Onassis: OnASSiS (Ontology Annotations and Semantic Similarity...

In eugeniaeueu/Onassis: OnASSIs Ontology Annotation and Semantic SImilarity software

Description

OnASSiS (Ontology Annotations and Semantic Similarity software) is a package for the annotation of any given text with concepts from biomedical ontologies that also provides features to relate the concepts using semantic similarity metrics.

This constructor instantiates an Onassis object.

Usage

Onassis(dictionary = NA_character_, entities = data.frame(),
  similarity = matrix(), scores = matrix())

Arguments

dictionary	The path of the dictionary file
entities	a data frame to store entities
similarity	A matrix of the similarities between entities
scores	The result of comparisons of the elements in the entities

Details

OnASSiS package

OnASSiS (Ontology Annotations and Semantic Similarity software) is a package that uses Conceptmapper, an Apache UIMA (Unstructured Information Management Architecture) https://uima.apache.org/downloads/sandbox/ConceptMapperAnnotatorUserGuide/ConceptMapperAnnotatorUserGuide.html dictionary lookup tool to retrieve dictionary terms in a given text.

In particular a Conceptmapper wrapper specific for the biomedical domain, ccp-nlp, (https://github.com/UCDenver-ccp/ccp-nlp) has been personalized to retrieve concepts from OBO ontologies in a given text with different options.

The package also provides the possibility to annotate Gene Expression Omnibus (GEO) metadata for stored experiments and samples.

Different annotated sets of text can be then compared using semantic similarity metrics based on the structure of the biomedical ontologies. The semantic similarity module has been obtained using the Java slib (http://www.semantic-measures-library.org/sml/)

Value

An object of type Onassis that can be used to analyze metadata

Examples

onassis <- Onassis()

eugeniaeueu/Onassis documentation built on March 9, 2020, 8:17 a.m.