Adenine AI API Documentation

Documentation to access/integrate Adenine AI through Web-APIs.

API key

Please log in to view your API key.

Authentication

To access protected endpoints, you must authenticate your requests using an API key managed by Kong. Each user has a unique API key associated with their account, which can be passed in one of two ways:

1. Request header Recommended

Send the API key in the apikey request header. This keeps it out of URLs, browser history, and common request logs.

Example request

curl -H 'apikey: 'YOUR API KEY'' https://adenine.ai/api/v1/:path_params

2. Request parameter

A query parameter is supported for compatibility when a request header is not possible.

Example request

curl https://adenine.ai/api/v1/:path_params?apikey='YOUR API KEY'

Avoid query-string API keys for production integrations: URLs may be retained in browser history, proxy logs, analytics systems, and referrer headers.

Evidences

GET /:category/:entity/:search_term

This endpoint enables flexible, free-text style querying of genetic evidence by allowing users to search by gene, disease, or variation across different categories such as cases, series, or somatic reports.

Required Path Parameters

category

category

Type

enum

Description
The data category/evidence type you want to search Adenine AI for. These refer to the source or structure of medical genetics evidence.

Supported Values:
- cases
- serieses
- functionals
- somatic_fusions
- somatic_serieses
entity

entity

Type

enum

Description
Indicates the type of biomedical entity provided in :search_term. It helps unambiguously determine how to interpret and route the query.

Supported Values:
- genes
- diseases
- variations
search_term

search_term

Type

string

Description
The actual value to be searched for. Its interpretation depends on the :entity provided as a path parameter described above.

Expected Formats Based on Entity:
- When entity => genes
  - HGNC-approved symbols: ARSA, TP53, BRAF
  - HGNC identifiers: HGNC:783
- When entity => diseases
  - MONDO identifiers: MONDO_0016575
  - Free-text disease names: Krabbe, leukodystrophy
- When entity => variations
  - HGVS-like DNA notation (must be prefixed by gene symbol): ARSA:c.1232C>T
  - HGVS-like protein notation: ARSA:p.Thr411Ile
Note: Dots (.) and greater-than symbols (>) in variations must be URL-encoded when calling the API directly.

Response (example)

Request: GET https://adenine.ai/api/v1/cases/genes/HSF4?apikey='YOUR API KEY'

