Dasty2

Omar Pera

Background

Dasty2

Features

AdvancedSearch page

Configurationsystem

DemonstrationA web client for visualizingprotein sequence features

Omar Pera Mira

ECCB 2008 in Sardinia, Italy

Dasty2

Omar Pera

Background

Dasty2

Features

AdvancedSearch page

Configurationsystem

Demonstration

Outline of the presentation

Background: DASDasty2FeaturesAdvanced search page: MyDastyMyDasty configuration systemAcknowledgmentsDemonstration

Dasty2

Omar Pera

Background

Dasty2

Features

AdvancedSearch page

Configurationsystem

Demonstration

Background: DAS

Distributed Annotation System.RESTful web service (XML data through HTTPrequests)Uniform access to multiple repositories of biologicaldataDifferent biological data types:

GenomeProtein sequenceProtein annotations..

Widely adopted systemURL: http://biodas.org

Dasty2

Omar Pera

Background

Dasty2

Features

AdvancedSearch page

Configurationsystem

Demonstration

Background: DAS

Ilustration of Andreas KähäriThe Distributed Annotation System, 2001 Dowell et al; BMC

Bioinformatics. 2001; 2: 7. Published online 2001 October 10.

Dasty2

Omar Pera

Background

Dasty2

Features

AdvancedSearch page

Configurationsystem

Demonstration

Dasty2

Dasty2 is a web client for visualizing protein sequencefeature information using DAS.

LightweightHighly customizableMakes use of AJAX (asynchronous loading + localcaching)Easy to integrate in other systemsExtensibleOpen Source: http://sourceforge.net/projects/dasty/URL : http://www.ebi.ac.uk/dasty

Dasty2

Omar Pera

Background

Dasty2

Features

AdvancedSearch page

Configurationsystem

Demonstration

Dasty2

Dasty2

Omar Pera

Background

Dasty2

Features

AdvancedSearch page

Configurationsystem

Demonstration

Dasty2

Dasty2

Omar Pera

Background

Dasty2

Features

AdvancedSearch page

Configurationsystem

Demonstration

Dasty2

Dasty2

Omar Pera

Background

Dasty2

Features

AdvancedSearch page

Configurationsystem

Demonstration

Dasty2

Dasty2

Omar Pera

Background

Dasty2

Features

AdvancedSearch page

Configurationsystem

Demonstration

Dasty2

Dasty2

Omar Pera

Background

Dasty2

Features

AdvancedSearch page

Configurationsystem

Demonstration

Dasty2

Dasty2

Omar Pera

Background

Dasty2

FeaturesProtein sequencevisualization

3D protein structureviewer

DAS ontologyintegration

AdvancedSearch page

Configurationsystem

Demonstration

FeaturesProtein sequence visualization

Positional features

Non Positional features

Dasty2

Omar Pera

Background

Dasty2

FeaturesProtein sequencevisualization

3D protein structureviewer

DAS ontologyintegration

AdvancedSearch page

Configurationsystem

Demonstration

Features3D protein structure viewer

Annotation on 3D protein space:

Highlight annotation on the 3Dstructure

Select 3D regions and highlightcorrespondence in the protein

3D structure rotation, zoom, etc..

Dasty2

Omar Pera

Background

Dasty2

FeaturesProtein sequencevisualization

3D protein structureviewer

DAS ontologyintegration

AdvancedSearch page

Configurationsystem

Demonstration

FeaturesDAS ontology integration for data manipulation

In order to classify protein annotations, a proteinfeature ontology is avaliable in DAS.

Dasty2

Omar Pera

Background

Dasty2

FeaturesProtein sequencevisualization

3D protein structureviewer

DAS ontologyintegration

AdvancedSearch page

Configurationsystem

Demonstration

FeaturesDAS ontology integration for data manipulation

In order to classify protein annotations, a proteinfeature ontology is avaliable in DAS.Dasty2 integrates DAS ontology information found inthe current protein to filter annotations by:

Protein feature typesEvidence

Dasty2

Omar Pera

Background

Dasty2

Features

AdvancedSearch pageDas sourcesselection

Filtering annotations

Mapping proteinaccessions fromother databases

Configurationsystem

Demonstration

Advanced Search page: MyDasty

MyDasty is an extension of the search page that makesDasty2 a more configurable and powerful application.

Dasty2

Omar Pera

Background

Dasty2

Features

AdvancedSearch pageDas sourcesselection

Filtering annotations

Mapping proteinaccessions fromother databases

Configurationsystem

Demonstration

MyDasty

Let users have more control over the search beforethe client starts.Give the option to save and restore yourconfiguration.Easy to extend with other ’plugins’Independent from Dasty2Developed recently, not yet in production

Dasty2

Omar Pera

Background

Dasty2

Features

AdvancedSearch pageDas sourcesselection

Filtering annotations

Mapping proteinaccessions fromother databases

Configurationsystem

Demonstration

FeaturesDas sources selection

Full control of the DAS sources Dasty2 retrieves proteinannotations from using DAS registry:

Select individually which DAS servers are queried forfeatures.Filter the servers by label in order to make easier theselection.Insert test or private DAS sources to display on Dasty2.Sort the selected DAS sources: Dasty2 graphic.

