Introducing the Brassica Information Portal: Towards integrating genotypic and phenotypic Brassica crop data

Annemarie H. Eckes, Tomasz Gubała, Piotr Nowakowski, Tomasz Szymczyszyn, Rachel Wells, Judith A. Irwin, Carlos Horro, John M. Hancock, Graham King, Sarah C. Dyer, Wiktor Jurkowski
2017 F1000Research  
The Brassica Information Portal (BIP) is a centralised repository for Brassica phenotypic data. Trait data associated with Brassica research and breeding experiments conducted on Brassica crops, used as vegetables, for livestock fodder and biofuels, is hosted on the site, together with information on the experimental plant materials used, as well as trial design. BIP is an open access and open source project, built on the schema of CropStoreDB, and as such can provide trait data management
more » ... egies for any crop data. A new user interface and programmatic submission/retrieval system helps to simplify data access for scientists and breeders. BIP opens up the opportunity to apply big data analyses to data generated by the Brassica Research Community. Here, we present a short description of the current status of the repository. PubMed Abstract | Publisher Full Text | Free Full Text 4. Edgar R, Domrachev M, Lash AE: Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res. 2002; 30(1): 207-210. PubMed Abstract | Publisher Full Text | Free Full Text 5. Leinonen R, Akhtar R, Birney E, et al.: The European Nucleotide Archive. Nucleic Acids Res. 2011; 39(Database issue): D28-D31. PubMed Abstract | Publisher Full Text | Free Full Text 6. Leinonen R, Sugawara H, Shumway M: The Sequence Read Archive. Nucleic Acids Res. 2011; 39(Database issue): D19-D21. PubMed Abstract | Publisher Full Text | Free Full Text 7. Cheng F, Liu S, Wu J, et al.: BRAD, the genetics and genomics database for Brassica plants. BMC Plant Biol. 2011; 11(1): 136. PubMed Abstract | Publisher Full Text | Free Full Text 8. Usadel B, Schwacke R, Nagel A, et al.: GabiPD -The GABI Primary Database integrates plant proteomic data with gene-centric information. Front Plant Sci. 2012; 3: 154. PubMed Abstract | Publisher Full Text | Free Full Text 9. Huala E, Dickerman AW, Garcia-Hernandez M, et al.: The Arabidopsis Information Resource (TAIR): a comprehensive database and web-based information retrieval, analysis, and visualization system for a model plant. Nucleic Acids Res. 2001; 29(1): 102-105. PubMed Abstract | Publisher Full Text | Free Full Text 10. Krishnakumar V, Hanlon MR, Contrino S, et al.: Araport: the Arabidopsis information portal. Nucleic Acids Res. 2015; 43(Database issue): D1003-9. PubMed Abstract | Publisher Full Text | Free Full Text 11. The 1001 Genomes Consortium: 1,135 Genomes Reveal the Global Pattern of Polymorphism in Arabidopsis thaliana. Cell. 2016; 166(2): 481-491. PubMed Abstract | Publisher Full Text | Free Full Text 12. Love CG, Andongabo AE, Wang J, et al.: InterStoreDB: a generic integration resource for genetic and genomic data. J Integr Plant Biol. 2012; 54(5): 345-355. PubMed Abstract | Publisher Full Text 13. Bancroft L, Barnes S, Li JY, et al.: Establishment of an Integrated Marker System for Oilseed Rape Breeding (IMSORB). 2006. Publisher Full Text 14. Trick M, et al.: Brassicadb is a database of genetic and molecular information derived from key brassica species. 2003. Reference Source 15. Qiu D, Morgan C, Shi J, et al.: A comparative linkage map of oilseed rape and its use for QTL analysis of seed oil and erucic acid content. Theor Appl Genet. 114(1): 67-80. PubMed Abstract | Publisher Full Text 16. Shrestha R, Matteis L, Skofic M, et al.: Bridging the phenotypic and genetic data useful for integrated breeding through a data annotation using the Crop Ontology developed by the crop communities of practice. Front Physiol. 2012; 3: 326. PubMed Abstract | Publisher Full Text | Free Full Text Ontologies. Comp Funct Genomics. 2002; 3(2): 137-142. PubMed Abstract | Publisher Full Text | Free Full Text 18. Thompson JD, Higgins DG, Gibson TJ: CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 1994; 22(22): 4673-4680. PubMed Abstract | Publisher Full Text | Free Full Text 19. Krajewski P, Chen D, C´wiek H, et al.: Towards recommendations for metadata and data handling in plant phenotyping. J Exp Bot. 2015; 66(18): 5417-5427. PubMed Abstract | Publisher Full Text 20. Ćwiek-Kupczyńska H, Altmann T, Arend D, et al.: Measures for interoperability of phenotypic data: minimum information requirements and formatting. Plant Methods. 2016; 12(1): 44. PubMed Abstract | Publisher Full Text | Free Full Text 21. Davey RP, Thanki AS, Bian X: Tgac browser: visualisation solutions for big data in the genomic era. 2016. Reference Source 22. Tello-Ruiz MK, Stein J, Wei S, et al.: Gramene 2016: comparative plant genomics and pathway resources. Nucleic Acids Res. 2016; 44(D1): D1133-40. PubMed Abstract | Publisher Full Text | Free Full Text 23. Gubała T, Szymczyszyn T, Nowakowski P, et al.: TGAC/brassica: v1.0.0. Zenodo. 2017. Data Source
doi:10.12688/f1000research.11301.1 pmid:28529710 pmcid:PMC5428495 fatcat:zppbrzq3kvejrlzx6oob6ila3e