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- 1. IntAct editor - an effective Interaction curation tool. Jyoti Khadake Proteomic Services Team
- 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 2012 2
- 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 25/04/12 3
- 4. What is a molecular interaction? Physical interactions • Types • Self • Binary: homomeric or heteromeric • N-nary complexes • Co-localisations • Enzymatic assays • Purified protein interactions 25/04/12 4
- 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 2012 5
- 6. Details of an interaction
- 7. Is it a duck or a rabbit? 25/04/12 7
- 8. Data Model Participant3 Interaction1 Protein1 Participant1 Experiment1 Interaction2 Participant2 Interaction3 Protein2 Publication Experiment2 Interaction4 . Roles . Features Participant . Preparations 8
- 9. How do databases store Interactions 25/04/12 9
- 10. www.ebi.ac.uk/ols for controlled vocabularies
- 11. How do we curate and manage data • We use – The New Editor. 25/04/12 11
- 12. Publication & Experiment 25/04/12 12
- 13. Publication View 25/04/12 13
- 14. Experiment view 25/04/12 14
- 15. Interaction 25/04/12 15
- 16. Interaction View 25/04/12 16
- 17. Participant 17
- 18. Feature 25/04/12 18
- 19. Participant View 25/04/12 19
- 20. Interactor 25/04/12 20
- 21. Interactor View 25/04/12 21
- 22. IntAct Curation management “Lifecycle of an Interaction” Ready for rechecking validator accept reject exp Publication In progress accept (full text) . p2 Publish I p1 check CVs Curation manual reject curator Super curator Author Master headline
- 23. 25/04/12 23
- 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. 25/04/12 25
- 26. Proteomic Services Team Thank you! Questions? 25/04/12 26 Pablo Dave
- 27. 25/04/12 27
- 28. The five EMBL sites
- 29. The Wellcome Trust Genome Campus Data centre Sanger Institute Sulston building Sanger labs / informatics Cairns Pavilion (shared) EMBL-EBI © John Freebury 29
- 30. New types of data Literature Genomes Protein sequence Nucleotide sequence Proteomes Gene expression Protein structure Protein families, domains and motifs Chemical entities Molecular interactions Pathways Systems 30
- 31. Format for storage and exchange – PSI-MI XML 2.5 31
- 32. Main objects - Experiment Literature references Controlled by Ontologies Confidence measures 32
- 33. Main objects - Participant Interactor e.g. enzyme target Building of Complex e.g. bait, prey Delivery method expression level… Interactor used experimentally 33
Notes de l'éditeur
- An interaction can have one (auto-phosphorylation) or many participants (binary or n-ary) It can involve protein, but also small molecule, DNA, RNA… A participant is the specific instance of the interactor (eg. protein) in the context of an interaction eg. Interactor: P12345, Participant: P12345 with GST tag and mutated residue
- Take Bind out Tell them that we also export some data for text-miners !
- We’re the second largest of the five EMBL sites; there is the main lab and administrative centre in Heidelberg; structural biology labs in Hamburg and Grenoble; mouse biology in Monterotondo, near Rome, and bioinformatics in Hinxton. There are around 1,500 staff within EMBL and about 500 of those work at the EBI.
- We’re based on the Wellcome Trust Genome Campus in Hinxton, south of Cambridge, UK, which we share with the Wellcome Trust Sanger Institute. This is a good strategic fit as the Sanger is a major sequencing centre (most famous for sequencing 1/3 of the human genome) with a strong programme in functional genomics.
- The EBI is probably unique in the world for its range of data resources and tools, spanning everything from DNA and protein sequence to complex pathways and networks. At the EBI, we separate resource development and provision, which we call services, and research although these two are closely related. Both the research areas and services follow the different areas of focus as shown on the slide. Some of the types of data that are now being collected in a high-throughput way, presenting new challenges for how we organise and store this data.