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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  
In 2015, the MaizeGDB team completed a multi-year effort to update the MaizeGDB resource by reorganizing existing data, upgrading hardware and infrastructure, creating new tools, incorporating new data  ...  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.  ...  Assistance and guidance from the MaizeGDB Editorial Board, Maize Nomenclature Committee, and Maize Genetics Executive Committee also are appreciated.  ... 
doi:10.1093/nar/gkv1007 pmid:26432828 pmcid:PMC4702771 fatcat:5ywbtkiv5ncw5nr3ewvlcjqmxu

MaizeGDB becomes 'sequence-centric'

T. Z. Sen, C. M. Andorf, M. L. Schaeffer, L. C. Harper, M. E. Sparks, J. Duvick, V. P. Brendel, E. Cannon, D. A. Campbell, C. J. Lawrence
2009 Database: The Journal of Biological Databases and Curation  
MaizeGDB is the maize research community's central repository for genetic and genomic information about the crop plant and research model Zea mays ssp. mays.  ...  Disciplines Bioinformatics | Biometry | Computational Biology | Plant Breeding and Genetics Comments This article is from Database MaizeGDB is the maize research community's central repository for genetic  ...  Acknowledgements We thank the MGSC and MaizeSequence.org groups (especially Shiran Pasternak and Doreen Ware) for sharing the maize genome sequence data and their analyzed data sets with us and with the  ... 
doi:10.1093/database/bap020 pmid:21847242 pmcid:PMC2964019 fatcat:4jpww5npp5cmfgvowtyj4o4fj4

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, the maize research community's Model Organism Database (MOD) is charged to integrate much of these data and to provide an access point that serves data representations [e.g. the MaizeGDB Genome  ...  MaizeGDB will redefine oligo probe sets for updates to gene models; and PLEXdb will re-normalize the raw expression data for the updated probe sets.  ... 
doi:10.1093/database/bar022 pmid:21624896 pmcid:PMC3104940 fatcat:tkuppcl4bng2hoc7g5icli2lxa

MaizeGDB 2018: the maize multi-genome genetics and genomics database

John L Portwood, Margaret R Woodhouse, Ethalinda K Cannon, Jack M Gardiner, Lisa C Harper, Mary L Schaeffer, Jesse R Walsh, Taner Z Sen, Kyoung Tak Cho, David A Schott, Bremen L Braun, Miranda Dietze (+9 others)
2018 Nucleic Acids Research  
Since its 2015 update, MaizeGDB, the Maize Genetics and Genomics database, has expanded to support the sequenced genomes of many maize inbred lines in addition to the B73 reference genome assembly.  ...  MaizeGDB also continues to be the community hub for maize research, coordinating activities and providing technical support to the maize research community.  ...  We would like to give a special thank you to Ed Coe as not only the founder of the original Maize Genetics Database and continued contributor to the database, but also for his contribution to the generation  ... 
doi:10.1093/nar/gky1046 pmid:30407532 fatcat:4kigm7hldzfxpmy6zpwwxsqki4

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  
The overall goals of MaizeGDB are to facilitate access to the outcomes of maize research by integrating new maize data into the database and to support the maize research community by coordinating group  ...  MaizeGDB is the maize research community's central repository for genetics and genomics information.  ...  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

MaizeGDB's new data types, resources and activities

C. J. Lawrence, M. L. Schaeffer, T. E. Seigfried, D. A. Campbell, L. C. Harper
2007 Nucleic Acids Research  
MaizeGDB is the Maize Genetics and Genomics Database.  ...  Reported here are data updates, improvements to interfaces and changes to standard operating procedures that have been made during the past 2 years.  ...  NEW FUNCTIONALITIES Along with additions of new data, MaizeGDB personnel remain committed to maintaining and improving upon the interface to the database.  ... 
doi:10.1093/nar/gkl1048 pmid:17202174 pmcid:PMC1899092 fatcat:c2c5vu4a4bgtlcufrr7szv6ohi

MaizeDIG: Maize Database of Images and Genomes

Kyoung Tak Cho, John L. Portwood, Jack M. Gardiner, Lisa C. Harper, Carolyn J. Lawrence-Dill, Iddo Friedberg, Carson M. Andorf
2019 Frontiers in Plant Science  
The maize genetics and genomics database (MaizeGDB, www.maizegdb.org) provides an array of useful resources for diverse data types including thousands of images related to mutant phenotypes in Zea mays  ...  This is accomplished through an updated interface allowing users to create image-to-gene links and is accessible via the image search tool.  ...  KC and JP developed the software and data visualization tools. JG and LH provided data curation.  ... 
doi:10.3389/fpls.2019.01050 pmid:31555312 pmcid:PMC6724615 fatcat:c3bno4adzvahjnxukki7kuiq4y

A pan-genomic approach to genome databases using maize as a model system

Margaret R. Woodhouse, Ethalinda K. Cannon, John L. Portwood, Lisa C. Harper, Jack M. Gardiner, Mary L. Schaeffer, Carson M. Andorf
2021 BMC Plant Biology  
MaizeGDB introduces a pan-genomic approach to hosting genomic data, leveraging the large number of diverse maize genomes and their associated datasets to quickly and efficiently connect genomes, gene models  ...  We believe our framework is unique and provides a template for any genomic database poised to host large-scale pan-genomic data.  ...  In hosting the NAM founder genomes and their data, MaizeGDB achieved in a single database update 26 new genome project/metadata pages; over 1 million new gene model pages; hundreds of new downloadable  ... 
doi:10.1186/s12870-021-03173-5 pmid:34416864 pmcid:PMC8377966 fatcat:bshsrovtofd67lgnookuowuox4

