mydasty, advanced search page for dasty2

MyDasty

Omar Pera

Background

Objetives

Features

Userconfiguration

Storagesystem

Technologiesin use

Extra possiblefeatures

Presentation of the project:MyDasty

Omar Pera Mira

European Bioinformatics Institute

July 24, 2008

MyDasty

Omar Pera

Background

Objetives

Features

Userconfiguration

Storagesystem

Technologiesin use

Extra possiblefeatures

Outline of the presentation

BackgroundObjectivesFeaturesUser configurationStorage systemTechnologies in useExtra features

MyDasty

Omar Pera

Background

Objetives

Features

Userconfiguration

Storagesystem

Technologiesin use

Extra possiblefeatures

BackgroundDasty2

Dasty2 is a powerful web client for visualizing proteinsequence features using the DAS protocol.

MyDasty

Omar Pera

Background

Objetives

Features

Userconfiguration

Storagesystem

Technologiesin use

Extra possiblefeatures

BackgroundDasty2 process

The general process that takes Dasty2 to visualize proteinsequence information is:

The client establishes an initial connection to the DASRegistry and retrieves a list of available DASannotation servers.Connects to the Uniprot DAS reference server andretrieves sequence information.

It accepts Uniprot accession numbers or Uniprot ID’s.

Retrieves feature information from one or more DASannotation servers filtered by label.Merges the collected data and provides the user with aview of the sequence and its annotated features.

MyDasty

Omar Pera

Background

Objetives

Features

Userconfiguration

Storagesystem

Technologiesin use

Extra possiblefeatures

BackgroundDasty2 process

The general process that takes Dasty2 to visualize proteinsequence information is:

The client establishes an initial connection to the DASRegistry and retrieves a list of available DASannotation servers.Connects to the Uniprot DAS reference server andretrieves sequence information.

It accepts Uniprot accession numbers or Uniprot ID’s.

Retrieves feature information from one or more DASannotation servers filtered by label.Merges the collected data and provides the user with aview of the sequence and its annotated features.

MyDasty

Omar Pera

Background

Objetives

Features

Userconfiguration

Storagesystem

Technologiesin use

Extra possiblefeatures

BackgroundDasty2 process

The general process that takes Dasty2 to visualize proteinsequence information is:

The client establishes an initial connection to the DASRegistry and retrieves a list of available DASannotation servers.Connects to the Uniprot DAS reference server andretrieves sequence information.

It accepts Uniprot accession numbers or Uniprot ID’s.

Retrieves feature information from one or more DASannotation servers filtered by label.Merges the collected data and provides the user with aview of the sequence and its annotated features.

MyDasty

Omar Pera

Background

Objetives

Features

Userconfiguration

Storagesystem

Technologiesin use

Extra possiblefeatures

BackgroundDasty2 process

The general process that takes Dasty2 to visualize proteinsequence information is:

The client establishes an initial connection to the DASRegistry and retrieves a list of available DASannotation servers.Connects to the Uniprot DAS reference server andretrieves sequence information.

It accepts Uniprot accession numbers or Uniprot ID’s.

Retrieves feature information from one or more DASannotation servers filtered by label.Merges the collected data and provides the user with aview of the sequence and its annotated features.

MyDasty

Omar Pera

Background

Objetives

Features

Userconfiguration

Storagesystem

Technologiesin use

Extra possiblefeatures

BackgroundDasty2 process

The general process that takes Dasty2 to visualize proteinsequence information is:

The client establishes an initial connection to the DASRegistry and retrieves a list of available DASannotation servers.Connects to the Uniprot DAS reference server andretrieves sequence information.

It accepts Uniprot accession numbers or Uniprot ID’s.

Retrieves feature information from one or more DASannotation servers filtered by label.Merges the collected data and provides the user with aview of the sequence and its annotated features.

MyDasty

Omar Pera

Background

Objetives

Features

Userconfiguration

Storagesystem

Technologiesin use

Extra possiblefeatures

BackgroundDasty2 search page

Main page which retrieves a Protein Accession number orID and executes Dasty.

MyDasty

Omar Pera

Background

Objetives

Features

Userconfiguration

Storagesystem

Technologiesin use

Extra possiblefeatures

How to improve this search page?

MyDasty

MyDasty

Omar Pera

Background

Objetives

Features

Userconfiguration

Storagesystem

Technologiesin use

Extra possiblefeatures

How to improve this search page?

MyDasty

MyDasty

Omar Pera

Background

Objetives

Features

Userconfiguration

Storagesystem

Technologiesin use

Extra possiblefeatures

MyDasty

It is an extension of the search page that makes Dasty2 amore configurable and powerful application.

