The art of curation at a biological database: Principles and application

Carollo, 2005, GrainGenes 2. 0. an improved resource for the small-grains community, Plant Physiol., 139, 643, 10.1104/pp.105.064485 Lamesch, 2012, The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools, Nucleic Acids Res., 40, D1202, 10.1093/nar/gkr1090 Andorf, 2016, MaizeGDB update: new tools, data and interface for the maize model organism database, Nucleic Acids Res., 44, D1195, 10.1093/nar/gkv1007 Tello-Ruiz, 2016, Gramene 2016: comparative plant genomics and pathway resources, Nucleic Acids Res., 44, D1133, 10.1093/nar/gkv1179 Fernandez-Pozo, 2015, The sol genomics network (SGN)?from genotype to phenotype to breeding, Nucleic Acids Res., 43, D1036, 10.1093/nar/gku1195 Grant, 2010, SoyBase, the USDA-ARS soybean genetics and genomics database, Nucleic Acids Res., 38, D843, 10.1093/nar/gkp798 Lazo, 2004, Development of an expressed sequence tag (EST) resource for wheat (Triticum aestivum L.): EST generation, unigene analysis, probe selection and bioinformatics for a 16, 000-locus bin-delineated map, Genetics, 168, 585, 10.1534/genetics.104.034777 Blake, 2016, The triticeae toolbox: combining phenotype and genotype data to advance small-grains breeding, Plant Genome, 9 Youens-Clark, 2009, CMap 1.01: a comparative mapping application for the Internet, Bioinformatics, 25, 3040, 10.1093/bioinformatics/btp458 Buels, 2016, JBrowse: a dynamic web platform for genome visualization and analysis, Genome Biol., 17, 66, 10.1186/s13059-016-0924-1 Howe, 2008, Big data: the future of biocuration, Nature, 455, 47, 10.1038/455047a Wilkinson, 2016, The FAIR Guiding Principles for scientific data management and stewardship, Sci. Data, 3, 160018, 10.1038/sdata.2016.18 Campbell, 1999, Quantitative trait loci associated with kernel traits in a soft × hard wheat cross, Crop Sci., 39, 1184, 10.2135/cropsci1999.0011183X003900040039x Dholakia, 2003, Molecular marker analysis of kernel size and shape in bread wheat, Plant Breed., 122, 392, 10.1046/j.1439-0523.2003.00896.x Breseghello, 2006, Association mapping of kernel size and milling quality in wheat (Triticum aestivum L.) cultivars, Genetics, 172, 1165, 10.1534/genetics.105.044586 Sun, 2008, QTL analysis of kernel shape and weight using recombinant inbred lines in wheat, Euphytica, 165 Su, 2011, Identification and development of a functional marker of TaGW2 associated with grain weight in bread wheat (Triticum aestivum L.), Theor. Appl. Genet., 122, 211, 10.1007/s00122-010-1437-z Song, 2007, A QTL for rice grain width and weight encodes a previously unknown RING-type E3 ubiquitin ligase, Nat. Genet., 39, 623, 10.1038/ng2014 Simmonds, 2016, A splice acceptor site mutation in TaGW2-A1 increases thousand grain weight in tetraploid and hexaploid wheat through wider and longer grains, Theor. Appl. Genet., 129, 1099, 10.1007/s00122-016-2686-2 Jaiswal, 2015, Identification of novel SNP in promoter sequence of taGW2-6A associated with grain weight and other agronomic traits in wheat (Triticum aestivum L.), PLoS One, 10, e0129400, 10.1371/journal.pone.0129400 Zhang, 2013, Association analysis of genomic loci important for grain weight control in elite common wheat varieties cultivated with variable water and fertiliser supply, PLoS One, 8, e57853, 10.1371/journal.pone.0057853 Xu, 2014, Mapping QTLs for yield and nitrogen-related traits in wheat: influence of nitrogen and phosphorus fertilization on QTL expression, Theor. Appl. Genet., 127, 59, 10.1007/s00122-013-2201-y Simmonds, 2014, Identification and independent validation of a stable yield and thousand grain weight QTL on chromosome 6A of hexaploid wheat (Triticum aestivum L.), BMC Plant Biol., 14, 191, 10.1186/s12870-014-0191-9 Huang, 2004, Advanced