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Dasty2

 Omar Pera

Background

Dasty2

Features

Advanced
Search page

Configuration
system
                A web client for visualizing
Demonstration
                protein sequence features
                        Omar Pera Mira

                  ECCB 2008 in Sardinia, Italy
Outline of the presentation

   Dasty2
                    Background: DAS
 Omar Pera
                    Dasty2
Background
                    Features
Dasty2

                    Advanced search page: MyDasty
Features

Advanced
                    MyDasty configuration system
Search page

                    Acknowledgments
Configuration
system

                    Demonstration
Demonstration
Background: DAS

   Dasty2
                   Distributed Annotation System.
 Omar Pera
                   RESTful web service (XML data through HTTP
Background
                   requests)
Dasty2
                   Uniform access to multiple repositories of biological
Features
                   data
Advanced
Search page
                   Different biological data types:
Configuration
                       Genome
system
                       Protein sequence
Demonstration
                       Protein annotations
                       ..
                   Widely adopted system
                   URL: http://biodas.org
Background: DAS

   Dasty2

 Omar Pera

Background

Dasty2

Features

Advanced
Search page

Configuration
system

Demonstration

                                                   The Distributed Annotation System, 2001 Dowell et al; BMC
                  Ilustration of Andreas Kähäri   Bioinformatics. 2001; 2: 7. Published online 2001 October 10.
Dasty2

                Dasty2 is a web client for visualizing protein sequence
   Dasty2

                feature information using DAS.
 Omar Pera

Background
                    Lightweight
Dasty2
                    Highly customizable
Features

                    Makes use of AJAX (asynchronous loading + local
Advanced
Search page
                    caching)
Configuration
system
                    Easy to integrate in other systems
Demonstration
                    Extensible
                    Open Source: http://sourceforge.net/projects/dasty/
                    URL : http://www.ebi.ac.uk/dasty
Dasty2

   Dasty2

 Omar Pera

Background

Dasty2

Features

Advanced
Search page

Configuration
system

Demonstration
Dasty2

   Dasty2

 Omar Pera

Background

Dasty2

Features

Advanced
Search page

Configuration
system

Demonstration
Dasty2

   Dasty2

 Omar Pera

Background

Dasty2

Features

Advanced
Search page

Configuration
system

Demonstration
Dasty2

   Dasty2

 Omar Pera

Background

Dasty2

Features

Advanced
Search page

Configuration
system

Demonstration
Dasty2

   Dasty2

 Omar Pera

Background

Dasty2

Features

Advanced
Search page

Configuration
system

Demonstration
Dasty2

   Dasty2

 Omar Pera

Background

Dasty2

Features

Advanced
Search page

Configuration
system

Demonstration
Features
                       Protein sequence visualization

    Dasty2

                                                 Positional features
 Omar Pera

Background

Dasty2

Features
Protein sequence
visualization
3D protein structure
viewer
DAS ontology
integration


                                              Non Positional features
Advanced
Search page

Configuration
system

Demonstration
Features
                       3D protein structure viewer

    Dasty2

 Omar Pera

Background
                                                     Annotation on 3D protein space:
Dasty2

Features
                                                         Highlight annotation on the 3D
Protein sequence

                                                         structure
visualization
3D protein structure
viewer

                                                         Select 3D regions and highlight
DAS ontology
integration

                                                         correspondence in the protein
Advanced
Search page
                                                         3D structure rotation, zoom, etc..
Configuration
system

Demonstration
Features
                       DAS ontology integration for data manipulation

    Dasty2
                             In order to classify protein annotations, a protein
 Omar Pera
                             feature ontology is avaliable in DAS.
Background

Dasty2

Features
Protein sequence
visualization
3D protein structure
viewer
DAS ontology
integration

Advanced
Search page

Configuration
system

Demonstration
Features
                       DAS ontology integration for data manipulation

