TermController API Wrapper

get_hierarchical_parent(term::Term; preferred_parent::Union{Missing,Term}=missing)

Fetches the hierarchical parent of a given term.

Arguments

• term::Term: The term for which to fetch the hierarchical parent.
• preferred_parent::Union{Missing,Term} (optional): The preferred parent term to be returned, if multiple parents are found.
• encode_iri::Bool (optional): Whether to encode the IRI before making the request. Default is true since IRI are usually stored non-encode in Term struct.

Returns

• If a single parent is found, returns the hierarchical parent as a Term object.
• If multiple parents are found and a preferred parent is specified, returns the preferred parent as a Term object.
• If multiple parents are found and no preferred parent is specified, returns the first parent as a Term object.
• If an error occurs while fetching the parents, returns missing.

get_parents(term::Term)

Fetches the parent terms for a given term.

Arguments

• term::Term: The term for which to fetch the parent terms.
• encode_iri::Bool (optional): Whether to encode the IRI before making the request. Default is true since IRI are usually stored non-encode in Term struct.

Returns

An array of Term objects representing the parent terms of the given term, or missing if an error occurs.

onto_term(ontogy_id::AbstractString, iri::AbstractString; [lang="en", encode_iri=true])

Fetches the term information from the specified ontology using the given IRI.

Arguments

• ontogy_id::AbstractString: The name of the ontology.
• iri::AbstractString: The IRI (Internationalized Resource Identifier) of the term.
• lang::AbstractString: (optional) The language code for the term description. Default is "en".
• encode_iri::Bool (optional): Whether to encode the IRI before making the request. Default is true.

Returns

• If the term is found, returns a Term object containing the term information.
• If there is an error fetching the term, a warning is issued and missing is returned.

onto_terms(ontogy_id::AbstractString;
           [id::AbstractString="",
           iri::AbstractString="",
           short_from::AbstractString="",
           obo_id="",
           obsoletes::Bool=false,
           lang::AbstractString="en"])

Fetches ontology terms from the OLS API based on the specified parameters.

Arguments

• ontogy_id::AbstractString: The name of the ontology to fetch terms from.
• id::AbstractString: (optional) The ID of the term.
• iri::AbstractString: (optional) The IRI of the term.
• short_from::AbstractString: (optional) The short form of the term.
• obo_id: (optional) The OBO ID of the term.
• obsoletes::Bool: (optional) Whether to include obsoleted terms. Default is false.
• lang::AbstractString: (optional) The language of the term. Default is "en".

Returns

A dictionary of terms, where the keys are the OBO IDs of the terms and the values are Term objects.