WikiPathways SPARQL Endpoint

WikiPathways was established to facilitate the contribution and maintenance of pathway information by the biology community. WikiPathways is an open, collaborative platform dedicated to the curation of biological pathways. WikiPathways thus presents a new model for pathway databases that enhances and complements ongoing efforts, such as KEGG, Reactome and Pathway Commons. Building on the same MediaWiki software that powers Wikipedia, we added a custom graphical pathway editing tool and integrated databases covering major gene, protein, and small-molecule systems. The familiar web-based format of WikiPathways greatly reduces the barrier to participate in pathway curation. More importantly, the open, public approach of WikiPathways allows for broader participation by the entire community, ranging from students to senior experts in each field. This approach also shifts the bulk of peer review, editorial curation, and maintenance to the community.

For end-users
For developers
Type:
Database / data source
Categories:
Knowledge bases
Applicability domain:
Bioinformatics
Topic:
Information extraction
Biological area:
Acute toxicity, Carcinogenicity, Mutagenicity, Genotoxicity, Skin sensitisation, Omics, Transcriptomics
Targeted industry:
Chemicals, Nanotechnology, Drugs, Cosmetics, Food, Other consumer products
Targeted users:
Software Developers, Risk assessors, Researchers, Students
Relevant OpenRiskNet case study:
AOPLink - Identification and Linking of Data related to AOPWiki

Provided by:
Maastricht University
Licence:
Apache 2.0 (None)
Login required:
No
Implementation status:
Available as web service
Integration status:
Integration in progress
Service integration operations completed:
Utilises the OpenRiskNet APIs to ensure that each service is accessible to our proposed interoperability layer.
Is annotated according to the semantic interoperability layer concept using defined ontologies.
Is containerised for easy deployment in virtual environments of OpenRiskNet instances.
Has documented scientific and technical background.
Is deployed into the OpenRiskNet reference environment.
Is listed in the OpenRiskNet discovery services.
Is listed in other central repositories like eInfraCentral, bio.tools and TeSS (ELIXIR).
Provides legal and ethical statements on how the service can be used.

Resources & Training

Peer-reviewed publication
Introducing WikiPathways as a data-source to support Adverse Outcome Pathways for regulatory risk assessment of chemicals and nanomaterials
Marvin Martens, Tim Verbruggen, Penny Nymark, Roland Grafström, Lyle D. Burgoon, Hristo Aladjov, Fernando Torres Andón, Chris T. Evelo, Egon L. Willighagen
4 Dec 2018
Abstract:
A paradigm shift is taking place in risk assessment to replace animal models, reduce the number of economic resources, and refine the methodologies to test the growing number of chemicals and nanomaterials. Therefore, approaches such as transcriptomics, proteomics, and metabolomics have become valuable tools in toxicological research, and are finding their way into regulatory toxicity. One promising framework to bridge the gap between the molecular-level measurements and risk assessment is the concept of Adverse Outcome Pathways (AOPs). These pathways comprise mechanistic knowledge and connect biological events from a molecular level towards an adverse effect outcome after exposure to a chemical. However, the implementation of omics-based approaches in the AOPs and their acceptance by the risk assessment community is still a challenge.
Related services:
WikiPathways SPARQL Endpoint

Published in: Frontiers in Genetics
Publisher: Frontiers
Target audience: Risk assessors, Researchers, Regulators, Bioinformaticians
Organisations involved: UM
Peer-reviewed publication