ArticleNAR genomics and bioinformatics2022
Comparison of functional classification systems.
Article in NAR genomics and bioinformatics, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
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Who cites it
8 citing papers in PubMed.
- Microbiome functional gene pathways are indicative of cognitive performance in older adults at risk for Alzheimer's disease.Gut microbes · 2026Article
- Redundancy maintains microbial ecosystem functional potential despite taxonomic shifts between serpentine and nonserpentine soils.Microbial genomics · 2026Article
- 2Pipe starts with a question: matching you with the correct pipeline for MAG reconstruction.mSystems · 2026Review
- Computational function prediction of bacteria and phage proteins.Microbiology and molecular biology reviews : MMBR · 2025Review
- Comprehensive analysis of orthologous genes reveals functional dynamics and energy metabolism in the rhizospheric microbiome of Moringa oleifera.Functional & integrative genomics · 2025Article
- Metabolic pathways associated with Firmicutes prevalence in the gut of multiple livestock animals and humans.Animal microbiome · 2025Article
- Insights into the microbiome of mine drainage from the Mária mine in Rožňava, Slovakia: a metagenomic approach.Frontiers in microbiology · 2025Article
- Comparison of functional classification systems.NAR genomics and bioinformatics · 2022Article
Corrections and comments
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
In microbiome analysis, functional profiling is based on assigning reads or contigs to terms or nodes in a functional classification system. There are a number of large, general-purpose functional classifications that are in use, such as eggNOG, KEGG, InterPro and SEED. Smaller, special-purpose classifications include CARD, EC, MetaCyc and VFDB. Here, we compare the different classifications in terms of their overlap, redundancy, structure and assignment rates. We also provide mappings between main concepts in different classifications. For the large classifications, we find that eggNOG performs the best with respect to sequence redundancy and structure, SEED has the cleanest hierarchy, whereas KEGG and InterPro:BP might be more informative for medical applications. We illustrate the practical assignment rates for different classifications using a number of metagenomic samples.
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.