Pathway Ontology
Names
More detailed information about this field from each metasource.
Pathway Ontology
metasource: Fairsharing.org
version: FAIRsharing.org: PW; Pathway Ontology; DOI: https://doi.org/10.25504/FAIRsharing.f73xhd; Last edited: June 4, 2019, 12:04 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
metasource: Biontology / Bioportal
version: 7.65 extracted_at: 2022-11-04T11:10:15.597147, http://bioportal.bioontology.org/ontologies/PW
PW
metasource: Fairsharing.org
version: FAIRsharing.org: PW; Pathway Ontology; DOI: https://doi.org/10.25504/FAIRsharing.f73xhd; Last edited: June 4, 2019, 12:04 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
metasource: Biontology / Bioportal
version: 7.65 extracted_at: 2022-11-04T11:10:15.597147, http://bioportal.bioontology.org/ontologies/PW
Names
More detailed information about this field from each metasource.
Pathway Ontology
metasource: Fairsharing.orgversion: FAIRsharing.org: PW; Pathway Ontology; DOI: https://doi.org/10.25504/FAIRsharing.f73xhd; Last edited: June 4, 2019, 12:04 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
metasource: Biontology / Bioportal
version: 7.65 extracted_at: 2022-11-04T11:10:15.597147, http://bioportal.bioontology.org/ontologies/PW
PW
metasource: Fairsharing.orgversion: FAIRsharing.org: PW; Pathway Ontology; DOI: https://doi.org/10.25504/FAIRsharing.f73xhd; Last edited: June 4, 2019, 12:04 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
metasource: Biontology / Bioportal
version: 7.65 extracted_at: 2022-11-04T11:10:15.597147, http://bioportal.bioontology.org/ontologies/PW
Names
More detailed information about this field from each metasource.
Pathway Ontology
metasource: Fairsharing.orgversion: FAIRsharing.org: PW; Pathway Ontology; DOI: https://doi.org/10.25504/FAIRsharing.f73xhd; Last edited: June 4, 2019, 12:04 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
metasource: Biontology / Bioportal
version: 7.65 extracted_at: 2022-11-04T11:10:15.597147, http://bioportal.bioontology.org/ontologies/PW
PW
metasource: Fairsharing.orgversion: FAIRsharing.org: PW; Pathway Ontology; DOI: https://doi.org/10.25504/FAIRsharing.f73xhd; Last edited: June 4, 2019, 12:04 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
metasource: Biontology / Bioportal
version: 7.65 extracted_at: 2022-11-04T11:10:15.597147, http://bioportal.bioontology.org/ontologies/PW
The goal of the Pathway Ontology is to cover all types of biological pathways, including altered and disease pathways, and to capture the relationships between them within the hierarchical structure of a Directed Acyclic Graph (DAG). The five nodes of the ontology are: classic metabolic, regulatory, signaling, drug and disease pathways. An extensive survey of the review literature along with searches of existing pathway databases have been used to choose terms and their position within the tree. The ontology is continually expanding along with the development of Pathway and Disease Portals at RGD.
Description
More detailed information about this field from each metasource.
The goal of the Pathway Ontology is to cover all types of biological pathways, including altered and disease pathways, and to capture the relationships between them within the hierarchical structure of a Directed Acyclic Graph (DAG). The five nodes of the ontology are: classic metabolic, regulatory, signaling, drug and disease pathways. An extensive survey of the review literature along with searches of existing pathway databases have been used to choose terms and their position within the tree. The ontology is continually expanding along with the development of Pathway and Disease Portals at RGD.
metasource: Fairsharing.orgversion: FAIRsharing.org: PW; Pathway Ontology; DOI: https://doi.org/10.25504/FAIRsharing.f73xhd; Last edited: June 4, 2019, 12:04 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
The goal of the Pathway Ontology is to cover all types of biological pathways, including altered and disease pathways, and to capture the relationships between them within the hierarchical structure of a Directed Acyclic Graph (DAG). The five nodes of the ontology are: classic metabolic, regulatory, signaling, drug and disease pathways. An extensive survey of the review literature along with searches of existing pathway databases have been used to choose terms and their position within the tree. The ontology is continually expanding along with the development of Pathway and Disease Portals at RGD. Mapping of pathways in other databases to terms in PW as synonyms further increased the content of the ontology. It also provided the means to bring in annotations made by these databases and link to their sites via automatic pipelines built at RGD. The ontology allows for the standardized annotation of rat as well as human and mouse genes to pathway terms. It also serves as a vehicle to connect between genes and ontology reports, between reports and interactive pathway diagrams, between pathways that directly connect to one another within a diagram or between pathways that in some fashion are globally related in pathway suites and suite networks. Metabolic, regulatory or signaling pathway terms have associated terms for the altered version of the pathway and the level at which the alteration(s) may occur. Proteins with mutations known to affect a particular pathway can be annotated to the normal and altered version(s) of the pathway and to a disease pathway, if known. Both the provision of terms for the altered versions of pathways and the representation of disease pathway diagrams as a collection of altered pathways are unique to the PW ontology and RGD's pathway data. The Pathway ontology is distributed under the terms of the Creative Commons Attribution license version 3.0 Unported (CC BY 3.0), see http://creativecommons.org/licenses/by/3.0 for details.
