Gramene Collaborators, Contributors & Sources

We work closely with several groups who share our interest in improving the quality of electronic resources available to plant biologists. These groups are identified in the table below, along with their role and the data they share.

* Collaborates with Gramene in designing and planning the database and creating software
** Provides their data and work with Gramene Curators to format it for inclusion in the Gramene Database.
*** Has data that is included in Gramene - usually downloaded from public databases by Gramene developers.
Click here for abbreviated table

Source *Collaborator **Contributor ***Data source Contact ID Affiliation Data Reference
Affymetrix Rice_ArrayConsensus_Affy57K, Wheat_ArrayConsensus_Affy61K Maize_ArrayConsensus_Affy18K
AGI (Arizona Genomics Institute) Cari Soderland University of Arizona Discussion and collaboration on an integrated view of the rice physical map. Maize FPC map"Chen, M., G. Presting, W. Barbazuk, J. Goicoechea, B. Blackmon, H. Kim, G. Fang, D. Frisch, Y. Yu, S. Higingbottom, J. Phimphilai, D. Phimphilai, S. Thurmond, B. Gaudette, P. Li, J. Liu, J. Hatfield, S. Sun, K. Farrar, C. Henderson, L. Barnett, R. Costa, B. Williams, J. Gilbert, S. Walser, M. Atkins, C. Hall, I. Bancroft, J. Salse, F. Regad, T. Mohapatra, N. Singh, A. Tyagi, C. Soderlund, R. Dean, R. Wing (2002). An Integrated physical and genetic map of the rice genome. Plant Cell 14:537-545.

