ArticleBMC genomics2013
Dovetailing biology and chemistry: integrating the Gene Ontology with the ChEBI chemical ontology.
Article in BMC genomics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed.
- A general strategy for generating expert-guided, simplified views of ontologies.Scientific data · 2026Article
- Achieving bottom-up ethical, legal, and societal implications and responsible research and innovation in the synthetic biology research community from the Japanese context.Frontiers in genetics · 2026Article
- Chemical classification program synthesis using generative artificial intelligence.Journal of cheminformatics · 2025Article
- A general strategy for generating expert-guided, simplified views of ontologies.bioRxiv : the preprint server for biology · 2025Article
- Dynamic Retrieval Augmented Generation of Ontologies using Artificial Intelligence (DRAGON-AI).Journal of biomedical semantics · 2024Article
- Challenges and perspectives for naming lipids in the context of lipidomics.Metabolomics : Official journal of the Metabolomic Society · 2024Review
- Improved characterisation of clinical text through ontology-based vocabulary expansion.Journal of biomedical semantics · 2021Article
- Learning chemistry: exploring the suitability of machine learning for the task of structure-based chemical ontology classification.Journal of cheminformatics · 2021Article
- BiPOm: a rule-based ontology to represent and infer molecule knowledge from a biological process-centered viewpoint.BMC bioinformatics · 2020Article
- ROBOT: A Tool for Automating Ontology Workflows.BMC bioinformatics · 2019Article
- Using OWL reasoning to support the generation of novel gene sets for enrichment analysis.Journal of biomedical semantics · 2018Article
- From Affective Science to Psychiatric Disorder: Ontology as a Semantic Bridge.Frontiers in psychiatry · 2018Article
- The bacterial interlocked process ONtology (BiPON): a systemic multi-scale unified representation of biological processes in prokaryotes.Journal of biomedical semantics · 2017Article
- Using the Gene Ontology to Annotate Key Players in Parkinson's Disease.Neuroinformatics · 2016Article
- Functional Profiling of Human MeCP2 by Automated Data Comparison Analysis and Computerized Expression Pathway Modeling.Healthcare informatics research · 2016Article
- ChEBI in 2016: Improved services and an expanding collection of metabolites.Nucleic acids research · 2016Article
- Modeling biochemical pathways in the gene ontology.Database : the journal of biological databases and curation · 2016Article
- Updates in Rhea--a manually curated resource of biochemical reactions.Nucleic acids research · 2015Article
- A method for increasing expressivity of Gene Ontology annotations using a compositional approach.BMC bioinformatics · 2014Article
- The European Bioinformatics Institute's data resources 2014.Nucleic acids research · 2014Article
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Authors and funding
19 authors.
Funding
Abstract
backgroundThe Gene Ontology (GO) facilitates the description of the action of gene products in a biological context. Many GO terms refer to chemical entities that participate in biological processes. To facilitate accurate and consistent systems-wide biological representation, it is necessary to integrate the chemical view of these entities with the biological view of GO functions and processes. We describe a collaborative effort between the GO and the Chemical Entities of Biological Interest (ChEBI) ontology developers to ensure that the representation of chemicals in the GO is both internally consistent and in alignment with the chemical expertise captured in ChEBI.
resultsWe have examined and integrated the ChEBI structural hierarchy into the GO resource through computationally-assisted manual curation of both GO and ChEBI. Our work has resulted in the creation of computable definitions of GO terms that contain fully defined semantic relationships to corresponding chemical terms in ChEBI.
conclusionsThe set of logical definitions using both the GO and ChEBI has already been used to automate aspects of GO development and has the potential to allow the integration of data across the domains of biology and chemistry. These logical definitions are available as an extended version of the ontology from http://purl.obolibrary.org/obo/go/extensions/go-plus.owl.
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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.