Campus Units

Electrical and Computer Engineering, Genetics, Development and Cell Biology, Bioinformatics and Computational Biology

Document Type

Article

Publication Version

Published Version

Publication Date

2014

Journal or Book Title

BMC Systems Biology

Volume

8

First Page

115

DOI

10.1186/s12918-014-0115-1

Abstract

Background
BioCyc databases are an important resource for information on biological pathways and genomic data. Such databases represent the accumulation of biological data, some of which has been manually curated from literature. An essential feature of these databases is the continuing data integration as new knowledge is discovered. As functional annotations are improved, scalable methods are needed for curators to manage annotations without detailed knowledge of the specific design of the BioCyc database.

Results
We have developed CycTools, a software tool which allows curators to maintain functional annotations in a model organism database. This tool builds on existing software to improve and simplify annotation data imports of user provided data into BioCyc databases. Additionally, CycTools automatically resolves synonyms and alternate identifiers contained within the database into the appropriate internal identifiers.

Conclusions
Automating steps in the manual data entry process can improve curation efforts for major biological databases. The functionality of CycTools is demonstrated by transferring GO term annotations from MaizeCyc to matching proteins in CornCyc, both maize metabolic pathway databases available at MaizeGDB, and by creating strain specific databases for metabolic engineering.

Comments

This article is from BMC Systems Biology 8 (2014): 115, doi:10.1186/s12918-014-0115-1.

Rights

Works produced by employees of the U.S. Government as part of their official duties are not copyrighted within the U.S. The content of this document is not copyrighted.

Language

en

File Format

application/pdf

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