Phenomics – background

The Australian National University (ANU) is lead agent for The Australian Phenomics Network (APN). The 11 university and research institution partners of the APN contribute their expertise and infrastructure for the production of mouse models, as well as providing cryopreservation and pathology services. In addition, the APN is working with the Atlas of Living Australia (ALA) to develop a framework for Australia’s e-science infrastructure to improve the capture, annotation and dissemination of research data.

As part of APN, the ANU is closely engaged in the development of the Phenomics Ontology Driven Data (PODD) repository. PODD is a web based data repository developed to meet the data management requirements of The Australian Plant Phenomics Facility (APPF) and the APN. These requirements are to capture, manage, secure, distribute and publish raw and analysed data from the phenotyping platforms run by these facilities, as well as capture sufficient contextual information (metadata) to support data discovery and analysis services. In turn, PODD intends to provide metadata to the ALA, so that the information generated by the APN and the APPF could be represented in the ALA as scientific reference collections. In any case, both the ANU Data Store and PODD will be able to feed RDA directly.

The ANU has a number of Phenomics and Genomics research groups. Publication of this metadata to the ANU Data Store will facilitate the reuse of the data within the ANU and the resubmission of datasets for further analyses both within Australia and overseas.

APN’s core expertise and infrastructure is also extended by key national and international partnerships. The John Curtin School of Medical Research (JCSMR) has received EIF funding to further develop its DNA sequencing capability, currently managed within the Australian Cancer Research Foundation Biomolecular Resource Facility (ACRF BRF), and to establish a bioinformatics capability alongside the sequencing facility. Along with support from Bioplatforms Australia and contributions from ANU research areas, this funding will support the establishment of the Genomics Discovery Unit (GDU). The ACRF BRF / GDU will be working with multiple platforms and techniques to meet the genomics needs of the plant, mouse and human research disciplines and provides service to clients across the ANU campus and beyond. The GDU aims to develop a single SNP (Single Nucleotide Polymorphism) detection pipeline for the capture, management and distribution of metadata and sequence data for its broad client base.

Context

The Australian National University is the lead organisation for The Australian Phenomics Network (APN). The 11 university and research institution partners of the APN contribute their expertise and infrastructure for the production of mouse models, as well as providing cryopreservation and pathology services. In addition, the APN is working with the Atlas of Living Australia to develop a framework for Australia’s e-science infrastructure to improve the capture, annotation and dissemination of research data.

As part of the APN, ANU is closely engaged in the development of  PODD, the Phenomics Ontology Driven Data repository.

The Phenomics Ontology Driven Data repository project is a two year data management software development project, funded by NeAT, the National eResearch Infrastructure Taskforce. The PODD system is a web based data repository developed to meet the data management requirements of the NCRIS 5.2 funded phenomics facilities: The Australian Plant Phenomics Facility; and the Australian Phenomics Network.

These requirements are to capture, manage, secure, distribute and publish raw and analysed data from the phenotyping platforms run by these facilities, as well as capture sufficient contextual information (metadata) to support data discovery and analysis services. In turn, PODD will provide metadata to the Atlas of Living Australia, so that the information generated by the APN and the APPF may be represented in the ALA as scientific reference collections.

The APN’s core expertise and infrastructure is also extended by key national and international partnerships.

The John Curtin School of Medical Research has received EIF funding to further develop its DNA sequencing capability, currently managed within the Australian Cancer Research Foundation Biomolecular Resource Facility (ACRF BRF), and to establish alongside the sequencing facility a bioinformatics capability. Along with support from Bioplatforms Australia and contributions from ANU research areas this funding will support the establishment of the Genomics Discovery Unit (GDU). The ACRF BRF / GDU will be working with multiple platforms and techniques to meet the genomics needs of the plant, mouse and human research disciplines and provides service to clients across the ANU campus and beyond. The GDU aims to develop a single SNP (Single Nucleiotide Polymorphism) detection pipeline for the capture, management and distribution of metadata and sequence data for its broad client base.

At a more fine-grained level, the objective of this project is to link the JCSMR / ACRF BRF genomic data sets with APN phenomic datasets through storage in PODD so the metadata and data is discoverable and longevity, use and reuse of the data is assured.