Data integration in ENFIN using standards. The EnCore DAS service.
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DAS workshop. 7–9 April 2010.
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Data integration in ENFIN using standards. The EnCore DAS service.
- 1. Data integration in ENFIN using standards The EnCore DAS service 7–9 April 2010 Rafael Jimenez rafael@ebi.ac.uk EnCORE presentation
- 2. Genesis 11:1-9 1 And the whole earth was of one language, and of one speech. 2 And it came to pass, as they journeyed from the east, that they found a plain in the land of Shinar; and they dwelt there. 3 And they said one to another, Go to, let us make brick, and burn them thoroughly. And they had brick for stone, and slime had they for mortar. 4 And they said, Go to, let us build us a city and a tower, whose top may reach unto heaven; and let us make us a name, lest we be scattered abroad upon the face of the whole earth. 5 And the Lord came down to see the city and the tower, which the children built. 6 And the Lord said, Behold, the people is one, and they have all one language; and this they begin to do; and now nothing will be restrained from them, which they have imagined to do. 7 Go to, let us go down, and there confound their language, that they may not understand one another's speech. 8 So the Lord scattered them abroad from thence upon the face of all the earth: and they left off to build the city. 9 Therefore is the name of it called Babel; because the Lord did there confound the language of all the earth: and from thence did the Lord scatter them abroad upon the face of all the earth. People God
- 3. Tower of Babel Pieter Bruegel the Elder
- 4. Diverse service world SOAP, REST, Java API, Perl API, FTP, GUI, … External data sources Different formats 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. 23.08.185 Utility of bioinformaticsScientificimpact Too little bioinformatics Too many databases Too diverse interfaces Tim Hubbard
- 6. 23.08.18 6 Utility of bioinformatics Scientificimpact Too little bioinformatics Too many databases Too diverse interfaces Integration of
- 7. 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
- 8. • 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 ENFIN Network of Excellence
- 9. 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 Standard EnXML format User input output SOAP
- 10. 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
- 11. EnCORE services From Inputs to Outputs Positive Negative Input/Query Output/Results Program/Service EnCORE dataset EnCORE results EnCORE webservice • Enfin-IntAct • Enfin-PRIDE • Enfin-Affy2UniProt • Enfin-PICR • Enfin-Reactome • Enfin-ArrayExpress • Enfin-UniProt • Enfin-BioModels • Enfin-KEGG • Enfin-G:GOSt • Enfin-CellMINT • Enfin-DOMAINATION • Enfin-FuncNet • Enfin-molecularInteractions • Enfin-proteinAnnotations • Database IDs • Sequences • Experiment: Identifies the result • Sets: Contains the structure of the result • Molecules: Includes the results • Features: Describe details of the result
- 12. Experiment Set Molecule Feature EnXML structure Identifies the result Contains the structure of the result Includes the results Describe details of the result
- 13. EnCORE services Example Positive Negative Input/Query Output/Results Program/Service EnCORE dataset EnCORE results EnCORE webservice • Encore webservice Enfin-IntAct • 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
- 14. EnCORE services Building workflows Input Result Positive result Negative resultWebservice Input selection
- 15. 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
- 16. 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
- 17. ~1440 resources Traditional EnCore approach Domain 5 Domain …Domain 4 Domain 2 Domain 3Domain 1
- 18. New EnCore approach Standards and Federation Domain 1 External data sources Federated systems / Standards EnVISION pages WS WS Web interface EnCORE wrapper
- 19. New EnCore approach Standards and Federation Domain 5 Domain …Domain 4 Domain 2 Domain 3Domain 1
- 20. New EnCore approach Standards and Federation • Less development • More sources • Domain data integration • Comparable results • Automatic inclusion of new data sources • Less maintenance • More stable formats • Easy to control changes • Facilitates validation • Extra value to the original data
- 21. New role for EnCore and EnVision Extra value to the original data • Integration of sources. • Filtering redundancy (whenever possible) • Interconnect results. • Data analysis • More visualization Domain 5 Domain …Domain 4 Domain 2 Domain 3Domain 1
- 22. Standards and Federation in EnCORE
- 23. 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,*]
- 24. 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 EnVision
- 26. Envison interface • Results for Pride, Uniprot, Intact, Reactome, CellMint, PICR, Biomodels, … http://www.ebi.ac.uk/~rafael/enfin/presentations/EnVISION2_01.ppt http://www.enfin.org/dokuwiki/ EnCORE tutorial Results per service Example
- 27. EnVISION Pathways result Positive results Negative results Example
- 28. Integrating standards into EnCore/EnVision Molecular interactions service Preview
- 29. Integrating standards into EnCore/EnVision Molecular interactions service Preview
- 30. Integrating standards into EnCore/EnVision Molecular interactions service Preview
- 31. 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
- The Tower of Babel - Story Summary: Up until this point in the Bible, the whole world had one language - one common speech for all people. The people of the earth became skilled in construction and decided to build a city with a tower that would reach to heaven. By building the tower they wanted to make a name for themselves and also prevent their city from being scattered. God came to see their city and the tower they were building. He perceived their intentions, and in His infinite wisdom, He knew this "stairway to heaven" would only lead the people away from God. He noted the powerful force within their unity of purpose. As a result, God confused their language, causing them to speak different languages so they would not understand each other. By doing this, God thwarted their plans. He also scattered the people of the city all over the face of the earth. God says in Genesis 11:6, "If as one people speaking the same language they have begun to do this, then nothing they plan to do will be impossible for them." (NIV) God realizes that when people are unified in purpose they can accomplish impossible feats, both noble and ignoble. This is why unity in the body of Christ is so important.
- We are exposed to a very diverse service world
- The idea behind EnCORE is simplified in this picture Input (our query) is contained in a XML standard format called EnXML We can run different services over this input. We get results contained in the same EnXML format The Outputs can be use as inputs of other services.
- 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
- EnCORE facilitates building workflows
- 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
- 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.
- 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.