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
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
20. New EnCore approach
Standards and Federation
Domain 1
External data sources
Federated systems / Standards
EnVISION pages
WS
WS
Web interface
EnCORE wrapper
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
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
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
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.