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      Advancing drug safety science by integrating molecular knowledge with post‐marketing adverse event reports

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          Abstract

          Promising drug development efforts may frequently fail due to unintended adverse reactions. Several methods have been developed to analyze such data, aiming to improve pharmacovigilance and drug safety. In this work, we provide a brief review of key directions to quantitatively analyzing adverse events and explore the potential of augmenting these methods using additional molecular data descriptors. We argue that molecular expansion of adverse event data may provide a path to improving the insights gained through more traditional pharmacovigilance approaches. Examples include the ability to assess statistical relevance with respect to underlying biomolecular mechanisms, the ability to generate plausible causative hypotheses and/or confirmation where possible, the ability to computationally study potential clinical trial designs and/or results, as well as the further provision of advanced features incorporated in innovative methods, such as machine learning. In summary, molecular data expansion provides an elegant way to extend mechanistic modeling, systems pharmacology, and patient‐centered approaches for the assessment of drug safety. We anticipate that such advances in real‐world data informatics and outcome analytics will help to better inform public health, via the improved ability to prospectively understand and predict various types of drug‐induced molecular perturbations and adverse events.

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          Most cited references81

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          KEGG: kyoto encyclopedia of genes and genomes.

          M Kanehisa (2000)
          KEGG (Kyoto Encyclopedia of Genes and Genomes) is a knowledge base for systematic analysis of gene functions, linking genomic information with higher order functional information. The genomic information is stored in the GENES database, which is a collection of gene catalogs for all the completely sequenced genomes and some partial genomes with up-to-date annotation of gene functions. The higher order functional information is stored in the PATHWAY database, which contains graphical representations of cellular processes, such as metabolism, membrane transport, signal transduction and cell cycle. The PATHWAY database is supplemented by a set of ortholog group tables for the information about conserved subpathways (pathway motifs), which are often encoded by positionally coupled genes on the chromosome and which are especially useful in predicting gene functions. A third database in KEGG is LIGAND for the information about chemical compounds, enzyme molecules and enzymatic reactions. KEGG provides Java graphics tools for browsing genome maps, comparing two genome maps and manipulating expression maps, as well as computational tools for sequence comparison, graph comparison and path computation. The KEGG databases are daily updated and made freely available (http://www. genome.ad.jp/kegg/).
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            STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets

            Abstract Proteins and their functional interactions form the backbone of the cellular machinery. Their connectivity network needs to be considered for the full understanding of biological phenomena, but the available information on protein–protein associations is incomplete and exhibits varying levels of annotation granularity and reliability. The STRING database aims to collect, score and integrate all publicly available sources of protein–protein interaction information, and to complement these with computational predictions. Its goal is to achieve a comprehensive and objective global network, including direct (physical) as well as indirect (functional) interactions. The latest version of STRING (11.0) more than doubles the number of organisms it covers, to 5090. The most important new feature is an option to upload entire, genome-wide datasets as input, allowing users to visualize subsets as interaction networks and to perform gene-set enrichment analysis on the entire input. For the enrichment analysis, STRING implements well-known classification systems such as Gene Ontology and KEGG, but also offers additional, new classification systems based on high-throughput text-mining as well as on a hierarchical clustering of the association network itself. The STRING resource is available online at https://string-db.org/.
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              UniProt: the universal protein knowledgebase in 2021

              Abstract The aim of the UniProt Knowledgebase is to provide users with a comprehensive, high-quality and freely accessible set of protein sequences annotated with functional information. In this article, we describe significant updates that we have made over the last two years to the resource. The number of sequences in UniProtKB has risen to approximately 190 million, despite continued work to reduce sequence redundancy at the proteome level. We have adopted new methods of assessing proteome completeness and quality. We continue to extract detailed annotations from the literature to add to reviewed entries and supplement these in unreviewed entries with annotations provided by automated systems such as the newly implemented Association-Rule-Based Annotator (ARBA). We have developed a credit-based publication submission interface to allow the community to contribute publications and annotations to UniProt entries. We describe how UniProtKB responded to the COVID-19 pandemic through expert curation of relevant entries that were rapidly made available to the research community through a dedicated portal. UniProt resources are available under a CC-BY (4.0) license via the web at https://www.uniprot.org/.
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                Author and article information

                Contributors
                thsoldat@gmail.com
                sarahkim@cop.ufl.edu
                SSchmidt@cop.ufl.edu
                LLesko@cop.ufl.edu
                david.jackson@molecularhealth.com
                Journal
                CPT Pharmacometrics Syst Pharmacol
                CPT Pharmacometrics Syst Pharmacol
                10.1002/(ISSN)2163-8306
                PSP4
                CPT: Pharmacometrics & Systems Pharmacology
                John Wiley and Sons Inc. (Hoboken )
                2163-8306
                20 February 2022
                May 2022
                : 11
                : 5 ( doiID: 10.1002/psp4.v11.5 )
                : 540-555
                Affiliations
                [ 1 ] Molecular Health GmbH Heidelberg Germany
                [ 2 ] Department of Pharmaceutics Center for Pharmacometrics and Systems Pharmacology University of Florida Orlando Florida USA
                Author notes
                [*] [* ] Correspondence

                David B. Jackson, Molecular Health GmbH, Kurfürsten‑Anlage 21, 69115 Heidelberg, Germany.

                Email: david.jackson@ 123456molecularhealth.com

                Author information
                https://orcid.org/0000-0001-6051-6605
                https://orcid.org/0000-0002-9179-0735
                Article
                PSP412765
                10.1002/psp4.12765
                9124355
                35143713
                395a3c77-9a1e-47cd-8be5-d9fe75842e03
                © 2022 The Authors. CPT: Pharmacometrics & Systems Pharmacology published by Wiley Periodicals LLC on behalf of American Society for Clinical Pharmacology and Therapeutics.

                This is an open access article under the terms of the http://creativecommons.org/licenses/by-nc/4.0/ License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited and is not used for commercial purposes.

                History
                : 20 December 2021
                : 30 September 2021
                : 17 January 2022
                Page count
                Figures: 2, Tables: 4, Pages: 16, Words: 8156
                Categories
                Review
                Reviews
                Review
                Custom metadata
                2.0
                May 2022
                Converter:WILEY_ML3GV2_TO_JATSPMC version:6.1.6 mode:remove_FC converted:22.05.2022

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