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