metasource: Biontology / Bioportalversion: 7.65 extracted_at: 2022-11-04T11:10:15.597147, http://bioportal.bioontology.org/ontologies/PW
Webpage:
https://rgd.mcw.edu/rgdweb/ontology/view.html?acc_id=PW:0000001Webpage
More detailed information about this field from each metasource.
https://rgd.mcw.edu/rgdweb/ontology/view.html?acc_id=PW:0000001
metasource: Fairsharing.orgversion: FAIRsharing.org: PW; Pathway Ontology; DOI: https://doi.org/10.25504/FAIRsharing.f73xhd; Last edited: June 4, 2019, 12:04 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
https://rgd.mcw.edu/rgdweb/ontology/search.html
metasource: Biontology / Bioportalversion: 7.65 extracted_at: 2022-11-04T11:10:15.597147, http://bioportal.bioontology.org/ontologies/PW
Licence:
Name: Creative Commons Attribution 4.0 International (CC BY 4.0)Licence name
More detailed information about this field from each metasource.
Creative Commons Attribution 4.0 International (CC BY 4.0)
metasource: Fairsharing.orgversion: FAIRsharing.org: PW; Pathway Ontology; DOI: https://doi.org/10.25504/FAIRsharing.f73xhd; Last edited: June 4, 2019, 12:04 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
Licence URL
More detailed information about this field from each metasource.
https://creativecommons.org/licenses/by/4.0/
metasource: Fairsharing.orgversion: FAIRsharing.org: PW; Pathway Ontology; DOI: https://doi.org/10.25504/FAIRsharing.f73xhd; Last edited: June 4, 2019, 12:04 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
Publications:
Publications
More detailed information about this field from each metasource.
The pathway ontology - updates and applications
PMID: 24499703
metasource: Fairsharing.org
version: FAIRsharing.org: PW; Pathway Ontology; DOI: https://doi.org/10.25504/FAIRsharing.f73xhd; Last edited: June 4, 2019, 12:04 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
Disease pathways at the Rat Genome Database Pathway Portal: genes in context-a network approach to understanding the molecular mechanisms of disease
PMID: 25265995
metasource: Fairsharing.org
version: FAIRsharing.org: PW; Pathway Ontology; DOI: https://doi.org/10.25504/FAIRsharing.f73xhd; Last edited: June 4, 2019, 12:04 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
http://rgd.mcw.edu/wg/home/pathway2/molecular-pathways/#pwrpubs
metasource: Biontology / Bioportal
version: 7.65 extracted_at: 2022-11-04T11:10:15.597147, http://bioportal.bioontology.org/ontologies/PW
Publications
More detailed information about this field from each metasource.
The pathway ontology - updates and applications
PMID: 24499703
metasource: Fairsharing.org
version: FAIRsharing.org: PW; Pathway Ontology; DOI: https://doi.org/10.25504/FAIRsharing.f73xhd; Last edited: June 4, 2019, 12:04 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
Disease pathways at the Rat Genome Database Pathway Portal: genes in context-a network approach to understanding the molecular mechanisms of disease
PMID: 25265995
metasource: Fairsharing.org
version: FAIRsharing.org: PW; Pathway Ontology; DOI: https://doi.org/10.25504/FAIRsharing.f73xhd; Last edited: June 4, 2019, 12:04 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
http://rgd.mcw.edu/wg/home/pathway2/molecular-pathways/#pwrpubs
metasource: Biontology / Bioportalversion: 7.65 extracted_at: 2022-11-04T11:10:15.597147, http://bioportal.bioontology.org/ontologies/PW
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The pathway ontology - updates and applications
PubMed citations: 41.
