Universität zu Köln

Mueller, Bernd, Castro, Leyla Jael ORCID: 0000-0003-3986-0510 and Rebholz-Schuhmann, Dietrich (2022). Ontology-based identification and prioritization of candidate drugs for epilepsy from literature. J. Biomed. Semant., 13 (1). LONDON: BMC. ISSN 2041-1480

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Abstract

Background Drug repurposing can improve the return of investment as it finds new uses for existing drugs. Literature-based analyses exploit factual knowledge on drugs and diseases, e.g. from databases, and combine it with information from scholarly publications. Here we report the use of the Open Discovery Process on scientific literature to identify non-explicit ties between a disease, namely epilepsy, and known drugs, making full use of available epilepsy-specific ontologies. Results We identified characteristics of epilepsy-specific ontologies to create subsets of documents from the literature; from these subsets we generated ranked lists of co-occurring neurological drug names with varying specificity. From these ranked lists, we observed a high intersection regarding reference lists of pharmaceutical compounds recommended for the treatment of epilepsy. Furthermore, we performed a drug set enrichment analysis, i.e. a novel scoring function using an adaptive tuning parameter and comparing top-k ranked lists taking into account the varying length and the current position in the list. We also provide an overview of the pharmaceutical space in the context of epilepsy, including a final combined ranked list of more than 70 drug names. Conclusions Biomedical ontologies are a rich resource that can be combined with text mining for the identification of drug names for drug repurposing in the domain of epilepsy. The ranking of the drug names related to epilepsy provides benefits to patients and to researchers as it enables a quick evaluation of statistical evidence hidden in the scientific literature, useful to validate approaches in the drug discovery process.

Item Type:	Journal Article
Creators:	Creators Email ORCID ORCID Put Code Mueller, Bernd UNSPECIFIED UNSPECIFIED UNSPECIFIED Castro, Leyla Jael UNSPECIFIED orcid.org/0000-0003-3986-0510 UNSPECIFIED Rebholz-Schuhmann, Dietrich UNSPECIFIED UNSPECIFIED UNSPECIFIED
URN:	urn:nbn:de:hbz:38-662719
DOI:	10.1186/s13326-021-00258-w
Journal or Publication Title:	J. Biomed. Semant.
Volume:	13
Number:	1
Date:	2022
Publisher:	BMC
Place of Publication:	LONDON
ISSN:	2041-1480
Language:	English
Faculty:	Unspecified
Divisions:	Unspecified
Subjects:	no entry
Uncontrolled Keywords:	Keywords Language FISH OIL; MAGNESIUM; SEIZURES; VISUALIZATION; DISCOVERY; MIGRAINE; DISEASE Multiple languages Mathematical & Computational Biology Multiple languages
URI:	http://kups.ub.uni-koeln.de/id/eprint/66271