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
Publications:
PMID:33211851
Training datasets:
Documentation and user guide:
Download / Web-service link:
Source code repository:
Programming languages:
R
Platforms:
Windows,
Linux,
MacOS
Output formats:
GPML,
For data analysis
RDF,
For data analysis
XGMML,
For data analysis
GMT,
For data analysis
TXT,
For data analysis
BioPAX,
For modeling languages
SBGN,
For modeling languages
SBML,
For modeling languages
PNG,
SVG,
PDF
Input formats:
GPML
Graphical pathway markup language
Web platform:
Yes
Desktop client:
Yes
CLI:
Yes
API/SPARQL Endpoint
GUI:
Yes
License:
CC-0 for pathway model content
Tasks
7.3)
Pathway and network solutions
Data visualization:
Interactive pathway graphs comprising involved lipids and genes/proteins
Links to other databases:
LIPID MAPS LMSD,
CAS,
ChEBI,
Chemspider,
HMDB,
InChiKey,
PubChem,
Wikidata
Links to related genes proteins:
Related genes/proteins with links to UniProtKB, GO, WikiGenes identifiers
Pathway mapping strategy:
Pathway browsing, searchable by species, keywords.
Pathway editing:
Via PathVisio
Covered species:
Human, mouse (and >20 other, not all covering lipids)
Available biopathways:
Lipid metabolic pathways including lipid biosynthesis and remodelling (e.g. sphingolipid metabolism)
Input style:
LIPID MAPS, ChEBI, HMDB