Text Mining and Data Modeling of Karyotypes to aid in Drug Repurposing Efforts

Zachary B. Abrams, Andrea L. Peabody, Nyla A. Heerema, Philip R.O. Payne

Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review

4 Scopus citations

Abstract

Karyotyping, or visually examining and recording chromosomal abnormalities, is commonly used to diagnose and treat disease. Karyotypes are written in the International System for Human Cytogenetic Nomenclature (ISCN), a computationally non-readable language that precludes full analysis of these genomic data. In response, we developed a cytogenetic platform that transfers the ISCN karyotypes to a machine-readable model available for computational analysis. Here we use cytogenetic data from the National Cancer Institute (NCI)-curated Mitelman database1 to create a structured karyotype language. Then, drug-gene-disease triplets are generated via a computational pipeline connecting public drug-gene interaction data sources to identify potential drug repurposing opportunities.

Original languageEnglish
Title of host publicationMEDINFO 2015
Subtitle of host publicationeHealth-Enabled Health - Proceedings of the 15th World Congress on Health and Biomedical Informatics
EditorsAndrew Georgiou, Indra Neil Sarkar, Paulo Mazzoncini de Azevedo Marques
PublisherIOS Press
Pages1037
Number of pages1
ISBN (Electronic)9781614995630
DOIs
StatePublished - 2015
Event15th World Congress on Health and Biomedical Informatics, MEDINFO 2015 - Sao Paulo, Brazil
Duration: Aug 19 2015Aug 23 2015

Publication series

NameStudies in Health Technology and Informatics
Volume216
ISSN (Print)0926-9630
ISSN (Electronic)1879-8365

Conference

Conference15th World Congress on Health and Biomedical Informatics, MEDINFO 2015
Country/TerritoryBrazil
CitySao Paulo
Period08/19/1508/23/15

Keywords

  • Cytogenetics
  • Drug repurposing
  • Karyotype
  • Text mining

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