» Articles » PMID: 36147662

The Potential of a Data Centred Approach & Knowledge Graph Data Representation in Chemical Safety and Drug Design

Overview
Specialty Biotechnology
Date 2022 Sep 23
PMID 36147662
Authors
Affiliations
Soon will be listed here.
Abstract

Big Data pervades nearly all areas of life sciences, yet the analysis of large integrated data sets remains a major challenge. Moreover, the field of life sciences is highly fragmented and, consequently, so is its data, knowledge, and standards. This, in turn, makes integrated data analysis and knowledge gathering across sub-fields a demanding task. At the same time, the integration of various research angles and data types is crucial for modelling the complexity of organisms and biological processes in a holistic manner. This is especially valid in the context of drug development and chemical safety assessment where computational methods can provide solutions for the urgent need of fast, effective, and sustainable approaches. At the same time, such computational methods require the development of methodologies suitable for an integrated and data centred Big Data view. Here we discuss Knowledge Graphs (KG) as a solution to a data centred analysis approach for drug and chemical development and safety assessment. KGs are knowledge bases, data analysis engines, and knowledge discovery systems all in one, allowing them to be used from simple data retrieval, over meta-analysis to complex predictive and knowledge discovery systems. Therefore, KGs have immense potential to advance the data centred approach, the re-usability, and informativity of data. Furthermore, they can improve the power of analysis, and the complexity of modelled processes, all while providing knowledge in a natively human understandable network data model.

Citing Articles

A curated gene and biological system annotation of adverse outcome pathways related to human health.

Saarimaki L, Fratello M, Pavel A, Korpilahde S, Leppanen J, Serra A Sci Data. 2023; 10(1):409.

PMID: 37355733 PMC: 10290716. DOI: 10.1038/s41597-023-02321-w.

References
1.
Chang A, Jeske L, Ulbrich S, Hofmann J, Koblitz J, Schomburg I . BRENDA, the ELIXIR core data resource in 2021: new developments and updates. Nucleic Acids Res. 2020; 49(D1):D498-D508. PMC: 7779020. DOI: 10.1093/nar/gkaa1025. View

2.
Kuhn M, Letunic I, Jensen L, Bork P . The SIDER database of drugs and side effects. Nucleic Acids Res. 2015; 44(D1):D1075-9. PMC: 4702794. DOI: 10.1093/nar/gkv1075. View

3.
Upreti V, Venkatakrishnan K . Model-Based Meta-Analysis: Optimizing Research, Development, and Utilization of Therapeutics Using the Totality of Evidence. Clin Pharmacol Ther. 2019; 106(5):981-992. DOI: 10.1002/cpt.1462. View

4.
Freires I, Sardi J, de Castro R, Rosalen P . Alternative Animal and Non-Animal Models for Drug Discovery and Development: Bonus or Burden?. Pharm Res. 2016; 34(4):681-686. DOI: 10.1007/s11095-016-2069-z. View

5.
Wang M, Wang H, Liu X, Ma X, Wang B . Drug-Drug Interaction Predictions via Knowledge Graph and Text Embedding: Instrument Validation Study. JMIR Med Inform. 2021; 9(6):e28277. PMC: 8277366. DOI: 10.2196/28277. View