SmartGraph API: Programmatic Knowledge Mining in Network-Pharmacology Setting.

IF 5.6 2区化学 Q1 CHEMISTRY, MEDICINAL

Journal of Chemical Information and Modeling Pub Date : 2024-12-04 DOI:10.1021/acs.jcim.4c00789

Gergely Zahoránszky-Kőhalmi, Brandon Walker, Nathan Miller, Brett Yang, Dhatri V L Penna, Jessica Maine, Timothy Sheils, Ke Wang, Jennifer King, Hythem Sidky, Sridhar Vuyyuru, Jeyaraman Soundarajan, Samuel G Michael, Alexander G Godfrey, Tudor I Oprea

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Abstract

The recent SmartGraph platform facilitates the execution of complex drug-discovery workflows with ease in the network-pharmacology paradigm. However, at the time of its publication we identified the need for the development of an Application Programming Interface (API) that could promote biomedical data integration and hypothesis generation in an automated manner. This need was magnified at the time of the COVID-19 pandemic. This study addresses the absence of such an API. Accordingly, most functionalities of the original platform were implemented within the SmartGraph API. We demonstrate that by using the API it is possible to transform the original semiautomated workflow behind the Neo4COVID19 database to a fully automated one. The availability of the SmartGraph API lends a significant improvement to the programmatic integration of network-pharmacology-oriented knowledge graphs and analytics, as well as predictive functionalities and workflows.

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来源期刊

Journal of Chemical Information and Modeling 化学-化学综合

CiteScore

9.80

自引率

10.70%

发文量

529

审稿时长

1.4 months

期刊介绍： The Journal of Chemical Information and Modeling publishes papers reporting new methodology and/or important applications in the fields of chemical informatics and molecular modeling. Specific topics include the representation and computer-based searching of chemical databases, molecular modeling, computer-aided molecular design of new materials, catalysts, or ligands, development of new computational methods or efficient algorithms for chemical software, and biopharmaceutical chemistry including analyses of biological activity and other issues related to drug discovery. Astute chemists, computer scientists, and information specialists look to this monthly’s insightful research studies, programming innovations, and software reviews to keep current with advances in this integral, multidisciplinary field. As a subscriber you’ll stay abreast of database search systems, use of graph theory in chemical problems, substructure search systems, pattern recognition and clustering, analysis of chemical and physical data, molecular modeling, graphics and natural language interfaces, bibliometric and citation analysis, and synthesis design and reactions databases.