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.

Homepage https://rgd.mcw.edu/rgdweb/ontology/view.html?acc_id=PW:0000001

Countries that developed this resource United States

Created in 2009

Taxonomic range

Homo sapiens

Mus musculus

Rattus norvegicus

Knowledge Domains

Subjects

How to cite this record FAIRsharing.org: PW; Pathway Ontology; DOI: https://doi.org/10.25504/FAIRsharing.f73xhd; Last edited: June 4, 2019, 12:04 p.m.; Last accessed: Dec 07 2019 5:01 p.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.

Show edit history

Edits to 'https://fairsharing.org/FAIRsharing.f73xhd' by 'The FAIRsharing Team' at 18:25, 20 May 2019 (approved):

	'supportLinks' has been modified:
		Before:
			online documentation|ftp://ftp.rgd.mcw.edu/pub/data_release/PathwayOntology_introduction.doc
		After:
			contact form|https://rgd.mcw.edu/contact/index.shtml
			online documentation|ftp://ftp.rgd.mcw.edu/pub/data_release/PathwayOntology_introduction.doc
		Added:
			contact form|https://rgd.mcw.edu/contact/index.shtml
		Removed:

	'dataProcesses' has been modified:
		Before:
			FTP download page
		After:
			FTP download page
			Browser
		Added:
			Browser
		Removed:

Edits to 'https://fairsharing.org/FAIRsharing.f73xhd' by 'The FAIRsharing Team' at 17:19, 20 May 2019 (approved):

	'onto_disciplines' has been modified:
		Before:
			Drug Metabolism
			Life Sciences
		After:
			Drug Metabolism
			Life Sciences
			Ontology and Terminology
		Added:
			Ontology and Terminology
		Removed:

	'homepage' has been modified:
		Before: http://rgd.mcw.edu/wg/home/pathway2
		After: https://rgd.mcw.edu/rgdweb/ontology/view.html?acc_id=PW:0000001

	'contactORCID' has been modified:
		Before: 
		After: 0000-0002-5540-8498

Edits to 'https://fairsharing.org/FAIRsharing.f73xhd' by 'The FAIRsharing Team' at 14:48, 12 Mar 2019 (approved):

	'organizations' has been modified:
		Before:
			PW administrators|http://rgd.mcw.edu/tools/ontology/ont_search.cgi|Maintains
		After:
			Medical College of Wisconsin (MCW), Wisconsin, USA|http://www.mcw.edu|Maintains
			National Heart, Lung and Blood Institute (NHLBI), National Institutes of Health (NIH), Bethesda, MD, USA|http://www.nhlbi.nih.gov/|Funds
		Added:
			Medical College of Wisconsin (MCW), Wisconsin, USA|http://www.mcw.edu|Maintains
			National Heart, Lung and Blood Institute (NHLBI), National Institutes of Health (NIH), Bethesda, MD, USA|http://www.nhlbi.nih.gov/|Funds
		Removed:
			PW administrators|http://rgd.mcw.edu/tools/ontology/ont_search.cgi|Maintains

	'supportLinks' has been modified:
		Before:
			schema file|ftp://ftp.rgd.mcw.edu/pub/ontology/pathway/
		After:
			online documentation|ftp://ftp.rgd.mcw.edu/pub/data_release/PathwayOntology_introduction.doc
		Added:
			online documentation|ftp://ftp.rgd.mcw.edu/pub/data_release/PathwayOntology_introduction.doc
		Removed:
			schema file|ftp://ftp.rgd.mcw.edu/pub/ontology/pathway/

	'licences' has been modified:
		Before:
			Free for academic and non-profit use|http://dibs.enzim.ttk.mta.hu/help.php|Data
		After:
			Creative Commons Attribution 4.0 International (CC BY 4.0)|https://creativecommons.org/licenses/by/4.0/|Data
			Creative Commons Attribution 3.0 Unported (CC BY 3.0)|https://creativecommons.org/licenses/by/3.0/|Data
		Added:
			Creative Commons Attribution 4.0 International (CC BY 4.0)|https://creativecommons.org/licenses/by/4.0/|Data
			Creative Commons Attribution 3.0 Unported (CC BY 3.0)|https://creativecommons.org/licenses/by/3.0/|Data
		Removed:
			Free for academic and non-profit use|http://dibs.enzim.ttk.mta.hu/help.php|Data

	'onto_disciplines' has been modified:
		Before:
			Life Sciences
		After:
			Drug Metabolism
			Life Sciences
		Added:
			Drug Metabolism
		Removed:

	'dataProcesses' has been modified:
		Before:
			FTP download page
			web interface
		After:
			FTP download page
		Added:
		Removed:
			web interface

	'grants' has been modified:
		Before:
		After:
			HL64541
		Added:
			HL64541
		Removed:

	'onto_domains' has been modified:
		Before:
			Mathematical model
			enzymatic reaction
			molecular entity
			pathway
			None
		After:
			Mathematical model
			biological regulation
			disease
			drug
			enzymatic reaction
			molecular entity
			pathway
			signaling
			None
		Added:
			biological regulation
			disease
			drug
			signaling
		Removed:

Support

General

contact form	General inquiry
online documentation	Pathway Ontology Introduction (doc)

Additional Information

Contact

Victoria Petri ORCID

External Links

Bioportal	http://bioportal.bioontology.org/ontologies/PW
OBO	http://obofoundry.org/ontology/pw.html

Tools

No tools defined

Schemas

No XSD schemas defined

Access / Retrieve Data

Conditions of Use

Applies to: Data use

Data Release

FTP download page

ftp://ftp.rgd.mcw.edu/pub/ontology/pathway/

Data Access

Browser

https://rgd.mcw.edu/rgdweb/ontology/view.html?acc_id=PW:0000001

REST Web Services

Ontology Web Service

https://rest.rgd.mcw.edu/rgdws/swagger-ui.html#/Ontology

Publications

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

PW Ontology Display

View in BioPortal.

Disclaimer: This widget assumes the availability of the ontology resources in the NCBO BioPortal.

View in OBO Foundry.

Related Standards

Reporting Guidelines

No guidelines defined

Terminology Artifacts

Domain Resource Application Ontology

Models and Formats

No syntax standards defined

Identifier Schemas

No identifier schema standards defined

Metrics

No metrics standards defined

Implementing Databases (5)

Rat Genome Database
The Rat Genome Database is the premier site for genetic, genomic, phenotype, and disease data generated from rat research. It provides easy access to corresponding human and mouse data for cross-species comparison and its comprehensive data and innovative software tools make it a valuable resource for researchers worldwide.

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.

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.

Implementing Policies

This record is not implemented by any policy.

Credit

Record Maintainer

This record is in need of a maintainer. If you login, you'll be able to claim this record.

Funds

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

Maintains

Medical College of Wisconsin (MCW), Wisconsin, USA (University) Lead

Grant Number(s)

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

Pathway Ontology

We need your help!

Developed by

Contact Us

About FAIRsharing