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13.09.2014. Master title. Molecular Interactions – the IntAct Database Sandra Orchard EMBL-EBI. 5. EBI is an Outstation of the European Molecular Biology Laboratory. IntAct goals & achievements.

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Master title

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  1. 13.09.2014 Master title • Molecular Interactions – the IntAct Database • Sandra Orchard • EMBL-EBI 5 EBI is an Outstation of the European Molecular Biology Laboratory.

  2. IntAct goals & achievements • Publicly available repository of molecular interactions (mainly PPIs) - >275K binary interactions taken from >5,000 publications (September 2011) • Data is standards-compliant and available via our website, for download at our ftp site or via PSICQUIC • Provide open-access versions of the software to allow installation of local IntAct nodes. 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. Sanity Checks(nightly) reject Public web site . exp annotate accept FTP site p2 I p1 IMEx check CVs Curation manual Mint DIP MatrixDB report report Super curator curator IntAct Curation “Lifecycle of an Interaction” Publication (full text) Master headline

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

  5. Relationship with UniProtKB Other IMEx databases Interaction curation Protein sequence Data filters In place Early 2012 High confidence PPIs Master headline

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

  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 Data, Standards and Tools EBI Walthrough May 2009 EBI

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

  10. Performing a Simple Search

  11. Visualizing - networkView From search to networkView…

  12. Extend and Visualise your Search

  13. Visualizing - networkView

  14. 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

  15. Visualization Opening the network in Cytoscape… Master headline

  16. Visualization Applying a better graph layout… Master headline

  17. Visualization Applying a better graph layout… Master headline

  18. Visualization Highlighting network properties… Master headline

  19. Visualization Highlighting network properties… Master headline

  20. Visualization Highlighting network properties… Master headline

  21. Visualization Highlighting network properties… Master headline

  22. Cytoscape Plugins

  23. Exploring a single interaction in more depth

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

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

  26. Changing the tabular view

  27. Participant information Search result for ‘RAD1’

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

  29. Viewing Interaction Details Additional information

  30. Interaction Details

  31. IntAct – Home Page-Quick Search

  32. Advanced search: Fields Filtering options Add more filtering options

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

  34. Browsing – Molecule View Binary view of o60671_human

  35. Browsing – extending your search

  36. ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?

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