Reporting biological assay screening results for maximum impact

Bolton, Evan

doi:10.1016/j.ddtec.2015.03.004

Cited by 5 publications

(4 citation statements)

References 25 publications

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“…We have shown how to process samples and managing libraries in IPK herein. In order to allow screening campaigns to find hits or drug candidates from different types of assays, it is essential to provide sufficient information regarding the sample space . The constituency of the library, an indication of the size or number of libraries and management of samples for the assay should be included.…”

Section: Resultsmentioning

confidence: 99%

Strategic Expansion and Management of Chemical Libraries for Drug Discovery

Choi

Lee

et al. 2018

Bulletin Korean Chem Soc

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The extensive chemical space provides options of selecting molecules that are unique and diverse to build a truly custom made screening chemical library. Finding the right compound from a high-throughput screening (HTS) that could be optimized to a drug candidate is no simple task. Selecting meaningful compounds from a multitude of commercially available compounds is critical; over the years Institut Pasteur Korea (IPK), whose mission is to eliminate the global threat of infectious disease, had built a selected chemical library of commercially available and proprietary compounds sensitive to encompass structural diversity aspect. To obtain structural diversity, lead-like Bemis-Murcko substructures were generated from IPK legacy collections, and those compounds with different Bemis-Murcko substructures were selected. Furthermore, structural fingerprints were used to select diverse subsets of compounds. Based on the analyses of whole structures and substructures, we selected a diverse set to utilize against several infectious diseases models provided at IPK. We implemented a strategic approach to managing the chemical library by taking into consideration the stability of compounds while maintaining compounds integrity. Automated liquid handlers were used to compress and replicate the chemical libraries into various concentrations. Emerging infectious diseases are on the rise and unpredictable in the global health landscape; using unique and carefully selected compounds for screening can make a difference in finding our next drug candidate at IPK.

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Section: Resultsmentioning

confidence: 99%

Strategic Expansion and Management of Chemical Libraries for Drug Discovery

Choi

Lee

et al. 2018

Bulletin Korean Chem Soc

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“…The pharmaceutical industry, public and private research institutions, peer‐reviewed journals, and regulatory agencies have all recognized and responded to this crisis through multiple measures. Recent initiatives include incentivizing transparency, enhancing oversight, and standardizing protocols and reporting measures through open‐access databases and specific guidelines issued by scientific journals (Bolton, 2015; Olsen, 2014; Prescott & Civil, 2013; Reiss, 2017; Worthy, 2015). Table 1 describes several key projects begun toward addressing the reproducibility crisis.…”

Section: Introductionmentioning

confidence: 99%

Introduction to the Use of Linear and Nonlinear Regression Analysis in Quantitative Biological Assays

Jarantow,

Pisors,

Chiu

2023

Current Protocols

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Biological assays are essential tools in biomedical and pharmaceutical research. In simplest terms, such an assay is an analytical method used to measure or predict a response in a biological system in the presence of a given stimulus (e.g., drug). The inherent complexity involved in evaluating a biological system requires the use of rigorous and appropriate tools for data analysis. Linear and nonlinear regression models represent critically important statistical analyses used to define the relationships between variables of interest in biological systems. Recent challenges relating to the reproducibility of published data suggest the absence of standardized and routine use of statistics to support experimental results across a wide range of scientific disciplines. The current situation warrants an introductory review of basic regression concepts using current, practical examples, along with references to in-depth resources. The goal is to provide the necessary information to help standardize the analysis of biological assays in academic research and drug discovery and development, elevating their utility and increasing data transparency and reproducibility.

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“…While these issues with scalability could be described as a relatively minor nuisance in a small laboratory, the field of drug discovery has lately been undergoing a renaissance of open data (Clark, Williams & Ekins, 2015;Hersey, Senger & Overington, 2012;Ecker & Williams-Jones, 2012;Williams, Wilbanks & Ekins, 2012). Services such as PubChem provide a truly massive resource (Helal et al, 2016); PubChem alone provides more than a million unique bioassay descriptions, and is growing rapidly (Bolton, 2015). 1 Such data are supplemented by carefully curated resources like ChEMBL (Gaulton et al, 2012), which are much smaller but have strict quality control mechanisms in place.…”

Section: Introductionmentioning

confidence: 99%

BioAssay Templates for the semantic web

Clark¹,

Litterman²,

Kranz³

et al. 2016

PeerJ Computer Science

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Annotation of bioassay protocols using semantic web vocabulary is a way to make experiment descriptions machine-readable. Protocols are communicated using concise scientific English, which precludes most kinds of analysis by software algorithms. Given the availability of a sufficiently expressive ontology, some or all of the pertinent information can be captured by asserting a series of facts, expressed as semantic web triples (subject, predicate, object). With appropriate annotation, assays can be searched, clustered, tagged and evaluated in a multitude of ways, analogous to other segments of drug discovery informatics. The BioAssay Ontology (BAO) has been previously designed for this express purpose, and provides a layered hierarchy of meaningful terms which can be linked to. Currently the biggest challenge is the issue of content creation: scientists cannot be expected to use the BAO effectively without having access to software tools that make it straightforward to use the vocabulary in a canonical way. We have sought to remove this barrier by: (1) defining a BioAssay Template (BAT) data model; (2) creating a software tool for experts to create or modify templates to suit their needs; and (3) designing a common assay template (CAT) to leverage the most value from the BAO terms. The CAT was carefully assembled by biologists in order to find a balance between the maximum amount of information captured vs. low degrees of freedom in order to keep the user experience as simple as possible. The data format that we use for describing templates and corresponding annotations is the native format of the semantic web (RDF triples), and we demonstrate some of the ways that generated content can be meaningfully queried using the SPARQL language. We have made all of these materials available as open source (http://github.com/cdd/ bioassay-template), in order to encourage community input and use within diverse projects, including but not limited to our own commercial electronic lab notebook products.

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Reporting biological assay screening results for maximum impact

Cited by 5 publications

References 25 publications

Strategic Expansion and Management of Chemical Libraries for Drug Discovery

Strategic Expansion and Management of Chemical Libraries for Drug Discovery

Introduction to the Use of Linear and Nonlinear Regression Analysis in Quantitative Biological Assays

BioAssay Templates for the semantic web

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