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 proteins | BarleyBase - 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 Library | useful 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, UK | useful 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 | ||
| 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, Japan | Collaboration 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, UK | useful 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 |