41 articles citing: The pathway ontology - updates and applications
The AOP-DB RDF: Applying FAIR Principles to the Semantic Integration of AOP Data Using the Research Description Framework. PMID:35295213
NETME: on-the-fly knowledge network construction from biomedical literature. PMID:35013714
Potential Molecular Mechanisms and Remdesivir Treatment for Acute Respiratory Syndrome Corona Virus 2 Infection/COVID 19 Through RNA Sequencing and Bioinformatics Analysis. PMID:34992355
Pathway Enrichment Analysis of Microarray Data. PMID:34902127
DecoPath: a web application for decoding pathway enrichment analysis. PMID:34568823
Ten simple rules for creating reusable pathway models for computational analysis and visualization. PMID:34411100
Mapping gene and gene pathways associated with coronary artery disease: a CARDIoGRAM exome and multi-ancestry UK biobank analysis. PMID:34385509
emiRIT: a text-mining-based resource for microRNA information. PMID:34048547
Application of multiple omics and network projection analyses to drug repositioning for pathogenic mosquito-borne viruses. PMID:33980888
Establishing a consensus for the hallmarks of cancer based on gene ontology and pathway annotations. PMID:33823788
Identification of potential and novel target genes in pituitary prolactinoma by bioinformatics analysis. PMID:33709028
Bioinformatics analyses of significant genes, related pathways, and candidate diagnostic biomarkers and molecular targets in SARS-CoV-2/COVID-19. PMID:33553808
Identification of potential mRNA panels for severe acute respiratory syndrome coronavirus 2 (COVID-19) diagnosis and treatment using microarray dataset and bioinformatics methods. PMID:33251083
Pathway information extracted from 25 years of pathway figures. PMID:33168034
Analysis of Differentially Expressed Genes in Coronary Artery Disease by Integrated Microarray Analysis. PMID:31881747
Identification of important invasion and proliferation related genes in adrenocortical carcinoma. PMID:31321566
Exploring the Molecular Mechanism of the Drug-Treated Breast Cancer Based on Gene Expression Microarray. PMID:31311202
Pathway Interactions Based on Drug-Induced Datasets. PMID:31205412
Predicting instances of pathway ontology classes for pathway integration. PMID:31196182
Identification of Crucial Candidate Genes and Pathways in Glioblastoma Multiform by Bioinformatics Analysis. PMID:31137733
Identification of Important Invasion-Related Genes in Non-functional Pituitary Adenomas. PMID:30982163
Mining Featured Biomarkers Linked with Epithelial Ovarian CancerBased on Bioinformatics. PMID:30970615
Drug repositioning for dengue haemorrhagic fever by integrating multiple omics analyses. PMID:30679503
ComPath: an ecosystem for exploring, analyzing, and curating mappings across pathway databases. PMID:30564458
Identifying High-Priority Proteins Across the Human Diseasome Using Semantic Similarity. PMID:30256117
A Primer for the Rat Genome Database (RGD). PMID:29761460
BIOPYDB: A Dynamic Human Cell Specific Biochemical Pathway Database with Advanced Computational Analyses Platform. PMID:29547394
The bacterial interlocked process ONtology (BiPON): a systemic multi-scale unified representation of biological processes in prokaryotes. PMID:29169408
Evaluating phenotype-driven approaches for genetic diagnoses from exomes in a clinical setting. PMID:29044180
Mutations in folate transporter genes and risk for human myelomeningocele. PMID:28948692
Rat Genome and Model Resources. PMID:28838068
Microarray analysis reveals key genes and pathways in Tetralogy of Fallot. PMID:28713939
Exploring human disease using the Rat Genome Database. PMID:27736745
Disease, Models, Variants and Altered Pathways-Journeying RGD Through the Magnifying Glass. PMID:27602200
Comprehensive coverage of cardiovascular disease data in the disease portals at the Rat Genome Database. PMID:27287925
Reactome from a WikiPathways Perspective. PMID:27203685
The Chinchilla Research Resource Database: resource for an otolaryngology disease model. PMID:27173523
Semantic interrogation of a multi knowledge domain ontological model of tendinopathy identifies four strong candidate risk genes. PMID:26804977
The clinical trial landscape in oncology and connectivity of somatic mutational profiles to targeted therapies. PMID:26772741
OVA: integrating molecular and physical phenotype data from multiple biomedical domain ontologies with variant filtering for enhanced variant prioritization. PMID:26272982
Disease pathways at the Rat Genome Database Pathway Portal: genes in context-a network approach to understanding the molecular mechanisms of disease. PMID:25265995 -
Disease pathways at the Rat Genome Database Pathway Portal: genes in context-a network approach to understanding the molecular mechanisms of disease
PubMed citations: 6.