backcross QTL analysis in progenies derived from a cross between a German elite winter wheat variety and a synthetic wheat (Triticum aestivum L.), Theor. Appl. Genet., 109, 933, 10.1007/s00122-004-1708-7 Huang, 2006, Molecular detection of QTLs for agronomic and quality traits in a doubled haploid population derived from two Canadian wheats (Triticum aestivum L.), Theor. Appl. Genet., 113, 753, 10.1007/s00122-006-0346-7 Hong, 2014, Transcript suppression of TaGW2 increased grain width and weight in bread wheat, Funct. Integr. Genomics, 14, 341, 10.1007/s10142-014-0380-5 Qin, 2017, TaGW2, a good reflection of wheat polyploidization and evolution, Front. Plant Sci., 8, 318, 10.3389/fpls.2017.00318 Qin, 2014, Homologous haplotypes, expression, genetic effects and geographic distribution of the wheat yield gene TaGW2, BMC Plant Biol., 14, 107, 10.1186/1471-2229-14-107 Bednarek, 2012, Down-regulation of the TaGW2 gene by RNA interference results in decreased grain size and weight in wheat, J. Exp. Bot., 63, 5945, 10.1093/jxb/ers249 Wei, 2013, PubTator: a web-based text mining tool for assisting biocuration, Nucleic Acids Res., 41, W518, 10.1093/nar/gkt441 Cooper, 2016, The plant ontology: a tool for plant genomics, Methods Mol. Biol., 1374, 89, 10.1007/978-1-4939-3167-5_5 Benson, 2017, GenBank, Nucleic Acids Res., 10.1093/nar/gkw1070 Chao, 2017, Evaluation of genetic diversity and host resistance to stem rust in USDA NSGC durum wheat accessions, Plant Genome, 10 Singh, 2015, Emergence and spread of new races of wheat stem rust fungus: continued threat to food security and prospects of genetic control, Phytopathology, 105, 872, 10.1094/PHYTO-01-15-0030-FI Rahmatov, 2016, A new 2DS.2RL Robertsonian translocation transfers stem rust resistance gene Sr59 into wheat, Theor. Appl. Genet., 129, 1383, 10.1007/s00122-016-2710-6 Zhang, 2017, Identification and characterization of Sr13, a tetraploid wheat gene that confers resistance to the Ug99 stem rust race group, Proc. Natl. Acad. Sci. U. S. A., 114, E9483, 10.1073/pnas.1706277114 Wang, 2014, Characterization of polyploid wheat genomic diversity using a high-density 90,000 single nucleotide polymorphism array, Plant Biotechnol. J., 12, 787, 10.1111/pbi.12183 Montenegro, 2017, The pangenome of hexaploid bread wheat, Plant J., 90, 1007, 10.1111/tpj.13515 Mascher, 2017, A chromosome conformation capture ordered sequence of the barley genome, Nature, 544, 427, 10.1038/nature22043 Bauer, 2017, Towards a whole-genome sequence for rye (Secale cereale L.), Plant J., 89, 853, 10.1111/tpj.13436 Avni, 2017, Wild emmer genome architecture and diversity elucidate wheat evolution and domestication, Science, 357, 93, 10.1126/science.aan0032 Chalupska, 2008, Acc homoeoloci and the evolution of wheat genomes, Proc. Natl. Acad. Sci. U. S. A., 105, 9691, 10.1073/pnas.0803981105 Dvorak, 1993, The evolution of polyploid wheats: identification of the A genome donor species, Genome, 36, 21, 10.1139/g93-004 Dvorak, 2005, Tempos of gene locus deletions and duplications and their relationship to recombination rate during diploid and polyploid evolution in the Aegilops-Triticum alliance, Genetics, 171, 323, 10.1534/genetics.105.041632 Dvorak, 1990, Variation in repeated nucleotide sequences sheds light on the phylogeny of the wheat B and G genomes, Proc. Natl. Acad. Sci. U. S. A., 87, 9640, 10.1073/pnas.87.24.9640 Willcox, 2013, Anthropology. The roots of cultivation in southwestern Asia, Science, 341, 39, 10.1126/science.1240496 Toronto International Data Release Workshop, 2009, Prepublication data sharing, Nature, 461, 168, 10.1038/461168a Altschul, 1997, Gapped BLAST and PSI-BLAST: a new generation of protein database search programs, Nucleic Acids Res., 25, 3389, 10.1093/nar/25.17.3389