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| { | |
| "type": "object", | |
| "properties": { | |
| "pmid": { | |
| "type": "string", | |
| "description": "The PubMed ID of the paper being analyzed." | |
| }, | |
| "entities": { | |
| "type": "array", | |
| "description": "Biomedical entities identified in the abstract.", | |
| "items": { | |
| "type": "object", | |
| "properties": { | |
| "type": { | |
| "type": "string", | |
| "enum": ["Gene", "Protein", "Compound", "Pathway", "Phenotype", "Mechanism"], | |
| "description": "Category of the biomedical entity." | |
| }, | |
| "name": { | |
| "type": "string", | |
| "description": "Exact name as it appears in the text." | |
| }, | |
| "confidence": { | |
| "type": "number", | |
| "minimum": 0.0, | |
| "maximum": 1.0, | |
| "description": "Confidence that this is correctly identified (1.0 = unambiguous)." | |
| }, | |
| "mentions": { | |
| "type": "integer", | |
| "minimum": 1, | |
| "description": "Number of times this entity is mentioned in the abstract." | |
| } | |
| }, | |
| "required": ["type", "name", "confidence", "mentions"] | |
| } | |
| }, | |
| "relationships": { | |
| "type": "array", | |
| "description": "Relationships between entities identified in the abstract.", | |
| "items": { | |
| "type": "object", | |
| "properties": { | |
| "source": { | |
| "type": "string", | |
| "description": "Name of the source entity (must match an entity in the entities list)." | |
| }, | |
| "target": { | |
| "type": "string", | |
| "description": "Name of the target entity (must match an entity in the entities list)." | |
| }, | |
| "type": { | |
| "type": "string", | |
| "enum": ["BINDS", "INHIBITS", "ASSOCIATED_WITH", "TESTED_IN", "EXPRESSED_IN", "CO_OCCURS"], | |
| "description": "Type of relationship between source and target." | |
| }, | |
| "evidence_text": { | |
| "type": "string", | |
| "description": "Brief excerpt from the abstract that supports this relationship." | |
| } | |
| }, | |
| "required": ["source", "target", "type", "evidence_text"] | |
| } | |
| } | |
| }, | |
| "required": ["pmid", "entities", "relationships"] | |
| } | |