    Dasty2
                             In order to classify protein annotations, a protein
 Omar Pera
                             feature ontology is avaliable in DAS.
Background
                             Dasty2 integrates DAS ontology information found in
Dasty2
                             the current protein to filter annotations by:
Features
Protein sequence
                                   Protein feature types
visualization
3D protein structure
                                   Evidence
viewer
DAS ontology
integration

Advanced
Search page

Configuration
system

Demonstration
Advanced Search page: MyDasty

    Dasty2

                          MyDasty is an extension of the search page that makes
 Omar Pera

                           Dasty2 a more configurable and powerful application.
Background

Dasty2

Features

Advanced
Search page
Das sources
selection
Filtering annotations
Mapping protein
accessions from
other databases

Configuration
system

Demonstration
MyDasty

    Dasty2
                           Let users have more control over the search before
 Omar Pera
                           the client starts.
Background
                           Give the option to save and restore your
Dasty2
                           configuration.
Features

                           Easy to extend with other ’plugins’
Advanced
Search page
                           Independent from Dasty2
Das sources
selection
Filtering annotations
                           Developed recently, not yet in production
Mapping protein
accessions from
other databases

Configuration
system

Demonstration
Features
                        Das sources selection


                         Full control of the DAS sources Dasty2 retrieves protein
    Dasty2

                         annotations from using DAS registry:
 Omar Pera

Background
                              Select individually which DAS servers are queried for
Dasty2
                              features.
Features
                              Filter the servers by label in order to make easier the
Advanced
                              selection.
Search page
Das sources
selection
                              Insert test or private DAS sources to display on Dasty2.
Filtering annotations
Mapping protein
accessions from
                              Sort the selected DAS sources: Dasty2 graphic.
other databases

Configuration
system

Demonstration
Features
                        Das sources selection

    Dasty2

 Omar Pera

Background

Dasty2

Features

Advanced
Search page
Das sources
selection
Filtering annotations
Mapping protein
accessions from
other databases

Configuration
system

Demonstration
Features
                        Filtering annotations using the DAS ontology


                         Pre-configure Dasty2 to just display annotations of a
    Dasty2

                         certain type or category.
 Omar Pera

Background

Dasty2

Features

Advanced
Search page
Das sources
selection
Filtering annotations
Mapping protein
accessions from
other databases

Configuration
system

Demonstration
Features
                        Mapping protein accessions from other databases


                         Protein Identifier Cross-Reference service ( PICR ) is a
    Dasty2

                         tool capable of mapping protein identifiers to a large list of
 Omar Pera

                         databases.
Background

Dasty2

Features
                         MyDasty uses PICR to:
Advanced
Search page
                              Map from different source databases such as IPI,
Das sources
selection
                              Ensembl, TrEMBL or PIR to Uniprot protein accession
Filtering annotations
Mapping protein
                              number, extending the possibilities of Dasty2
accessions from
other databases

Configuration
system

Demonstration
Features
                        Mapping protein accessions from other databases


                         Protein Identifier Cross-Reference service ( PICR ) is a
    Dasty2

                         tool capable of mapping protein identifiers to a large list of
 Omar Pera

                         databases.
Background

Dasty2

Features
                         MyDasty uses PICR to:
Advanced
Search page
                              Map from different source databases such as IPI,
Das sources
selection
                              Ensembl, TrEMBL or PIR to Uniprot protein accession
Filtering annotations
Mapping protein
                              number, extending the possibilities of Dasty2
accessions from
other databases

Configuration
system

Demonstration
Configuration system

                We have to consider two types of users on MyDasty:
   Dasty2

 Omar Pera
                Anonymous: Users that just want to customize their current
Background
                          search. No need to store the config for future
Dasty2
                          uses.
Features
                Registered: They are users who want to save their
Advanced
                            configuration on the server. It means that all
Search page

Configuration
                            the parameters configured on myDasty could
system
                            be restored in the future.
Demonstration
Registered users
                OpenID

