ArticleBMC microbiology2014
An ontology for microbial phenotypes.
Article in BMC microbiology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers, 1 of them a synthesis that pooled it.
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Who cites it
27 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Pooled it
- Advancing FAIR data towards comparable, organized, predictive AI-ready data for community validation.Communications biology · 2026Review
- metaTraits: a large-scale integration of microbial phenotypic trait information.Nucleic acids research · 2026Article
- Clinical considerations on antimicrobial resistance potential of complex microbiological samples.PeerJ · 2025Article
- Mycobacteriaceae Phenome Atlas (MPA): A Standardized Atlas for the Mycobacteriaceae Phenome Based on Heterogeneous Sources.Phenomics (Cham, Switzerland) · 2023Article
- Genome annotation: From human genetics to biodiversity genomics.Cell genomics · 2023Review
- Omnicrobe, an open-access database of microbial habitats and phenotypes using a comprehensive text mining and data fusion approach.PloS one · 2023Article
- Semantics of Dairy Fermented Foods: A Microbiologist's Perspective.Foods (Basel, Switzerland) · 2022Article
- Inferring microbiota functions from taxonomic genes: a review.GigaScience · 2022Review
- ECO: the Evidence and Conclusion Ontology, an update for 2022.Nucleic acids research · 2022Article
- Insights from the reanalysis of high-throughput chemical genomics data for Escherichia coli K-12.G3 (Bethesda, Md.) · 2021Article
- ECO-CollecTF: A Corpus of Annotated Evidence-Based Assertions in Biomedical Manuscripts.Frontiers in research metrics and analytics · 2021Article
- Lessons Learnt From Using the Machine Learning Random Forest Algorithm to Predict Virulence inFrontiers in cellular and infection microbiology · 2021Review
- Leveraging Experimental Strategies to Capture Different Dimensions of Microbial Interactions.Frontiers in microbiology · 2021Review
- Organizing genome engineering for the gigabase scale.Nature communications · 2020Review
- OHMI: the ontology of host-microbiome interactions.Journal of biomedical semantics · 2019Article
- Visualization and prediction of CRISPR incidence in microbial trait-space to identify drivers of antiviral immune strategy.The ISME journal · 2019Article
- Text mining tools for extracting information about microbial biodiversity in food.Food microbiology · 2019Article
- Phenotype annotation with the ontology of microbial phenotypes (OMP).Journal of biomedical semantics · 2019Article
- ECO, the Evidence & Conclusion Ontology: community standard for evidence information.Nucleic acids research · 2019Article
Corrections and comments
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Authors and funding
9 authors.
Funding
Abstract
backgroundPhenotypic data are routinely used to elucidate gene function in organisms amenable to genetic manipulation. However, previous to this work, there was no generalizable system in place for the structured storage and retrieval of phenotypic information for bacteria.
resultsThe Ontology of Microbial Phenotypes (OMP) has been created to standardize the capture of such phenotypic information from microbes. OMP has been built on the foundations of the Basic Formal Ontology and the Phenotype and Trait Ontology. Terms have logical definitions that can facilitate computational searching of phenotypes and their associated genes. OMP can be accessed via a wiki page as well as downloaded from SourceForge. Initial annotations with OMP are being made for Escherichia coli using a wiki-based annotation capture system. New OMP terms are being concurrently developed as annotation proceeds.
conclusionsWe anticipate that diverse groups studying microbial genetics and associated phenotypes will employ OMP for standardizing microbial phenotype annotation, much as the Gene Ontology has standardized gene product annotation. The resulting OMP resource and associated annotations will facilitate prediction of phenotypes for unknown genes and result in new experimental characterization of phenotypes and functions.
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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.