ArticleBioinformatics (Oxford, England)2020
UniRule: a unified rule resource for automatic annotation in the UniProt Knowledgebase.
Article in Bioinformatics (Oxford, England), 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 45 papers.
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Who cites it
45 citing papers in PubMed.
- Article
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- The Gene Ontology knowledgebase in 2026.Nucleic acids research · 2026Article
- The PROSITE database for protein families, domains, and sites.Nucleic acids research · 2026Article
- A Systematic Review of Drug-Related InteractionsUtilizing Deep Learning and LLMs for Prediction and Mitigation.ACS omega · 2025Review
- Computational approaches to enzymatic reaction assignment: a review of methods, validations, and future directions.Briefings in bioinformatics · 2025Review
- Limitations of current machine learning models in predicting enzymatic functions for uncharacterized proteins.G3 (Bethesda, Md.) · 2025Article
- Protein functional site annotation using local structure embeddings.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Chromosome-level genome assembly of the Durum wheat cultivar Langdon.Scientific data · 2025Article
- C11orf54 catalyzes L-xylulose formation in human metabolism.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- mettannotator: a comprehensive and scalable Nextflow annotation pipeline for prokaryotic assemblies.Bioinformatics (Oxford, England) · 2025Article
- Testing the Capability of Embedding-Based Alignments on the GST Superfamily Classification: The Role of Protein Length.Molecules (Basel, Switzerland) · 2024Article
- High-throughput screening for cell binding and repulsion peptides on multifunctionalized surfaces.Communications biology · 2024Article
- Genetic admixture drives climate adaptation in the bank vole.Communications biology · 2024Article
- Biocatalytic Stereoselective Oxidation of 2-Arylindoles.Journal of the American Chemical Society · 2024Article
- Bioinformatics analysis and alternative polyadenylation in Heat Shock Proteins 70 (HSP70) family members.International journal of physiology, pathophysiology and pharmacology · 2024Article
- Local adaptation and future climate vulnerability in a wild rodent.Nature communications · 2023Article
- Biofilm formation and cell plasticity drive diazotrophy in an anoxygenic phototrophic bacterium.Applied and environmental microbiology · 2023Article
Corrections and comments
- Erratum issued
Authors and funding
31 authors.
Funding
Abstract
motivationThe number of protein records in the UniProt Knowledgebase (UniProtKB: https://www.uniprot.org) continues to grow rapidly as a result of genome sequencing and the prediction of protein-coding genes. Providing functional annotation for these proteins presents a significant and continuing challenge.
resultsIn response to this challenge, UniProt has developed a method of annotation, known as UniRule, based on expertly curated rules, which integrates related systems (RuleBase, HAMAP, PIRSR, PIRNR) developed by the members of the UniProt consortium. UniRule uses protein family signatures from InterPro, combined with taxonomic and other constraints, to select sets of reviewed proteins which have common functional properties supported by experimental evidence. This annotation is propagated to unreviewed records in UniProtKB that meet the same selection criteria, most of which do not have (and are never likely to have) experimentally verified functional annotation. Release 2020_01 of UniProtKB contains 6496 UniRule rules which provide annotation for 53 million proteins, accounting for 30% of the 178 million records in UniProtKB. UniRule provides scalable enrichment of annotation in UniProtKB. AVAILABILITY AND IMPLEMENTATION: UniRule rules are integrated into UniProtKB and can be viewed at https://www.uniprot.org/unirule/. UniRule rules and the code required to run the rules, are publicly available for researchers who wish to annotate their own sequences. The implementation used to run the rules is known as UniFIRE and is available at https://gitlab.ebi.ac.uk/uniprot-public/unifire.
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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.