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PMID: 21624896 Published · epublish English Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S.

MaizeGDB: curation and outreach go hand-in-hand.

Database : the journal of biological databases and curation ·Vol. 2011 ·2011-00-00 ·Pages bar022

Schaeffer ML, Harper LC, Gardiner JM, Andorf CM, Campbell DA, Cannon EK, Sen TZ, Lawrence CJ

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.

MeSH Terms
Databases, Genetic Genome, Plant/genetics Genomics Molecular Sequence Annotation Zea mays/genetics
Authors & Affiliations
8 authors, click to expand affiliations / ORCID
Schaeffer Mary L
USDA-ARS Plant Genetics Research Unit and Division of Plant Sciences, Department of Agronomy, University of Missouri, Columbia, MO 65211, USA. mary.schaeffer@ars.usda.gov
Harper Lisa C
Gardiner Jack M
Andorf Carson M
Campbell Darwin A
Cannon Ethalinda K S
Sen Taner Z
Lawrence Carolyn J
References (55)
55 references, click to expand
  1. Complexity and coordination of root growth at low water potentials: recent advances from transcriptomic and proteomic analyses.
    Plant Cell Environ. 2010 Apr;33(4):590-603 PMID: 19895398
  2. The physical and genetic framework of the maize B73 genome.
    PLoS Genet. 2009 Nov;5(11):e1000715 PMID: 19936061
  3. MaizeGDB.
    Methods Mol Biol. 2007;406:331-45 PMID: 18287701
  4. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium.
    Nat Genet. 2000 May;25(1):25-9 PMID: 10802651
  5. Reactivation of an inactive centromere reveals epigenetic and structural components for centromere specification in maize.
    Plant Cell. 2009 Jul;21(7):1929-39 PMID: 19602622
  6. PlantGDB: a resource for comparative plant genomics.
    Nucleic Acids Res. 2008 Jan;36(Database issue):D959-65 PMID: 18063570
  7. MaizeGDB becomes 'sequence-centric'.
    Database (Oxford). 2009;2009:bap020 PMID: 21847242
  8. Global gene expression analysis of the shoot apical meristem of maize (Zea mays L.).
    Plant J. 2007 Nov;52(3):391-404 PMID: 17764504
  9. Genetic properties of the maize nested association mapping population.
    Science. 2009 Aug 7;325(5941):737-40 PMID: 19661427
  10. Genetic and QTL analysis of maize tassel and ear inflorescence architecture.
    Theor Appl Genet. 2006 Feb;112(4):592-606 PMID: 16395569
  11. SoyBase, the USDA-ARS soybean genetics and genomics database.
    Nucleic Acids Res. 2010 Jan;38(Database issue):D843-6 PMID: 20008513
  12. Basic local alignment search tool.
    J Mol Biol. 1990 Oct 5;215(3):403-10 PMID: 2231712
  13. Involving undergraduates in the annotation and analysis of global gene expression studies: creation of a maize shoot apical meristem expression database.
    Genetics. 2007 Jun;176(2):741-7 PMID: 17409087
  14. Textpresso: an ontology-based information retrieval and extraction system for biological literature.
    PLoS Biol. 2004 Nov;2(11):e309 PMID: 15383839
  15. Genome-wide distribution of transposed Dissociation elements in maize.
    Plant Cell. 2010 Jun;22(6):1667-85 PMID: 20581308
  16. RNA-mediated trans-communication can establish paramutation at the b1 locus in maize.
    Proc Natl Acad Sci U S A. 2010 Jul 20;107(29):12986-91 PMID: 20616013
  17. Heterosis is prevalent for multiple traits in diverse maize germplasm.
    PLoS One. 2009 Oct 13;4(10):e7433 PMID: 19823591
  18. Maize SUT1 functions in phloem loading.
    Plant Signal Behav. 2010 Jun;5(6):687-90 PMID: 20404497
  19. yrGATE: a web-based gene-structure annotation tool for the identification and dissemination of eukaryotic genes.
    Genome Biol. 2006;7(7):R58 PMID: 16859520
  20. The Locus Lookup tool at MaizeGDB: identification of genomic regions in maize by integrating sequence information with physical and genetic maps.
    Bioinformatics. 2010 Feb 1;26(3):434-6 PMID: 20124413
  21. Genome-wide atlas of transcription during maize development.
    Plant J. 2011 May;66(4):553-63 PMID: 21299659
  22. Genome-wide patterns of genetic variation among elite maize inbred lines.
    Nat Genet. 2010 Nov;42(11):1027-30 PMID: 20972441
  23. The B73 maize genome: complexity, diversity, and dynamics.
    Science. 2009 Nov 20;326(5956):1112-5 PMID: 19965430
  24. A first-generation haplotype map of maize.
    Science. 2009 Nov 20;326(5956):1115-7 PMID: 19965431
  25. The maize genetics and genomics database. The community resource for access to diverse maize data.
    Plant Physiol. 2005 May;138(1):55-8 PMID: 15888678
  26. Cornfests, cornfabs and cooperation: the origins and beginnings of the maize genetics cooperation news letter.
    Genetics. 2005 Apr;169(4):1787-97 PMID: 15879515
  27. High-throughput linkage analysis of Mutator insertion sites in maize.
