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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.

Learn how to use Monarch Initiative effectively! Here are a few example prompts, tips, and the documentation of available commands.

Example prompts

  1. Prompt 1: "What are some diseases related to cystic fibrosis?"

  2. Prompt 2: "Find genes associated with Alzheimer's disease."

  3. Prompt 3: "Search for phenotypes related to autism."

  4. Prompt 4: "Can you provide information about the gene BRCA1?"

  5. Prompt 5: "Find diseases associated with the phenotype 'short stature'."

Features and commands

Feature/CommandDescription
search_entityThis 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_profilesThis 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_entitiesThis 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_associationsThis 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_associationsThis 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_associationsThis 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_associationsThis 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_associationsThis 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_associationsThis 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.

Configuration

User authenticationNo user authentication
API documentation

For AI

Namemonarch
DescriptionSearch and retrieve basic information from the Monarch Initiative knowledge graph. You can search for entities such as genes, diseases, and phenotypes by name to get the associated ontology identifier. You can retrieve associations between entities via their identifiers, get general information about sets of entities, and search for genes and diseases related to phenotypic profiles. Users may use synonyms for these such as 'illness' or 'symptom'. Do not assume the user is familiar with biomedical terminology, and always add additional information such as lay descriptions of phenotypes. Use your best judgement for setting the offset and limit parameters to answer the users' questions, for example by retrieving more associations if the user asks for a summary. IMPORTANT: indicate the total number of results available so the user is not led to believe that the results are exhaustive. IMPORTANT: include the text 'Monarch Initiative data is not intended to be used for clinical decision making, diagnoses, or other medical advice.' Do not repeat this disclaimer in every response. IMPORTANT: Include links to the Monarch Initiative for all results. For example, instead of 'Irregular hyperpigmentation', include a markdown link: '[Irregular hyperpigmentation](https://monarchinitiative.org/phenotype/HP:0007400)', and instead of 'Cystic Fibrosis', use '[Cystic Fibrosis](https://monarchinitiative.org/disease/MONDO:0009061)'.

Updates

First added24 July 2023

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