Dasty2

Omar Pera

Background

Dasty2

Features

AdvancedSearch pageDas sourcesselection

Filtering annotations

Mapping proteinaccessions fromother databases

Configurationsystem

Demonstration

FeaturesDas sources selection

Dasty2

Omar Pera

Background

Dasty2

Features

AdvancedSearch pageDas sourcesselection

Filtering annotations

Mapping proteinaccessions fromother databases

Configurationsystem

Demonstration

FeaturesFiltering annotations using the DAS ontology

Pre-configure Dasty2 to just display annotations of acertain type or category.

Dasty2

Omar Pera

Background

Dasty2

Features

AdvancedSearch pageDas sourcesselection

Filtering annotations

Mapping proteinaccessions fromother databases

Configurationsystem

Demonstration

FeaturesMapping protein accessions from other databases

Protein Identifier Cross-Reference service ( PICR ) is atool capable of mapping protein identifiers to a large list ofdatabases.

MyDasty uses PICR to:Map from different source databases such as IPI,Ensembl, TrEMBL or PIR to Uniprot protein accessionnumber, extending the possibilities of Dasty2

Dasty2

Omar Pera

Background

Dasty2

Features

AdvancedSearch pageDas sourcesselection

Filtering annotations

Mapping proteinaccessions fromother databases

Configurationsystem

Demonstration

FeaturesMapping protein accessions from other databases

Protein Identifier Cross-Reference service ( PICR ) is atool capable of mapping protein identifiers to a large list ofdatabases.

MyDasty uses PICR to:Map from different source databases such as IPI,Ensembl, TrEMBL or PIR to Uniprot protein accessionnumber, extending the possibilities of Dasty2

Dasty2

Omar Pera

Background

Dasty2

Features

AdvancedSearch page

Configurationsystem

Demonstration

Configuration system

We have to consider two types of users on MyDasty:

Anonymous: Users that just want to customize their currentsearch. No need to store the config for futureuses.

Registered: They are users who want to save theirconfiguration on the server. It means that allthe parameters configured on myDasty couldbe restored in the future.

Dasty2

Omar Pera

Background

Dasty2

Features

AdvancedSearch page

Configurationsystem

Demonstration

Registered usersOpenID

It is a shared identity servicethat makes use of a singledigital identity, eliminatingthe need for a different username and password for eachsite.

Dasty2

Omar Pera

Background

Dasty2

Features

AdvancedSearch page

Configurationsystem

Demonstration

Registered usersOptions

History of the previous proteins inserted onmyDasty.

Dasty2

Omar Pera

Background

Dasty2

Features

AdvancedSearch page

Configurationsystem

Demonstration

Registered usersOptions

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

Dasty2

Omar Pera

Background

Dasty2

Features

AdvancedSearch page

Configurationsystem

Demonstration

Registered usersOptions

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

Dasty2

Omar Pera

Background

Dasty2

Features

AdvancedSearch page

Configurationsystem

Demonstration

Registered usersOptions

History of the previous proteins inserted on myDasty.Save multiple configurations of myDasty with a specificname.Update, delete, change name or create newconfigurations.

Dasty2

Omar Pera

Background

Dasty2

Features

AdvancedSearch page

Configurationsystem

Demonstration

Acknowledgments

SupervisionHenning Hermjakob,EMBL-EBI, UK

DevelopmentRafael C. Jimenez,EMBL-EBI, UKNBN central node, South AfricaCiPF, Spain

Antony Quinn,EMBL-EBI, UK

DevelopmentRafael C. Jimenez,EMBL-EBI, UNBN central node, South AfricaCiPF, SpainAntony Quinn,EMBL-EBI, UK Antony Quinn,EMBL-EBI, UK

Funding and collaborations

Participation and collaborationPhil Jones,EMBL-EBI, UK

Lennart Martens,EMBL-EBI, UK

Florian Reisinger,EMBL-EBI, UK

Eugene Kulesha,EMBL-EBI, UK

Andreas Prlic,Sanger Institute,UK

Alberto Labarga,EMBL-EBI, UK

Nisha Vinod,EMBL-EBI, UK

Dan Jacobson,NBN central node,South Africa

Andreas Kahari,EMBL-EBI, UK

Dasty2

Omar Pera

Background

Dasty2

Features

AdvancedSearch page

Configurationsystem

Demonstration

Demonstration

Demonstration