epos

Epilepsy Ontology Similarities

Analysis and visualization of similarities between epilepsy ontologies based on text mining results by comparing ranked lists of co-occurring drug terms in the corpus of LIVIVO. The ranked result lists of neurological drug terms co-occurring with named entities from the epilepsy ontologies EpSO, ESSO, and EPILONT are aggregated in order to generate two different results: an overview table of drugs that are relevant to epilepsy created with the method createNeuroTable, and a plot of tanimoto similarity coefficients between the aggregated list of drug terms against the list of drug terms from each of the ontologies created with the method createTanimotoBaseline(). The alignment of the Top-K Ranked Lists is conducted using the R-package TopKLists <https://cran.r-project.org/package=TopKLists>. The source data to create the ranked lists of drug names is produced using the text mining workflows described in Mueller, Bernd and Hagelstein, Alexandra (2016) <doi:10.4126/FRL01-006408558> and Mueller, Bernd et al. (2017) <doi:10.1007/978-3-319-58694-6_22>.

Total

581

Last month

240

Last week

55

Average per day

8

Daily downloads

Total downloads

Description file content

Package
epos
Type
Package
Title
Epilepsy Ontology Similarities
Version
0.1.0
Author
Bernd Müller
Maintainer
Bernd Mueller
Depends
R (>= 2.10)
Description
Analysis and visualization of similarities between epilepsy ontologies based on text mining results by comparing ranked lists of co-occurring drug terms in the corpus of LIVIVO. The ranked result lists of neurological drug terms co-occurring with named entities from the epilepsy ontologies EpSO, ESSO, and EPILONT are aggregated in order to generate two different results: an overview table of drugs that are relevant to epilepsy created with the method createNeuroTable, and a plot of tanimoto similarity coefficients between the aggregated list of drug terms against the list of drug terms from each of the ontologies created with the method createTanimotoBaseline(). The alignment of the Top-K Ranked Lists is conducted using the R-package TopKLists . The source data to create the ranked lists of drug names is produced using the text mining workflows described in Mueller, Bernd and Hagelstein, Alexandra (2016) and Mueller, Bernd et al. (2017) .
License
MIT + file LICENSE
Encoding
UTF-8
LazyData
true
RoxygenNote
6.1.0
Imports
hashmap, ggplot2, tidyr, dplyr, testthat, gridExtra, TopKLists, stringr, xtable
Suggests
knitr, rmarkdown
NeedsCompilation
no
Packaged
2018-10-08 10:27:05 UTC; muellerb
Repository
CRAN
Date/Publication
2018-10-08 14:20:06 UTC

install.packages('epos')

0.1.0

2 months ago

Bernd Mueller

MIT + file LICENSE

Depends on

R (>= 2.10)

Imports

hashmap, ggplot2, tidyr, dplyr, testthat, gridExtra, TopKLists, stringr, xtable

Suggests

knitr, rmarkdown

Discussions