ArticleBMC bioinformatics2010
Formalization of taxon-based constraints to detect inconsistencies in annotation and ontology development.
Article in BMC bioinformatics, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers.
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Who cites it
36 citing papers in PubMed.
- Proteome Remodeling of a Carbapenem-Resistant Escherichia coli Strain upon Meropenem Exposure.Journal of proteome research · 2026Article
- Evaluating completeness, coherence, and consistency of genome-scale function annotations.Briefings in bioinformatics · 2026Review
- The Cell Ontology in the age of single-cell omics.Scientific data · 2026Article
- Go Big or go home: a new gene ontology subset that improves plant gene function prediction.Plant methods · 2026Article
- Article
- Integration of background knowledge for automatic detection of inconsistencies in gene ontology annotation.Bioinformatics (Oxford, England) · 2024Article
- A roadmap for the functional annotation of protein families: a community perspective.Database : the journal of biological databases and curation · 2022Article
- JaponicusDB: rapid deployment of a model organism database for an emerging model species.Genetics · 2022Article
- PANTHER: Making genome-scale phylogenetics accessible to all.Protein science : a publication of the Protein Society · 2022Review
- Computational Methods for Prediction of Human Protein-Phenotype Associations: A Review.Phenomics (Cham, Switzerland) · 2021Review
- The Gene Ontology resource: enriching a GOld mine.Nucleic acids research · 2021Article
- Detecting Gene Ontology misannotations using taxon-specific rate ratio comparisons.Bioinformatics (Oxford, England) · 2020Article
- Benchmarking gene ontology function predictions using negative annotations.Bioinformatics (Oxford, England) · 2020Article
- The Plant Ontology Facilitates Comparisons of Plant Development Stages Across Species.Frontiers in plant science · 2019Article
- Fast Genome-Wide Functional Annotation through Orthology Assignment by eggNOG-Mapper.Molecular biology and evolution · 2017Article
- Article
- Eliciting the Functional Taxonomy from protein annotations and taxa.Scientific reports · 2016Article
- Sex-biased gene expression and sequence conservation in Atlantic and Pacific salmon lice (Lepeophtheirus salmonis).BMC genomics · 2016Article
- Using the Gene Ontology to Annotate Key Players in Parkinson's Disease.Neuroinformatics · 2016Article
- Canto: an online tool for community literature curation.Bioinformatics (Oxford, England) · 2014Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
backgroundThe Gene Ontology project supports categorization of gene products according to their location of action, the molecular functions that they carry out, and the processes that they are involved in. Although the ontologies are intentionally developed to be taxon neutral, and to cover all species, there are inherent taxon specificities in some branches. For example, the process 'lactation' is specific to mammals and the location 'mitochondrion' is specific to eukaryotes. The lack of an explicit formalization of these constraints can lead to errors and inconsistencies in automated and manual annotation.
resultsWe have formalized the taxonomic constraints implicit in some GO classes, and specified these at various levels in the ontology. We have also developed an inference system that can be used to check for violations of these constraints in annotations. Using the constraints in conjunction with the inference system, we have detected and removed errors in annotations and improved the structure of the ontology.
conclusionsDetection of inconsistencies in taxon-specificity enables gradual improvement of the ontologies, the annotations, and the formalized constraints. This is progressively improving the quality of our data. The full system is available for download, and new constraints or proposed changes to constraints can be submitted online at https://sourceforge.net/tracker/?atid=605890&group_id=36855.
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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.