Response code: 200

{
	  "hits": [
	    {
	      "_id": "67a9264132642c0cd3a98c11",
	      "patient": {
	        "ethnicity": [
	          "iranian"
	        ]
	      },
	      "genes": [
	        "HGNC:5227"
	      ],
	      "symptoms": [
	        "HP_0000518"
	      ],
	      "zygosity": "homozygous",
	      "consanguineous_parents": true,
	      "publication_year": "2016",
	      "pmid": "26490182",
	      "score": 15,
	      "has_variation_information": true,
	      "cpdots_flat": [
	        "HSF4:c.521T>C",
	        "HSF4:p.Leu174Pro"
	      ]
	    },
	    {
	      "_id": "67a9264032642c0cd3a9679b",
	      "patient": {
	        "ethnicity": [
	          "chinese"
	        ]
	      },
	      "genes": [
	        "HGNC:5227"
	      ],
	      "symptoms": [
	        "HP_0000519"
	      ],
	      "zygosity": "heterozygous",
	      "publication_year": "2014",
	      "pmid": "24637349",
	      "score": 13,
	      "has_variation_information": true,
	      "cpdots_flat": [
	        "HSF4:c.69G>T",
	        "HSF4:p.Lys23Asn"
	      ]
	    },
	    {
	      "_id": "67a9264232642c0cd3a9a9d6",
	      "patient": {
	        "ethnicity": [
	          "british"
	        ]
	      },
	      "genes": [
	        "HGNC:5227"
	      ],
	      "diseases": [
	        "MONDO_0007290"
	      ],
	      "publication_year": "2018",
	      "pmid": "29243736",
	      "score": 12,
	      "has_variation_information": true,
	      "cpdots_flat": [
	        "HSF4:c.190A>G",
	        "HSF4:p.Lys64Glu"
	      ]
	    },
	    {
	      "_id": "67a9263f32642c0cd3a92f4c",
	      "patient": {
	        "ethnicity": [
	          "chinese"
	        ]
	      },
	      "genes": [
	        "HGNC:5227"
	      ],
	      "publication_year": "2006",
	      "pmid": "16876512",
	      "score": 11,
	      "has_variation_information": true,
	      "cpdots_flat": [
	        "HSF4:c.217C>T",
	        "HSF4:p.Arg73Cys",
	        "HSF4:c.221G>A",
	        "HSF4:p.Arg74His"
	      ]
	    },
	    {
	      "_id": "67a9264132642c0cd3a97240",
	      "patient": {
	        "ethnicity": [
	          "chinese"
	        ]
	      },
	      "genes": [
	        "HGNC:5227"
	      ],
	      "publication_year": "2015",
	      "pmid": "25877371",
	      "score": 9,
	      "has_variation_information": true,
	      "cpdots_flat": [
	        "HSF4:c.331C>T",
	        "HSF4:p.Arg111Cys"
	      ]
	    },
	    {
	      "_id": "67a9264232642c0cd3a9ac43",
	      "genes": [
	        "HGNC:5227"
	      ],
	      "patient": {},
	      "publication_year": "2018",
	      "pmid": "30316871",
	      "score": 9,
	      "has_variation_information": true,
	      "cpdots_flat": [
	        "HSF4:p.Ser299Ala",
	        "HSF4:p.Ser299Asp"
	      ]
	    },
	    {
	      "_id": "67a9264432642c0cd3aa19cd",
	      "genes": [
	        "HGNC:7146",
	        "HGNC:1393",
	        "HGNC:4042",
	        "HGNC:3603",
	        "HGNC:2200",
	        "HGNC:5227",
	        "HGNC:4281",
	        "HGNC:7103",
	        "HGNC:11724"
	      ],
	      "patient": {},
	      "publication_year": "2024",
	      "pmid": "38315492",
	      "score": 6,
	      "has_variation_information": false
	    }
	  ],
	  "facets": {
	    "publication_year": {
	      "2006": 1,
	      "2014": 1,
	      "2015": 1,
	      "2016": 1,
	      "2018": 2,
	      "2024": 1
	    },
	    "genes": {
	      "HGNC:5227": 7,
	      "HGNC:7146": 1,
	      "HGNC:1393": 1,
	      "HGNC:4042": 1,
	      "HGNC:3603": 1,
	      "HGNC:2200": 1,
	      "HGNC:4281": 1,
	      "HGNC:7103": 1,
	      "HGNC:11724": 1
	    },
	    "diseases": {
	      "MONDO_0007290": 1
	    },
	    "patient.sex": {},
	    "patient.ethnicity": {
	      "iranian": 1,
	      "chinese": 3,
	      "british": 1
	    },
	    "zygosity": {
	      "homozygous": 1,
	      "heterozygous": 1,
	      "other": 5
	    },
	    "age_group": {
	      "pediatric": 0,
	      "adults": 0,
	      "geriatric": 0,
	      "unknown": 7
	    },
	    "de_novo": {
	      "de Novo Mutation": 0,
	      "Unknown Origin": 7
	    },
	    "has_variations": {
	      "Yes": 6,
	      "No": 1
	    }
	  },
	  "mapping_help": {
	    "genes": {
	      "HGNC:11724": "TEK",
	      "HGNC:1393": "CACNA1F",
	      "HGNC:2200": "COL2A1",
	      "HGNC:3603": "FBN1",
	      "HGNC:4042": "FZD4",
	      "HGNC:4281": "GJA8",
	      "HGNC:5227": "HSF4",
	      "HGNC:7103": "MIP",
	      "HGNC:7146": "TRPM1"
	    },
	    "diseases": {
	      "MONDO_0007290": "cataract 5 multiple types"
	    },
	    "symptoms": {
	      "HP_0000518": "Cataract",
	      "HP_0000519": "Developmental cataract"
	    }
	  }
	}

Response (example)

Request: GET https://adenine.ai/api/v1/cases/diseases/metachromatic?apikey='YOUR API KEY'

