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      The IUPHAR/BPS Guide to PHARMACOLOGY in 2024

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          Abstract

          The IUPHAR/BPS Guide to PHARMACOLOGY (GtoPdb; https://www.guidetopharmacology.org) is an open-access, expert-curated, online database that provides succinct overviews and key references for pharmacological targets and their recommended experimental ligands. It includes over 3039 protein targets and 12 163 ligand molecules, including approved drugs, small molecules, peptides and antibodies. Here, we report recent developments to the resource and describe expansion in content over the six database releases made during the last two years. The database update section of this paper focuses on two areas relating to important global health challenges. The first, SARS-CoV-2 COVID-19, remains a major concern and we describe our efforts to expand the database to include a new family of coronavirus proteins. The second area is antimicrobial resistance, for which we have extended our coverage of antibacterials in partnership with AntibioticDB, a collaboration that has continued through support from GARDP. We discuss other areas of curation and also focus on our external links to resources such as PubChem that bring important synergies to the resources.

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          Most cited references46

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          The FAIR Guiding Principles for scientific data management and stewardship

          There is an urgent need to improve the infrastructure supporting the reuse of scholarly data. A diverse set of stakeholders—representing academia, industry, funding agencies, and scholarly publishers—have come together to design and jointly endorse a concise and measureable set of principles that we refer to as the FAIR Data Principles. The intent is that these may act as a guideline for those wishing to enhance the reusability of their data holdings. Distinct from peer initiatives that focus on the human scholar, the FAIR Principles put specific emphasis on enhancing the ability of machines to automatically find and use the data, in addition to supporting its reuse by individuals. This Comment is the first formal publication of the FAIR Principles, and includes the rationale behind them, and some exemplar implementations in the community.
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            Global burden of bacterial antimicrobial resistance in 2019: a systematic analysis

            (2022)
            Summary Background Antimicrobial resistance (AMR) poses a major threat to human health around the world. Previous publications have estimated the effect of AMR on incidence, deaths, hospital length of stay, and health-care costs for specific pathogen–drug combinations in select locations. To our knowledge, this study presents the most comprehensive estimates of AMR burden to date. Methods We estimated deaths and disability-adjusted life-years (DALYs) attributable to and associated with bacterial AMR for 23 pathogens and 88 pathogen–drug combinations in 204 countries and territories in 2019. We obtained data from systematic literature reviews, hospital systems, surveillance systems, and other sources, covering 471 million individual records or isolates and 7585 study-location-years. We used predictive statistical modelling to produce estimates of AMR burden for all locations, including for locations with no data. Our approach can be divided into five broad components: number of deaths where infection played a role, proportion of infectious deaths attributable to a given infectious syndrome, proportion of infectious syndrome deaths attributable to a given pathogen, the percentage of a given pathogen resistant to an antibiotic of interest, and the excess risk of death or duration of an infection associated with this resistance. Using these components, we estimated disease burden based on two counterfactuals: deaths attributable to AMR (based on an alternative scenario in which all drug-resistant infections were replaced by drug-susceptible infections), and deaths associated with AMR (based on an alternative scenario in which all drug-resistant infections were replaced by no infection). We generated 95% uncertainty intervals (UIs) for final estimates as the 25th and 975th ordered values across 1000 posterior draws, and models were cross-validated for out-of-sample predictive validity. We present final estimates aggregated to the global and regional level. Findings On the basis of our predictive statistical models, there were an estimated 4·95 million (3·62–6·57) deaths associated with bacterial AMR in 2019, including 1·27 million (95% UI 0·911–1·71) deaths attributable to bacterial AMR. At the regional level, we estimated the all-age death rate attributable to resistance to be highest in western sub-Saharan Africa, at 27·3 deaths per 100 000 (20·9–35·3), and lowest in Australasia, at 6·5 deaths (4·3–9·4) per 100 000. Lower respiratory infections accounted for more than 1·5 million deaths associated with resistance in 2019, making it the most burdensome infectious syndrome. The six leading pathogens for deaths associated with resistance (Escherichia coli, followed by Staphylococcus aureus, Klebsiella pneumoniae, Streptococcus pneumoniae, Acinetobacter baumannii, and Pseudomonas aeruginosa) were responsible for 929 000 (660 000–1 270 000) deaths attributable to AMR and 3·57 million (2·62–4·78) deaths associated with AMR in 2019. One pathogen–drug combination, meticillin-resistant S aureus, caused more than 100 000 deaths attributable to AMR in 2019, while six more each caused 50 000–100 000 deaths: multidrug-resistant excluding extensively drug-resistant tuberculosis, third-generation cephalosporin-resistant E coli, carbapenem-resistant A baumannii, fluoroquinolone-resistant E coli, carbapenem-resistant K pneumoniae, and third-generation cephalosporin-resistant K pneumoniae. Interpretation To our knowledge, this study provides the first comprehensive assessment of the global burden of AMR, as well as an evaluation of the availability of data. AMR is a leading cause of death around the world, with the highest burdens in low-resource settings. Understanding the burden of AMR and the leading pathogen–drug combinations contributing to it is crucial to making informed and location-specific policy decisions, particularly about infection prevention and control programmes, access to essential antibiotics, and research and development of new vaccines and antibiotics. There are serious data gaps in many low-income settings, emphasising the need to expand microbiology laboratory capacity and data collection systems to improve our understanding of this important human health threat. Funding Bill & Melinda Gates Foundation, Wellcome Trust, and Department of Health and Social Care using UK aid funding managed by the Fleming Fund.
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              UniProt: the Universal Protein Knowledgebase in 2023

