Epilepsy Ontologies' Similarities
Calculate the cosine similarity metric for two lists a and b
Calculate the dice similarity metric for two lists a and b
Calculate dsea scores of one list in comparison to reference list
Calculate enrichment of one list in comparison to reference list
Calculate the jaccard coefficient for two lists a and b
Calculate cosine similarity metric
Main function to call everything and produce the results
Creates a vector with an X at each position where a drug from the drug...
Creates the plot for all jaccard coefficients amongst the three epilep...
Creates the plot for all jaccard coefficients amongst the three epilep...
Create the final resulting data frame
Creates the plot for all jaccard coefficients amongst the three epilep...
Calculate dice similarity metric
Does the full plot on one page
Create quad Venn Diagramm for overlapping concepts between EpSO, ESSO,...
Create quintuple Venn Diagramm for shared documents with co-occurrence...
Create quad Venn Diagramm for shared documents with co-occurrences of ...
Create quad Venn Diagramm for shared synonyms between EpSO, ESSO, EPIL...
Create quintuple Venn Diagramm for overlapping concepts between EpSO, ...
Create quintuple Venn Diagramm for shared documents between EpSO, ESSO...
Create quintuple Venn Diagramm for shared documents with co-occurrence...
Create quintuple Venn Diagramm for shared synonyms between EpSO, ESSO,...
Create plot_grid from multiple plots
Filter a given list of drug names for having an ATC code, if not they ...
Filter a given list of drug names for having an ATC code starting with...
Clears object that was loaded from harddrive into a list of terms sort...
Retrieve the list of drugs from the union of all reference lists
Receives a sorted hashmap with found entities from a dictionary
Calculate jaccard similarity metric for two sets a and b
Plotting functions for DSEA lists
Plotting functions for enrichment lists
Print Top 10 Drugs
Processes the input file db-atc.map to form a HashMap containing the d...
Processes the input file db-atc.map to form a HashMap containing the d...
Read the second level ATC classes from the file atc-secondlevel.map
Sort table by scoring for each row
Analysis and visualization of similarities between epilepsy ontologies based on text mining results by comparing ranked lists of co-occurring drug terms in the BioASQ corpus. The ranked result lists of neurological drug terms co-occurring with terms from the epilepsy ontologies EpSO, ESSO, EPILONT, EPISEM and FENICS undergo further analysis. 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>, Mueller, Bernd et al. (2017) <doi:10.1007/978-3-319-58694-6_22>, Mueller, Bernd and Rebholz-Schuhmann, Dietrich (2020) <doi:10.1007/978-3-030-43887-6_52>, and Mueller, Bernd et al. (2022) <doi:10.1186/s13326-021-00258-w>.