annotate_text
Identify ontology terms in text for biological analysis using configurable parameters like semantic types, class hierarchies, and stop words to refine results.
Instructions
Analyze text and identify relevant ontology terms with configurable parameters
Input Schema
| Name | Required | Description | Default |
|---|---|---|---|
| class_hierarchy_max_level | No | Maximum hierarchy depth (default: 0) | |
| exclude_numbers | No | Exclude numeric matches (default: false) | |
| exclude_synonyms | No | Exclude synonym matches (default: false) | |
| expand_class_hierarchy | No | Include class ancestors in annotation (default: false) | |
| expand_mappings | No | Use manual mappings (UMLS, REST, CUI, OBOXREF) (default: false) | |
| expand_semantic_types_hierarchy | No | Include children of semantic types (default: false) | |
| longest_only | No | Return only longest matches (default: false) | |
| minimum_match_length | No | Minimum character length for matches | |
| ontologies | No | Comma-separated ontology acronyms to use for annotation | |
| semantic_types | No | Comma-separated semantic types to filter by | |
| stop_words | No | Comma-separated custom stop words | |
| text | Yes | Text to annotate with ontology terms | |
| whole_word_only | No | Match whole words only (default: true) |