Difference between revisions of "ORB term request prototype"

From phenoscape
(Project plan)
(Project plan)
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To establish ORB web-interface for searching, viewing and updating the requested terms
 
To establish ORB web-interface for searching, viewing and updating the requested terms
*Design and implement the web-interface of ORB new term services  
+
*Design and implement the web-interface of ORB new term services
 
*Create functions to collate the user provided information from the interface and load into the ORB server database √
 
*Create functions to collate the user provided information from the interface and load into the ORB server database √
  
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'''List of remaining tasks in the last stretch of project'''
 
'''List of remaining tasks in the last stretch of project'''
 +
*Sending an email to the term requester and the community mailing list  on term submission by ORB
 +
*Sending an E-mail to an ontology gatekeeper by an ORB administrator
 +
*Enable an automated e-mail generation to the requester and community whenever term status changes
 +
*Build an administrator protected interface for editing terms
 +
*Enable multiple addition of comments on a given term
 +
*Enable auto-complete service using the OBO relations at the term submission page the term relations 
 +
*Allow for user, status,name and ontology filtered queries
 +
*Develop the ORB client API for interaction with other applications
 +
*Allow the output of terms in XML format
 +
*Enable the submission of more than one relation per term request
  
 
== Links & Resources ==
 
== Links & Resources ==

Revision as of 21:33, 18 November 2009

Introduction

The vision of this project is to develop an application that will allow data curators to use new ontology terms without creating a workflow bottleneck.

Background

There is a need for applications that will expedite the annotation of phenotypic characters using ontologies and also promote community participation in the expansion and refinement of ontologies. One particular need that has arisen within Phenoscape and other projects is for an Ontology Request Broker (ORB), an application that can launch new ontology term requests within existing data curation workflows, record term provenance and community discussion, enable temporary terms to be used in data annotation, and update temporary terms once a request has been resolved.

Scope

This document describes the design of a prototype ORB application involving only a term request web-service. ORB is envisioned to be a web-service with an API for custom integration into multiple data curation software applications.

Diagrams

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ORB requirements specification

System behavior

ORB will allow users to submit (and view?) requests for new ontology terms. In the prototype, communication between the client and server will be effected via RESTful web-services. Functionality will be demonstrated via a custom web interface and widget in Phenex. The integration in Phenex will be a demonstration of the ORB’s “integratability” with other related applications via the API.

Term submission

Term submission use case'

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Via the web interface or the ORB widget in Phenex a user will have to submit a term’s

  • name,
  • definition, and
  • parent relationship.

The optional fields will be:

  • database references,
  • citations,
  • other relationships,
  • synonym(s), and
  • comments.

A user will be required to submit their e-mail addresses and their names (optional).

On term submission, ORB will:

  • Validate if the required fields are provided, send the user an invalid term request message and return to the submission interface.

If the user’s submission is successful, the application will:

  • Notify the user of successful submission
  • Set the status of the term to “Pending”
  • Assign a temporary ID (ORB:xxxxxx) and store in a database. The xes in the temporary ID represent an auto-generated unique number
  • Automatically send notification messages to the ontology gate keeper(s)
  • Send the term request to the community through the relevant mailing lists at source forge (http://sourceforge.net/projects/obo/support).

Input from the BBOP group

  • There isn't really a reason that "temporary terms" can't be added to the ontology directly, with some kind of status that prevents them from showing in editors etc.
  • Term status values:
    • User trial
    • Requested but unreviewed
    • Reviewed and accepted
    • Obsolete
  • Request types:
    • New term
    • Definition revision
    • Graph placement change
    • Obsoletion

Term processing

Term Resolution Use Case

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If a term is resolved (i.e. a reviewer(s) either accepts a term requested or provides a more accurate term as an alternative) the ontology gatekeeper will provide the new term plus all the information provided by the expert via ORB’s web service.

The application will subsequently:

  • Update the status of the new term to “Resolved”
  • Assign the term a permanent ID as provided by the ontology gatekeeper
  • Generate a notification mail to the user and community and the resolution.

If a term is rejected (i.e. the expert(s) and community concur that the requested term is not acceptable and no alternative exists for the request), the gatekeepers will submit this feedback plus any explanations, comments etc. that may have been availed by the expert(s). In this case ORB will:

  • Set the term status to “Rejected”,
  • Send notification e-mail to the user and community.

