ArticleDatabase : the journal of biological databases and curation2016
Modeling biochemical pathways in the gene ontology.
Article in Database : the journal of biological databases and curation, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- Brain metastases converge on shared geometric architecture and transcriptomic landscape yet remain distinct from gliomas.iScience · 2026Article
- Weighted network analysis of adverse outcome pathways decodes the multiscale mechanisms of environmental toxicity.Environmental science and ecotechnology · 2026Article
- Genotype and phenotype data standardization, utilization and integration in the big data era for agricultural sciences.Database : the journal of biological databases and curation · 2023Review
- Article
- Biochemical Pathways Represented by Gene Ontology Causal Activity Models Identify Distinct Phenotypes Resulting from Mutations in Pathways.bioRxiv : the preprint server for biology · 2023Article
- Synergistic suppressive effects on triple-negative breast cancer by the combination of JTC-801 and sodium oxamate.American journal of cancer research · 2023Article
- Identification of hub genes and pathways in bladder cancer using bioinformatics analysis.American journal of clinical and experimental urology · 2022Article
- GO functional similarity clustering depends on similarity measure, clustering method, and annotation completeness.BMC bioinformatics · 2019Article
- Identification of key genes in human airway epithelial cells in response to respiratory pathogens using microarray analysis.BMC microbiology · 2018Article
- Exploring autophagy with Gene Ontology.Autophagy · 2018Review
- The bacterial interlocked process ONtology (BiPON): a systemic multi-scale unified representation of biological processes in prokaryotes.Journal of biomedical semantics · 2017Article
- Establishment of apoptotic regulatory network for genetic markers of colorectal cancer.Saudi journal of biological sciences · 2017Article
- Expansion of the Gene Ontology knowledgebase and resources.Nucleic acids research · 2017Article
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
The concept of a biological pathway, an ordered sequence of molecular transformations, is used to collect and represent molecular knowledge for a broad span of organismal biology. Representations of biomedical pathways typically are rich but idiosyncratic presentations of organized knowledge about individual pathways. Meanwhile, biomedical ontologies and associated annotation files are powerful tools that organize molecular information in a logically rigorous form to support computational analysis. The Gene Ontology (GO), representing Molecular Functions, Biological Processes and Cellular Components, incorporates many aspects of biological pathways within its ontological representations. Here we present a methodology for extending and refining the classes in the GO for more comprehensive, consistent and integrated representation of pathways, leveraging knowledge embedded in current pathway representations such as those in the Reactome Knowledgebase and MetaCyc. With carbohydrate metabolic pathways as a use case, we discuss how our representation supports the integration of variant pathway classes into a unified ontological structure that can be used for data comparison and analysis.
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Registered trials
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