robot_extract
Extract a subset module from an ontology by specifying seed terms and choosing an extraction method (STAR, BOT, TOP, MIREOT, or subset).
Instructions
Extract a subset module from a larger ontology.
Methods:
STAR: minimal module with seed terms and direct relationships
BOT: seed terms plus all superclasses
TOP: seed terms plus all subclasses
MIREOT: hierarchy-preserving extraction with upper/lower boundaries
subset: seed terms with materialized existential relationships
Specify seed terms via term (list of CURIEs/IRIs) or term_file.
Input Schema
| Name | Required | Description | Default |
|---|---|---|---|
| input | No | ||
| output | No | ||
| method | No | STAR | |
| term | No | ||
| term_file | No | ||
| upper_term | No | ||
| lower_term | No | ||
| branch_from_term | No | ||
| imports | No | ||
| individuals | No | ||
| intermediates | No | ||
| copy_ontology_annotations | No | ||
| annotate_with_source | No | ||
| sources | No | ||
| working_directory | No | ||
| catalog | No | ||
| prefixes | No | ||
| add_prefix | No | ||
| noprefixes | No | ||
| verbose | No | ||
| strict | No | ||
| xml_entities | No | ||
| extra_args | No |
Output Schema
| Name | Required | Description | Default |
|---|---|---|---|
No arguments | |||