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How to Develop a Drug Target Ontology: KNowledge Acquisition and Representation Methodology (KNARM)

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Bioinformatics and Drug Discovery

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1939))

Abstract

Technological advancements in many fields have led to huge increases in data production, including data volume, diversity, and the speed at which new data is becoming available. In accordance with this, there is a lack of conformity in the ways data is interpreted. This era of “big data” provides unprecedented opportunities for data-driven research and “big picture” models. However, in-depth analyses—making use of various data types and data sources and extracting knowledge—have become a more daunting task. This is especially the case in life sciences where simplification and flattening of diverse data types often lead to incorrect predictions. Effective applications of big data approaches in life sciences require better, knowledge-based, semantic models that are suitable as a framework for big data integration, while avoiding oversimplifications, such as reducing various biological data types to the gene level. A huge hurdle in developing such semantic knowledge models, or ontologies, is the knowledge acquisition bottleneck. Automated methods are still very limited, and significant human expertise is required. In this chapter, we describe a methodology to systematize this knowledge acquisition and representation challenge, termed KNowledge Acquisition and Representation Methodology (KNARM). We then describe application of the methodology while implementing the Drug Target Ontology (DTO). We aimed to create an approach, involving domain experts and knowledge engineers, to build useful, comprehensive, consistent ontologies that will enable big data approaches in the domain of drug discovery, without the currently common simplifications.

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Acknowledgments and Funding

This work was supported by NIH grants U54CA189205 (Illuminating the Druggable Genome Knowledge Management Center, IDG-KMC), U24TR002278 (Illuminating the Druggable Genome Resource Dissemination and Outreach Center, IDG-RDOC), U54HL127624 (BD2K LINCS Data Coordination and Integration Center, DCIC), and U01LM012630-02 (BD2K, Enhancing the efficiency and effectiveness of digital curation for biomedical “big data ”). The IDG-KMC and IDG-RDOC (http://druggablegenome.net/) are components of the Illuminating the Druggable Genome (IDG) project (https://commonfund.nih.gov/idg) awarded by the National Cancer Institute (NCI) and National Center for Advancing Translational Sciences (NCATS), respectively. The BD2K LINC DCIC is awarded by the National Heart, Lung, and Blood Institute through funds provided by the trans-NIH Library of Integrated Network-Based Cellular Signatures (LINCS ) Program (http://www.lincsproject.org/) and the trans-NIH Big Data to Knowledge (BD2K) initiative (https://commonfund.nih.gov/bd2k). IDG, LINCS, and BD2K are NIH Common Fund projects.

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Authors and Affiliations

  1. Department of Computer Science, University of Miami, Coral Gables, FL, USA

    Hande Küçük McGinty & Ubbo Visser

  2. Collaborative Drug Discovery, Inc., Burlingame, CA, USA

    Hande Küçük McGinty

  3. Department of Molecular and Cellular Pharmacology, Miller School of Medicine, University of Miami, Miami, FL, USA

    Stephan Schürer

  4. Center for Computational Science, University of Miami, Coral Gables, FL, USA

    Stephan Schürer

Authors
  1. Hande Küçük McGinty
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  2. Ubbo Visser
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  3. Stephan Schürer
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Corresponding author

Correspondence to Stephan Schürer .

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Editors and Affiliations

  1. Department of Pathology, University of New Mexico, Albuquerque, NM, USA

    Richard S. Larson

  2. Department of Internal Medicine, University of New Mexico, Albuquerque, NM, USA

    Tudor I. Oprea

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Küçük McGinty, H., Visser, U., Schürer, S. (2019). How to Develop a Drug Target Ontology: KNowledge Acquisition and Representation Methodology (KNARM). In: Larson, R., Oprea, T. (eds) Bioinformatics and Drug Discovery. Methods in Molecular Biology, vol 1939. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-9089-4_4

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  • DOI: https://doi.org/10.1007/978-1-4939-9089-4_4

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  • Publisher Name: Humana Press, New York, NY

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