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ready Pathway Ontology

Abbreviation: PW

General Information
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.

How to cite this record PW; Pathway Ontology; DOI:; Last edited: June 4, 2019, 12:04 p.m.; Last accessed: Jan 23 2022 11:50 a.m.

Publication for citation  The pathway ontology - updates and applications. Petri V,Jayaraman P,Tutaj M,Hayman GT,Smith JR,De Pons J,Laulederkind SJ,Lowry TF,Nigam R,Wang SJ,Shimoyama M,Dwinell MR,Munzenmaier DH,Worthey EA,Jacob HJ; J Biomed Semantics ; 2014; 10.1186/2041-1480-5-7;

Record updated: May 20, 2019, 6:25 p.m. by The FAIRsharing Team.

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The pathway ontology - updates and applications.

Petri V,Jayaraman P,Tutaj M,Hayman GT,Smith JR,De Pons J,Laulederkind SJ,Lowry TF,Nigam R,Wang SJ,Shimoyama M,Dwinell MR,Munzenmaier DH,Worthey EA,Jacob HJ
J Biomed Semantics 2014

View Paper (PubMed) View Publication

Disease pathways at the Rat Genome Database Pathway Portal: genes in context-a network approach to understanding the molecular mechanisms of disease.

Petri V,Hayman GT,Tutaj M,Smith JR,Laulederkind SJ,Wang SJ,Nigam R,De Pons J,Shimoyama M,Dwinell MR,Worthey EA,Jacob HJ
Hum Genomics 2014

View Paper (PubMed) View Publication

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Related Databases (6)
Rat Genome Database
The Rat Genome Database stores genetic, genomic, phenotype, and disease data generated from rat research. It provides access to corresponding data for eight other species, allowing cross-species comparison. Data curation is performed both manually and via an automated pipeline, giving RGD users integrated access to a wide variety of data to support their research.

Pathway Interaction Database
The Pathway Interaction Database is a highly-structured, curated collection of information about known biomolecular interactions and key cellular processes assembled into signaling pathways.

Kyoto Encyclopedia of Genes and Genomes
KEGG is a database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism and the ecosystem, from molecular-level information, especially large-scale molecular datasets generated by genome sequencing and other high-throughput experimental technologies.

Alliance of Genome Resources
The primary mission of the Alliance of Genome Resources (the Alliance) is to develop and maintain sustainable genome information resources that facilitate the use of diverse model organisms in understanding the genetic and genomic basis of human biology, health and disease.

OBO Foundry
The Open Biological and Biomedical Ontology (OBO) Foundry is a collective of ontology developers that are committed to collaboration and adherence to shared principles. The mission of the OBO Foundry is to develop a family of interoperable ontologies that are both logically well-formed and scientifically accurate. To achieve this, OBO Foundry participants voluntarily adhere to and contribute to the development of an evolving set of principles including open use, collaborative development, non-overlapping and strictly-scoped content, and common syntax and relations, based on ontology models that work well, such as the Gene Ontology (GO). The OBO Foundry is overseen by an Operations Committee with Editorial, Technical and Outreach working groups.

BIOchemical PathwaY DataBase
BIOPYDB is a manually-curated database of human cell specific biochemical pathway data. The information within BIOPYDB is primarily extracted from published scientific literature and a selection of databases. The reconstructed pathways contain information about proteins, protein complexes, inorganic molecules, mutated and onco-proteins of signalling, disease and immunological pathways. Every molecule and interaction listed in the database contains at least one reference in a peer reviewed journal.

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Grant Number(s)

  • HL64541 (National Heart, Lung and Blood Institute (NHLBI), National Institutes of Health (NIH), Bethesda, MD, USA)