Symphonies of metabolomics DOI Creative Commons
Denise Slenter

Published: Jan. 1, 2024

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

Language: Английский

Unveiling the chemical complexity of food-risk components: A comprehensive data resource guide in 2024 DOI Creative Commons
Dachuan Zhang, Dongliang Liu,

Jiayi Jing

et al.

Trends in Food Science & Technology, Journal Year: 2024, Volume and Issue: 148, P. 104513 - 104513

Published: April 26, 2024

With the influence of climate change, environmental pollution, industrial development, and new agricultural practices, increasing amounts chemical substances with potential risks—both anthropogenic biogenic—enter food supply chain ultimately affect human health, entailing challenges to safety security. Although some food-risk components (FRCs) have been accessed regulated, toxicity exposure level numerous detected in remain unknown, leaving questions on their effect safety. Therefore, multiple databases emerging FRCs constructed aid risk assessment, regulation, communication; however, focus areas, data content, quality, accessibility not systematically summarized, which hinders development applications data-driven methods field. The major objective this review is comprehensively introduce representative FRC different along presentation, quality availability, successful applications. Over past decades, over 50 released widely used hazard identification, prediction, contributing significantly scientific research, policymaking, education. However, our analysis unveils persistent such as delayed updates, concerns, reproducibility issues, suboptimal inadequate coverage underdeveloped regions. To address these shortcomings, we propose an initiative aimed at enhancing future FRC-related resources, prioritizing principles findability, accessibility, interoperability, reusability. Additionally, highlight strategies, e.g., natural language processing, cheminformatics, suspect non-targeted analysis, genome mining, for detection outside existing databases. By embracing initiatives lay groundwork a robust framework facilitating enhanced assessment informed decision-making face evolving challenges.

Language: Английский

Citations

5
Knowledge graph and its application in the study of neurological and mental disorders DOI Creative Commons
Qizheng Wang, Fan Yang, Quan Li

et al.

Frontiers in Psychiatry, Journal Year: 2025, Volume and Issue: 16

Published: March 18, 2025

Neurological disorders (e.g., Alzheimer's disease and Parkinson's disease) mental depression anxiety), pose huge challenges to global public health. The pathogenesis of these diseases can usually be attributed many factors, such as genetic, environmental socioeconomic status, which make the diagnosis treatment difficult. As research on advances, so does body medical data. accumulation data provides unique opportunities for basic clinical study diseases, but vast diverse nature also it difficult physicians researchers precisely extract information utilize in their work. A powerful tool necessary knowledge from large amounts is graph (KG). KG, an organized form information, has great potential neurological when paired with big deep learning technologies. In this study, we reviewed application KGs common recent years. We discussed current state graphs, highlighting obstacles constraints that still need overcome.

Language: Английский

Citations

0
Symphonies of metabolomics DOI Creative Commons
Denise Slenter

Published: Jan. 1, 2024

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

Language: Английский

Citations

1