Fusheng Wei, Ed Coe, William Nelson, Arvind Bharti, Fred Engler, Ed Butler, HyeRan Kim, Jose Luis Goicoechea, Mingsheng Chen, Seunghee Lee, Galina Fuks, Hector Sanchez-Villeda, Steven Schroeder, Zhiwei Fang, Michael McMullen, Georgia Davis, John Bowers, Andrew Paterson, Mary Schaeffer, Jack Gardiner, Karen Cone, Jo Messing, Carol Soderlund, and Rod Wing (2007) Physical and Genetic Structure of the Maize Genome Reflects its Complex Evolutionary History. PLoS Genetics. In press"
AGI (Arizona Genomics Institute) Rod Wing University of Arizona RICE BAC PHYSICAL MAP
BarleyBase/PlexDB Julie Dickerson Iowa State University sequences and proteinsBarleyBase - An expression profiling database for plant genomics'. Lishuang Shen, Jian Gong, Rico A. Caldo, Dan Nettleton, Dianne Cook, Roger P. Wise and Julie A. Dickerson. Nucleic Acids Research, 2005, Vol. 33, Database issue D614-D618. PubMed: 15608273
BarleyBase/PlexDB Roger Wise Iowa State University sequences and proteins
BarleyBase/PlexDB Roger Wise and Stacy Turner Dept. of Plant Pathology; Center for Plant Responses to Environmental Stresses Barley_ArrayConsensus_Affy22K, Barley_ArrayExemplar_Affy22k, Barley GeneChip A New Resource for Cereal Genomics: 22K Barley GeneChip Comes of Age. Timothy J. Close, Steve I. Wanamaker, Rico A. Caldo, Stacy M. Turner, Daniel A. Ashlock, Julie A. Dickerson, Rod A. Wing, Gary J. Muehlbauer, Andris Kleinhofs and Roger P. Wise. Plant Physiology 134:960-968 (2004).
Beijing Genomics Institute, BTN (Bioinformatics Technology Network Rice_ind_cluster RiceIndica_ESTcluster_BGI, Rice_ind_est RiceIndica_EST_BGI
CIMMYT Suketoshi Taba useful discussions about the devolopment of a controlled vocabularies to be used in describing plant anatomy, agronomic traits and morphology.
Cornell University Tim Lynch Mann Libraryuseful discussions about accessing reference databases and automating citation procedures in Gramene, and for providing opportunities to collaborate on outreach through The Essential Electronic Agricultural Library (TEEAL) project.
Cornell University Kathy Chiang Mann Library
Cornell University Jon Corson-Rikert Mann Library
Cornell University Mary Ochs TEEAL (The Essential Electronic Agricultural Lib.)
Cornell University McCouch Lab, Cornell University Rice diversity data, rice markers, nonRice_rflp_marker nonRice_MarkerRFLP
Ensembl Ewan Birney Wellcome Trust Sanger Institute Software development
Interpro Nicola Mulder EBI, UK sequences and proteins
"UniProt Knowledgebase (UniProtKB) which is composed of two sections, UniProtKB/Swiss-Prot and UniProtKB/TrEMBL" Sequences and Proteins "The Universal Protein Resource (UniProt) The UniProt Consortium. Nucleic Acids Research, 2007, Vol. 35, Database issue D193–D197. doi:10.1093/nar/gkl929 "
GenBank "Barley_est, Maize_EST, Maize_HiCot_Bennetzen, Maize_meth_filt_CSHL_Mccombie, Methyl-filtered CSHL maize sequence, Maize_meth_filt_TIGR Maize_MethylFilter_Orion, Methyl-filtered TIGR maize sequence, Maize_FSTMu, Millet_EST, RiceBrachyantha_BACend_OMAP, RiceJaponica_BACend_OMAP, Rice_BAC, Rice_CDS, Rice_EST, Rice_FSTtransposon, RiceJaponica_cDNA_KOME , Rice_FSTtos17, Rice_FST-TDNA, Sorghum_EST, RiceAlta_BACend_OMAP, RiceAustraliensis_BACend_OMAP, RiceCoarctata_BACend_OMAP, RiceGlaberrima_BACend_OMAP, RiceMinuta_BACend_OMAP , RicePunctata_BACend_OMAP, RiceRufipogon_BACend_OMAP, Sugarcane_est, Wheat_est, Sorghum_CDNA " Genbank. Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Wheeler DL. Nucleic Acids Research 2006 Jan 1;34(Database issue):D16-20. pubmedid=16381837
Gene Ontology Consortium Michael Ashburner EBI, UKuseful discussions about the devolopment of a controlled vocabularies to be used in describing plant anatomy, agronomic traits and morphology. The Gene Ontology Consortium. Gene Ontology: tool for the unification of biology. Nature Genet. (2000) 25: 25-29.
Gene Ontology Consortium MIDORI HARRIS
Gene Ontology Consortium Software Development/Consortium Tools The Gene Ontology Consortium. Gene Ontology: tool for the unification of biology. Nature Genet. (2000) 25: 25-29.
GMOD/CMap Ben Faga, Scott Cain CSHL Software Development
Graingenes Dave Matthews USDA-ARS, Ithaca, NY Wheat and Barley Maps Matthews DE et al. (2003) GrainGenes, the genome database for small-grain crops Nucleic Acids Research 31:183-186. http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12519977
Graingenes Victoria Carollo USDA-ARS, Bozeman, MT
GRIN (NPGS/GRIN) Rice germplasms passport data --Diversity database
Haplotype Polymorphism in Polyploid Wheats and Their Diploid Ancestors project Wheat diversity database
Hokkaido Univ, Japan Toshiro Kinoshita collaboration on the development of a standard nomenclature system for rice mutants, for descriptions of mutant phenotypes, and for map information about rice mutants. Gene symbols for dwarfness. Kamijima-O, Tanisaka-T, Kinoshita-T. Rice Genetics Newsletter , 1996, 13, pp.19-25
Institute for Plant Genomics and Biology John Mullet Texas A&M Sorghum genetic / physical maps"Menz, M.A., R.R. Klein, J.E. Mullet, J.A. Obert, N.C. Unruh and P.E. Klein (2002) A High-density Genetic Map of Sorghum bicolor (L.) Moench based on 2926 AFLP, RFLP and SSR Markers.  Plant Mol. Biol. 48: 483-499.

