ArticleACS omega2023
OntoPESScan: An Ontology for Potential Energy Surface Scans.
Article in ACS omega, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
What it found
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Who cites it
5 citing papers in PubMed, 12 citations in OpenAlex.
- Inverse Design of Metal-Organic Polyhedra through Molecular Fragmentation and Evolutionary Optimisation.Journal of chemical information and modeling · 2026Article
- Integrative Network Pharmacology, Molecular Docking, and Dynamics Simulations Reveal the Mechanisms ofCurrent issues in molecular biology · 2024Article
- Leveraging Text-to-Text Pretrained Language Models for Question Answering in Chemistry.ACS omega · 2024Article
- Study on the Effect of Cations on the Surface Energy of Nano-SiOMolecules (Basel, Switzerland) · 2024Article
- Chemical Species Ontology for Data Integration and Knowledge Discovery.Journal of chemical information and modeling · 2023Article
Corrections and comments
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Authors and funding
7 authors at 4 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
In this work, a new OntoPESScan ontology is developed for the semantic representation of one-dimensional potential energy surface (PES) scans, a central concept in computational chemistry. This ontology is developed in line with knowledge graph principles and The World Avatar (TWA) project. OntoPESScan is linked to other ontologies for chemistry in TWA, including OntoSpecies, which helps uniquely identify species along the PES and access their properties, and OntoCompChem, which allows the association of potential energy surfaces with quantum chemical calculations and the concepts used to derive them. A force-field fitting agent is also developed that makes use of the information in the OntoPESScan ontology to fit force fields to reactive surfaces of interest on the fly by making use of the empirical valence bond methodology. This agent is demonstrated to successfully parametrize two cases, namely, a PES scan on ethanol and a PES scan on a localized π-radical PAH hypothesized to play a role in soot formation during combustion. OntoPESScan is an extension to the capabilities of TWA and, in conjunction with potential further ontological support for molecular dynamics and reactions, will further progress toward an open, continuous, and self-growing knowledge graph for chemistry.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.