128 lines
3.5 KiB
Markdown
128 lines
3.5 KiB
Markdown
---
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title: "OMIM (Online Mendelian Inheritance in Man) API Reference"
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task: ""
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lineage_type: import
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upstream_source: https://github.com/K-Dense-AI/scientific-agent-skills/blob/9c9bd2e9/skills/database-lookup/references/omim.md
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upstream_sha: 9c9bd2e9
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imported_at: 2026-06-26
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prompt_class: prompt
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upstream_changes: accepted
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author: upstream
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validated: false
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---
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# OMIM (Online Mendelian Inheritance in Man) API Reference
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## Base URL
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```
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https://api.omim.org/api
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```
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## Authentication
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**API key REQUIRED.** Request at https://omim.org/api (free for academic/non-commercial use).
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- Pass as query parameter: `?apiKey=YOUR_API_KEY`
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- All requests require the key; unauthenticated requests are rejected.
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## Rate Limits
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Not publicly documented in detail. Reasonable usage expected per terms of service.
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## Response Format
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JSON (with `&format=json`) or XML (default). Always append `&format=json` for JSON responses.
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## Key Endpoints
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### 1. Entry Lookup (by MIM number)
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```
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GET https://api.omim.org/api/entry?mimNumber={mim_number}&apiKey={key}&format=json
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```
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Example:
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```
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GET https://api.omim.org/api/entry?mimNumber=141900&apiKey=YOUR_KEY&format=json
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```
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Returns entry with title, text, gene map, allelic variants, references.
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### 2. Entry with Specific Includes
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```
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GET https://api.omim.org/api/entry?mimNumber=141900&include=text&include=allelicVariantList&include=geneMap&apiKey={key}&format=json
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```
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Include options: `text`, `clinicalSynopsis`, `geneMap`, `allelicVariantList`, `referenceList`, `existFlags`, `externalLinks`.
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### 3. Search Entries
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```
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GET https://api.omim.org/api/entry/search?search={query}&apiKey={key}&format=json
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```
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Example — search for "Marfan syndrome":
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```
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GET https://api.omim.org/api/entry/search?search=marfan+syndrome&apiKey=YOUR_KEY&format=json&start=0&limit=10
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```
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### 4. Search with Filters
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```
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GET https://api.omim.org/api/entry/search?search={query}&filter=gene&apiKey={key}&format=json
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```
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Filter options: `gene`, `phenotype`, `clinical_synopsis`, etc.
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### 5. Gene Map Lookup
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```
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GET https://api.omim.org/api/geneMap?chromosome={chrom}&apiKey={key}&format=json
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```
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Example:
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```
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GET https://api.omim.org/api/geneMap?chromosome=17&apiKey=YOUR_KEY&format=json&start=0&limit=10
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```
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### 6. Gene Map Search
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```
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GET https://api.omim.org/api/geneMap/search?search={query}&apiKey={key}&format=json
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```
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### 7. Clinical Synopsis Search
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```
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GET https://api.omim.org/api/clinicalSynopsis/search?search={query}&apiKey={key}&format=json
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```
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## Response Structure
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```json
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{
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"omim": {
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"version": "1.0",
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"entryList": [
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{
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"entry": {
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"mimNumber": 141900,
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"status": "live",
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"titles": {
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"preferredTitle": "HEMOGLOBIN S; HBS",
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"alternativeTitles": "SICKLE CELL ANEMIA"
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},
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"textSectionList": [...],
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"geneMap": {
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"chromosome": "11",
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"cytoLocation": "11p15.4",
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"geneSymbols": "HBB"
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}
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}
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}
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]
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}
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}
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```
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## Pagination
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Use `start` and `limit` query parameters:
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```
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&start=0&limit=20
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```
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## MIM Number Types
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- **Asterisk (*)**: Gene
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- **Plus (+)**: Gene with known phenotype
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- **Number sign (#)**: Phenotype (molecular basis known)
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- **Percent (%)**: Phenotype (molecular basis unknown)
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- **Null**: Other entry types
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## Notes
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- OMIM data is copyrighted; API access is free for academic use but requires registration.
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- The API does not support bulk downloads; use OMIM downloads page with separate agreement.
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- Cross-reference MIM numbers with ClinVar, NCBI Gene, and HPO for integrated disease analysis.
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