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Monarch Initiative

API Documentation

The Monarch Initiative is a cutting-edge tool that harnesses data and computational power to facilitate biomedical research. With an approach that is friendly to both experts and novices, it allows you to delve into a comprehensive knowledge graph to explore relationships between genes, diseases, and phenotypes. Point your cursor towards the familiar or unusual--say 'cystic fibrosis' or 'irregular hyperpigmentation'--and it will present you with an ontology identifier, essentially a digital DNA for that entity. But the tool doesn’t stop there. It can offer connections, linking entities to generate new insights. It's also practical for sorting through the colossal data sets akin to biomedical research. Further, the results come with links to detailed information within the Monarch Initiative, serving both your curious mind and responsible research. However, keep in mind, while the Monarch Initiative is a treasure trove of data, always remember, it is not intended to be used for clinical decision making, diagnoses, or other medical advice. This platform is all about revelation, not prescription.




Example Prompts


Find diseases related to the gene HGNC:


Search for phenotypes associated with disease MONDO:


Get information about the entity MONDO:


Look up genes associated with the phenotype HP:


Search for entities with the term "cystic fibrosis" in the Monarch knowledge graph.


Perform semantic similarity search for gene and disease IDs ["HGNC:


Retrieve information on diseases associated with the gene HGNC:


Find phenotypes related to the gene HGNC:


Get a list of diseases associated with the phenotype HP:


Search for genes related to the disease MONDO:

Description for AI

Search 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', and instead of 'Cystic Fibrosis', use 'Cystic Fibrosis'.

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