GrameneMart: the BioMart data portal for the Gramene project - PubMed (original) (raw)

GrameneMart: the BioMart data portal for the Gramene project

William Spooner et al. Database (Oxford). 2012.

Abstract

Gramene is a well-established resource for plant comparative genome analysis. Data are generated through automated and curated analyses and made available through web interfaces such as GrameneMart. The Gramene project was an early adopter of the BioMart software, which remains an integral and well-used component of the Gramene website. BioMart accessible data sets include plant gene annotations, plant variation catalogues, genetic markers, physical mapping entities, public DNA/mRNA sequences of various types and curated quantitative trait loci for various species. DATABASE URL: http://www.gramene.org/biomart/martview.

PubMed Disclaimer

Figures

Figure 1.

Growth in the number of species represented in Gramene's genomes module.

Similar articles

• Gramene: a resource for comparative grass genomics.
  Ware D, Jaiswal P, Ni J, Pan X, Chang K, Clark K, Teytelman L, Schmidt S, Zhao W, Cartinhour S, McCouch S, Stein L. Ware D, et al. Nucleic Acids Res. 2002 Jan 1;30(1):103-5. doi: 10.1093/nar/30.1.103. Nucleic Acids Res. 2002. PMID: 11752266 Free PMC article.
• Gramene: a growing plant comparative genomics resource.
  Liang C, Jaiswal P, Hebbard C, Avraham S, Buckler ES, Casstevens T, Hurwitz B, McCouch S, Ni J, Pujar A, Ravenscroft D, Ren L, Spooner W, Tecle I, Thomason J, Tung CW, Wei X, Yap I, Youens-Clark K, Ware D, Stein L. Liang C, et al. Nucleic Acids Res. 2008 Jan;36(Database issue):D947-53. doi: 10.1093/nar/gkm968. Epub 2007 Nov 4. Nucleic Acids Res. 2008. PMID: 17984077 Free PMC article.
• Gramene database in 2010: updates and extensions.
  Youens-Clark K, Buckler E, Casstevens T, Chen C, Declerck G, Derwent P, Dharmawardhana P, Jaiswal P, Kersey P, Karthikeyan AS, Lu J, McCouch SR, Ren L, Spooner W, Stein JC, Thomason J, Wei S, Ware D. Youens-Clark K, et al. Nucleic Acids Res. 2011 Jan;39(Database issue):D1085-94. doi: 10.1093/nar/gkq1148. Epub 2010 Nov 13. Nucleic Acids Res. 2011. PMID: 21076153 Free PMC article.
• Gramene, a tool for grass genomics.
  Ware DH, Jaiswal P, Ni J, Yap IV, Pan X, Clark KY, Teytelman L, Schmidt SC, Zhao W, Chang K, Cartinhour S, Stein LD, McCouch SR. Ware DH, et al. Plant Physiol. 2002 Dec;130(4):1606-13. doi: 10.1104/pp.015248. Plant Physiol. 2002. PMID: 12481044 Free PMC article. Review.
• Biological ontologies in rice databases. An introduction to the activities in Gramene and Oryzabase.
  Yamazaki Y, Jaiswal P. Yamazaki Y, et al. Plant Cell Physiol. 2005 Jan;46(1):63-8. doi: 10.1093/pcp/pci505. Epub 2005 Jan 19. Plant Cell Physiol. 2005. PMID: 15659431 Review.

Cited by

• WikiPathways for plants: a community pathway curation portal and a case study in rice and arabidopsis seed development networks.
  Hanumappa M, Preece J, Elser J, Nemeth D, Bono G, Wu K, Jaiswal P. Hanumappa M, et al. Rice (N Y). 2013 May 29;6(1):14. doi: 10.1186/1939-8433-6-14. Rice (N Y). 2013. PMID: 24280312 Free PMC article.
• Gene Ontology Meta Annotator for Plants (GOMAP).
  Wimalanathan K, Lawrence-Dill CJ. Wimalanathan K, et al. Plant Methods. 2021 May 25;17(1):54. doi: 10.1186/s13007-021-00754-1. Plant Methods. 2021. PMID: 34034755 Free PMC article.
• Genome-wide computational prediction and analysis of core promoter elements across plant monocots and dicots.
  Kumari S, Ware D. Kumari S, et al. PLoS One. 2013 Oct 29;8(10):e79011. doi: 10.1371/journal.pone.0079011. eCollection 2013. PLoS One. 2013. PMID: 24205361 Free PMC article.
• POEAS: Automated Plant Phenomic Analysis Using Plant Ontology.
  Shameer K, Naika MB, Mathew OK, Sowdhamini R. Shameer K, et al. Bioinform Biol Insights. 2014 Dec 21;8:209-14. doi: 10.4137/BBI.S19057. eCollection 2014. Bioinform Biol Insights. 2014. PMID: 25574136 Free PMC article.
• Sequencing and de novo transcriptome assembly of Brachypodium sylvaticum (Poaceae).
  Fox SE, Preece J, Kimbrel JA, Marchini GL, Sage A, Youens-Clark K, Cruzan MB, Jaiswal P. Fox SE, et al. Appl Plant Sci. 2013 Mar 5;1(3):apps.1200011. doi: 10.3732/apps.1200011. eCollection 2013 Mar. Appl Plant Sci. 2013. PMID: 25202520 Free PMC article.

References

1. 1. Youens-Clark K, Buckler E, Casstevens T, et al. Gramene database in 2010: updates and extensions. Nucleic Acids Res. 2011;39:D1085–1094. - PMC - PubMed
2. 1. Flicek P, Amode MR, Barrell D, et al. Ensembl 2011. Nucleic Acids Res. 2011;39:D800–D806. - PMC - PubMed
3. 1. Smedley D, Haider S, Ballester B, et al. BioMart - biological queries made easy. BMC Genomics. 2009;10:22. - PMC - PubMed
4. 1. Kersey PJ, Lawson D, Birney E, et al. Ensembl Genomes: Extending Ensembl across the taxonomic space. Nucleic Acids Res. 2010;38:D563–D569. - PMC - PubMed
5. 1. Cochrane G, Akhtar R, Aldebert P, et al. Priorities for nucleotide trace, sequence and annotation data capture at the Ensembl Trace Archive and the EMBL Nucleotide Sequence Database. Nucleic Acids Res. 2007;36:D5–D12. - PMC - PubMed

Publication types

MeSH terms

Substances

LinkOut - more resources

• Full Text Sources

  • Europe PubMed Central
  • PubMed Central
  • Silverchair Information Systems