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ontoFAST (version 1.0.0)

Interactive Annotation of Characters with Biological Ontologies

Description

Tools for annotating characters (character matrices) with anatomical and phenotype ontologies. Includes functions for visualising character annotations and creating simple queries using ontological relationships.

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Install

install.packages('ontoFAST')

Monthly Downloads

181

Version

1.0.0

License

GPL (>= 2)

Issues

2

Pull Requests

0

Stars

2

Forks

0

Maintainer

Sergei Tarasov

Last Published

April 29th, 2021

Functions in ontoFAST (1.0.0)

get_onto_id

Get IDs for ontology names
list2edges

Convert list to edge matrix
paths_sunburst

Return ontology paths for characters
onto_process

Shortcut to process characters and ontology
table2list

Converts a table to list
Scarab

A modified Hymenoptera Anatomy Ontology (HAO) to accommodate anatomy of dung beetles
HAO

Hymenoptera Anatomy Ontology (HAO)
get_ancestors_chars

Get ancestal ontology terms for a set of characters
get_descendants_chars

Get characters that descendants of selected ontology term
make_shiny_in

Make an ontology object for visualization
runOntoFast

Run ontoFAST interactively
get_onto_name

Get names for ontology IDs
syn_extract

Link synonyms with ontology terms
export_cytoscape

Export to Cytoscape format
export_annotations

Export annotation data
Tarasov_2017_annot

Dung beetle characters annotated with ontology terms
annot_all_chars

Annotate all character statements with ontology terms
chars_per_term

Get number of chracters per each ontology term
edges2list

Convert edge matrix to list
annot_char_grep

Annotate a character statement with ontology terms
Sharkey_2011

Hymenoptera character statements
Sharkey_2011_annot

Hymenoptera characters annotated with ontology terms
exclude_terms

Ontology terms to exclude for sunburst plot