How to develop a drug target ontology

KNowledge acquisition and representation methodology (KNARM)

Hande Küçük McGinty, Ubbo E Visser, Stephan C Schuerer

Research output: Chapter in Book/Report/Conference proceedingChapter

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.

Original languageEnglish (US)
Title of host publicationMethods in Molecular Biology
PublisherHumana Press Inc.
Pages49-69
Number of pages21
DOIs
StatePublished - Jan 1 2019

Publication series

NameMethods in Molecular Biology
Volume1939
ISSN (Print)1064-3745

Fingerprint

Biological Science Disciplines
Semantics
Pharmaceutical Preparations
Information Storage and Retrieval
Drug Discovery
Research
Genes

Keywords

  • Big data
  • Drug target ontology
  • KNARM
  • Knowledge acquisition
  • Ontology
  • Semantic model
  • Semantic web

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics

Cite this

Küçük McGinty, H., Visser, U. E., & Schuerer, S. C. (2019). How to develop a drug target ontology: KNowledge acquisition and representation methodology (KNARM). In Methods in Molecular Biology (pp. 49-69). (Methods in Molecular Biology; Vol. 1939). Humana Press Inc.. https://doi.org/10.1007/978-1-4939-9089-4_4

How to develop a drug target ontology : KNowledge acquisition and representation methodology (KNARM). / Küçük McGinty, Hande; Visser, Ubbo E; Schuerer, Stephan C.

Methods in Molecular Biology. Humana Press Inc., 2019. p. 49-69 (Methods in Molecular Biology; Vol. 1939).

Research output: Chapter in Book/Report/Conference proceedingChapter

Küçük McGinty, H, Visser, UE & Schuerer, SC 2019, How to develop a drug target ontology: KNowledge acquisition and representation methodology (KNARM). in Methods in Molecular Biology. Methods in Molecular Biology, vol. 1939, Humana Press Inc., pp. 49-69. https://doi.org/10.1007/978-1-4939-9089-4_4
Küçük McGinty H, Visser UE, Schuerer SC. How to develop a drug target ontology: KNowledge acquisition and representation methodology (KNARM). In Methods in Molecular Biology. Humana Press Inc. 2019. p. 49-69. (Methods in Molecular Biology). https://doi.org/10.1007/978-1-4939-9089-4_4
Küçük McGinty, Hande ; Visser, Ubbo E ; Schuerer, Stephan C. / How to develop a drug target ontology : KNowledge acquisition and representation methodology (KNARM). Methods in Molecular Biology. Humana Press Inc., 2019. pp. 49-69 (Methods in Molecular Biology).
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