MyDasty

Omar Pera

Background

Objetives

Features

Userconfiguration

Storagesystem

Technologiesin use

Extra possiblefeatures

Objectives

Let users have more control over the search beforethe client starts.Facilitate users to configure Dasty2 with their ownrequirements.Give the option to save and restore the configurationdone on MyDasty.Improve Dasty2 with extra features such as not onlyaccept Uniprot accession numbers or ID’s.

MyDasty

Omar Pera

Background

Objetives

FeaturesSelection of DASsources

Filtering features bytype and category

Mapping proteinaccessions fromother databases

Userconfiguration

Storagesystem

Technologiesin use

Extra possiblefeatures

Features

In order to achieve this objectives we proposed severalfeatures:

Full control about which DAS servers Dasty2 retrievesprotein annotations from.Pre-configure Dasty2 to just display features of acertain type or category.Mapping protein accessions from other databases (IPI,ENSEMBL, etc.) to Uniprot accession.

MyDasty

Omar Pera

Background

Objetives

FeaturesSelection of DASsources

Filtering features bytype and category

Mapping proteinaccessions fromother databases

Userconfiguration

Storagesystem

Technologiesin use

Extra possiblefeatures

Features

In order to achieve this objectives we proposed severalfeatures:

Full control about which DAS servers Dasty2 retrievesprotein annotations from.Pre-configure Dasty2 to just display features of acertain type or category.Mapping protein accessions from other databases (IPI,ENSEMBL, etc.) to Uniprot accession.

MyDasty

Omar Pera

Background

Objetives

FeaturesSelection of DASsources

Filtering features bytype and category

Mapping proteinaccessions fromother databases

Userconfiguration

Storagesystem

Technologiesin use

Extra possiblefeatures

Features

In order to achieve this objectives we proposed severalfeatures:

Full control about which DAS servers Dasty2 retrievesprotein annotations from.Pre-configure Dasty2 to just display features of acertain type or category.Mapping protein accessions from other databases (IPI,ENSEMBL, etc.) to Uniprot accession.

MyDasty

Omar Pera

Background

Objetives

FeaturesSelection of DASsources

Filtering features bytype and category

Mapping proteinaccessions fromother databases

Userconfiguration

Storagesystem

Technologiesin use

Extra possiblefeatures

Features

In order to achieve this objectives we proposed severalfeatures:

Full control about which DAS servers Dasty2 retrievesprotein annotations from.Pre-configure Dasty2 to just display features of acertain type or category.Mapping protein accessions from other databases (IPI,ENSEMBL, etc.) to Uniprot accession.

MyDasty

Omar Pera

Background

Objetives

FeaturesSelection of DASsources

Filtering features bytype and category

Mapping proteinaccessions fromother databases

Userconfiguration

Storagesystem

Technologiesin use

Extra possiblefeatures

Selection of DAS sourcesContext

By default, Dasty2 retrievesfeatures filtered byBiosapiens label.There is no possibility todisplay features fromprivate DAS servers.There are more than 60DAS servers that containprotein annotations.

MyDasty

Omar Pera

Background

Objetives

FeaturesSelection of DASsources

Filtering features bytype and category

Mapping proteinaccessions fromother databases

Userconfiguration

Storagesystem

Technologiesin use

Extra possiblefeatures

Selection of DAS sources

We will use DAS registry to allow the user:Select from which DAS servers you want to retrieveannotations.Display features from private or test DAS servers givingthe URL.Possibility to display specific DAS sources first on thegraphic.

MyDasty

Omar Pera

Background

Objetives

FeaturesSelection of DASsources

Filtering features bytype and category

Mapping proteinaccessions fromother databases

Userconfiguration

Storagesystem

Technologiesin use

Extra possiblefeatures

Selection of DAS sources

We will use DAS registry to allow the user:Select from which DAS servers you want to retrieveannotations.Display features from private or test DAS servers givingthe URL.Possibility to display specific DAS sources first on thegraphic.

MyDasty

Omar Pera

Background

Objetives

FeaturesSelection of DASsources

Filtering features bytype and category

Mapping proteinaccessions fromother databases

Userconfiguration

Storagesystem

Technologiesin use

Extra possiblefeatures

Selection of DAS sources

We will use DAS registry to allow the user:Select from which DAS servers you want to retrieveannotations.Display features from private or test DAS servers givingthe URL.Possibility to display specific DAS sources first on thegraphic.

MyDasty

Omar Pera

Background

Objetives

FeaturesSelection of DASsources

Filtering features bytype and category

Mapping proteinaccessions fromother databases

Userconfiguration

Storagesystem

Technologiesin use

Extra possiblefeatures

Selection of DAS sources

We will use DAS registry to allow the user:Select from which DAS servers you want to retrieveannotations.Display features from private or test DAS servers givingthe URL.Possibility to display specific DAS sources first on thegraphic.