Klein, P.E., R.R. Klein, S.W. Cartinhour, P.E. Ulanch, J.M. Dong, J.A. Obert, D.T. Morishige, S.D. Schlueter, K.L. Childs, M. Ale, and J.E. Mullet (2000) A High Throughput AFLP-based Method for Constructing Integrated Genetic and Physical Maps: Progress Toward a Sorghum Genome Map.  Genome Res. 10: 789-807. "
Institute for Plant Genomics and Biology Patricia Klein Texas A&M Sorghum genetic / physical maps, Sorghum_GSS_Klein
Institute for Plant Genomics and Biology ROBERT KLEIN USDA-ARS Sorghum genetic / physical maps
ICIS Graham McLaren IRRI useful discussions about the devolopment of a controlled vocabularies to be used in describing plant anatomy, agronomic traits and morphology. McLaren CG, Bruskiewich RM, Portugal AM, Cosico AB. 2005. The International Rice Information System: a platform for meta-analysis of rice crop data. Plant Physio. 139 (2): 637-642
The Institute for Genomic Diversity (IGD) Sorghum diversity database
INGER Contact Edwin L. Javier (retired) IRRI useful discussions about the development of a controlled vocabularies to be used in describing plant anatomy, agronomic traits and morphology.
IRIS Rice germaplams passport data --Diversity database Linking genotype to phenotype: the International Rice Information System (IRIS). Richard M. Bruskiewich 1,*, Alexander B. Cosico 1, William Eusebio 1, Arllet M. Portugal 1, Luralyn M. Ramos 1, Ma. Teresa Reyes 1, May Ann B. Sallan 1, Victor Jun M. Ulat 1, Xusheng Wang 1,3, Kenneth L. McNally 2, Ruaraidh Sackville Hamilton 2 and Christopher Graham McLaren. Bioinformatics Vol. 19 Suppl. 1 2003. Pages i63-i65
IRRI Richard Bruskiewich useful discussions about the devolopment of a controlled vocabularies to be used in describing plant anatomy, agronomic traits and morphology.
IRRI Arllet Portugal useful discussions about the devolopment of a controlled vocabularies to be used in describing plant anatomy, agronomic traits and morphology.
JGI (Joint Genome Institute) Maize_wgs_JGI Maize_WGS_JGI
Lab. for Genomics and Bioinformatics Lee H. Pratt University of Georgia sequences and proteins "Cordonnier-Pratt, M-M., C. Liang, H. Wang, D. Kolychev, F. Sun, R. Freeman, R. Sullivan and L. H. Pratt. 2004. MAGIC Database and interfaces: an integrated package for gene discovery and expression. Comparative and Functional Genomics 5:268-275.

Pratt, L. H., C. Liang, M. Shah, F. Sun, H. Wang, St. P. Reid, A. R. Gingle, A. H. Paterson, R. Wing, R. Dean, R. Klein, H. T. Nguyen, H-M. Ma, X. Zhao and M-M. Cordonnier-Pratt. 2005. Sorghum expressed sequence tags provide a milestone set of 16,801 unique clusters and identify signature genes for drought, pathogenesis and etiolation. Plant Physiology 139:869-884.

Liang, C., F. Sun, H. Wang, J. Qu, R. M. Freeman Jr., L. H. Pratt and M-M. Cordonnier-Pratt. 2006. MAGIC-SPP: a database-driven DNA sequence processing package with associated management tools. BMC Bioinformatics 7:115."
Lab. for Genomics and Bioinformatics M-M Cordonnier-Pratt University of Georgia sequences and proteins, Sorghum_ESTCluster3P_LGBPratt
MAGI (Maize Assembled Genomic Island) Maize_MAGI_ISU Maize_MAGI_ISU Maize_ISU_MAGIs_3_1_w_singleton
MaizeGDB Leszek Vincent University of Missouri-Columbia useful discussions about the devolopment of a controlled vocabularies to be used in describing plant anatomy, agronomic traits and morphology. "Anuradha Pujar, Pankaj Jaiswal, Elizabeth A. Kellogg, Katica Ilic, Leszek Vincent, Shulamit Avraham, Peter Stevens, Felipe Zapata, Leonore Reiser, Seung Y. Rhee, Martin M. Sachs, Mary Schaeffer, Lincoln Stein, Doreen Ware and Susan McCouch. Whole-Plant Growth Stage Ontology for Angiosperms and Its Application in Plant Biology. Plant Physiology, 2006, 142: 414-428. "
MaizeGDB Mary Schaeffer, f/k/a Mary Polacco USDA-ARS and University of Missouri sequences and proteins, maps, QTL, genes, Maize_BACend, Maize_consensus Maize_ESTcluster_MMPconsensus, MaizeDB Unigenes "PMID: 15020742 2004 Plant Physiol 134:1317-1326"
MaizeGDB Carolyn Lawrence USDA-ARS, Ames, Iowa QTL, genes, etc. "Lawrence, CJ, Schaeffer, ML, Seigfried, TE, Campbell, DA, and Harper, LC. (2007) MaizeGDB's new data types, resources and activities. Nucleic Acids Research 35:D895-900.

