ArticleJournal of biomedical informatics2011
Cross-product extensions of the Gene Ontology.
Article in Journal of biomedical informatics, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 66 papers.
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Who cites it
66 citing papers in PubMed.
- Dynamic Retrieval Augmented Generation of Ontologies using Artificial Intelligence (DRAGON-AI).Journal of biomedical semantics · 2024Article
- Creating an ignorance-base: Exploring known unknowns in the scientific literature.Journal of biomedical informatics · 2023Article
- Semantic similarity and machine learning with ontologies.Briefings in bioinformatics · 2021Review
- Genome-wide transcriptome profiling indicates the putative mechanism underlying enhanced grain size in a wheat mutant.3 Biotech · 2021Article
- A comprehensive survey of integron-associated genes present in metagenomes.BMC genomics · 2020Article
- Semantic characterization of adverse outcome pathways.Aquatic toxicology (Amsterdam, Netherlands) · 2020Article
- Formal axioms in biomedical ontologies improve analysis and interpretation of associated data.Bioinformatics (Oxford, England) · 2020Article
- Phenotype annotation with the ontology of microbial phenotypes (OMP).Journal of biomedical semantics · 2019Article
- Repository of Enriched Structures of Proteins Involved in the Red Blood Cell Environment (RESPIRE).PloS one · 2019Article
- Improving Interpretation of Cardiac Phenotypes and Enhancing Discovery With Expanded Knowledge in the Gene Ontology.Circulation. Genomic and precision medicine · 2018Article
- Improving the interoperability of biomedical ontologies with compound alignments.Journal of biomedical semantics · 2018Article
- A new method for evaluating the impacts of semantic similarity measures on the annotation of gene sets.PloS one · 2018Article
- Exploring autophagy with Gene Ontology.Autophagy · 2018Review
- Single subject transcriptome analysis to identify functionally signed gene set or pathway activity.Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing · 2018Article
- Article
- Gold-standard ontology-based anatomical annotation in the CRAFT Corpus.Database : the journal of biological databases and curation · 2017Article
- The environment ontology in 2016: bridging domains with increased scope, semantic density, and interoperation.Journal of biomedical semantics · 2016Article
- The Cell Ontology 2016: enhanced content, modularization, and ontology interoperability.Journal of biomedical semantics · 2016Article
- Using the Gene Ontology to Annotate Key Players in Parkinson's Disease.Neuroinformatics · 2016Article
- Modeling biochemical pathways in the gene ontology.Database : the journal of biological databases and curation · 2016Article
6 more citing papers are in PubMed but not listed here.
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Authors and funding
8 authors.
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Abstract
The Gene Ontology (GO) consists of nearly 30,000 classes for describing the activities and locations of gene products. Manual maintenance of ontology of this size is a considerable effort, and errors and inconsistencies inevitably arise. Reasoners can be used to assist with ontology development, automatically placing classes in a subsumption hierarchy based on their properties. However, the historic lack of computable definitions within the GO has prevented the user of these tools. In this paper, we present preliminary results of an ongoing effort to normalize the GO by explicitly stating the definitions of compositional classes in a form that can be used by reasoners. These definitions are partitioned into mutually exclusive cross-product sets, many of which reference other OBO Foundry candidate ontologies for chemical entities, proteins, biological qualities and anatomical entities. Using these logical definitions we are gradually beginning to automate many aspects of ontology development, detecting errors and filling in missing relationships. These definitions also enhance the GO by weaving it into the fabric of a wider collection of interoperating ontologies, increasing opportunities for data integration and enhancing genomic analyses.
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