ArticleJournal of biomedical semantics2014
TermGenie - a web-application for pattern-based ontology class generation.
Article in Journal of biomedical semantics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- Extending and using anatomical vocabularies in the stimulating peripheral activity to relieve conditions project.Frontiers in neuroinformatics · 2022Article
- Ontological and Non-Ontological Resources for Associating Medical Dictionary for Regulatory Activities Terms to SNOMED Clinical Terms With Semantic Properties.Frontiers in pharmacology · 2019Article
- Using OWL reasoning to support the generation of novel gene sets for enrichment analysis.Journal of biomedical semantics · 2018Article
- The eXtensible ontology development (XOD) principles and tool implementation to support ontology interoperability.Journal of biomedical semantics · 2018Review
- Article
- Exploring autophagy with Gene Ontology.Autophagy · 2018Review
- Dead simple OWL design patterns.Journal of biomedical semantics · 2017Article
- Expansion of the Gene Ontology knowledgebase and resources.Nucleic acids research · 2017Article
- Article
- The environment ontology in 2016: bridging domains with increased scope, semantic density, and interoperation.Journal of biomedical semantics · 2016Article
- Gene Ontology synonym generation rules lead to increased performance in biomedical concept recognition.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
- Integrating Biodiversity Data into Botanic Collections.Biodiversity data journal · 2016Article
- The cellular microscopy phenotype ontology.Journal of biomedical semantics · 2016Article
- Webulous and the Webulous Google Add-On--a web service and application for ontology building from templates.Journal of biomedical semantics · 2016Article
- Representing virus-host interactions and other multi-organism processes in the Gene Ontology.BMC microbiology · 2015Article
- Moving the mountain: analysis of the effort required to transform comparative anatomy into computable anatomy.Database : the journal of biological databases and curation · 2015Article
- Gene Ontology Consortium: going forward.Nucleic acids research · 2015Article
Corrections and comments
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Authors and funding
8 authors.
Funding
Abstract
backgroundBiological ontologies are continually growing and improving from requests for new classes (terms) by biocurators. These ontology requests can frequently create bottlenecks in the biocuration process, as ontology developers struggle to keep up, while manually processing these requests and create classes.
resultsTermGenie allows biocurators to generate new classes based on formally specified design patterns or templates. The system is web-based and can be accessed by any authorized curator through a web browser. Automated rules and reasoning engines are used to ensure validity, uniqueness and relationship to pre-existing classes. In the last 4 years the Gene Ontology TermGenie generated 4715 new classes, about 51.4% of all new classes created. The immediate generation of permanent identifiers proved not to be an issue with only 70 (1.4%) obsoleted classes.
conclusionTermGenie is a web-based class-generation system that complements traditional ontology development tools. All classes added through pre-defined templates are guaranteed to have OWL equivalence axioms that are used for automatic classification and in some cases inter-ontology linkage. At the same time, the system is simple and intuitive and can be used by most biocurators without extensive training.
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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 Socratic graph.