Lawrence, CJ, Seigfried, TE, and Brendel, V. (2005) The Maize Genetics and Genomics Database. The community resource for access to diverse maize data. Plant Physiology 138:55-58.

http://www.lawrencelab.org"
MGOS - Magnaporthe Grisea Oryza Sativa Database Rice_SageTag_MGOS
Monsanto useful discussions about the development of a controlled vocabularies to be used in describing plant anatomy, agronomic traits and morphology.
MPSS Blake Meyers Rice_MpssTag, Sequences and Proteins Nobuta K, Venu RC, Lu C, Belo A, Vemaraju K, Kulkarni K, Wang W, Pillay M, Green PJ,Wang GL, Meyers BC. An expression atlas of rice mRNAs and small RNAs. Nat Biotechnol. 2007 Apr;25(4):473-7. Epub 2007 Mar 11.
National Center for Gene Research, China Bin Han Rice Chromosome 4
National Center for Gene Research, China Qiang Zhao Rice Chromosome 4
NCBI Unigene, dbSNP Sequences and Proteins
Nottingham Arabidopsis Stock Centre (NASC Arabidopsis) Arabidopsis genome view in Ensembl
OMAP (Oryza Map Alignment Project) Bonnie Hurwitz FPC maps (curated and phase 1) from the wild rices; BES (BAC end sequences) from the wild rices; do curation on the BES to get clone and contig positions to put into CMap.
Orion Genomics webmaster "Sorghum GeneThresher ® Reads, Ryegrass_Assembly Ryegrass_MethylFilterCluster_Orion Ryegrass_Sequence Ryegrass_MethylFilter_Orion, Sorghum_orion Sorghum_MethylFilter_Orion Sorghum_Orion_Genethresher_reads"
Oryzabase Yukiko Yamazaki National Institute of Genetics, JapanCollaboration on the development of a standard nomenclature system for rice genes, for descriptions of mutant phenotypes, and for map information about rice genes
Oryzabase Atsushi Yoshimura Kyushu University, Japan
Molecular and Functional Diversity of the Maize Genome project. Panzea database maize diversity data, software development
Panzea Maize_Seq_Panzea
Pioneer Software Development, useful discussions about the devolopment of a controlled vocabularies to be used in describing plant anatomy, agronomic traits and morphology.
Plant GDB Barley_ESTCluster_PlantGDB
Plant GDB " Maize_ESTCluster_PlantGDB "
Plant GDB Rice_ESTCluster_PlantGDB
Plant GDB Sorghum_ESTCluster_PlantGDB
Plant GDB Wheat_ESTCluster_PlantGDB
Plant Ontology Consortium useful discussions about the devolopment of a controlled vocabularies to be used in describing plant anatomy, agronomic traits and morphology.
Published papers Various professional journals multiple authors Gramene Curational databases: genes, QTL, markers, Cmap, diversity, pathways, literature
NSF Rice Oligonucleotide Array Project Rice_ESToligo_TIGR (20,230 oligo sequences
SAGE Carie Soderland sequences and proteins "Gowda M., R-C. Venu, H. Li, C. Jantasuriyarat, S. Chen, M. Bellizzi, V. Pampanwar, H. Kim, R. A. Dean , E. Stahlberg, R. Wing, C. Soderlund, G. Wang (2007). Magnaporthe grisea Infection Triggers RNA Variation and Antisense Transcript Expression in Rice. Plant Physiology, in press. "
SAGE Guoliang Wang sequences and proteins
SCRI (Scottish Crop Research Institute) Arnis Druka Dundee, Scotland, UKuseful discussions about the devolopment of a controlled vocabularies to be used in describing plant anatomy, agronomic traits and morphology.
SCRI (Scottish Crop Research Institute) Dave Marshall Dundee, Scotland, UK
Seoul National University, Korea Hee-Jong Koh collaboration on the development of a standard nomenclature system for rice mutants, for descriptions of mutant phenotypes, and for map information about rice mutants.
SRI Pathways tool Software Development
TAIR LEONORE REISER, Stanford University useful discussions about the devolopment of a controlled vocabularies to be used in describing plant anatomy, agronomic traits and morphology.
TAIR AraCyc Peifen Zhang Carnegie Institute of Washington AraCyc
TIGR Barley_GI, Barley_ESTcluster_TIGR
TIGR " Maize_ArrayTarget_NSF58K, Maize_ArrayGene_NSF58K"
TIGR Maize_GI, Maize_ESTcluster_TIGR
TIGR Maize_meth_filt_hi_cot_cluster, Maize_HiCotMethylFilterCluster_TIGR
TIGR Maize_hi_cot_TIGR Maize_HiCotCluster_TIGR
TIGR Rice_GI, Rice_ESTcluster_TIGR
TIGR Sorghum_GI, Sorghum_ESTcluster_TIGR
TIGR Wheat_GI, Wheat_ESTcluster_TIGR
University of Georgia Andrew Paterson Sorghum Genetic map, Sorghum_Markers Sorghum_Marker
Yale Virtual Center for Cellular Expression Profiling of Rice Timothy Nelson Rice_ArrayOligo_Yale58K Rice_ArrayOligo_Yale58K