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The MaizeGDB Genome Browser tutorial: one example of database outreach to biologists via video

L. C. Harper, M. L. Schaeffer, J. Thistle, J. M. Gardiner, C. M. Andorf, D. A. Campbell, E. K. S. Cannon, B. L. Braun, S. M. Birkett, C. J. Lawrence, T. Z. Sen
2011 Database: The Journal of Biological Databases and Curation  
Acknowledgements MaizeGDB would like to acknowledge a diverse group of individuals, organizations and funding agencies whose enduring support makes the mission of MaizeGDB possible.  ...  Core funding for MaizeGDB is provided by the USDA-ARS. Conflict of interest. None declared.  ...  Content of the tutorial video: 'Using the MaizeGDB Genome Browser' This video describes how the maize genome was sequenced, assembled and how the sequence can be viewed and used via the MaizeGDB Genome  ... 
doi:10.1093/database/bar016 pmid:21565781 pmcid:PMC3096322 fatcat:5ngsev4hvndqbopkwseglbjhum

MaizeGDB update: new tools, data and interface for the maize model organism database

Carson M. Andorf, Ethalinda K. Cannon, John L. Portwood, Jack M. Gardiner, Lisa C. Harper, Mary L. Schaeffer, Bremen L. Braun, Darwin A. Campbell, Abhinav G. Vinnakota, Venktanaga V. Sribalusu, Miranda Huerta, Kyoung Tak Cho (+7 others)
2015 Nucleic Acids Research  
MaizeGDB is a highly curated, community-oriented database and informatics service to researchers focused on the crop plant and model organism Zea mays ssp. mays.  ...  Although some form of the maize community database has existed over the last 25 years, there have only been two major releases. In 1991, the original maize genetics database MaizeDB was created.  ...  ACKNOWLEDGEMENTS The MaizeGDB redesign was guided by suggestions from the MaizeGDB Working Group as well as the MaizeGDB Redesign Beta Testers.  ... 
doi:10.1093/nar/gkv1007 pmid:26432828 pmcid:PMC4702771 fatcat:5ywbtkiv5ncw5nr3ewvlcjqmxu

GrainGenes: a data-rich repository for small grains genetics and genomics

Eric Yao, Victoria C Blake, Laurel Cooper, Charlene P Wight, Steve Michel, H Busra Cagirici, Gerard R Lazo, Clay L Birkett, David J Waring, Jean-Luc Jannink, Ian Holmes, Amanda J Waters (+2 others)
2022 Database: The Journal of Biological Databases and Curation  
We provide an example of an expression quantitative trait loci track on the International Wheat Genome Sequencing Consortium Chinese Spring wheat browser to demonstrate how genome browser tracks can be  ...  To help users benefit more from its data, GrainGenes created four tutorials available on YouTube.  ...  The opinions in this study are those of the authors and do not necessarily represent the opinions or policies of PepsiCo, Inc. All URLs were accessed in November 2021.  ... 
doi:10.1093/database/baac034 pmid:35616118 pmcid:PMC9216595 fatcat:zdbhbx32vfcpdejmxovf7uyhce

SorghumBase: a web-based portal for sorghum genetic information and community advancement

Nicholas Gladman, Andrew Olson, Sharon Wei, Kapeel Chougule, Zhenyuan Lu, Marcela Tello-Ruiz, Ivar Meijs, Peter Van Buren, Yinping Jiao, Bo Wang, Vivek Kumar, Sunita Kumari (+8 others)
2022 Planta  
SorghumBase offers sorghum investigators improved data collation and access that will facilitate the growth of a robust research community to support genomics-assisted breeding.  ...  databases; and (5) a content management system to support access to community news and training materials.  ...  Acknowledgements We thank the sorghum community members, domestic and international, for initial discussions about community needs, contribution of data sets, and feedback on the site.  ... 
doi:10.1007/s00425-022-03821-6 pmid:35015132 pmcid:PMC8752523 fatcat:a72aufr6enfy7gsuxmg3s5dhpm