Choosing a genome browser for a Model Organism Database: surveying the Maize community

Taner Z. Sen, Lisa C. Harper, Mary L. Schaeffer, Carson M. Andorf, Trent E. Seigfried, Darwin A. Campbell, Carolyn J. Lawrence
2010 Database: The Journal of Biological Databases and Curation  
Last, but not least, we deeply appreciate and thank the maize community for their continuous support. Conflict of interest. None declared.  ...  Acknowledgements We thank USDA-ARS for its sustained funding, past and present members of the MaizeGDB Working Group (Volker Brendel Wang, and Cesar Alvarez-Mejia), without whose comments and suggestions  ...  ) for sharing and displaying distributed data sets on any publicly available Ensembl instance GBrowse The Generic Model Organism Database Project (GMOD) (http://gmod.org) has the mission to build tools  ... 
doi:10.1093/database/baq007 pmid:20627860 pmcid:PMC2911842 fatcat:6ihbvxcmdnfypo2clanjfma5vq

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  ...  , and all maize researchers who have contributed  ... 
doi:10.1155/2011/923035 pmid:22253616 pmcid:PMC3255282 fatcat:qke2v5v3erh7jep4btmzx47pue

The Plant Ontology Database: a community resource for plant structure and developmental stages controlled vocabulary and annotations

Shulamit Avraham, Chih-Wei Tung, Katica Ilic, Pankaj Jaiswal, Elizabeth A. Kellogg, Susan McCouch, Anuradha Pujar, Leonore Reiser, Seung Y Rhee, Martin M Sachs, Mary Schaeffer, Lincoln Stein (+4 others)
2008 Nucleic Acids Research  
In this report, we present a brief description of resources available from the website, changes to the interfaces, data updates, community activities and future enhancement.  ...  The Consortium has also implemented new functionalities to facilitate the application of PO in genomic research and updated the website to keep the contents current.  ...  ACKNOWLEDGEMENTS The Plant Ontology Consortium gratefully acknowledges the Gene Ontology Consortium for the contributed infrastructure, software and kind support.  ... 
doi:10.1093/nar/gkm908 pmid:18194960 pmcid:PMC2238838 fatcat:4pct3qkkrzabbgrud45bpbwroy

A computational platform to maintain and migrate manual functional annotations for BioCyc databases

Jesse R Walsh, Taner Z Sen, Julie A Dickerson
2014 BMC Systems Biology  
Results We have developed CycTools, a software tool which allows curators to maintain functional annotations in a model organism database.  ...  Results: We have developed CycTools, a software tool which allows curators to maintain functional annotations in a model organism database.  ...  Acknowledgements We thank the MaizeGDB team for sharing their insights and expertise. The MaizeGDB group also created a use case for this software and provided user feedback.  ... 
doi:10.1186/s12918-014-0115-1 pmid:25304126 pmcid:PMC4203924 fatcat:vc3quvywa5bytfyyznyeu7rmgy

PLEXdb: gene expression resources for plants and plant pathogens

S. Dash, J. Van Hemert, L. Hong, R. P. Wise, J. A. Dickerson
2011 Nucleic Acids Research  
The PLEXdb team also thanks Ethalinda Cannon of MaizeGDB for her work mapping expression probes to the maize v2 (5b.60) assembly.  ...  ACKNOWLEDGEMENTS The PLEXdb team would like to thank the following undergraduate students who have helped develop tools and import experimental data: Jodan Goldie, Royce Blackledge, Jack (Pu) Hou, Joseph  ...  For example, the Nimblegen Maize platform is being mapped to the gene models from the maize RefGen V2 build in collaboration with MaizeGDB.  ... 
doi:10.1093/nar/gkr938 pmid:22084198 pmcid:PMC3245067 fatcat:udchdlk5nrbt7mkzlw2z3irzpq

FPC Web Tools for Rice, Maize, and Distribution

V. Pampanwar
2005 Plant Physiology  
For additional FPC support, we have developed an FPC module for BioPerl and an FPC browser using the Generic Model Organism Project (GMOD) genome browser (GBrowse), where the FPC BioPerl module generates  ...  The tools have been implemented for both the rice (Oryza sativa) and maize (Zea mays) FPC maps, which both contain the locations of clones, markers, genetic markers, and sequenced clone (along with links  ...  As an example, for the Maize Mapping Project (www.maizemap.org), the WebAGCoL tools were regularly updated as new clones were fingerprinted.  ... 
doi:10.1104/pp.104.056291 pmid:15888684 fatcat:khai6teabvfutp7u7igirux2ie

ZEAMAP, a comprehensive database adapted to the maize multi-omics era [article]

Songtao Gui, Linfeng Yang, Jianbo Li, Jingyun Luo, Xiaokai Xu, Jianyu Yuan, Lu Chen, Wenqiang Li, Xin Yang, Shenshen Wu, Shuyan Li, Yuebin Wang (+4 others)
2020 bioRxiv   pre-print
With advances in high-throughput detection of various omics data, a wealth of multi-dimensional and multi-omics information has been accumulated for maize and its wild relative, teosinte.  ...  As one of the most extensively cultivated crops, maize (Zea mays L.) has been extensively studied by researchers and breeders for over a century.  ...  ACKNOWLEDGEMENTS The authors would like to thank Dr Qing Li and Ms Jing Xu (National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University) for providing the DNA methylation data  ... 
doi:10.1101/2020.01.04.894626 fatcat:f7rzhmwb6ffxdglnkzvfyksacy
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