6 articles citing: Disease pathways at the Rat Genome Database Pathway Portal: genes in context-a network approach to understanding the molecular mechanisms of disease
Genetic Dissection of Femoral and Tibial Microarchitecture. PMID:31844829
Rat Genome and Model Resources. PMID:28838068
Long Evans rat spermatogonial lines are effective germline vectors for transgenic rat production. PMID:28608322
Disease, Models, Variants and Altered Pathways-Journeying RGD Through the Magnifying Glass. PMID:27602200
Histone Modifier Genes Alter Conotruncal Heart Phenotypes in 22q11.2 Deletion Syndrome. PMID:26608785
The Rat Genome Database 2015: genomic, phenotypic and environmental variations and disease. PMID:25355511 - http://rgd.mcw.edu/wg/home/pathway2/molecular-pathways/#pwrpubs
Tags:
Tags
More detailed information about this field from each metasource.
biological regulation
metasource: Fairsharing.org
version: FAIRsharing.org: PW; Pathway Ontology; DOI: https://doi.org/10.25504/FAIRsharing.f73xhd; Last edited: June 4, 2019, 12:04 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
disease
metasource: Fairsharing.org
version: FAIRsharing.org: PW; Pathway Ontology; DOI: https://doi.org/10.25504/FAIRsharing.f73xhd; Last edited: June 4, 2019, 12:04 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
drug
metasource: Fairsharing.org
version: FAIRsharing.org: PW; Pathway Ontology; DOI: https://doi.org/10.25504/FAIRsharing.f73xhd; Last edited: June 4, 2019, 12:04 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
enzymatic reaction
metasource: Fairsharing.org
version: FAIRsharing.org: PW; Pathway Ontology; DOI: https://doi.org/10.25504/FAIRsharing.f73xhd; Last edited: June 4, 2019, 12:04 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
mathematical model
metasource: Fairsharing.org
version: FAIRsharing.org: PW; Pathway Ontology; DOI: https://doi.org/10.25504/FAIRsharing.f73xhd; Last edited: June 4, 2019, 12:04 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
molecular entity
metasource: Fairsharing.org
version: FAIRsharing.org: PW; Pathway Ontology; DOI: https://doi.org/10.25504/FAIRsharing.f73xhd; Last edited: June 4, 2019, 12:04 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
network model
metasource: Fairsharing.org
version: FAIRsharing.org: PW; Pathway Ontology; DOI: https://doi.org/10.25504/FAIRsharing.f73xhd; Last edited: June 4, 2019, 12:04 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
pathway model
metasource: Fairsharing.org
version: FAIRsharing.org: PW; Pathway Ontology; DOI: https://doi.org/10.25504/FAIRsharing.f73xhd; Last edited: June 4, 2019, 12:04 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
signaling
metasource: Fairsharing.org
version: FAIRsharing.org: PW; Pathway Ontology; DOI: https://doi.org/10.25504/FAIRsharing.f73xhd; Last edited: June 4, 2019, 12:04 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
Tags
More detailed information about this field from each metasource.
biological regulation
metasource: Fairsharing.orgversion: FAIRsharing.org: PW; Pathway Ontology; DOI: https://doi.org/10.25504/FAIRsharing.f73xhd; Last edited: June 4, 2019, 12:04 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
disease
metasource: Fairsharing.orgversion: FAIRsharing.org: PW; Pathway Ontology; DOI: https://doi.org/10.25504/FAIRsharing.f73xhd; Last edited: June 4, 2019, 12:04 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
drug
metasource: Fairsharing.orgversion: FAIRsharing.org: PW; Pathway Ontology; DOI: https://doi.org/10.25504/FAIRsharing.f73xhd; Last edited: June 4, 2019, 12:04 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
enzymatic reaction
metasource: Fairsharing.orgversion: FAIRsharing.org: PW; Pathway Ontology; DOI: https://doi.org/10.25504/FAIRsharing.f73xhd; Last edited: June 4, 2019, 12:04 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
mathematical model
metasource: Fairsharing.orgversion: FAIRsharing.org: PW; Pathway Ontology; DOI: https://doi.org/10.25504/FAIRsharing.f73xhd; Last edited: June 4, 2019, 12:04 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
molecular entity
metasource: Fairsharing.orgversion: FAIRsharing.org: PW; Pathway Ontology; DOI: https://doi.org/10.25504/FAIRsharing.f73xhd; Last edited: June 4, 2019, 12:04 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
network model
metasource: Fairsharing.orgversion: FAIRsharing.org: PW; Pathway Ontology; DOI: https://doi.org/10.25504/FAIRsharing.f73xhd; Last edited: June 4, 2019, 12:04 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
pathway model
metasource: Fairsharing.orgversion: FAIRsharing.org: PW; Pathway Ontology; DOI: https://doi.org/10.25504/FAIRsharing.f73xhd; Last edited: June 4, 2019, 12:04 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
signaling
metasource: Fairsharing.orgversion: FAIRsharing.org: PW; Pathway Ontology; DOI: https://doi.org/10.25504/FAIRsharing.f73xhd; Last edited: June 4, 2019, 12:04 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
biological regulation disease drug enzymatic reaction mathematical model molecular entity network model pathway model signaling
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