A focused wrapper around map_concepts that restricts all
ontology lookups to the EDAM ontology. The LLM is instructed to search
within EDAM only and to identify which EDAM sub-tree applies (topic,
operation, data, or format); the OLS4 REST label search is also constrained
to EDAM regardless of the LLM's response.
Arguments
- query
character(1) free-text input containing one or more biological or medical concepts.
- ...
additional arguments passed to
map_concepts, e.g.max_concepts,deduplicate,definition.
Value
a data.frame as returned by map_concepts, with all
rows from the EDAM ontology.
Details
Scope and curation. EDAM covers bioinformatics operations, data
types, file formats, and computational biology topics. Concepts outside
this scope — including spatial statistics, clinical phenotypes, chemical
entities, and general study designs — have little or no EDAM coverage.
When the input text contains such concepts the LLM may return a spurious
EDAM term rather than admitting no match exists. All outputs should
be reviewed by a domain expert before use: check that each
term_label is semantically appropriate for its input_text,
and discard rows where the mapping is implausible. The
map_concepts function (unrestricted ontology) may give better
coverage for mixed or clinically-oriented texts.
Examples
if (interactive()) {
map_concepts_edam("RNA-Seq workflow with variant calling and primer trimming",
max_concepts = 8)
}