DAS Writeback: A Collaborative Annotation System

Gustavo A Salazar,Nicola Mulder,Alexander Garcia,Henning Hermjakob,Rafael C Jimenez,Edwin Blake

doi:10.1186/1471-2105-12-143

Gustavo A Salazar, Nicola Mulder + Show 4 more

Open Access

https://doi.org/10.1186/1471-2105-12-143

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Abstract

BackgroundCentralised resources such as GenBank and UniProt are perfect examples of the major international efforts that have been made to integrate and share biological information. However, additional data that adds value to these resources needs a simple and rapid route to public access. The Distributed Annotation System (DAS) provides an adequate environment to integrate genomic and proteomic information from multiple sources, making this information accessible to the community. DAS offers a way to distribute and access information but it does not provide domain experts with the mechanisms to participate in the curation process of the available biological entities and their annotations.ResultsWe designed and developed a Collaborative Annotation System for proteins called DAS Writeback. DAS writeback is a protocol extension of DAS to provide the functionalities of adding, editing and deleting annotations. We implemented this new specification as extensions of both a DAS server and a DAS client. The architecture was designed with the involvement of the DAS community and it was improved after performing usability experiments emulating a real annotation task.ConclusionsWe demonstrate that DAS Writeback is effective, usable and will provide the appropriate environment for the creation and evolution of community protein annotation.

Highlights

Centralised resources such as GenBank and UniProt are perfect examples of the major international efforts that have been made to integrate and share biological information
The extensions performed in Dasty3 in order to support the writeback capabilities are divided below into reading and writing functions, i.e. if annotations are requested or if a change/creation is submitted, respectively: Reading Functions The writeback server behaves like any other Distributed Annotation System (DAS) source when a set of features is requested
All the groups that participated in the experiment were able to Create/Update DAS annotations from a published paper, so we consider this to demonstrate that our system is effective, usable and will provide the appropriate environment for the creation and development of a protein annotation community

Summary

Introduction

Centralised resources such as GenBank and UniProt are perfect examples of the major international efforts that have been made to integrate and share biological information. DAS offers a way to distribute and access information but it does not provide domain experts with the mechanisms to participate in the curation process of the available biological entities and their annotations. The annotation of biological data is a common task in different fields of the life sciences, and can be classified into two types: manual and automatic [1]. Automatic annotation is required because of the flood of data that can not be handled manually; genome projects, among others, are able to generate terabytes of information on a daily. We have designed and implemented the Distributed Annotation System (DAS) Writeback, which enables community-based manual annotation of public data. Our approach makes the process of manual annotation a collaborative task, whereby any individual can participate by sharing their knowledge in the form of new or edited annotations

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