   Dasty2
                  It is a shared identity service
                  that makes use of a single
 Omar Pera

                  digital identity, eliminating
Background

                  the need for a different user
Dasty2

                  name and password for each
Features

                  site.
Advanced
Search page

Configuration
system

Demonstration
Registered users
                Options

   Dasty2
                      History of the previous proteins inserted on
 Omar Pera
                      myDasty.
Background

Dasty2

Features

Advanced
Search page

Configuration
system

Demonstration
Registered users
                Options

   Dasty2
                      History of the previous proteins inserted on myDasty.
 Omar Pera
                      Save multiple configurations with a specific name.
Background

Dasty2

Features

Advanced
Search page

Configuration
system

Demonstration
Registered users
                Options

   Dasty2
                      History of the previous proteins inserted on myDasty.
 Omar Pera
                      Save multiple configurations with a specific name.
Background

Dasty2

Features

Advanced
Search page

Configuration
system

Demonstration
Registered users
                Options

   Dasty2
                      History of the previous proteins inserted on myDasty.
 Omar Pera
                      Save multiple configurations of myDasty with a specific
Background
                      name.
Dasty2
                      Update, delete, change name or create new
Features

                      configurations.
Advanced
Search page

Configuration
system

Demonstration
Acknowledgments

   Dasty2

                                                         Funding and collaborations
 Omar Pera
                 Supervision
Background
                        Henning Hermjakob,
                        EMBL-EBI, UK
Dasty2

Features
                 Development
Advanced
                        Rafael C. Jimenez,
Search page
                        EMBL-EBI, UK
Configuration            NBN central node, South Africa
system                  CiPF, Spain
                                                         Participation and collaboration
                        Antony Quinn,
Demonstration
                        EMBL-EBI, UK                         Phil Jones,
                                                             EMBL-EBI, UK         Alberto Labarga,
                 Development                                                      EMBL-EBI, UK
                                                             Lennart Martens,
                                                             EMBL-EBI, UK         Nisha Vinod,
                 Rafael C. Jimenez,                                               EMBL-EBI, UK
                                                             Florian Reisinger,
                 EMBL-EBI, U
                                                             EMBL-EBI, UK         Dan Jacobson,
                 NBN central node, South Africa
                                                                                  NBN central node,
                 CiPF, Spain                                 Eugene Kulesha,
                                                                                  South Africa
                 Antony Quinn,                               EMBL-EBI, UK
                 EMBL-EBI, UK Antony Quinn,                                       Andreas Kahari,
                                                             Andreas Prlic,
                 EMBL-EBI, UK                                                     EMBL-EBI, UK
                                                             Sanger Institute,
                                                             UK
Demonstration

   Dasty2

                                Demonstration
 Omar Pera

Background

Dasty2

Features

Advanced
Search page

Configuration
system

Demonstration

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Dasty2, a web client for visualizing protein sequence features

