Table 2.

Vocabulary and interactive tools used in DES-RedoxVasc.

Vocabulary and interactive tools	Definition
Concepts	Biological words or phrases (e.g., inflammation, oxidative stress, and hydrogen peroxide) found in this topic-specific literature, organized into thematic dictionaries, and used to mine the literature
Concept Pairs	Cooccurring “Enriched Concepts” (e.g., cell fate determination and TAL1; Wnt receptor and CELSR2; and BMP2K and coronary artery endothelial cell) that may or may not have a biological association/connection
FDR	“To be enriched, a concept or a pair has to have an FDR (false discovery rate) < 0.05 in the DES-RedoxVasc corpus. The FDR is obtained by correcting the enrichment P values for multiplicity testing based on the Benjamini-Hochberg procedure”
Literature	Provides the literature set used in the development of this KB
Network	A tool for the visualization of concept associations as a graph of interlinked nodes
Concept Co-occurrences	A list of concepts which cooccur in the literature with the concept in question. Concepts are regarded as cooccurring in the text if they are within a 200-character distance from each other (refer to rationale below). Only enriched pairs are shown in this list
Knowledge base	A store of information or data that is available to draw on
Dictionaries	A set of topic-specific vocabularies made up of words or phrases used for the purpose of text mining
kb_frequency	Frequency of a concept within the KB literature corpus
bkg_freq	Refers to background frequency: frequency of a concept within the whole PubMed/PMC literature corpus
Density	KB frequency divided by background frequency