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Bc2012 jyotiebi poster44ec82

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Biocurator Conference Presentation Easy chair number 82 by Jyoti khadake from EMBL-EBI

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Bc2012 jyotiebi poster44ec82

  1. 1. IntAct editor - an effective Interactioncuration tool.Jyoti KhadakeProteomic Services Team
  2. 2. Overview • What is IntAct molecular interaction database • What is a Molecular Interaction • Data Model • Standardized Schema and CV • Editor and management of entries 25 April 20122
  3. 3. What is IntAct? • IntAct is a database of molecular interaction • Capture interactions from literature • It is Manually Curated • Is extensively cross-referenced • Provides tools to query, analyze and visualize data • Open source and open access 25/04/123
  4. 4. What is a molecular interaction? Physical interactions • Types • Self • Binary: homomeric or heteromeric • N-nary complexes • Co-localisations • Enzymatic assays • Purified protein interactions 25/04/124
  5. 5. Interaction details captured from literature • Pubmed ID – Source of data • The interactors • Experimental conditions of interactions • Type of interaction • Properties of interactors 25 April 20125
  6. 6. Details of an interaction
  7. 7. Is it a duck or a rabbit? 25/04/127
  8. 8. Data Model Participant3 Interaction1 Protein1 Participant1 Experiment1 Interaction2 Participant2 Interaction3 Protein2Publication Experiment2 Interaction4 . Roles . Features Participant . Preparations8
  9. 9. How do databases store Interactions 25/04/129
  10. 10. www.ebi.ac.uk/ols for controlled vocabularies
  11. 11. How do we curate and manage data • We use – The New Editor. 25/04/1211
  12. 12. Publication & Experiment 25/04/1212
  13. 13. Publication View 25/04/1213
  14. 14. Experiment view 25/04/1214
  15. 15. Interaction 25/04/1215
  16. 16. Interaction View 25/04/1216
  17. 17. Participant17
  18. 18. Feature 25/04/1218
  19. 19. Participant View 25/04/1219
  20. 20. Interactor 25/04/1220
  21. 21. Interactor View 25/04/1221
  22. 22. IntAct Curation management “Lifecycle of an Interaction” Ready for rechecking validator accept reject expPublication In progress accept (full text) . p2 Publish I p1 checkCVs Curation manual reject curator Super curator Author Master headline
  23. 23. 25/04/1223
  24. 24. Databases using Editor
  25. 25. Summary • IntAct editor is based on the PSI-MI schema v2.5 • This enables us to capture details of Interaction data • Allows us to manage curation process • It is used by various other databases. 25/04/1225
  26. 26. Proteomic Services Team Thank you! Questions? 25/04/1226 Pablo Dave
  27. 27. 25/04/1227
  28. 28. The five EMBL sites
  29. 29. The Wellcome Trust Genome CampusData centre Sanger Institute Sulston buildingSangerlabs /informatics Cairns Pavilion (shared) EMBL-EBI © John Freebury29
  30. 30. New types of data LiteratureGenomes Protein sequenceNucleotide sequence Proteomes Gene expression Protein structure Protein families, domains and motifs Chemical entities Molecular interactions Pathways Systems 30
  31. 31. Format for storage and exchange – PSI-MI XML 2.531
  32. 32. Main objects - Experiment Literature references Controlled by Ontologies Confidence measures32
  33. 33. Main objects - Participant Interactor e.g. enzyme target Building of Complex e.g. bait, prey Delivery method expression level… Interactor used experimentally33

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