Monarch Initiative
Search and retrieve basic information from the Monarch Initiative knowledge graph.
Search the Monarch Initiative knowledge graph for basic information on genes, diseases, and phenotypes. Retrieve ontology identifiers, associations between entities, general entity information, and genes and diseases related to phenotypic profiles. Use lay descriptions to ensure users can understand biomedical terminology. Set appropriate offset and limit parameters to answer user questions and provide a summary. Remember to include the total number of results available and add the disclaimer that the data is not intended for clinical decision making. All results will include links to the Monarch Initiative website.
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API docs
Learn how to use Monarch Initiative effectively! Here are a few example prompts, tips, and the documentation of available commands.
Example prompts
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Prompt 1: "What are some diseases related to cystic fibrosis?"
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Prompt 2: "Find genes associated with Alzheimer's disease."
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Prompt 3: "Search for phenotypes related to autism."
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Prompt 4: "Can you provide information about the gene BRCA1?"
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Prompt 5: "Find diseases associated with the phenotype 'short stature'."
Features and commands
| Feature/Command | Description |
|---|---|
search_entity | This command allows you to search for entities such as genes, diseases, and phenotypes by name to get the associated ontology identifier. You can specify the term to search for and the category (e.g., Disease, PhenotypicQuality, Gene). |
search_phenotype_profiles | This command allows you to perform a semantic similarity search between genes and/or diseases. You provide a list of gene and/or disease ontology identifiers and the command will return matching phenotypes. |
get_entities | This command returns information about arbitrary entities by their identifier. You need to provide a list of entity ids (e.g., MONDO:0005737, HP:0002721, HGNC:1884) and the command will provide details such as name, description, synonyms, categories, and counts of associations to other entities. |
get_disease_gene_associations | This command retrieves a list of genes associated with a disease. You need to provide the ontology identifier of the disease and can optionally specify the maximum number of associations to return. |
get_disease_phenotype_associations | This command retrieves a list of phenotypes associated with a disease. You need to provide the ontology identifier of the disease and can optionally specify the maximum number of associations to return. |
get_gene_disease_associations | This command retrieves a list of diseases associated with a gene. You need to provide the identifier of the gene and can optionally specify the maximum number of associations to return. |
get_gene_phenotype_associations | This command retrieves a list of phenotypes associated with a gene. You need to provide the ontology identifier of the gene and can optionally specify the maximum number of associations to return. |
get_phenotype_disease_associations | This command retrieves a list of diseases associated with a phenotype. You need to provide the ontology identifier of the phenotype and can optionally specify the maximum number of associations to return. |
get_phenotype_gene_associations | This command retrieves a list of genes associated with a phenotype. You need to provide the ontology identifier of the phenotype and can optionally specify the maximum number of associations to return. |