ORB term request prototype

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

Term submission

ORB will be a web application for users to submit, view and update new ontology terms. In the prototype, term submission will be effected via a widget in Phenex and each term will be required to have; name; definition, a parent relationship and users e-mail address. Synonyms, comments and any relevant databases references will be provided as optional fields for the requests. On submission, 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 x’es 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. ORB will automatically send notification messages to the ontology gate keeper(s) and 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 and generate a notification mail to the user and community. In instances where the expert and community reject a term (i.e. 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). ORB will then set the term status to “Rejected” and send notification e-mail to the user and community. From the web-service, users will be able to request for all the terms; names, status, temporary IDs, status, relationship, plus any of the information provided during submission and resolution. With an ORB ID, a user can obtain the name, status, temporary ID plus any other information provided by the requester or gatekeeper. In this prototype, the functionality of ORB and the cycle will be exemplified by working with the Teleost Anatomy and Development Ontology gatekeeper (http://www.berkeleybop.org/ontologies/owl/TAO).

Implementation

Contacts

Name: Mtakai Ngara

E-mail: mtakai@nescent.org