e-infrastructure Roadmap for Open Science in Agriculture

A bibliometric study

The e-ROSA project seeks to build a shared vision of a future sustainable e-infrastructure for research and education in agriculture in order to promote Open Science in this field and as such contribute to addressing related societal challenges. In order to achieve this goal, e-ROSA’s first objective is to bring together the relevant scientific communities and stakeholders and engage them in the process of coelaboration of an ambitious, practical roadmap that provides the basis for the design and implementation of such an e-infrastructure in the years to come.

This website highlights the results of a bibliometric analysis conducted at a global scale in order to identify key scientists and associated research performing organisations (e.g. public research institutes, universities, Research & Development departments of private companies) that work in the field of agricultural data sources and services. If you have any comment or feedback on the bibliometric study, please use the online form.

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An FDA bioinformatics tool for microbial genomics research on molecular characterization of bacterial foodborne pathogens using microarrays


Background: Advances in microbial genomics and bioinformatics are offering greater insights into the emergence and spread of foodborne pathogens in outbreak scenarios. The Food and Drug Administration (FDA) has developed a genomics tool, ArrayTrack (TM), which provides extensive functionalities to manage, analyze, and interpret genomic data for mammalian species. ArrayTrack (TM) has been widely adopted by the research community and used for pharmacogenomics data review in the FDA's Voluntary Genomics Data Submission program. Results: ArrayTrack (TM) has been extended to manage and analyze genomics data from bacterial pathogens of human, animal, and food origin. It was populated with bioinformatics data from public databases such as NCBI, Swiss-Prot, KEGG Pathway, and Gene Ontology to facilitate pathogen detection and characterization. ArrayTrack (TM)'s data processing and visualization tools were enhanced with analysis capabilities designed specifically for microbial genomics including flag-based hierarchical clustering analysis (HCA), flag concordance heat maps, and mixed scatter plots. These specific functionalities were evaluated on data generated from a custom Affymetrix array (FDA-ECSG) previously developed within the FDA. The FDA-ECSG array represents 32 complete genomes of Escherichia coli and Shigella. The new functions were also used to analyze microarray data focusing on antimicrobial resistance genes from Salmonella isolates in a poultry production environment using a universal antimicrobial resistance microarray developed by the United States Department of Agriculture (USDA). Conclusion: The application of ArrayTrack (TM) to different microarray platforms demonstrates its utility in microbial genomics research, and thus will improve the capabilities of the FDA to rapidly identify foodborne bacteria and their genetic traits (e. g., antimicrobial resistance, virulence, etc.) during outbreak investigations. ArrayTrack (TM) is free to use and available to public, private, and academic researchers at http://www.fda.gov/ArrayTrack.

  • US
  • USDA_ARS_Agr_Res_Serv (US)
  • US_FDA_US_Food_&_Drug_Adm (US)
Data keywords
  • ontology
Agriculture keywords
  • agriculture
Data topic
  • big data
  • information systems
  • semantics
Document type

Inappropriate format for Document type, expected simple value but got array, please use list format

Institutions 10 co-publis
  • USDA_ARS_Agr_Res_Serv (US)
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e-ROSA - e-infrastructure Roadmap for Open Science in Agriculture has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 730988.
Disclaimer: The sole responsibility of the material published in this website lies with the authors. The European Union is not responsible for any use that may be made of the information contained therein.