WikiPathways (lipid portal)

Resource for (lipid) pathway models

Description

WikiPathways (https://www.wikipathways.org) is a collaborative database platform to collect and curate biological pathway models by the research community, embracing open science approaches. A dedicated portal (http://lipids.wikipathways.org) is available to browse current data, download all lipid pathways for analysis (in PathVisio or Cytsocape), access the content through semantic web technologies (RDF SPARQL endpoint) or programming interface (API). Pathways are available for human (Homo sapiens) and mouse (Mus musculus) species and can be converted to other species (to integrate with other -omics data).

Technical Information

Website:
https://www.wikipathways.org/index.php/Download_Pathways

Publications:
PMID:33211851

Documentation:
http://help.wikipathways.org/

Download / Web-service:
https://www.wikipathways.org/index.php/Download_Pathways

Source code:
https://github.com/wikipathways/wikipathways.org

Programming languages:
R

Platforms:
Windows, linux, macOS

Input formats:
GPML

Output formats:
GPML, RDF, XGMML, GMT, TXT, BioPAX, SBGN, SBML, PNG, SVG, PDF

Interface:
Web platform, GUI, CLI, Desktop

Licence:
CC-0 for pathway model content

Sections

Section 7.3 — Pathway and Network Solutions

Species covered:
Human, mouse (and >20 other, not all covering lipids)

Data visualisation:
Interactive pathway graphs comprising involved lipids and genes/proteins

Visualisation export:
Yes

Pathway mapping:
Pathway browsing, searchable by species, keywords.

Pathway mapping strategy:
Pathway browsing, searchable by species, keywords.

Pathway editing:
No

Available biopathways:
Lipid metabolic pathways including lipid biosynthesis and remodelling (e.g. sphingolipid metabolism)

Links to related genes/proteins:
related genes/proteins with links to UniProtKB, GO, WikiGenes identifiers

Up/down regulation on maps:
No

Direct projection of identification results:
No