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

Abstract

WikiPathways (wikipathways.org) captures the collective knowledge represented in biological pathways. By providing a database in a curated, machine readable way, omics data analysis and visualization is enabled. WikiPathways and other pathway databases are used to analyze experimental data by research groups in many fields. Due to the open and collaborative nature of the WikiPathways platform, our content keeps growing and is getting more accurate, making WikiPathways a reliable and rich pathway database. Previously, however, the focus was primarily on genes and proteins, leaving many metabolites with only limited annotation. Recent curation efforts focused on improving the annotation of metabolism and metabolic pathways by associating unmapped metabolites with database identifiers and providing more detailed interaction knowledge. Here, we report the outcomes of the continued growth and curation efforts, such as a doubling of the number of annotated metabolite nodes in WikiPathways. Furthermore, we introduce an OpenAPI documentation of our web services and the FAIR (Findable, Accessible, Interoperable and Reusable) annotation of resources to increase the interoperability of the knowledge encoded in these pathways and experimental omics data. New search options, monthly downloads, more links to metabolite databases, and new portals make pathway knowledge more effortlessly accessible to individual researchers and research communities.

Stem cell-derived retinal pigment epithelium from patients with age-related macular degeneration exhibit reduced metabolism and matrix interactions

“…The results indicate that the gene profiling of iPSC‐derived RPE cells from AMD patients were different from normal controls. In RPE cells derived from AMD patients, altered gene expression patterns were related to metabolic and signal transduction pathways . The mRNAs that were significantly lower in AMD samples included voltage‐dependent calcium channel (CACNA1D), epidermal growth factor receptor (EGFR), fibroblast growth factor 14 (FGF14), forkhead box protein O1 (FOXO1), laminin alpha 5 subunit (LAMA5), and transient receptor potential cation channel subfamily V member 4 (TRPV4).…”

Integrative analysis of highly mutated genes in hepatitis B virus‐related hepatic carcinoma

“…Gene ontology (GO) analysis was utilized to identify the molecular functions of enriched highly mutated genes . Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway and WIKI pathway analysis, were carried out to determine the significant biological pathways with the clusters of highly mutated genes. In addition, GO analysis was measured with the g:Profiler online tool as described previously .…”

RNA expression preoperatively and postoperatively following total knee replacement: a pilot study in patients with and without chronic postsurgical pain

“…Biological pathways of the upregulated or downregulated genes were determined by searching WikiPathways (WikiPathways.org) 19. Significance of the genes in the pathways was determined using a Fisher’s exact test of the 2×2 contingency table of the number of overlapping genes in the pathway of the identified genes that passed the filter criteria, the number of non-overlapping genes in the pathway that passed the filter criteria, the number of genes in the pathway that did not pass the filter criteria, and the number of genes not in the pathway that did not pass the filter criteria.…”