  • 1. Dasty2 Omar Pera Background Dasty2 Features Advanced Search page Configuration system A web client for visualizing Demonstration protein sequence features Omar Pera Mira ECCB 2008 in Sardinia, Italy
  • 2. Outline of the presentation Dasty2 Background: DAS Omar Pera Dasty2 Background Features Dasty2 Advanced search page: MyDasty Features Advanced MyDasty configuration system Search page Acknowledgments Configuration system Demonstration Demonstration
  • 3. Background: DAS Dasty2 Distributed Annotation System. Omar Pera RESTful web service (XML data through HTTP Background requests) Dasty2 Uniform access to multiple repositories of biological Features data Advanced Search page Different biological data types: Configuration Genome system Protein sequence Demonstration Protein annotations .. Widely adopted system URL: http://biodas.org
  • 4. Background: DAS Dasty2 Omar Pera Background Dasty2 Features Advanced Search page Configuration system Demonstration The Distributed Annotation System, 2001 Dowell et al; BMC Ilustration of Andreas Kähäri Bioinformatics. 2001; 2: 7. Published online 2001 October 10.
  • 5. Dasty2 Dasty2 is a web client for visualizing protein sequence Dasty2 feature information using DAS. Omar Pera Background Lightweight Dasty2 Highly customizable Features Makes use of AJAX (asynchronous loading + local Advanced Search page caching) Configuration system Easy to integrate in other systems Demonstration Extensible Open Source: http://sourceforge.net/projects/dasty/ URL : http://www.ebi.ac.uk/dasty
  • 6. Dasty2 Dasty2 Omar Pera Background Dasty2 Features Advanced Search page Configuration system Demonstration
  • 7. Dasty2 Dasty2 Omar Pera Background Dasty2 Features Advanced Search page Configuration system Demonstration
  • 8. Dasty2 Dasty2 Omar Pera Background Dasty2 Features Advanced Search page Configuration system Demonstration
  • 9. Dasty2 Dasty2 Omar Pera Background Dasty2 Features Advanced Search page Configuration system Demonstration
  • 10. Dasty2 Dasty2 Omar Pera Background Dasty2 Features Advanced Search page Configuration system Demonstration
  • 11. Dasty2 Dasty2 Omar Pera Background Dasty2 Features Advanced Search page Configuration system Demonstration
  • 12. Features Protein sequence visualization Dasty2 Positional features Omar Pera Background Dasty2 Features Protein sequence visualization 3D protein structure viewer DAS ontology integration Non Positional features Advanced Search page Configuration system Demonstration
  • 13. Features 3D protein structure viewer Dasty2 Omar Pera Background Annotation on 3D protein space: Dasty2 Features Highlight annotation on the 3D Protein sequence structure visualization 3D protein structure viewer Select 3D regions and highlight DAS ontology integration correspondence in the protein Advanced Search page 3D structure rotation, zoom, etc.. Configuration system Demonstration
  • 14. Features DAS ontology integration for data manipulation Dasty2 In order to classify protein annotations, a protein Omar Pera feature ontology is avaliable in DAS. Background Dasty2 Features Protein sequence visualization 3D protein structure viewer DAS ontology integration Advanced Search page Configuration system Demonstration
  • 15. Features DAS ontology integration for data manipulation Dasty2 In order to classify protein annotations, a protein Omar Pera feature ontology is avaliable in DAS. Background Dasty2 integrates DAS ontology information found in Dasty2 the current protein to filter annotations by: Features Protein sequence Protein feature types visualization 3D protein structure Evidence viewer DAS ontology integration Advanced Search page Configuration system Demonstration
  • 16. Advanced Search page: MyDasty Dasty2 MyDasty is an extension of the search page that makes Omar Pera Dasty2 a more configurable and powerful application. Background Dasty2 Features Advanced Search page Das sources selection Filtering annotations Mapping protein accessions from other databases Configuration system Demonstration
  • 17. MyDasty Dasty2 Let users have more control over the search before Omar Pera the client starts. Background Give the option to save and restore your Dasty2 configuration. Features Easy to extend with other ’plugins’ Advanced Search page Independent from Dasty2 Das sources selection Filtering annotations Developed recently, not yet in production Mapping protein accessions from other databases Configuration system Demonstration