MyDasty

Omar Pera

Background

Objetives

FeaturesSelection of DASsources

Filtering features bytype and category

Mapping proteinaccessions fromother databases

Userconfiguration

Storagesystem

Technologiesin use

Extra possiblefeatures

Filtering features by type and categoryContext

Biosapiens Ontologies has provided an effective wayof structuring feature annotation.Dasty2 already gives the option to filter protein featuresby Biosapiens ontologies.

MyDasty

Omar Pera

Background

Objetives

FeaturesSelection of DASsources

Filtering features bytype and category

Mapping proteinaccessions fromother databases

Userconfiguration

Storagesystem

Technologiesin use

Extra possiblefeatures

Filtering features by type and category

The main objective of this feature is allow the user to allowconfigure a more accurate search before the clientstarts:

We will use Biosapiens Ontologies to display onlyspecific features filtered by:

TypeCategory

MyDasty

Omar Pera

Background

Objetives

FeaturesSelection of DASsources

Filtering features bytype and category

Mapping proteinaccessions fromother databases

Userconfiguration

Storagesystem

Technologiesin use

Extra possiblefeatures

Mapping protein accessions from otherdatabasesContext

Dasty2 only accepts Uniprot accession numbers orUniprot ID’s.When you request features or structural data from aprotein ID, it could happen that some information onlymaps to his protein accession number.Protein Identifier Cross-Reference service ( PICR )is a tool capable to map protein identifiers to a large listof databases.

MyDasty

Omar Pera

Background

Objetives

FeaturesSelection of DASsources

Filtering features bytype and category

Mapping proteinaccessions fromother databases

Userconfiguration

Storagesystem

Technologiesin use

Extra possiblefeatures

Mapping protein accessions from otherdatabases

We will use PICR to:Map Uniprot protein ID’s to protein accession number.Mapping from different source databases such as IPI,Ensembl, TrEMBL or PIR to Uniprot protein accessionnumber, extending the possibilities of Dasty2

MyDasty

Omar Pera

Background

Objetives

FeaturesSelection of DASsources

Filtering features bytype and category

Mapping proteinaccessions fromother databases

Userconfiguration

Storagesystem

Technologiesin use

Extra possiblefeatures

Mapping protein accessions from otherdatabases

We will use PICR to:Map Uniprot protein ID’s to protein accession number.Mapping from different source databases such as IPI,Ensembl, TrEMBL or PIR to Uniprot protein accessionnumber, extending the possibilities of Dasty2

MyDasty

Omar Pera

Background

Objetives

FeaturesSelection of DASsources

Filtering features bytype and category

Mapping proteinaccessions fromother databases

Userconfiguration

Storagesystem

Technologiesin use

Extra possiblefeatures

Mapping protein accessions from otherdatabases

We will use PICR to:Map Uniprot protein ID’s to protein accession number.Mapping from different source databases such as IPI,Ensembl, TrEMBL or PIR to Uniprot protein accessionnumber, extending the possibilities of Dasty2

MyDasty

Omar Pera

Background

Objetives

FeaturesSelection of DASsources

Filtering features bytype and category

Mapping proteinaccessions fromother databases

Userconfiguration

Storagesystem

Technologiesin use

Extra possiblefeatures

Mapping protein accessions from otherdatabases

We will use PICR to:Map Uniprot protein ID’s to protein accession number.Mapping from different source databases such as IPI,Ensembl, TrEMBL or PIR to Uniprot protein accessionnumber, extending the possibilities of Dasty2

MyDasty

Omar Pera

Background

Objetives

Features

Userconfiguration

Storagesystem

Technologiesin use

Extra possiblefeatures

User configuration

We need to solve the problem of configuring theparameters of MyDasty each time we want to runDasty2.

MyDasty

Omar Pera

Background

Objetives

Features

Userconfiguration

Storagesystem

Technologiesin use

Extra possiblefeatures

User configuration

We have to consider two types of users on the system:

Anonymous: Users who don’t want to retrieve theirconfiguration in another time.

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

MyDasty

Omar Pera

Background

Objetives

Features

Userconfiguration

Storagesystem

Technologiesin use

Extra possiblefeatures

User configuration

We have to consider two types of users on the system:

Anonymous: Users who don’t want to retrieve theirconfiguration in another time.

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

MyDasty

Omar Pera

Background

Objetives

Features

Userconfiguration

Storagesystem

Technologiesin use

Extra possiblefeatures

User configuration

We have to consider two types of users on the system:

Anonymous: Users who don’t want to retrieve theirconfiguration in another time.

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

MyDasty

Omar Pera

Background

Objetives

Features

Userconfiguration

Storagesystem

Technologiesin use

Extra possiblefeatures

User configurationRegistered users

There is a neeed of an account with user/pass for eachuser who wants to save his configuration.