Response code: 200

{
  "message": "More than one diseases matched with the query, the preferred name of the diseases are metachromatic leukodystrophy due to saposin B deficiency (MONDO_0009590), metachromatic leukodystrophy, juvenile form (MONDO_0009591), metachromatic leukodystrophy, adult form (MONDO_0017730), metachromatic leukodystrophy, late infantile form (MONDO_0017729), metachromatic leukodystrophy (MONDO_0018868)}"
}

Response (example)

Request: GET https://adenine.ai/api/v1/cases/diseases/gregory?apikey='YOUR API KEY'

Response code: 200

{"message":"The disease 'gregory' did not resolve to any diseases. Make sure the disease name is a valid."}

Evidence (requires apikey, see authentication)

GET /:category/:id

This endpoint returns a single curated article by its document ID from the specified evidence :category. It is useful when retrieving an exact case, functional study, somatic series, or other evidence record by ID.

Required Path Parameters

category

category

Type

enum

Description
Specifies the evidence collection to search.

Supported Values:
- cases
- serieses
- functionals
- somatic_fusions
- somatic_serieses
id

id

Type

string

Description

The unique document ID to retrieve from the given category (e.g. MongoDB ObjectId).

Response (example)

Request: GET https://adenine.ai/api/v1/cases/67a9263f32642c0cd3a9248c?apikey='YOUR API KEY'