  • 18. Features Das sources selection Full control of the DAS sources Dasty2 retrieves protein Dasty2 annotations from using DAS registry: Omar Pera Background Select individually which DAS servers are queried for Dasty2 features. Features Filter the servers by label in order to make easier the Advanced selection. Search page Das sources selection Insert test or private DAS sources to display on Dasty2. Filtering annotations Mapping protein accessions from Sort the selected DAS sources: Dasty2 graphic. other databases Configuration system Demonstration
  • 19. Features Das sources selection Dasty2 Omar Pera Background Dasty2 Features Advanced Search page Das sources selection Filtering annotations Mapping protein accessions from other databases Configuration system Demonstration
  • 20. Features Filtering annotations using the DAS ontology Pre-configure Dasty2 to just display annotations of a Dasty2 certain type or category. Omar Pera Background Dasty2 Features Advanced Search page Das sources selection Filtering annotations Mapping protein accessions from other databases Configuration system Demonstration
  • 21. Features Mapping protein accessions from other databases Protein Identifier Cross-Reference service ( PICR ) is a Dasty2 tool capable of mapping protein identifiers to a large list of Omar Pera databases. Background Dasty2 Features MyDasty uses PICR to: Advanced Search page Map from different source databases such as IPI, Das sources selection Ensembl, TrEMBL or PIR to Uniprot protein accession Filtering annotations Mapping protein number, extending the possibilities of Dasty2 accessions from other databases Configuration system Demonstration
  • 22. Features Mapping protein accessions from other databases Protein Identifier Cross-Reference service ( PICR ) is a Dasty2 tool capable of mapping protein identifiers to a large list of Omar Pera databases. Background Dasty2 Features MyDasty uses PICR to: Advanced Search page Map from different source databases such as IPI, Das sources selection Ensembl, TrEMBL or PIR to Uniprot protein accession Filtering annotations Mapping protein number, extending the possibilities of Dasty2 accessions from other databases Configuration system Demonstration
  • 23. Configuration system We have to consider two types of users on MyDasty: Dasty2 Omar Pera Anonymous: Users that just want to customize their current Background search. No need to store the config for future Dasty2 uses. Features Registered: They are users who want to save their Advanced configuration on the server. It means that all Search page Configuration the parameters configured on myDasty could system be restored in the future. Demonstration
  • 24. Registered users OpenID Dasty2 It is a shared identity service that makes use of a single Omar Pera digital identity, eliminating Background the need for a different user Dasty2 name and password for each Features site. Advanced Search page Configuration system Demonstration
  • 25. Registered users Options Dasty2 History of the previous proteins inserted on Omar Pera myDasty. Background Dasty2 Features Advanced Search page Configuration system Demonstration
  • 26. Registered users Options Dasty2 History of the previous proteins inserted on myDasty. Omar Pera Save multiple configurations with a specific name. Background Dasty2 Features Advanced Search page Configuration system Demonstration
  • 27. Registered users Options Dasty2 History of the previous proteins inserted on myDasty. Omar Pera Save multiple configurations with a specific name. Background Dasty2 Features Advanced Search page Configuration system Demonstration
  • 28. Registered users Options Dasty2 History of the previous proteins inserted on myDasty. Omar Pera Save multiple configurations of myDasty with a specific Background name. Dasty2 Update, delete, change name or create new Features configurations. Advanced Search page Configuration system Demonstration
  • 29. Acknowledgments Dasty2 Funding and collaborations Omar Pera Supervision Background Henning Hermjakob, EMBL-EBI, UK Dasty2 Features Development Advanced Rafael C. Jimenez, Search page EMBL-EBI, UK Configuration NBN central node, South Africa system CiPF, Spain Participation and collaboration Antony Quinn, Demonstration EMBL-EBI, UK Phil Jones, EMBL-EBI, UK Alberto Labarga, Development EMBL-EBI, UK Lennart Martens, EMBL-EBI, UK Nisha Vinod, Rafael C. Jimenez, EMBL-EBI, UK Florian Reisinger, EMBL-EBI, U EMBL-EBI, UK Dan Jacobson, NBN central node, South Africa NBN central node, CiPF, Spain Eugene Kulesha, South Africa Antony Quinn, EMBL-EBI, UK EMBL-EBI, UK Antony Quinn, Andreas Kahari, Andreas Prlic, EMBL-EBI, UK EMBL-EBI, UK Sanger Institute, UK
  • 30. Demonstration Dasty2 Demonstration Omar Pera Background Dasty2 Features Advanced Search page Configuration system Demonstration