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MaizeGDB: curation and outreach go hand-in-hand

M. L. Schaeffer, L. C. Harper, J. M. Gardiner, C. M. Andorf, D. A. Campbell, E. K. S. Cannon, T. Z. Sen, C. J. Lawrence
2011 Database: The Journal of Biological Databases and Curation  
MaizeGDB curators, who also serve as outreach staff, (J.M.G., L.C.H. and M.L.S.) are located in areas where many maize geneticists are stationed: at the USDA-ARS Plant Gene Expression Center near the University  ...  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  ... 
doi:10.1093/database/bar022 pmid:21624896 pmcid:PMC3104940 fatcat:tkuppcl4bng2hoc7g5icli2lxa

MaizeGDB: The Maize Model Organism Database for Basic, Translational, and Applied Research

Carolyn J. Lawrence, Lisa C. Harper, Mary L. Schaeffer, Taner Z. Sen, Trent E. Seigfried, Darwin A. Campbell
2008 International Journal of Plant Genomics  
MaizeGDB is the maize research community's central repository for genetics and genomics information.  ...  In 2001 maize became the number one production crop in the world with the Food and Agriculture Organization of the United Nations reporting over 614 million tonnes produced.  ...  ACKNOWLEDGMENTS We are indebted to the community of maize researchers and the MaizeGDB Working Group (Drs.  ... 
doi:10.1155/2008/496957 pmid:18769488 pmcid:PMC2518694 fatcat:uti43cbtpbdgjf7klsqdogbuam

POPcorn: An Online Resource Providing Access to Distributed and Diverse Maize Project Data

Ethalinda K. S. Cannon, Scott M. Birkett, Bremen L. Braun, Sateesh Kodavali, Douglas M. Jennewein, Alper Yilmaz, Valentin Antonescu, Corina Antonescu, Lisa C. Harper, Jack M. Gardiner, Mary L. Schaeffer, Darwin A. Campbell (+10 others)
2011 International Journal of Plant Genomics  
database for maize genetic and genomic information: MaizeGDB.  ...  minimal data warehousing to search for sequence matches in online resources of diverse offsite projects, and (3) a set of tools that enables researchers to migrate their data to the long-term model organism  ...  Acknowledgments The authors thank Martin Spalding for helping with administrative aspects of project direction, Matthew Steven for contributing to the conceptualization of some of the BLAST capabilities, and  ... 
doi:10.1155/2011/923035 pmid:22253616 pmcid:PMC3255282 fatcat:qke2v5v3erh7jep4btmzx47pue

Plant Reactome: a knowledgebase and resource for comparative pathway analysis

2019 Nucleic Acids Research  
In addition to browsing plant pathways, users can upload and analyze their omics data, such as the gene-expression data, and overlay curated or experimental gene-gene interaction data to extend pathway  ...  The curation team actively engages researchers and students on gene and pathway curation by offering workshops and online tutorials.  ...  We extend our gratitude to the Ensembl Plants team at EBI for their support and interest in strong cross-platform data integration.  ... 
doi:10.1093/nar/gkz996 pmid:31680153 pmcid:PMC7145600 fatcat:ykzfjhf4hvgs7keopndswr5req

Plant Reactome: a resource for plant pathways and comparative analysis

Sushma Naithani, Justin Preece, Peter D'Eustachio, Parul Gupta, Vindhya Amarasinghe, Palitha D. Dharmawardhana, Guanming Wu, Antonio Fabregat, Justin L. Elser, Joel Weiser, Maria Keays, Alfonso Munoz-Pomer Fuentes (+4 others)
2016 Nucleic Acids Research  
We manually curate molecular details of pathways in these domains for reference species Oryza sativa (rice) supported by published literature and annotation of well-characterized genes.  ...  The database also offers data access via Application Programming Interfaces (APIs) and in various standardized pathway formats, such as SBML and BioPAX.  ...  The list of facets with check boxes in the left-hand menu allows additional query filters. One has an option to go further for a detailed view ( Figure 1B ) of the search on the COI1 set from rice.  ... 
doi:10.1093/nar/gkw932 pmid:27799469 pmcid:PMC5210633 fatcat:uxqy23gd4newjholwhkbbtmoju

A Community-Based Annotation Framework for Linking Solanaceae Genomes with Phenomes

N. Menda, R. M. Buels, I. Tecle, L. A. Mueller
2008 Plant Physiology  
Model organism databases (MODs) invest great efforts to functionally annotate genomes and phenomes by in-house curators.  ...  The amount of biological data available in the public domain is growing exponentially, and there is an increasing need for infrastructural and human resources to organize, store, and present the data in  ...  ACKNOWLEDGMENTS We would like to thank Esther Van Der Knaap, Roger Chetelat, and Dani Zamir and all submitters for contributing data to the phenotyped populations and locus database, and Anuradha Pujar  ... 
doi:10.1104/pp.108.119560 pmid:18539779 pmcid:PMC2492603 fatcat:idtk3vqar5he7j5756socytbiy

