the intact database sandra orchard & birgit meldal

The IntAct DatabaseThe IntAct Database

Sandra Orchard & Birgit Meldal

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1. Publicly available repository of molecular interactions (mainly PPIs) - >333K binary interactions taken from >6620 publications (Aug 2013)

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

3. Provide open-access editor for those who wish to curate molecular interactions.

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

://w

ww

.eb

i.u

nip

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org

/h

ttp

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org

/

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

Interaction curation

OtherDBs

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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:

Performing and visualing a Simple SearchPerforming and visualing a Simple Search

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IntAct – Home Pageh

ttp

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k/i

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htt

p:/

/ww

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Performing a Simple Search

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Visualizing - networkView

Fro

m s

earc

h t

o n

etw

ork

Vie

w…

Fro

m s

earc

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Vie

w…

Extend and Visualise your Search

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Visualisation – network view

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Cytoscape Web

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• 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

Visualisation

Master headline

Op

en

ing

th

e n

etw

ork

in

Cyto

scap

e…

Op

en

ing

th

e n

etw

ork

in

Cyto

scap

e…

Master headline

VisualizationVisualization

Ap

ply

ing

a b

ett

er

gra

ph

layou

t…A

pp

lyin

g a

bett

er

gra

ph

layou

t…

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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Exploring a single interaction in more depthExploring a single interaction in more depth

Interaction detail

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Choice of UniProtKBor Dasty ViewDetails of

interactionUniProt PubMed/IMEx ID

Detail of interaction

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Expansionmethod

Details of interaction

InteractionScore

Interaction Score

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• All evidences of Protein A interacting with Protein B are clustered.

• Evidences are scored according to

a. Interaction detection method

b. Interaction type

c. Number of publications interaction has been observed in

Score is normalised on 0-1 scale

Low score – low confidence interaction

High score – high confidence interaction

Participant information

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Searc

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lt f

or

‘RA

D1’

Searc

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lt f

or

‘RA

D1’

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Browsing – Molecule View

Bin

ary

vie

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f o60671_h

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an

Bin

ary

vie

w o

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um

an

Interaction detail

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Fir

st

searc

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rom

th

e h

om

e p

ag

e…

Fir

st

searc

h f

rom

th

e h

om

e p

ag

e…

Details of interaction

Viewing Interaction Details

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Additionalinformation

Interaction Details

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IntAct – Home Page-Quick Search

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Advanced search

Filtering options

Add more filtering options

Ontology search

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Searching with MIQLFir

st

searc

h f

rom

th

e h

om

e p

ag

e…

Fir

st

searc

h f

rom

th

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ag

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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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Network analysis

Analyzing protein-protein interaction networks. Koh GC , Porras P , Aranda B , Hermjakob H , Orchard SE PMID:22385417J Proteome Res [2012 (11) ] page info:2014-31

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www.ebi.ac.uk/training/online

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the intact database sandra orchard & birgit meldal

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