Difference between revisions of "ORB term request prototype"

From phenoscape
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*Create a function to enable downloading the searched term in different  formats
 
*Create a function to enable downloading the searched term in different  formats
  
'''Week 9
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Testing'''
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'''Testing''''''
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To make the web-service compartible with different technologies
 
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 Oses

Revision as of 01:20, 18 October 2009

Background

The need for applications that will expedite the annotation of Phenotypic characters using accurate ontologies and also promote community participation in the engineering ontological terms is crucial.There is need for applications that will; efficiently handle new ontology term requests, capture and provide term's community discussions, archive terms provenance and facilitate ea process for making easy accurate decisions during ontological annotations. Ontology Request Broker(ORB) application is founded on the premise of these challenges. It aims to provide; efficient mechanism for handling new term requests and term look up during ontology annotation, capture and avail ontology terms community discussions and provenance in a more robust manner. Here is ORB prototype which will mainly handle the new term request service.

Vision

To develop an application that will allow data curators to launch the process of community review for a new ontology term without creating a workflow bottleneck for themselves.

Scope

ORB will be a server-side application with an API for custom integration into data curation software

ORB requirements specification

Introduction

This is a documentation of all the requirements specification for the ORB prototype. ORB will provide a wide range of services that will facilitate efficient large-scale ontology annotation and decision making process by curators intuitive. In the prototype, only the term request web-services will be implemented hence this document is a description of only this aspect. The non-functional features of the application are not comprehensively addressed in this version but should be available in the subsequent additions.

System behavior

ORB will allow users to submit and view new ontology terms. In the prototype, term submission and accession will be effected via a widget in Phenex (https://www.nescent.org/phenoscape/Phenex) and also via the web interface. The integration in Phenex will be a demonstration of the ORB’s “integratability” with other related applications via the API.

Term submission

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).

Term processing

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 the name provided to allow the user to continually annotate entities using the requested terms without having to halt their work. -Send the temporary ID assigned to the user -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).


Term resolution

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 -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.


Term accession

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.

Design consideration

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 Restelet, 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 data models to the database.


Diagram

Center


Work plan

Week 1 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 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 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 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 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 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 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 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 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


Contacts

Name: Mtakai Ngara

E-mail: mtakai@nescent.org