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  
, curation and management, with the goal of creating database products that are more Findable, Accessible, Interoperable and Reusable.  ...  with regard to data curation.  ...  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

Tripal: a construction toolkit for online genome databases

S. P. Ficklin, L.-A. Sanderson, C.-H. Cheng, M. E. Staton, T. Lee, I.-H. Cho, S. Jung, K. E. Bett, D. Main
2011 Database: The Journal of Biological Databases and Curation  
Lab and Clemson's Cyberinfrastructure and Technology Integration (CITI) Group who provided assistance with early developments of Tripal for the Marine Genomics Project.  ...  Acknowledgements Special thanks are extended to Scott Cain and Dave Clements of the GMOD project team for logistical support and consultation, as well as, to the Marine Genomics Group at the Hollings Marine  ...  A search box in the top left-hand side is available for full-text searching of the site, and a login box is available for administrative and community logins.  ... 
doi:10.1093/database/bar044 pmid:21959868 pmcid:PMC3263599 fatcat:elbmyqg3qzcflcl3l3277gk2oq

Vision, challenges and opportunities for a Plant Cell Atlas

Plant Cell Atlas Consortium, Jahed Ahmed, Oluwafemi Alaba, Gazala Ameen, Vaishali Arora, Mario A Arteaga-Vazquez, Alok Arun, Julia Bailey-Serres, Laura E Bartley, George W Bassel, Dominique C Bergmann, Edoardo Bertolini (+137 others)
2021 eLife  
A workshop was convened to discuss the purpose and utility of such an initiative, resulting in a roadmap that acknowledges the current knowledge gaps and technical challenges, and underscores how the PCA  ...  This effort requires a conceptual and technological framework to identify and map all cell types, and to comprehensively annotate the localization and organization of molecules at cellular and tissue levels  ...  Acknowledgements The PCA community-building activities are funded in part by the National Science Foundation grant numbers MCB-1916797 and MCB-2052590, Carnegie Institution for Science, and BASF.  ... 
doi:10.7554/elife.66877 pmid:34491200 pmcid:PMC8423441 fatcat:xq6vypwp4rbbjfkhtl5l2ty35q

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  
resources NCBI, EBI, Araport, TAIR, MaizeGDB, Gene Ontology, etc.  ...  These curated data have been leveraged for annotating orthologous genetic components in other species and thus are invaluable resources.  ... 
doi:10.1104/pp.17.01490 pmid:29208732 pmcid:PMC5717721 fatcat:diocyqmgbvdm7dpoanfwxnlc4y

Vision, challenges and opportunities for a Plant Cell Atlas

Jahed Ahmed, Oluwafemi Alaba, Gazala Ameen, Vaishali Arora, Mario A Arteaga-Vazquez, Alok Arun, Julia Bailey-Serres, Laura E Bartley, George W Bassel, Dominique C Bergmann, Edoardo Bertolini, Kaushal Kumar Bhati (+134 others)
2021
A workshop was convened to discuss the purpose and utility of such an initiative, resulting in a roadmap that acknowledges the current knowledge gaps and technical challenges, and underscores how the PCA  ...  This effort requires a conceptual and technological framework to identify and map all cell types, and to comprehensively annotate the localization and organization of molecules at cellular and tissue levels  ...  Acknowledgements The PCA community-building activities are funded in part by the National Science Foundation grant numbers MCB-1916797 and MCB-2052590  ... 
doi:10.26181/6147ebc7d40dd fatcat:uu6gah3adbcm5jrchcdhs2af7y

NatioNal ScieNce Board Member ex officio NatioNal ScieNce Board committee oN ProgramS aNd PlaNS

Nina Fedoroff, Evan Hugh, Barry Barish, Elizabeth Hoffman, Douglas Randall, Jo Vasquez, Mesa, Dan Arvizu, Steven Beering, G Clough, Jon Strauss, Harvey College (+19 others)
2005 unpublished
Descriptive captions and credits for images on the cover of this report are provided inside the back cover.  ...  The task force's goal was to define and structure a strategy for the "curation" of primary research data in the UK. National Research Council. 1995.  ...  Lord, Philip, and Alison Macdonald. 2003. e-Science Curation Report--Data curation for e-Science in the UK: an audit to establish requirements for future curation and provision.  ... 
fatcat:4nldyixpindojd6klntnkwo5b4