Response code: 200

{
  "case": [
    {
      "_id": "67a9263f32642c0cd3a9248c",
      "patient": {
        "age": 10,
        "age_unit": "year",
        "sex": "female"
      },
      "interventions": {
        "unmapped_entities": [
          "vincristine"
        ]
      },
      "article": {
        "pmid": "15382281",
        "title": "Vincristine neuropathy: neurophysiological and genetic studies in a case of Wilms tumor.",
        "abstract": "We report a 10-year-old female with Wilms tumor (WT) who developed severe neuropathy after the fifth weekly dose of vincristine. The girl was previously asymptomatic and the family history was negative for inherited neuropathies. Neurophysiological studies and electrodiagnostic findings were suggestive of a axonal neuropathy with greater motor than sensory characteristics not typical of Charcot-Marie-Tooth (CMT) Type 1A. Genetic studies were performed in view of the degree of neurotoxicity. Duplication of 17p11.2 was found that supported the diagnosis of CMT Type 1A. The patient is alive without disease and with minimal weakness of the lower extremities after 42 months. Neurophysiological studies, repeated at 8 and 24 months, were negative. Although the association of asymptomatic CMT and vincristine neuropathy has been previously reported, the present case is of note because the reversible neuropathy occurred after five doses of vincristine, suggesting that possible more people suffering vincristine neurotoxicity may have underlying and asymptomatic CMT.",
        "year": "2004",
        "journal": "Pediatric blood & cancer"
      },
      "family_profiled": false,
      "diagnostic_procedures": {
        "unmapped_entities": [
          "Neurophysiological studies",
          "electrodiagnostic findings"
        ]
      },
      "curation_quality": {
        "number_of_mapped_terms": 7,
        "thickness": 10
      },
      "diseases": {
        "mapped_entities": [
          {
            "_id": "MONDO_0006058",
            "pref_name": "Wilms tumor",
            "source_uids": [
              "MEDGEN:10221",
              "MESH:D009396",
              "NCIT:C3267",
              "UMLS:C0027708"
            ],
            "definition": "An embryonal neoplasm characterized by the presence of epithelial, mesenchymal, and blastema components. The vast majority of cases arise from the kidney. A small number of cases with morphologic features resembling Wilms tumor of the kidney have been reported arising from the ovary and the cervix.",
            "synonyms": [
              "Wilms tumor",
              "Wilms' tumor",
              "Wilms' tumour",
              "Nephroblastoma",
              "NEPHROBLASTOMA",
              "nephroblastoma",
              "Nephroblastomas",
              "Nephroblastoma, NOS",
              "Nephroblastoma NOS",
              "KIDNEY, ADENOMYOSARCOMA, EMBRYONAL",
              "RENAL CANCER, WILMS",
              "KIDNEY, CARCINOSARCOMA, EMBRYONAL",
              "kidney; embryoma",
              "KIDNEY, EMBRYOMA",
              "embryoma; kidney",
              "KIDNEY, EMBRYONAL MIXED TUMOR",
              "Embryonal adenosarcoma",
              "Renal adenosarcoma",
              "Embryonal nephroma",
              "Nephroma",
              "nephroma",
              "Nephroma, NOS",
              "nephromas",
              "[M]Nephroblastoma NOS",
              "Wilms Tumor",
              "tumor, Wilms'",
              "tumor wilms'",
              "tumor wilms",
              "tumor; Wilms",
              "WILMS TUMOR",
              "wilms tumor",
              "wilms' tumor",
              "Wilms; tumor",
              "Wilm Tumor",
              "Wilm's Tumor",
              "Wilms' Tumor",
              "Wilm's tumor",
              "tumor wilm's",
              "tumor wilms's",
              "tumors wilm's",
              "tumors wilms",
              "wilm tumor",
              "wilm's tumor",
              "wilms tumour",
              "wilms' tumour",
              "Wilms tumour",
              "Tumor, Wilms'",
              "Tumor, Wilms",
              "Perlman syndrome",
              "Wilms Tumor 1",
              "WILMS TUMOR 1",
              "WT1",
              "Renal embryonic tumor",
              "Wilms tumor and other childhood kidney tumors",
              "Wilms' tumor and other childhood kidney tumors",
              "Nephroblastoma (M-89603)",
              "Nephroblastoma (morphologic abnormality)",
              "Wilms",
              "Kidney Wilms Tumor",
              "Wilms Tumor of the Kidney",
              "Wilms' Tumor of the Kidney",
              "Renal Wilms Tumor",
              "Renal Wilms' Tumor",
              "Nephroblastoma (Wilms tumor)",
              "Wilms tumor (nephroblastoma)",
              "nephroblastoma of kidney",
              "Kidney Nephroblastoma"
            ]
          },
          {
            "_id": "MONDO_0005244",
            "pref_name": "peripheral neuropathy",
            "source_uids": [
              "DOID:870",
              "EFO:0003100",
              "GARD:12192",
              "MEDGEN:18386",
              "MedDRA:10034606",
              "NCIT:C119734",
              "NCIT:C4731",
              "SCTID:386033004",
              "UMLS:C0031117"
            ],
            "definition": "A disorder affecting the peripheral nervous system. It manifests with pain, tingling, numbness, and muscle weakness. It may be the result of physical injury, toxic substances, viral diseases, diabetes, renal failure, cancer, and drugs.",
            "synonyms": [
              "neuropathy",
              "peripheral nerve disorder",
              "peripheral neuropathy",
              "Peripheral Neuropathy",
              "Neuropathy;peripheral",
              "Peripheral neuropathy",
              "PERIPHERAL NEUROPATHY",
              "Peripheral neuritis",
              "PN - Peripheral neuropathy",
              "Peripheral nerve damage",
              "peripheral neuropathy (physical finding)"
            ]
          }
        ]
      },
      "genes_mutation_context": {
        "mapped_entities": []
      },
      "symptoms": {
        "unmapped_entities": [
          "severe neuropathy after the fifth weekly dose of vincristine",
          "minimal weakness of the lower extremities"
        ],
        "mapped_entities": []
      },
      "genes_non_mutation_context": {
        "mapped_entities": [
          {
            "_id": "HGNC:9118",
            "cui": "C1418677",
            "pref_name": "PMP22 gene",
            "synonyms": [
              "PMP22 Gene",
              "PERIPHERAL MYELIN PROTEIN 22",
              "peripheral myelin protein 22",
              "PMP22",
              "GAS3",
              "Sp110",
              "Charcot-Marie-Tooth neuropathy 1A (greatly reduced nerve conduction velocity, hereditary motor sensory neuropathy Ia)",
              "Peripheral Myelin Protein 22 Gene",
              "HMSNIA",
              "CMT1A",
              "GROWTH ARREST-SPECIFIC 3",
              "HNPP"
            ],
            "source_uids": [
              "LNC:LP19757-1",
              "HGNC:9118",
              "MTH:NOCODE",
              "NCI:C75900",
              "OMIM:601097"
            ]
          }
        ]
      },
      "phenotype_mentions": {
        "unmapped_entities": [
          "Charcot-Marie-Tooth Type 1A"
        ],
        "mapped_entities": []
      }
    }
  ]
}

Aggregated Evidence

GET /aggregated_evidence/gd?gene=HGNC_XXXX&disease=MONDO_YYYYYYY

Returns aggregated evidence of association for a specific Gene–Disease pair. Accepts HGNC and MONDO identifiers and returns a JSON aggregation of the available evidence related to that association.

