IntAct editor - an effective Interactioncuration tool.Jyoti KhadakeProteomic Services Team
Overview    • What is IntAct molecular interaction      database    • What is a Molecular Interaction    • Data Model    •...
What is IntAct?    • IntAct is a database of molecular interaction    • Capture interactions from literature    • It is Ma...
What is a molecular interaction?    Physical interactions    • Types      • Self      • Binary: homomeric or heteromeric  ...
Interaction details captured from literature       • Pubmed ID – Source of data       • The interactors       • Experiment...
Details of an interaction
Is it a duck or a rabbit?    25/04/127
Data Model                                               Participant3                            Interaction1             ...
How do databases store Interactions         25/04/129
www.ebi.ac.uk/ols for controlled vocabularies
How do we curate and manage data     • We use – The New Editor.          25/04/1211
Publication & Experiment     25/04/1212
Publication View     25/04/1213
Experiment view     25/04/1214
Interaction     25/04/1215
Interaction View     25/04/1216
Participant17
Feature     25/04/1218
Participant View     25/04/1219
Interactor     25/04/1220
Interactor View     25/04/1221
IntAct Curation management                 “Lifecycle of an Interaction”                                         Ready for...
25/04/1223
Databases using Editor
Summary     • IntAct editor is based on the       PSI-MI schema v2.5     • This enables us to capture       details of Int...
Proteomic Services Team                Thank you!                Questions?     25/04/1226                Pablo   Dave
25/04/1227
The five EMBL sites
The Wellcome Trust Genome CampusData centre                                     Sanger Institute                          ...
New types of data                                LiteratureGenomes                                            Protein sequ...
Format for storage and exchange –     PSI-MI XML 2.531
Main objects - Experiment                                 Literature                                 references           ...
Main objects - Participant                                     Interactor                                        e.g. enzy...
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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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  • 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.
  • 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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