Programmatic Access to Biological Databases through EnCore and EnVision
•Download as PPT, PDF•
0 likes•36 views
Workshop. Programmatic Access To Biological Databases (Perl). 22–26 February 2010.
Recommended
Recommended
More Related Content
Similar to Programmatic Access to Biological Databases through EnCore and EnVision
Similar to Programmatic Access to Biological Databases through EnCore and EnVision (20)
More from Rafael C. Jimenez
More from Rafael C. Jimenez (20)
Recently uploaded
Recently uploaded (20)
Programmatic Access to Biological Databases through EnCore and EnVision
- 1. Data Integration through Enfin and EnCore Programmatic Access To Biological Databases (Perl) 22–26 February 2010 Rafael Jimenez rafael@ebi.ac.uk Updated: 12 February 2010 EnCORE presentation • EnCore • EnVision
- 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 EnCore
- 3. 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
- 4. 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
- 5. 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, …
- 6. 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
- 7. … – Input – Output – Input – Output – … … Input EnXML Output EnXML Service EnCORE WS
- 8. 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 • Database IDs • Sequences • Experiment: Identifies the result • Sets: Contains the structure of the result • Molecules: Includes the results • Features: 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 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
- 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
- 12. 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
- 13. 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
- 14. ~1440 resources Traditional EnCore approach Domain 5 Domain …Domain 4 Domain 2 Domain 3Domain 1
- 15. New EnCore approach Standards and Federation Domain 1 External data sources Federated systems / Standards EnVISION pages WS WS Web interface EnCORE wrapper
- 16. New EnCore approach Standards and Federation Domain 5 Domain …Domain 4 Domain 2 Domain 3Domain 1
- 17. 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
- 18. 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
- 19. Standards and Federation in EnCORE
- 20. 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
- 22. 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
- 23. EnVISION Pathways result Positive results Negative results Example
- 24. Integrating standards into EnCore/EnVision Molecular interactions service Preview
- 25. Integrating standards into EnCore/EnVision Molecular interactions service Preview
- 26. Integrating standards into EnCore/EnVision Molecular interactions service Preview
Editor's Notes
- 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
- The same results in a table
- 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.