ORB term request prototype
Contents
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
Here is a documentation of ORB term request service. ORB will be accessible via an online interface and programmatically through RESTful web-services.
ORB architecture overview
Requirements
Accessibility
- ORB will have a web interface for easy access via browsers
- It will also have REST-style web service for programmatic access
Actors and roles
Requester
Use cases
Specification
Activity
Database schema
REST services
Project plan
An agile approach will be used in ORB development. The sign √ indicates accomplished tasks while * indicates tasks which ought to have been implemented but haven't been
Week 1: 4 to 9 January, 2010 To review the ORB project, suggest any changes in light of existing technologies from literature review and input from the team and document the (including the changes).
- Revise the ORB project plan and milestones√
- Identify a suitable citation management tool and learn how to utilize it√
- Perform a comprehensive literature search and read the relevant papers and add to the ORB literature review√
Week 2: 10 to 16 January, 2010
Complete literature review, document and discuss with project team
- Perform further literature search, read and complete literature review*
- Document the project requirements (technologies to be used, architecture, behavior) in the project wiki*
- Hold an online meeting with NESCent team about progress and ORB implementation based on literature review and existing technologies√
Week 3: 17 to 23 January, 2010
Document ORB requirements and specification based on input from literature, discussion and research
- Revise the ORB requirements, specification and document it to the wiki
Week 4: 24 to 30 January, 2010
Revise, design and implement ORB data layer based on existing technologies, input from project team and implement the database.
- Design and implement the ORB database
- Document the ORB database schema
Week 5: 31st January to 6th February 2010
Design and implement ORB Application layer
- Identify and document the role of each server application
- Start implementing/coding the application layer
Week 6: 7 to 13 February, 2010
Continue implementing the application layer plus the unit test
- Continue implementing the application layer and unit tests
Week 7: 14 to 20 February, 2010
Continue implementing the application layer plus the unit test
- Continue implementing the application layer and unit tests
Week 8: 21 to 27 February, 2010
Continue implementing the application layer plus the unit test
- Continue implementing the application layer and unit tests
Week 9: 28th February to 6th March 2010
Continue implementing the application layer plus the unit test
- Continue implementing the application layer and unit tests
Week 10: 7th to 13th March 2010 Start working on the ORB user/client interface
- Identify and describe the user/client interface
- Begin implementing the user/client interface
Week 12: 21st to 27th March 2010
- Continue working on the user/client interface
Week 13: 28th March to 3rd April 2010
- Continue working on the user/client interface
Week 14: 4th to 10th April 2010
- Continue working on the user/client interface
Week 15: 11th to 17th April, 2010
- Continue working on the user/client interface
Week 16: 18th to 24th April, 2010
- Continue working on the user/client interface
Week 17: 25th April to 1st May 2010
Complete the ORB application
- Assemble all the ORB components and have a complete software
- Refine the code implementation and fix any bugs
Week 18: 2nd to 8th May 2010 Refinement and fix bugs
- Continue fixing bugs
Week 19: 9th to 15th May, 2010 Begin deployment
- Deploy ORB to a publicly accessible server
- Document ORB server
Week 20: 16th to 22nd May, 2010
*To be added
Week 21: 23rd to 29th May, 2010
*To be added
Week 22: 30th to 31st May, 2010
Meetings
Jan 19, 2010 (notes by Mtakai)
Present
- Paula Mubee
- Hilmar Lapp
- Wasila Dahdul
- Jim Bahloff
- Peter Midford
- Mtakai Ngara
Agenda
-
- ORB requirements
- Working modalities
Minutes
- ORB will be accessible via browsers and programmatically as REST web services
- Term requester and Ontology gatekeepers must create an account at the site
- A function to allow for submission of a term to multiple ontologies would useful
- Apart from term submission, definition revision, term obsoletion and graph placement should be implemented
- A casual user need not register at the site
- Function for uploading a file and downloading terms to be implemented
- Have a section within ORB site for updates on latest acivities
- Integrate ORB into phenex
- Host the ORB project at sourceforge on it's page
- Have a mechanism of checking if a term already exists in an ontology
- Communication via e-mail
- ORB meetings after each use case implementation
- Code will be shared via subversion repository for team review
- Action items
- Contact the Berkley group(BBPO) on ORB trial
- Have screen shots of ORB uploaded in the wiki to demonstrate functionality
Links & Resources
- Early and incomplete ORB implementation in Perl by Seth Carbon. This interfaces directly with the SourceForge tracker.
Contacts
Name: Mtakai Ngara
E-mail: mtakai@nescent.org