WikiPathways: a multifaceted pathway database bridging metabolomics to other omics research

A transcriptomics data-driven gene space accurately predicts liver cytopathology and drug-induced liver injury

(2017) Pekka Kohonen et al.   Nature Communications

Bayesian model of signal rewiring reveals mechanisms of gene dysregulation in acquired drug resistance in breast cancer

(2017) A. K. M. Azad et al.   PLoS One

Identifying known unknowns using the US EPA’s CompTox Chemistry Dashboard

(2016) Andrew D. McEachran et al.   ANALYTICAL AND BIOANALYTICAL CHEMISTRY

The metabolome 18 years on: a concept comes of age

(2016) Douglas B. Kell et al.   Metabolomics

Integration of targeted metabolomics and transcriptomics identifies deregulation of phosphatidylcholine metabolism in Huntington’s disease peripheral blood samples

(2016) Anastasios Mastrokolias et al.   Metabolomics

KEGG: new perspectives on genomes, pathways, diseases and drugs

(2016) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Reactome from a WikiPathways Perspective

(2016) Anwesha Bohler et al.   PLoS Computational Biology

Using the Semantic Web for Rapid Integration of WikiPathways with Other Biological Online Data Resources

(2016) Andra Waagmeester et al.   PLoS Computational Biology

The FAIR Guiding Principles for scientific data management and stewardship

(2016) Mark D. Wilkinson et al.   Scientific Data

ChEBI in 2016: Improved services and an expanding collection of metabolites

(2015) Janna Hastings et al.   NUCLEIC ACIDS RESEARCH

WikiPathways: capturing the full diversity of pathway knowledge

(2015) Martina Kutmon et al.   NUCLEIC ACIDS RESEARCH

The Reactome pathway Knowledgebase

(2015) Antonio Fabregat et al.   NUCLEIC ACIDS RESEARCH

PathVisio 3: An Extendable Pathway Analysis Toolbox

(2015) Martina Kutmon et al.   PLoS Computational Biology

The Application of the Open Pharmacological Concepts Triple Store (Open PHACTS) to Support Drug Discovery Research

(2014) Joseline Ratnam et al.   PLoS One

Mining and integration of pathway diagrams from imaging data

(2012) Sergey Kozhenkov et al.   BIOINFORMATICS

MetaboLights—an open-access general-purpose repository for metabolomics studies and associated meta-data

(2012) Kenneth Haug et al.   NUCLEIC ACIDS RESEARCH

The ConsensusPathDB interaction database: 2013 update

(2012) Atanas Kamburov et al.   NUCLEIC ACIDS RESEARCH

The value of data

(2011) Barend Mons et al.   NATURE GENETICS

BioPortal: enhanced functionality via new Web services from the National Center for Biomedical Ontology to access and use ontologies in software applications

(2011) P. L. Whetzel et al.   NUCLEIC ACIDS RESEARCH

The BridgeDb framework: standardized access to gene, protein and metabolite identifier mapping services

(2010) Martijn P van Iersel et al.   BMC BIOINFORMATICS

Biotransformation pathway maps in WikiPathways enable direct visualization of drug metabolism related expression changes

(2010) Danyel G.J. Jennen et al.   DRUG DISCOVERY TODAY

Update of the LIPID MAPS comprehensive classification system for lipids

(2008) Eoin Fahy et al.   JOURNAL OF LIPID RESEARCH

WikiPathways: Pathway Editing for the People

(2008) Alexander R Pico et al.   PLOS BIOLOGY