              (2022)
              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 publication we describe enhancements made to our data processing pipeline and to our website to adapt to an ever-increasing information content. The number of sequences in UniProtKB has risen to over 227 million and we are working towards including a reference proteome for each taxonomic group. We continue to extract detailed annotations from the literature to update or create reviewed entries, while unreviewed entries are supplemented with annotations provided by automated systems using a variety of machine-learning techniques. In addition, the scientific community continues their contributions of publications and annotations to UniProt entries of their interest. Finally, we describe our new website ( https://www.uniprot.org/ ), designed to enhance our users’ experience and make our data easily accessible to the research community. This interface includes access to AlphaFold structures for more than 85% of all entries as well as improved visualisations for subcellular localisation of proteins.
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                Author and article information

                Contributors
                Journal
                Nucleic Acids Res
                Nucleic Acids Res
                nar
                Nucleic Acids Research
                Oxford University Press
                0305-1048
                1362-4962
                05 January 2024
                28 October 2023
                28 October 2023
                : 52
                : D1
                : D1438-D1449
                Affiliations
                Centre for Discovery Brain Science, Deanery of Biomedical Sciences, University of Edinburgh , Edinburgh EH8 9XD, UK
                Centre for Discovery Brain Science, Deanery of Biomedical Sciences, University of Edinburgh , Edinburgh EH8 9XD, UK
                Centre for Discovery Brain Science, Deanery of Biomedical Sciences, University of Edinburgh , Edinburgh EH8 9XD, UK
                Centre for Discovery Brain Science, Deanery of Biomedical Sciences, University of Edinburgh , Edinburgh EH8 9XD, UK
                School of Life Sciences, University of Nottingham Medical School , Nottingham NG7 2UH, UK
                Experimental Medicine and Immunotherapeutics, University of Cambridge , Cambridge CB2 0QQ, UK
                Spedding Research Solutions SAS , Le Vésinet 78110, France
                Centre for Discovery Brain Science, Deanery of Biomedical Sciences, University of Edinburgh , Edinburgh EH8 9XD, UK
                Author notes
                To whom correspondence should be addressed. Tel: +44 131 650 3729; Email: simon.harding@ 123456ed.ac.uk

                The authors wish it to be known that, in their opinion, the first 4 authors should be regarded as joint First Authors.

                Author information
                https://orcid.org/0000-0002-9262-8318
                Article
                gkad944
                10.1093/nar/gkad944
                10767925
                37897341
                f4b7eee3-db86-4f1f-bd65-e9cb092dcae2
                © The Author(s) 2023. Published by Oxford University Press on behalf of Nucleic Acids Research.

                This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                : 18 October 2023
                : 09 October 2023
                : 14 September 2023
                Page count
                Pages: 12
                Funding
                Funded by: International Union of Basic and Clinical Pharmacology, DOI 10.13039/100009703;
                Funded by: British Pharmacological Society, DOI 10.13039/501100000559;
                Award ID: MED791
                Funded by: GARDP;
                Award ID: c-12440474
                Funded by: Medicines for Malaria Venture, DOI 10.13039/501100004167;
                Award ID: CT-5535
                Funded by: Antibiotic Research UK, DOI 10.13039/100011694;
                Award ID: ANTSRG 02/2019
                Funded by: Wellcome Trust, DOI 10.13039/100010269;
                Award ID: 108420/Z/15/Z
                Funded by: American Society for Pharmacology and Experimental Therapeutics, DOI 10.13039/100005497;
                Funded by: Laboratoires Servier, DOI 10.13039/501100011725;
                Funded by: The University of Edinburgh, DOI 10.13039/501100000848;
                Categories
                AcademicSubjects/SCI00010
                Database Issue

                Genetics
                Genetics

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