Data integration in Proteomics through EnVision and EnCore Web Services
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The document discusses EnCore, a platform developed by the ENFIN Network of Excellence to enable data integration across various biological domains and data sources. EnCore provides a set of web services and the EnVision interface to allow users to query multiple databases and analyze the results in a standardized format. It is moving towards a new approach based on standards and federation to access more external sources in a interoperable way and provide added value to the original data.
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Data integration in Proteomics through EnVision and EnCore Web Services
- 1. ECCB10 TT11 29 September 2010 Rafael Jimenez rafael@ebi.ac.uk EnCORE presentation Data integration in Proteomics through EnVision and EnCore Web Services
- 2. ENFIN Network of Excellence • Brings together experimentalists and computational biologists to develop the next generation of informatics resources for systems biology • Funded by the European Commission within its FP6 programme under the thematic area ‘Life sciences, genomics and biotechnology for health’ • 20 partners in 13 countries • www.enfin.org
- 3. EnCore • ENFIN Platform to enable mining data across various domains, sources, formats and types • Integrates database resources and analysis tools across different disciplines EnXML EnCORE services EnVISION pages EnXML User input output SOAP Web Services Web Client Interface Standard exchange format
- 4. Diverse service world SOAP, REST, Java API, Perl API, FTP, GUI, … External data sources Results Access interfaces User ?integration • Multiple manual connections • Multiple technologies • Multiple result files which have to be combined manually • Much work to reproduce XML, CSV, Plain Text, JSON, …
- 5. Standardized EnCORE world Heterogeneous external world Standardised EnCORE world EnXML External data sources EnCORE services EnVISION pages API, WS access Standard EnXML format User input output
- 6. EnCORE services From Inputs to Outputs Positive Negative Results / EnXML Web Services Protein identifications • pride Microarray probe mapping to Uniprot • probe2uniprot Protein Identifier Cross Reference Service • picr Biological Pathways • reactome • kegg Microarray experiments • arrayExpress Protein sequence information • uniprot • uniprot2proteinAnnotations Biological models • biomodels Gene ontology enrichment • gGost Cellular location • cellmint Protein domain analysis • domaination Protein function prediction • funcnet Molecular interactions • uniprot2molecularInteractions Protein • Database IDs • Sequences • Experiment: Identifies the result • Sets: Contains the structure of the result • Molecules: Includes the results • Features: Describe details of the result Input / EnXML
- 7. Experiment Set Molecule Feature EnXML structure Identifies the result Contains the structure of the result Includes the results Describe details of the result
- 9. EnCORE services Example Positive Negative Input/Query Output/Results Program/Service EnCORE dataset EnCORE results EnCORE webservice • Encore webservice uniprot2molecularInteractions • Database ID (Uniprot ID) P37173 • Experiment: ID4 • Sets: (1)EBI-296235, (2)EBI-1033040, (3) EBI- 902913, EBI-902937, (4) EBI-296166, EBI-296246, (5)EBI-902913 • Molecules: (1)O35613, (2)P10600, (3)P07200, (4)Q9UER7, (5)Q99K41 • Features: No features
- 10. EnCore services Example (Result on a table) Interactor A Interactor B Interaction IDs 1 P37173 O35613 EBI-296235 2 P37173 P10600 EBI-1033040 3 P37173 P07200 EBI-902913, EBI-902937 4 P37173 Q9UER7 EBI-296166, EBI-296246 5 P37173 Q99K41 EBI-902913 Input/Query Output/Results Program/Service Enfin-IntAct P37173
- 11. EnCore services Building workflows Input Result Positive result Negative resultWebservice Input selection
- 14. EnVision2 interface • Results for Pride, Uniprot, Intact, Reactome, CellMint, PICR, Biomodels, … Results per service
- 15. EnVision2 Pathways result Positive results Negative results
- 17. ENFIN Network of Excellence • Brings together experimentalists and computational biologists to develop the next generation of informatics resources for systems biology • Funded by the European Commission within its FP6 programme under the thematic area ‘Life sciences, genomics and biotechnology for health’ • 20 partners in 13 countries • www.enfin.org EnCore Adapting EnCORE to Standards and Federation
- 18. Molecular Biology Database resources Human Genes and Diseases 14% Proteomics Resources (20) 0% Other Molecular Biology Databases 3% Immunological databases 2% Plant databases 8% Organelle databases 2% Human and other Vertebrate Genomes 8% Nucleotide Sequence Databases 9% RNA sequence databases Protein sequence databases Structure Databases 9% Genomics -Databases (non (vertebrate Metabolic and Signaling Pathways 9% Nucleic Acids Research annual Database Issue and the NAR online Molecular Biology Database Collection in 2009MY Galperin, GR Cochrane - Nucleic Acids Research, 2008 ~1440 resources
- 19. ~1440 resources Traditional EnCore approach Domain 5 Domain …Domain 4 Domain 2 Domain 3Domain 1
- 20. New EnCore approach Standards and Federation Domain 1 External data sources Federated systems / Standards EnVISION pages WS WS Web interface EnCORE wrapper
- 21. New EnCore approach Standards and Federation Domain 5 Domain …Domain 4 Domain 2 Domain 3Domain 1
