molecule View

Bin

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Browsing – extending your search

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