医学公开数据库查询与登记

references/omim.md

Base URL

https://api.omim.org/api

Authentication

API key REQUIRED. Request at https://omim.org/api (free for academic/non-commercial use).

• Pass as query parameter: ?apiKey=YOUR_API_KEY
• All requests require the key; unauthenticated requests are rejected.

Rate Limits

Not publicly documented in detail. Reasonable usage expected per terms of service.

Response Format

JSON (with &format=json) or XML (default). Always append &format=json for JSON responses.

Key Endpoints

1. Entry Lookup (by MIM number)

GET https://api.omim.org/api/entry?mimNumber={mim_number}&apiKey={key}&format=json

Example:

GET https://api.omim.org/api/entry?mimNumber=141900&apiKey=YOUR_KEY&format=json

Returns entry metadata; request text, gene maps, allelic variants and references with the corresponding include options.

2. Entry with Specific Includes

GET https://api.omim.org/api/entry?mimNumber=141900&include=text&include=allelicVariantList&include=geneMap&apiKey={key}&format=json

Include options: text, clinicalSynopsis, geneMap, allelicVariantList, referenceList, existFlags, externalLinks.

3. Search Entries

GET https://api.omim.org/api/entry/search?search={query}&apiKey={key}&format=json

Example — search for "Marfan syndrome":

GET https://api.omim.org/api/entry/search?search=marfan+syndrome&apiKey=YOUR_KEY&format=json&start=0&limit=10

4. Search filters

/entry/search accepts a filter search expression, fields, operator=AND|OR, and sort. filter is not an enum of gene, phenotype, and clinical_synopsis. Use fielded OMIM search syntax from OMIM search help, or construct the query with the official API form. Do not invent unsupported filter values.

5. Gene Map Lookup

GET https://api.omim.org/api/geneMap?chromosome={chrom}&apiKey={key}&format=json

Example:

GET https://api.omim.org/api/geneMap?chromosome=17&apiKey=YOUR_KEY&format=json&start=0&limit=10

6. Gene Map Search

GET https://api.omim.org/api/geneMap/search?search={query}&apiKey={key}&format=json

7. Clinical Synopsis Search

GET https://api.omim.org/api/clinicalSynopsis/search?search={query}&apiKey={key}&format=json

Response Structure (illustrative; fields depend on requested includes)

{
  "omim": {
    "version": "1.0",
    "entryList": [
      {
        "entry": {
          "mimNumber": 141900,
          "status": "live",
          "titles": {
            "preferredTitle": "HEMOGLOBIN--BETA LOCUS; HBB"
          },
          "textSectionList": [...],
          "geneMap": {
            "chromosome": "11",
            "cytoLocation": "11p15.4",
            "geneSymbols": "HBB"
          }
        }
      }
    ]
  }
}

Pagination

Use start and limit query parameters:

&start=0&limit=20

MIM Number Types

• Asterisk (*): Gene
• Plus (+): Gene with known phenotype
• Number sign (#): Phenotype (molecular basis known)
• Percent (%): Phenotype (molecular basis unknown)
• Null: Other entry types

Notes

• OMIM data is copyrighted; API access is free for academic use but requires registration.
• The API does not support bulk downloads; use OMIM downloads page with separate agreement.
• Cross-reference MIM numbers with ClinVar, NCBI Gene, and HPO for integrated disease analysis.