- 22. New EnCore approach Standards and Federation • Less development • More sources • Data integration per domain • Comparable results • Automatic inclusion of new data sources • More stable formats • Validation • Extra value to the original data
- 23. New role for EnCore and EnVision Extra value to the original data • Integration of sources – Clustering results – Data analysis • Interconnect results • More visualization Domain 5 Domain …Domain 4 Domain 2 Domain 3Domain 1
- 24. Centralization VS Federation DB GUI API WS DB DB DB SP SP SP SP Federation Database Graphical User InterfaceGUI User Standard protocolSP DB GUI API WS Centralized database A AA A A A A A
- 25. Standards and Federation in EnCORE
- 26. Service broker Service consumer Service provider Service Contract ... ... Interact PublishFind Service Oriented Architecture DAS & PSICQUIC Implementation ... ... ... Registry DAS Clients Annotation sources Annotation sources Annotation sources DAS Clients Clients Protocol
- 27. 23.08.18 27 The Distributed Annotation System, 2001 Dowell et al; BMC Bioinformatics. 2001; 2: 7. Published online 2001 October 10. DAS, how it works illustration
- 28. 23.08.18 28 DAS Registry - list of protein annotation sources
- 29. EnCore DAS service for protein sequence annotations Protein DAS annotation sources Protein DAS annotation sources Experiment Set Molecule Feature Uniprot DAS reference source Uniprot DAS annotation source Protein information Protein feature information Protein DAS annotation sources Protein DAS annotation sources Protein DAS annotation sources • Service: • Name: uniprot2proteinannotations • URL: http://www.ebi.ac.uk/enfin-srv/encore/uniprot2proteinannotations/service • Input: List of Uniprot Acc numbers • Options: DAS Sources to query • Direct input (DAS feature URL) [0,*] • Registry LABEL [0,1] • Registry source URI (DS_XXX) [0,*]
- 30. PSICQUIC, how it works ….…. …..... ….…. …..... PSICQUIC PSICQUIC PSICQUIC Sample Observation error Interaction databases Publications PSICQUIC services Annotation error User PSICQUIC Registry PSICQUIC client
- 31. PSICQUIC Registry • 13 sources • 14.665.530 interactions
- 32. EnVision2, molecular interactions PSICQUIC client http://www.enfin.org/ PSICQUIC registry Query
- 36. EnCore APIs Example: Score distribution across several databases
- 39. Thank you! Questions? ENFIN partners: • Pascal Kahlem (project coordinator) • Bernd Brandt (IBIVU) • Christine Orengo (UCL) • Andrew Clegg (UCL) • Ioannis Xenarios (SIB) • Heinz Stockinger (SIB) • Jaak Vilo (QURETEC) • Jüri Reimand (QURETEC) • Gianni Cesareni (UNITOR) • Arnaud Ceol (UNITOR) • James Procter (UNIVDUN) • Ana Rojas Mendoza (CNIO)
Editor's Notes
- We are exposed to a very diverse service world
- This is a generic example of how an EnCORE service work
- An specific example The query is a protein Acc We run the Intact service We get the interactions result defined by the EnXML terminology
- The same results in a table
- EnCORE facilitates building workflows
- EnVISION is an EnCORE interface With just one click user can run different services get a quick overview for a dataset This example shows result for …
- Here an example of the potential of EnVISION In this example we used a dataset of more than 300 protein Acc. In this screenshot EnVISION was able to find more than 500 pathways for this dataset. EnVISION is capable to link and display positive results in a pathway map.
- EnVISION results are nice, but do not forget our initial integration problem For one domain (protein interaction, pathways, protein sequence …) we might have several databases providing data
- EnCORE provides a great solution however it is not complete if it can not include more resources For EnCORE it is not feasible to develop and maintain so many wrappers. Nonetheless EnCORE can overcome this problem using standards and federated systems
- Data producers have good reasons to have their own database. However among all of us have to think about ways to share our data and make it easily available to user. Federation provides an easy way to integrate data resources. 100% compatible with database providers continuing working with their own database structure, GUI, ...
- Integration of biological data of various types and development of adapted bioinformatics tools represent critical objectives to enable research at the systems level. The European Network of Excellence ENFIN is engaged in developing an adapted infrastructure to connect databases, and platforms to enable both generation of new bioinformatics tools and experimental validation of computational predictions. Beyond the use of common standards to format individual datasets, there is a need for sophisticated informatics platforms to enable mining data across various domains, sources, formats and types. The aim of the EnCORE project is to integrate across different disciplines an extensive list of database resources and analysis tools in a computationally accessible and extensible manner, facilitating automated data retrieval and processing with a special focus on systems biology. The EnCORE platform is available as a collection of webservices with a common standard format easy to integrate in Workflow management software such as Taverna. Additionally EnCORE services are also accessible thought EnVISION, a web graphical user interface providing elaborated information such as molecular interaction, biological pathways and computational models of pathways.