Plant Reactome: a knowledgebase and resource for comparative pathway analysis

2019 Nucleic Acids Research  
The curation team actively engages researchers and students on gene and pathway curation by offering workshops and online tutorials.  ...  It uses Oryza sativa (rice) as a reference species for manual curation of pathways and extends pathway knowledge to another 82 plant species via gene-orthology projection using the Reactome data model  ...  Plant genome browser.  ... 
doi:10.1093/nar/gkz996 pmid:31680153 pmcid:PMC7145600 fatcat:ykzfjhf4hvgs7keopndswr5req

The Next Generation of Training for Arabidopsis Researchers: Bioinformatics and Quantitative Biology

Joanna Friesner, Sarah M. Assmann, Ruth Bastow, Julia Bailey-Serres, Jim Beynon, Volker Brendel, C. Robin Buell, Alexander Bucksch, Wolfgang Busch, Taku Demura, Jose R. Dinneny, Colleen J. Doherty (+27 others)
2017 Plant Physiology  
The documentation provides many examples for standard imaging tasks. http://mahotas.readthedocs.io/en/latest/ Coelho (2013) DIRT tutorials and videos DIRT (for Digital Imaging of Root Traits) is an online  ...  next-generation sequencing data) Biological databases and resources NCBI, EBI, Araport, TAIR, MaizeGDB, Gene Ontology, etc.  ... 
doi:10.1104/pp.17.01490 pmid:29208732 pmcid:PMC5717721 fatcat:diocyqmgbvdm7dpoanfwxnlc4y

Double triage to identify poorly annotated genes in Maize: The missing link in community curation [article]

Marcela K Tello-Ruiz, Cristina F Marco, Fei-Man Hsu, Rajdeep S Khangura, Pengfei Qiao, Sirjan Sapkota, Michelle C Stitzer, Rachael Wasikowski, Hao Wu, Junpeng Zhan, Kapeel Chougule, Lindsay C Barone (+6 others)
2019 biorxiv/medrxiv   pre-print
The sophistication of gene prediction algorithms and the abundance of RNA-based evidence for the maize genome may suggest that manual curation of gene models is no longer necessary.  ...  Together with the Apollo graphical editor, our double triage provides an infrastructure to support the community curation of eukaryotic genomes by scientists, students, and potentially even citizen scientists  ...  We thank Monica Munoz-Torres for providing an annotation tutorial for the jamboree.  ... 
doi:10.1101/654848 fatcat:3agjmg7iujf2ldnvcv55rjrzzi

Double triage to identify poorly annotated genes in maize: The missing link in community curation

Marcela K. Tello-Ruiz, Cristina F. Marco, Fei-Man Hsu, Rajdeep S. Khangura, Pengfei Qiao, Sirjan Sapkota, Michelle C. Stitzer, Rachael Wasikowski, Hao Wu, Junpeng Zhan, Kapeel Chougule, Lindsay C. Barone (+7 others)
2019 PLoS ONE  
The sophistication of gene prediction algorithms and the abundance of RNA-based evidence for the maize genome may suggest that manual curation of gene models is no longer necessary.  ...  Together with the Apollo graphical editor, our double triage provides an infrastructure to support the community curation of eukaryotic genomes by scientists, students, and potentially even citizen scientists  ...  We thank Monica Munoz-Torres for providing an annotation tutorial for the jamboree.  ... 
doi:10.1371/journal.pone.0224086 pmid:31658277 pmcid:PMC6816542 fatcat:maafxbww4bblnhiiqjfy6rz2zm

AgBioData consortium recommendations for sustainable genomics and genetics databases for agriculture

Lisa Harper, Jacqueline Campbell, Ethalinda K S Cannon, Sook Jung, Monica Poelchau, Ramona Walls, Carson Andorf, Elizabeth Arnaud, Tanya Z Berardini, Clayton Birkett, Steve Cannon, James Carson (+40 others)
2018 Database: The Journal of Biological Databases and Curation  
The future of agricultural research depends on data. The sheer volume of agricultural biological data being produced today makes excellent data management essential.  ...  As a step toward this goal, we present the current state of biocuration, ontologies, metadata and persistence, database platforms, programmatic (machine) access to data, communication and sustainability  ...  Acknowledgements We acknowledge with thanks The National Science Foundation Plant Genome Research Program Award # 1444573 for funding the AgBioData Workshop and development and hosting of the AgBio-Data  ... 
doi:10.1093/database/bay088 pmid:30239679 pmcid:PMC6146126 fatcat:spcxmd66qrgdnos4larqfvf6ai