ArticleBriefings in bioinformatics2015
The role of ontologies in biological and biomedical research: a functional perspective.
Article in Briefings in bioinformatics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 103 papers.
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Who cites it
103 citing papers in PubMed.
- Standardizing Cell Ontology terms for cross-study integration in the female reproductive tract.Science advances · 2026Review
- How not to be seen: predicting unseen enzyme functions using contrastive learning.Bioinformatics (Oxford, England) · 2026Article
- A pragmatist approach to bridging tables and ontologies through LinkML and punning.Journal of biomedical semantics · 2026Article
- Reframing clinical research frameworks: Case for a shift from a biomedical to a biopsychosocial one.The Indian journal of medical research · 2026Article
- How Not to be Seen: Predicting Unseen Enzyme Functions using Contrastive Learning.bioRxiv : the preprint server for biology · 2026Article
- Improving data sharing and knowledge transfer via the Neuroelectrophysiology Analysis Ontology (NEAO).Scientific data · 2025Article
- New and revised gene ontology biological process terms describe multiorganism interactions critical for understanding microbial pathogenesis and sequences of concern.Journal of biomedical semantics · 2025Article
- The Unified Phenotype Ontology : a framework for cross-species integrative phenomics.Genetics · 2025Article
- Working in biocuration: contemporary experiences and perspectives.Database : the journal of biological databases and curation · 2025Article
- A review on Gene Ontology evaluations.Database : the journal of biological databases and curation · 2025Review
- The effectiveness of large language models with RAG for auto-annotating trait and phenotype descriptions.Biology methods & protocols · 2025Article
- A Community Effort to Develop Common Data Elements for Pre-Clinical Spinal Cord Injury Research.Neurotrauma reports · 2025Review
- The Unified Phenotype Ontology (uPheno): A framework for cross-species integrative phenomics.bioRxiv : the preprint server for biology · 2024Article
- Special supplement issue on quality assurance and enrichment of biological and biomedical ontologies and terminologies.BMC medical informatics and decision making · 2024Article
- The Immunopeptidomics Ontology (ImPO).Database : the journal of biological databases and curation · 2024Article
- An open source knowledge graph ecosystem for the life sciences.Scientific data · 2024Article
- EURO-NMD registry: federated FAIR infrastructure, innovative technologies and concepts of a patient-centred registry for rare neuromuscular disorders.Orphanet journal of rare diseases · 2024Review
- NCBI GEO: archive for gene expression and epigenomics data sets: 23-year update.Nucleic acids research · 2024Article
- Bayesian-knowledge driven ontologies: A framework for fusion of semantic knowledge under uncertainty and incompleteness.PloS one · 2024Article
- Refining Substance Use Classification: An Ontological Framework for Enhancing Large-Scale Data Collection.AMIA ... Annual Symposium proceedings. AMIA Symposium · 2024Article
43 more citing papers are in PubMed but not listed here.
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Authors and funding
3 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Ontologies are widely used in biological and biomedical research. Their success lies in their combination of four main features present in almost all ontologies: provision of standard identifiers for classes and relations that represent the phenomena within a domain; provision of a vocabulary for a domain; provision of metadata that describes the intended meaning of the classes and relations in ontologies; and the provision of machine-readable axioms and definitions that enable computational access to some aspects of the meaning of classes and relations. While each of these features enables applications that facilitate data integration, data access and analysis, a great potential lies in the possibility of combining these four features to support integrative analysis and interpretation of multimodal data. Here, we provide a functional perspective on ontologies in biology and biomedicine, focusing on what ontologies can do and describing how they can be used in support of integrative research. We also outline perspectives for using ontologies in data-driven science, in particular their application in structured data mining and machine learning applications.
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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.