Required Query Parameters

gene

gene

Type

string

Description

HGNC identifier of the gene. Both HGNC:1234 and HGNC_1234 forms are accepted.
disease

disease

Type

string

Description

MONDO identifier of the disease (e.g., MONDO_0019152). The form MONDO:0019152 is also accepted.

Response (example)

Request: GET https://adenine.ai/api/v1/aggregated_evidence/gd?gene=HGNC_10013&disease=MONDO_0019152&apikey='YOUR API KEY'

Response code: 200

{
  "evidence": {
    "cases": [
      { "_id": "67a9264132642c0cd3a982ee", "...": "..." },
      { "_id": "67a9264132642c0cd3a98c11", "...": "..." }
    ],
    "series": [
      { "_id": "67ab649b95718832c5cc7c4b", "...": "..." }
    ],
    "functional": [
      { "_id": "67a92666de51878901905827", "...": "..." }
    ]
  }
}

Response (missing params)

Request: GET https://adenine.ai/api/v1/aggregated_evidence/gd?gene=HGNC_10013

Response code: 400

{
  "error": "Missing required parameters",
  "required": ["gene", "disease"]
}

Evidence Tools & Retrieval

Read-only endpoints for evidence exploration, counts, and targeted retrieval. All requests use the same Kong API-key authentication described above.

Gene, disease, and fusion analysis

GET/aggregated_evidence/somatic_gd?gene=HGNC:7132&disease=MONDO:0016070

Returns aggregated somatic fusion and somatic series evidence for a gene–tumor pair. Gene and disease identifiers accept colon or underscore forms.

GET/evidence/germline/gene-summary?gene=HGNC:843

Returns the germline evidence summary for one gene across case reports, case series, and functional studies.

GET/summarize_somatic_hits?gene=HGNC:7132

Returns the somatic evidence summary for one gene.

GET/evidence/germline/disease-gene-counts?disease=MONDO:0016070

Counts germline case-report, cohort, and functional-study documents per gene for a disease.

GET/evidence/somatic/disease-gene-counts?disease=MONDO:0016070

Counts somatic fusion and somatic-series documents per gene for a disease.

GET/evidence/somatic/fusions/recurrent?min_count=2&max_count=15&max_genes_per_record=5

Returns recurrent somatic fusion pairs, constrained by recurrence and the number of genes in a record.

GET/analytics/germline/gene-counts?min_case_reports=5&max_case_reports=15

Returns corpus-level germline evidence counts by gene. Optional case-series bounds are min_case_series and max_case_series.

Targeted record retrieval

These read-only POST endpoints accept {"ids":["24-character Mongo IDs"]} and return only the requested records. Use IDs returned by search, timeline, PMID, fusion-partner, or curated-summary endpoints.

POST/evidence/germline/case-reports/summaries

Compact text summaries for germline case reports.

POST/evidence/germline/case-series/summaries

Compact text summaries for germline case series.

POST/evidence/functional-studies/summaries

Compact text summaries for functional studies.

POST/evidence/somatic/fusions/summaries

Compact text summaries for somatic fusion studies.

POST/evidence/somatic/case-series/records

Structured records for somatic case series; this source has no text-summary form.

POST/curated-summaries/records

Complete selected organized summaries.

Additional read-only lookup endpoints

GET/:category/lof_in_gene/:gene_symbol

Finds loss-of-function evidence within a gene. Categories follow the existing evidence category names.

GET/test

Simple authenticated API connectivity check. Returns {"success":true}.

GET https://adenine.ai/api/v1/evidence/germline/gene-summary?gene=HGNC:843&apikey='YOUR API KEY'

Evidence Timeline

GET /evidence/timeline

Returns recent evidence-document counts by publication year and evidence type. Supply a gene, disease, variation, or any combination; supplied biological filters are combined with AND.

Gene symbols and disease names are resolved by the UI gateway. The API receives canonical HGNC and MONDO identifiers.

