mydasty, advanced search page for dasty2
DESCRIPTION
MyDasty is an extension of the search page of Dasty2 that let users have more control over the search, facilitate users to configure Dasty2 and give the option to save and restore their configuration.TRANSCRIPT
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 ?