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Related Concept Videos

Multi-species Conserved Sequences02:51

Multi-species Conserved Sequences

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Next-generation sequencing technologies have created large genomic databases of a variety of animals and plants. Ever since the human genome project was completed, scientists studied the genome of primates, mammals, and other phylogenetically distant living beings. Such large-scale  studies have provided new insights into the evolutionary relationship between organisms.
Although the genome of each species varies greatly from each other, a few sequences are highly conserved. Such conserved...
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Genome Annotation and Assembly03:36

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The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.
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Updated: Oct 8, 2025

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Ontology-Enriched Specifications Enabling Findable, Accessible, Interoperable, and Reusable Marine Metagenomic

Kai L Blumberg1, Alise J Ponsero1, Matthew Bomhoff1

  • 1Department of Biosystems Engineering, University of Arizona, Tucson, AZ, United States.

Frontiers in Microbiology
|December 27, 2021
PubMed
Summary

Marine metagenomic data can now be made Findable, Accessible, Interoperable, and Reusable (FAIR) using a new specification. This enables automated discovery and reuse of global ocean datasets for microbial ecology research.

Keywords:
FAIRcyberinfrastructure (CI)marine microbiologymetagenomicsnext generation sequencing—NGSomicsontology

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Area of Science:

  • Marine microbial ecology
  • Bioinformatics
  • Oceanography

Background:

  • Marine microbial ecology relies on integrating biogeochemical and sequence data to understand microbial community dynamics.
  • Increasing metagenomic data necessitates standardized, Findable, Accessible, Interoperable, and Reusable (FAIR) datasets for cross-ecosystem analysis.
  • Current metadata standards are inconsistently applied, hindering data interoperability and machine actionability.

Purpose of the Study:

  • To develop a technical specification for encapsulating marine metagenomic and physicochemical datasets for FAIR reuse.
  • To enable machine-actionable discovery and reuse of environmental and omic data.
  • To facilitate meta-analyses addressing biological questions across diverse marine environments.

Main Methods:

  • Developed a novel specification for dataset encapsulation using Frictionless Data Packages.
  • Enriched data packages with environmental and life-science ontologies for variable and unit annotation.
  • Implemented the specification within the Planet Microbe cyberinfrastructure platform and web portal.

Main Results:

  • Successfully created a specification for FAIR dataset encapsulation of marine metagenomic and physicochemical data.
  • Demonstrated the implementation of this specification within the Planet Microbe portal.
  • Showcased data discovery and reuse for biological questions through meta-analyses.

Conclusions:

  • The proposed specification enables FAIR data principles for marine metagenomic datasets.
  • Automated discovery and reuse of global ocean data can be achieved through cyberinfrastructure adoption.
  • This approach advances marine metagenomic research by supporting broader, data-driven biological inquiries.