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RGMIMS: a web-based Laboratory Information Management System for plant functional genomics research

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Abstract

A robust Laboratory Information Management System (LIMS) is required for the efficient handling of data generated from large-scale insertional mutagenesis projects. The Rice Gene Machine Information Management System (RGMIMS), a web-based modular LIMS, developed in a rice functional genomics laboratory at CSIRO, currently has four core modules: Seed Management, Transformation Management, Plant/Progeny Management, Phenotype Management, and an ad hoc querying module. RGMIMS manages, preserves and tracks large inventories of transgenic germplasm and enables efficient and accurate record keeping of the large quantities of experimental data. RGMIMS automates and seamlessly integrates multi-step experimental processes. A web user interface, incorporating barcoding utilities, enables rapid data capture and tracking of biological resources. Ontologies from Gramene and Plant Ontology consortium are used to describe mutant phenotypes. RGMIMS supports generic research processes in plant mutagenesis and could readily be adapted to general LIMS for high-throughput plant research.

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Abbreviations

LIMS:

Laboratory Information Management System

PACLIMS:

Phenotype Assay Component LIMS

RGMIMS:

Rice Gene Machine Information Management System

TPM:

Transgenic plant monitor

References

  • Donofrio N, Rajagopalon R, Brown D et al. (2005) ‘PACLIMS’: a component LIM system for high-throughput functional genomic analysis. BMC Bioinformatics 6:94

    Article  PubMed  Google Scholar 

  • Jaiswal P, Ni J, Yap I, Ware D, Spooner W, Youens-Clark K, Ren L, Liang C, Zhao W, Ratnapu K, Faga B, Canaran P, Fogleman M, Hebbard C, Avraham S, Schmidt S, Casstevens TM, Buckler ES, Stein L, McCouch S (2006) Gramene: a bird’s eye view of cereal genomes. Nucleic Acids Res 34:D717–D723

    Article  PubMed  CAS  Google Scholar 

  • McLaren CG, Bruskiewich RM, Portugal AM, Cosico AB (2005) The International Rice Information System. A platform for meta-analysis of rice crop data. Plant Physiol 139:637–642

    Article  PubMed  CAS  Google Scholar 

  • The Plant Ontology™ Consortium (2002) The Plant Ontology™ Consortium and plant ontologies. Comp Funct Genomics 3(2):137–142

    Article  Google Scholar 

  • Scott R, Clark C, Mathews A, Yallop S, Davey MR, Lazzeri P, Mutasa-Göttgens E (2003) Transgenic plant monitor (TPM): a relational database for the management and analysis of information in plant tissue culture and transformation laboratories. Mol Breed 11:121–125

    Article  Google Scholar 

  • Upadhyaya NM, Zhu Q-H, Zhou X-R, Eamens AL, Hoque MS, Ramm K, Shivakkumar R, Smith KF, Pan S-T, Li S, Peng K Kim SJ, Dennis ES (2006) Dissociation (Ds) constructs, mapped Ds launch pads and a transiently expressed transposase system suitable for localized insertional mutagenesis in rice. Theor Appl Genet 112:1326–1341

    Article  PubMed  CAS  Google Scholar 

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Acknowledgements

We thank Drs. Robert Anderssen and Kathy Ruggiero for reviewing this manuscript, Drs. Elizabeth Dennis, David Mitchell and David Lovell for their support during the project, Drs. Ramesh Bhat and Shamsul Hoque for their feedback on software usability, and Bart Reardon and Michael James for IT support. This work was supported by the New South Wales Agricultural Genomics Centre.

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Authors and Affiliations

  1. CSIRO Mathematical and Information Sciences, ANU Campus, Canberra, ACT, 2601, Australia

    Leakha Henry

  2. CSIRO Plant Industry, Cnr. Clunies Ross Street and Barry Drive, GPO Box 1600, Canberra, ACT, 2601, Australia

    Kerrie Ramm, Qian-Hao Zhu & Narayana M. Upadhyaya

  3. New South Wales Agricultural Genomics Centre, Wagga Wagga, NSW, 2678, Australia

    Leakha Henry, Kerrie Ramm, Qian-Hao Zhu & Narayana M. Upadhyaya

Authors
  1. Leakha Henry
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  2. Kerrie Ramm
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  3. Qian-Hao Zhu
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  4. Narayana M. Upadhyaya
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Corresponding authors

Correspondence to Leakha Henry or Narayana M. Upadhyaya.

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Henry, L., Ramm, K., Zhu, QH. et al. RGMIMS: a web-based Laboratory Information Management System for plant functional genomics research. Mol Breeding 22, 151–157 (2008). https://doi.org/10.1007/s11032-008-9160-z

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  • DOI: https://doi.org/10.1007/s11032-008-9160-z

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