| [ |
| { |
| "type": "PubTatorTool", |
| "name": "PubTator3_EntityAutocomplete", |
| "description": "Provides suggestions for the best‐matching standardized PubTator IDs for a partial biomedical term (gene, disease, chemical, or variant). Use this tool first to convert free‐text names into the stable @IDs required by the other PubTator APIs.", |
| "endpoint_path": "/entity/autocomplete/", |
| "method": "GET", |
| "param_map": { |
| "text": "query", |
| "entity_type": "concept", |
| "max_results": "limit" |
| }, |
| "parameter": { |
| "type": "object", |
| "properties": { |
| "text": { |
| "type": "string", |
| "description": "A few characters or the full name of the biomedical concept you are trying to look up (e.g. “BRAF V6”)." |
| }, |
| "entity_type": { |
| "type": "string", |
| "description": "Optional filter to restrict suggestions to a single category such as GENE, DISEASE, CHEMICAL, or VARIANT." |
| }, |
| "max_results": { |
| "type": "integer", |
| "description": "Maximum number of suggestions to return (1 - 50, default = 10)." |
| } |
| }, |
| "required": ["text"] |
| }, |
| "fields": { |
| "tool_subtype": "PubTatorEntity" |
| } |
| }, |
| { |
| "type": "PubTatorTool", |
| "name": "PubTator3_LiteratureSearch", |
| "description": "Find PubMed articles that match a keyword, a PubTator entity ID (e.g. “@GENE_BRAF”), or an entity-to-entity relation expression (e.g. “relations:treat|@CHEMICAL_Doxorubicin|@DISEASE_Neoplasms”).", |
| "endpoint_path": "/search/", |
| "method": "GET", |
| "param_map": { |
| "query": "text", |
| "page": "page", |
| "page_size": "page_size" |
| }, |
| "parameter": { |
| "type": "object", |
| "properties": { |
| "query": { |
| "type": "string", |
| "description": "What you want to search for. This can be plain keywords, a single PubTator ID, or the special relation syntax shown above." |
| }, |
| "page": { |
| "type": "integer", |
| "description": "Zero-based results page (optional; default = 0)." |
| }, |
| "page_size": { |
| "type": "integer", |
| "description": "How many PMIDs to return per page (optional; default = 20, maximum = 200)." |
| } |
| }, |
| "required": ["query"] |
| }, |
| "fields": { |
| "tool_subtype": "PubTatorSearch" |
| } |
| } |
| ] |
|
|
