MaizeGDB: curation and outreach go hand-in-hand

M L Schaeffer,J M Gardiner,T Z Sen,D A Campbell,C M Andorf,E K S Cannon,L C Harper,C J Lawrence

doi:10.1093/database/bar022

Abstract

First released in 1991 with the name MaizeDB, the Maize Genetics and Genomics Database, now MaizeGDB, celebrates its 20th anniversary this year. MaizeGDB has transitioned from a focus on comprehensive curation of the literature, genetic maps and stocks to a paradigm that accommodates the recent release of a reference maize genome sequence, multiple diverse maize genomes and sequence-based gene expression data sets. The MaizeGDB Team is relatively small, and relies heavily on the research community to provide data, nomenclature standards and most importantly, to recommend future directions, priorities and strategies. Key aspects of MaizeGDB's intimate interaction with the community are the co-location of curators with maize research groups in multiple locations across the USA as well as coordination with MaizeGDB’s close partner, the Maize Genetics Cooperation—Stock Center. In this report, we describe how the MaizeGDB Team currently interacts with the maize research community and our plan for future interactions that will support updates to the functional and structural annotation of the B73 reference genome.

Highlights

We describe how the MaizeGDB Team currently interacts with the maize research community and our plan for future interactions that will support updates to the functional and structural annotation of the B73 reference genome
At MaizeGDB, we provide extensive outreach and other services to support continued development of the maize community, which are described in previous reports [4, 12,13,14] and in the accompanying Database (Oxford) article (Harper et al.)
Updated associations of gene models to standard ontologies for plant anatomy and development will be supplied to the Plant Ontology site, www.plantontology.org, where we have contributed to the initial development of this ontology, and have provided associations as part of our normal operating protocols for some years [52]

Summary

Original article

Priority is given to manuscripts suggested by the MaizeGDB Editorial Board (approximately five journal articles per month; http://www.maizegdb.org/ cgi-bin/editorial_board.cgi) and, as time permits, to newly sequenced genes with experimentally confirmed functions. In an effort to increase literature curation, implementation of Textpresso [6] is currently underway Textpresso will serve both as a tool to facilitate curational activities, as well as a mechanism for researchers to search publications based on biological categories such Gene Ontology terms [7], http://www.geneontology.org/. We envision this to become a model for similar community-based annotation efforts

MaizeGDB and the community

Genome annotation in the past

Leaf transcriptome

Genome annotation in the future

Summary