    Plant J. 2009 Jun;58(5):883-92 PMID: 19207214
  28. Kernel composition, starch structure, and enzyme digestibility of opaque-2 maize and quality protein maize.
    J Agric Food Chem. 2009 Mar 11;57(5):2049-55 PMID: 19206469
  29. Precise centromere mapping using a combination of repeat junction markers and chromatin immunoprecipitation-polymerase chain reaction.
    Genetics. 2006 Oct;174(2):1057-61 PMID: 16951073
  30. Following tetraploidy in maize, a short deletion mechanism removed genes preferentially from one of the two homologs.
    PLoS Biol. 2010 Jun 29;8(6):e1000409 PMID: 20613864
  31. Natural genetic variation in lycopene epsilon cyclase tapped for maize biofortification.
    Science. 2008 Jan 18;319(5861):330-3 PMID: 18202289
  32. Density-dependent and density-independent mortality of the western corn rootworm: impact on dose calculations of rootworm-resistant Bt corn.
    J Econ Entomol. 2010 Feb;103(1):77-84 PMID: 20214371
  33. Spatial configuration of transposable element Ac termini affects their ability to induce chromosomal breakage in maize.
    Plant Cell. 2010 Mar;22(3):744-54 PMID: 20228246
  34. Maintaining collections of mutants for plant functional genomics.
    Methods Mol Biol. 2003;236:311-26 PMID: 14501073
  35. MaizeGDB's new data types, resources and activities.
    Nucleic Acids Res. 2007 Jan;35(Database issue):D895-900 PMID: 17202174
  36. Involvement of the MADS-box gene ZMM4 in floral induction and inflorescence development in maize.
    Plant Physiol. 2008 Aug;147(4):2054-69 PMID: 18539775
  37. Genetic dissection of intermated recombinant inbred lines using a new genetic map of maize.
    Genetics. 2006 Nov;174(3):1671-83 PMID: 16951074
  38. Potentials of the National Corn Genome Initiative.
    Proc Natl Acad Sci U S A. 1998 Mar 3;95(5):2029-32 PMID: 9482830
  39. Choosing a genome browser for a Model Organism Database: surveying the maize community.
    Database (Oxford). 2010 Jul 06;2010:baq007 PMID: 20627860
  40. Quality assessment of maize assembled genomic islands (MAGIs) and large-scale experimental verification of predicted genes.
    Proc Natl Acad Sci U S A. 2005 Aug 23;102(34):12282-7 PMID: 16103354
  41. Emergence and patterning of the five cell types of the Zea mays anther locule.
    Dev Biol. 2011 Feb 1;350(1):32-49 PMID: 21070762
  42. Big data: The future of biocuration.
    Nature. 2008 Sep 4;455(7209):47-50 PMID: 18769432
  43. MaizeGDB: The maize model organism database for basic, translational, and applied research.
    Int J Plant Genomics. 2008;2008:496957 PMID: 18769488
  44. The maize SBP-box transcription factor encoded by tasselsheath4 regulates bract development and the establishment of meristem boundaries.
    Development. 2010 Apr;137(8):1243-50 PMID: 20223762
  45. Resistant-starch formation in high-amylose maize starch during Kernel development.
    J Agric Food Chem. 2010 Jul 14;58(13):8043-7 PMID: 20550134
  46. The Plant Ontology Database: a community resource for plant structure and developmental stages controlled vocabulary and annotations.
    Nucleic Acids Res. 2008 Jan;36(Database issue):D449-54 PMID: 18194960
  47. Sequencing, mapping, and analysis of 27,455 maize full-length cDNAs.
    PLoS Genet. 2009 Nov;5(11):e1000740 PMID: 19936069
  48. Maize AMEIOTIC1 is essential for multiple early meiotic processes and likely required for the initiation of meiosis.
    Proc Natl Acad Sci U S A. 2009 Mar 3;106(9):3603-8 PMID: 19204280
  49. The developmental dynamics of the maize leaf transcriptome.
    Nat Genet. 2010 Dec;42(12):1060-7 PMID: 21037569
  50. Plant SMU-1 and SMU-2 homologues regulate pre-mRNA splicing and multiple aspects of development.
    Plant Physiol. 2009 Nov;151(3):1498-512 PMID: 19734266
  51. Suppressor of sessile spikelets1 functions in the ramosa pathway controlling meristem determinacy in maize.
    Plant Physiol. 2009 Jan;149(1):205-19 PMID: 18997117
  52. Steady-state transposon mutagenesis in inbred maize.
    Plant J. 2005 Oct;44(1):52-61 PMID: 16167895
  53. From dwarves to giants? Plant height manipulation for biomass yield.
    Trends Plant Sci. 2009 Aug;14(8):454-61 PMID: 19616467
  54. Plant genome resources at the national center for biotechnology information.
    Plant Physiol. 2005 Jul;138(3):1280-8 PMID: 16010002
  55. BarleyBase/PLEXdb.
    Methods Mol Biol. 2007;406:347-63 PMID: 18287702
Article Info
Journal
Database : the journal of biological databases and curation
Abbr.
Database (Oxford)
ISSN
1758-0463
Published
2011-00-00
Epub
2011-00-29
Pages
bar022
Language
English
Region
England
NLM ID
101517697
PMCID
PMC3104940
Subset
IM
Analysis Services
Analysis Services

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