5 EBI is an Outstation of the European Molecular Biology Laboratory. Master title Molecular Interactions – the IntAct Database Sandra Orchard EMBL-EBI

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 ftp://ftp.ebi.ac.uk/pub/databases/intact

Master headline “Lifecycle of an Interaction” Publication (full text) Sanity Checks (nightly) IntAct Curation CVs curator report Curation manual. reject Super curator annotate p1 p2 I exp IMEx MatrixDB Mint DIP Public web site FTP site accept check

4 UniProt Knowledge Base 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

6 Data model Support for detailed features i.e. definition of interacting interface Interacting domains Overlay of Ranges on sequence:

7 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 Walthrough May 2009 EBI Data, Standards and Tools

9 IntAct – Home Page

Performing a Simple Search 10

11 Visualizing - networkView From search to networkView…

Extend and Visualise your Search 12

13 Visualizing - networkView

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 14

Master headline Visualization Opening the network in Cytoscape…

Master headline Visualization Applying a better graph layout…

Master headline Visualization Applying a better graph layout…

Master headline Visualization Highlighting network properties…

Master headline Visualization Highlighting network properties…

Master headline Visualization Highlighting network properties…

Master headline Visualization Highlighting network properties…

Cytoscape Plugins 22

EBI is an Outstation of the European Molecular Biology Laboratory. Exploring a single interaction in more depth

Interaction detail 24 First search from the home page… Choice of UniProtKB or Dasty View Details of interaction

Detail of interaction 25 UniProt Taxonomy PubMed Expansion method Details of interaction

Changing the tabular view 26

Participant information 27 Search result for ‘RAD1’

Interaction detail 28 First search from the home page… Details of interaction

29 Viewing Interaction Details Additional information

Interaction Details 30

IntAct – Home Page-Quick Search 31

Advanced search: Fields Filtering options Add more filtering options

33 Searching with MIQL First search from the home page… Using the Molecular Interaction Query Language (MIQL), one can also build complex queries List of terms one can query on :

34 Browsing – Molecule View Binary view of o60671_human

35 Browsing – extending your search

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