Implementation details

ORB will be a platform-independent web service with an exposed API for its integration into pre-existing ontology suites such as Phenex, OBO-edit, Phenote etc. Java will be the main language of development and application will be designed in a RESTful way using Restlet, a lightweight REST framework for Java applications.

The application will support GET, POST and PUT requests and the data will be stored in PostgreSQL, an object relational database management system. Hibernate library will be utilized to map the java persistent classes to the relational database. From ORB web-service interface (or Phenex widget) and using the term ID or name, users will be able to access information provided during submission and resolution.

In this prototype, the functionality of ORB term request services and the cycle will be exemplified by working with the Teleost Anatomy and Development Ontology (TAO) gatekeeper (http://www.berkeleybop.org/ontologies/owl/TAO) and TAO mailing list at source forge.

Project plan

An agile approach is used in ORB development. The sign √ indicates accomplished tasks while * indicates tasks yet to be implemented

Week 1: 21 to 26 September Preparation

To gather all the ORB requirements and set up a working IDE with all the required libraries.

  • Design and document a work plan √
  • Carry out interviews,consultation and document ORB requirements √
  • Write up the ORB specification document √
  • Set up java IDE,Apache—tomcat server and import the required libraries(restlet,json)√

Week 2: 28 to 2 October Term request server and skeleton web services

A working skeleton term request server, which responds to new term request and status queries, but with dummy data.

  • Create Restlet server project. √
  • Create a Restlet Application subclass which maps URLs to service resources.√
  • Create ServerResource subclasses which respond to HTTP requests for each web service. √

Week 3: 5 to 10 October Relational database for persisting term requests

Design and establish a server database for storing term requests.

  • Create ORB database schema √
  • Create application subclasses that store data submitted into the database √
  • Create application subclasses that retrieve and display data in the database √

Week 4: 12 to 17 October New term definition and creation

To define and create more suitable ontology terms and generate informative responses on term submission.

  • Create an application function that will take up the user provided required fields plus the different combinations of the optional fields and create terms and add to the database √
  • Create a function to validate if the user provided the required fields and if not generate an informative response to the user√
  • Create an application function to assign status on term submission√

Week 5: 19 to 23 October Term Resolution and generation informative of responses

To build application functions that will enable term updates and generate informative responses

  • Create an application function to facilitate updating a term requested in the database and change the term’s status appropriately √
  • Create a function to generate auto messages to the term requester *

Week 6: 26 to 31 October ORB community outreach and ontology gate-keepers notification

To build a function in ORB to facilitate the auto-generation of messages to the community mailing list at source forge and ontology gate keepers

  • Build an application function that will generate auto messages to the ontology gate-keepers when a term is submitted *
  • Create a function to send automated messages to the community mailing list both on term request and resolution *

Week 7 : 2 to 6 November Web-interface

To establish ORB web-interface for searching, viewing and updating the requested terms

  • Design and implement the web-interface of ORB new term services
  • Create functions to collate the user provided information from the interface and load into the ORB server database √

Week 8: 9 to 14 November Displaying and downloading search results

To create function to display term search results and enable downloading .

  • Build an application function to display the term search results and provide informative response in case the term being search is not found *
  • Create a function to enable downloading the searched term in different formats *

Week 9: 16 to 21 November Testing

To make the web-service compartible with different technologies

  • Test and edit the programs to enable smooth and uniform functionality in different Oses *
  • Test and edit the programs to enable smooth and uniform functionality in different browsers *

Week 10 and 11 : 23 November to December 5 Deployment

To deploy the ORB new term web-service to the NESCent server *

List of remaining tasks in the last stretch of project

  • Sending an email to the term requester and the community mailing list on term submission by ORB
  • Sending an E-mail to an ontology gatekeeper by an ORB administrator
  • Enable an automated e-mail generation to the requester and community whenever term status changes
  • Build an administrator protected interface for editing terms
  • Enable multiple addition of comments on a given term
  • Enable auto-complete service using the OBO relations at the term submission page the term relations
  • Allow for user, status,name and ontology filtered queries
  • Develop the ORB client API for interaction with other applications
  • Allow the output of terms in XML format
  • Enable the submission of more than one relation per term request

Links & Resources

Contacts

Name: Mtakai Ngara

E-mail: mtakai@nescent.org