It is more reasonable for this project to take advantageof the possibilities of OpenID.

MyDasty

Omar Pera

Background

Objetives

Features

Userconfiguration

Storagesystem

Technologiesin use

Extra possiblefeatures

User configurationRegistered users

There is a neeed of an account with user/pass for eachuser who wants to save his configuration.

It is more reasonable for this project to take advantageof the possibilities of OpenID.

MyDasty

Omar Pera

Background

Objetives

Features

Userconfiguration

Storagesystem

Technologiesin use

Extra possiblefeatures

User configurationOpenID

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

MyDasty

Omar Pera

Background

Objetives

Features

Userconfiguration

Storagesystem

Technologiesin use

Extra possiblefeatures

User configurationOpenID

The necessity of a database to save different users andpass on the system is solved with this service.The authentication is done by the OpenID providerof each user.This way makes our server much secure not storingany sensible information.

MyDasty

Omar Pera

Background

Objetives

Features

Userconfiguration

Storagesystem

Technologiesin use

Extra possiblefeatures

User configurationOpenID

The necessity of a database to save different users andpass on the system is solved with this service.The authentication is done by the OpenID providerof each user.This way makes our server much secure not storingany sensible information.

MyDasty

Omar Pera

Background

Objetives

Features

Userconfiguration

Storagesystem

Technologiesin use

Extra possiblefeatures

User configurationOpenID

The necessity of a database to save different users andpass on the system is solved with this service.The authentication is done by the OpenID providerof each user.This way makes our server much secure not storingany sensible information.

MyDasty

Omar Pera

Background

Objetives

Features

Userconfiguration

Storagesystem

Technologiesin use

Extra possiblefeatures

Storage system

In order to save the configuration done on MyDasty andcomunicate with Dasty2 we need a very simple storagesystem.

MyDasty

Omar Pera

Background

Objetives

Features

Userconfiguration

Storagesystem

Technologiesin use

Extra possiblefeatures

Storage system

We will give the option to choose about the followingtypes depending of the use of Dasty2:

Flat files Ideally for a local copy, just create adirectory and give permission to Apacheuser to write.

Database Focus on a massive use, a very simpledatabase with one table.

Independent of the system storage, we need to set theformat of the configuration data: XML, JSON..

MyDasty

Omar Pera

Background

Objetives

Features

Userconfiguration

Storagesystem

Technologiesin use

Extra possiblefeatures

Storage system

We will give the option to choose about the followingtypes depending of the use of Dasty2:

Flat files Ideally for a local copy, just create adirectory and give permission to Apacheuser to write.

Database Focus on a massive use, a very simpledatabase with one table.

Independent of the system storage, we need to set theformat of the configuration data: XML, JSON..

MyDasty

Omar Pera

Background

Objetives

Features

Userconfiguration

Storagesystem

Technologiesin use

Extra possiblefeatures

Storage system

We will give the option to choose about the followingtypes depending of the use of Dasty2:

Flat files Ideally for a local copy, just create adirectory and give permission to Apacheuser to write.

Database Focus on a massive use, a very simpledatabase with one table.

Independent of the system storage, we need to set theformat of the configuration data: XML, JSON..

MyDasty

Omar Pera

Background

Objetives

Features

Userconfiguration

Storagesystem

Technologiesin use

Extra possiblefeatures

Storage system

We will give the option to choose about the followingtypes depending of the use of Dasty2:

Flat files Ideally for a local copy, just create adirectory and give permission to Apacheuser to write.

Database Focus on a massive use, a very simpledatabase with one table.

Independent of the system storage, we need to set theformat of the configuration data: XML, JSON..

MyDasty

Omar Pera

Background

Objetives

Features

Userconfiguration

Storagesystem

Technologiesin use

Extra possiblefeatures

Technologies in use

Server:

PHP ( optional a database system )

Client:

XHTML and Cascading Style Sheets (CSS), interactionusing the Document Object Model (DOM), AJAX andJavascript to bind everything together.

MyDasty

Omar Pera

Background

Objetives

Features

Userconfiguration

Storagesystem

Technologiesin use

Extra possiblefeatures

Extra possible features

Allow to configure the layout of Dasty2 as well as thedefault properties.

Sort the panels, show or hide panels or columns of thegraphic, change the width of this columns, etc.

Create an option to configure which DAS referenceserver to use to retrieve sequence and annotations(choose between the different Protein coordinatessystem).Include an option to look for proteins accessions usingGO ontologies terms (via OntoDAS software)Display last proteins accession numbers requested onMyDasty for a certain user.

MyDasty

Omar Pera

Background

Objetives

Features

Userconfiguration

Storagesystem

Technologiesin use

Extra possiblefeatures

Any question, suggestion, idea ?