Import ontologies already having gene annotations

ontology_kw(
  organism = "human",
  gene_annotation = TRUE,
  verbose = simona_opt$verbose,
  ...
)

ontology_chebi(
  organism = c("human", "mouse", "rat", "pig", "dog"),
  gene_annotation = TRUE,
  verbose = simona_opt$verbose,
  ...
)

ontology_hp(
  organism = c("human", "mouse"),
  gene_annotation = TRUE,
  verbose = simona_opt$verbose,
  ...
)

ontology_pw(
  organism = c("human", "mouse", "rat", "pig", "dog", "chimpanzee"),
  gene_annotation = TRUE,
  verbose = simona_opt$verbose,
  ...
)

ontology_rdo(
  organism = c("human", "mouse", "rat", "pig", "dog", "chimpanzee"),
  gene_annotation = TRUE,
  verbose = simona_opt$verbose,
  ...
)

ontology_vt(
  organism = c("human", "mouse", "rat", "pig", "dog", "chimpanzee"),
  gene_annotation = TRUE,
  verbose = simona_opt$verbose,
  ...
)

ontology_go(...)

Arguments

organism: Organism.
gene_annotation: Whether to add gene annotations to the DAG.
verbose: Whether to print messages?
...: Pass to create_ontology_DAG().

Details

There are the following ontologies:

ontology_kw(): UniProt Keywords. The list of supported organisms can be found in UniProtKeywords::load_keyword_genesets().
ontology_chebi(): Chemical Entities of Biological Interest.
ontology_hp(): The Human Phenotype Ontology.
ontology_pw(): Pathway Ontology.
ontology_rdo(): RGD Disease Ontology.
ontology_vt(): Vertebrate Trait Ontology.

The source of the original files can be found with simona:::RGD_TB.

ontology_go() is an alias of create_ontology_DAG_from_GO_db(). All arguments go there.