1. The IntAct Database Sandra Orchard & Birgit Meldal

2. 2 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/intact ftp://ftp.ebi.ac.uk/pub/databases/intact www.ebi.ac.uk/Tools/webservices/psicquic/view/main.xhtml

3. 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. 4 UniProt Knowledge Base http://www.ebi.uniprot.org/ Interactions can be mapped to the canonical sequence….. to splice variants.... or to post- processed chains

5. Relationship with UniProtKB Master headline Protein sequence Data filters Other IMEx databases High confidence PPIs Interaction curation Other DBs

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

7. 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:

8. Performing and visualing a Simple Search

9. 9 IntAct – Home Page http://www.ebi.ac.uk/intact

10. Performing a Simple Search 10

11. 11 Visualizing - networkView From search to networkView…

12. Extend and Visualise your Search 12

13. Visualisation – network view 13

14. Cytoscape Web 14 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

15. Visualisation Master headline Opening the network in Cytoscape…

16. Master headline Visualization Applying a better graph layout…

17. Master headline Visualization Applying a better graph layout…

18. Master headline Visualization Highlighting network properties…

19. Master headline Visualization Highlighting network properties…

20. Master headline Visualization Highlighting network properties…

21. Master headline Visualization Highlighting network properties…

22. Cytoscape Plugins 22

23. Exploring a single interaction in more depth

24. Interaction detail 24 Choice of UniProtKB or Dasty View Details of interaction UniProt PubMed/IMEx ID

25. Detail of interaction 25 Expansion method Details of interaction Interaction Score

26. Interaction Score 26 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

27. Participant information 27 Search result for ‘RAD1’

28. 28 Browsing – Molecule View Binary view of o60671_human

29. Interaction detail 29 First search from the home page… Details of interaction

30. Viewing Interaction Details 30 Additional information

31. Interaction Details 31

32. IntAct – Home Page-Quick Search 32

33. Advanced search Filtering options Add more filtering options

34. Ontology search 34

35. 35 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 :

36. 36 Network analysis Analyzing protein-protein interaction networks. Koh GC, Porras P, Aranda B, Hermjakob H, Orchard SE PMID:22385417 J Proteome Res [2012 (11) ] page info:2014-31

37. 37 www.ebi.ac.uk/training/online

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