Query parameters

gene: gene symbol or HGNC identifier.
disease: disease name or MONDO identifier.
variation: exact variation text.
evidence_types: comma-separated cases, serieses, functionals, somatic_fusions, and/or somatic_serieses. Defaults to all types.
year: one four-digit publication year. Defaults to the current year.
start_year and end_year: inclusive range of no more than three publication years. These must be supplied together and cannot be combined with year.
include=ids: adds matching document IDs under each year and evidence type. id_limit defaults to 50 and may be from 1 to 100; ids_truncated identifies a capped list.

Response (example)

Request:

GET https://adenine.ai/api/v1/evidence/timeline?gene=BRCA1&evidence_types=cases,serieses,functionals&start_year=2024&end_year=2026&include=ids&apikey='YOUR API KEY'

{
  "query": {
    "gene": "HGNC:1100",
    "evidence_types": ["cases", "serieses", "functionals"],
    "start_year": 2024,
    "end_year": 2026,
    "include": ["ids"],
    "id_limit": 50
  },
  "years": [
    {
      "year": 2024,
      "total": 3,
      "cases": 2,
      "serieses": 1,
      "functionals": 0,
      "evidence_ids": { "cases": ["..."], "serieses": ["..."], "functionals": [] },
      "ids_truncated": { "cases": false, "serieses": false, "functionals": false }
    },
    {
      "year": 2025,
      "total": 0,
      "cases": 0,
      "serieses": 0,
      "functionals": 0,
      "evidence_ids": { "cases": [], "serieses": [], "functionals": [] },
      "ids_truncated": { "cases": false, "serieses": false, "functionals": false }
    },
    {
      "year": 2026,
      "total": 1,
      "cases": 0,
      "serieses": 0,
      "functionals": 1,
      "evidence_ids": { "cases": [], "serieses": [], "functionals": ["..."] },
      "ids_truncated": { "cases": false, "serieses": false, "functionals": false }
    }
  ],
  "mapping_help": { "genes": { "HGNC:1100": "BRCA1" } }
}

MCP Evidence Endpoints

These endpoints provide compact organized evidence for API and MCP consumers. All are available through the authenticated UI API surface.

Curated-summary search and related summaries

GET /curated-summaries/search proxies the paginated curated-summary search. It accepts q, gene_ids, disease_ids, summary_type, score filters, page, and per_page.

GET /curated-summaries/:id/related?limit=6 returns related organized summaries with reasons and stable summary IDs.

GET

https://adenine.ai/api/v1/curated-summaries/search?q=BRCA1&summary_type=gene_disease&page=1&per_page=20&apikey='YOUR API KEY'

Somatic fusion partners

GET /evidence/somatic/fusion-partners accepts a gene symbol or HGNC identifier, optional disease, and limit (1–100; default 20). Each result has partner and disease identifiers, document count, PMIDs, years, and evidence IDs. Document IDs and PMIDs are capped at 100 per partner, with truncation flags.

GET https://adenine.ai/api/v1/evidence/somatic/fusion-partners?gene=KMT2A&limit=20&apikey='YOUR API KEY'

Evidence by PMID

GET /evidence/by-pmid?pmid=12345678 returns compact curated records across all evidence types, with stable evidence IDs, article metadata, genes, diseases, variations, and mapping help. Use returned identifiers to retrieve summaries or related evidence.

GET https://adenine.ai/api/v1/evidence/by-pmid?pmid=12345678&apikey='YOUR API KEY'

Adenine AI API Documentation

API key

Authentication

1. Request header Recommended

2. Request parameter

Evidences

Required Path Parameters

Supported Values:

Supported Values:

Expected Formats Based on Entity:

Response (example)

Response (example)

Response (example)

Evidence (requires apikey, see authentication)

Required Path Parameters

Supported Values:

Response (example)

Aggregated Evidence

Required Query Parameters

Response (example)

Response (missing params)

Evidence Tools & Retrieval

Gene, disease, and fusion analysis

Targeted record retrieval

Additional read-only lookup endpoints

Evidence Timeline

Query parameters

Response (example)

MCP Evidence Endpoints

Curated-summary search and related summaries

Somatic fusion partners

Evidence by PMID