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PharmGKB, an Integrated Resource of Pharmacogenomic Knowledge.

ABSTRACT: The Pharmacogenomics Knowledgebase (PharmGKB) is an integrated online knowledge resource for the understanding of how genetic variation contributes to variation in drug response. Our focus includes not only pharmacogenomic information useful for clinical implementation (e.g., drug dosing guidelines and annotated drug labels), but also information to catalyze scientific research and drug discovery (e.g., variant-drug annotations and drug-centered pathways). As of April 2021, the annotated content of PharmGKB spans 715 drugs, 1761 genes, 227 diseases, 165 clinical guidelines, and 784 drug labels. We have manually curated data from more than 9000 published papers to generate the content of PharmGKB. Recently, we have also implemented an automated natural language processing (NLP) tool to broaden our coverage of the pharmacogenomic literature. This article contains a basic protocol describing how to navigate the PharmGKB website to retrieve information on how genes and genetic variations affect drug efficacy and toxicity. It also includes a protocol on how to use PharmGKB to facilitate interpretation of findings for a pharmacogenomic variant genotype or metabolizer phenotype. PharmGKB is freely available at http://www.pharmgkb.org. © 2021 Wiley Periodicals LLC. Basic Protocol 1: Navigating the homepage of PharmGKB and searching by drug Basic Protocol 2: Using PharmGKB to facilitate interpretation of pharmacogenomic variant genotypes or metabolizer phenotypes.

SUBMITTER: Gong L

PROVIDER: S-EPMC8650697 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:Interstitial lung diseases (ILDs) are a diverse group of ?200 acute and chronic pulmonary disorders that are characterized by variable amounts of inflammation, fibrosis and architectural distortion with substantial morbidity and mortality. Inaccurate and delayed diagnoses increase the risk, especially in developing countries. Studies have indicated the significant roles of genetic elements in ILDs pathogenesis. Therefore, the first genetic knowledge resource, ILDgenDB, has been developed with an objective to provide ILDs genetic data and their integrated analyses for the better understanding of disease pathogenesis and identification of diagnostics-based biomarkers. This resource contains literature-curated disease candidate genes (DCGs) enriched with various regulatory elements that have been generated using an integrated bioinformatics workflow of databases searches, literature-mining and DCGs-microRNA (miRNAs)-single nucleotide polymorphisms (SNPs) association analyses. To provide statistical significance to disease-gene association, ILD-specificity index and hypergeomatric test scores were also incorporated. Association analyses of miRNAs, SNPs and pathways responsible for the pathogenesis of different sub-classes of ILDs were also incorporated. Manually verified 299 DCGs and their significant associations with 1932 SNPs, 2966 miRNAs and 9170 miR-polymorphisms were also provided. Furthermore, 216 literature-mined and proposed biomarkers were identified. The ILDgenDB resource provides user-friendly browsing and extensive query-based information retrieval systems. Additionally, this resource also facilitates graphical view of predicted DCGs-SNPs/miRNAs and literature associated DCGs-ILDs interactions for each ILD to facilitate efficient data interpretation. Outcomes of analyses suggested the significant involvement of immune system and defense mechanisms in ILDs pathogenesis. This resource may potentially facilitate genetic-based disease monitoring and diagnosis.Database URL: http://14.139.240.55/ildgendb/index.php.

Project description:BackgroundThe introduction of the WHO's Integrated Management of Childhood Illnesses (IMCI) guidelines in the mid-1990s contributed to global reductions in under-five mortality. However, issues in quality of care have been reported. We aimed to determine resource availability and healthcare worker knowledge of IMCI guidelines in two districts in Malawi.MethodsWe conducted a mixed-methods study, including health facility audits to record availability and functionality of essential IMCI equipment and availability of IMCI drugs, healthcare provider survey and focus group discussions (FGDs) with facility staff. The study was conducted between January and April 2019 in Mchinji (central region) and Zomba (southern region) districts. Quantitative data were described using proportions and χ2 tests; linear regression was conducted to explore factors associated with IMCI knowledge. Qualitative data were analysed using a pragmatic framework approach. Qualitative and quantitative data were analysed and presented separately.ResultsForty-seven health facilities and 531 healthcare workers were included. Lumefantrine-Artemether and cotrimoxazole were the most available drugs (98% and 96%); while amoxicillin tablets and salbutamol nebuliser solution were the least available (28% and 36%). Respiratory rate timers were the least available piece of equipment, with only 8 (17%) facilities having a functional device. The mean IMCI knowledge score was 3.96 out of 10, and there was a statistically significant association between knowledge and having received refresher training (coeff: 0.42; 95% CI 0.01 to 0.82). Four themes were identified in the FGDs: IMCI implementation and practice, barriers to IMCI, benefits of IMCI and sustainability.ConclusionWe found key gaps in IMCI implementation; however, these were not homogenous across facilities, suggesting opportunities to learn from locally adapted IMCI best practices. Improving on-going mentorship, training and supervision should be explored to improve quality of care, and programming which moves away from vertical financing with short-term support, to a more holistic approach with embedded sustainability may address the balance of resources for different conditions.

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PharmGKB, an Integrated Resource of Pharmacogenomic Knowledge.

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