API for Genetic Diseases
The genetic diseases dataset was created by the National Center for Biomedical Information at the U.S. National Library of Medicine for the ClinVar public database. ClinVar is a freely accessible, public archive of reports of the relationships among human genetic variations and phenotypes, with supporting evidence.
This API returns the subset of the ClinVar disease names file whose entries have a value in the ConceptID field.
Source file: ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/disease_names
This service is provided "as is" and free of charge. Please see the Frequently Asked Questions page for more details on terms of service, etc.API Demo
The following demo shows how this API might be used with an autocompleter we've developed.
For further experimentation with the autocompleter and this API, try the autocompleter demo page.
API Documentation
API Base URL: https://clinicaltables.nlm.nih.gov/api/disease_names/v3/search (+ query string parameters)
This data set may also be accessed through the FHIR ValueSet $expand operation.
In addition to the base URL, you will need to specify other parameters. See the query string parameters section below for details.
Query String Parameters and Default Values
At a minimum, when using the above base URL, you will need to specify the "terms" parameter containing a word or partial word to match.
| Parameter Name | Default Value | Description |
|---|---|---|
| terms | (Required.) The search string (e.g., just a part of a word) for which to find matches in the list. More than one partial word can be present in "terms", in which case there is an implicit AND between them. | |
| maxList | 7 | Optional, with a default of 7. Specifies the number of results requested, up to the upper limit of 500. If present but the value is empty, 500 will be used. Note that this parameter does not support pagination, see "count" and "offset" below for details on pagination support. |
| count | 7 | The number of results to retrieve (page size). The maximum count allowed is 500, see "offset" below on pagination support. |
| offset | 0 | The starting result number (0-based) to retrieve. Use offset and count together for pagination. Note that the current limit on the total number of results that can be retrieved (offset + count) is 7,500. We reserve the right to decrease or increase this limit based on system capacity and/or other factors. Please see the FAQ page on how to sign up to our email list to be notified of any changes or new features. |
| q | An optional, additional query string used to further constrain the results returned by the "terms" field. Unlike the terms field, "q" is not automatically wildcarded, but can include wildcards and can specify field names. See the Elasticsearch query string page for documentation of supported syntax. | |
| df | DiseaseName | A comma-separated list of display
fields (from the fields section below) which are
intended for the user to see when looking at the results. The parameter "ef" (see below) may also be used to specify the data fields to retrieve. The main difference is that the value of "df" is always a string (for display), while the value for "ef" could be a json object when the field value has a complex structure. |
| sf | DiseaseName, ConceptID | A comma-separated list of fields to be searched. |
| cf | ConceptID | A field to regard as the "code" for the returned item data. |
| ef | A comma-separated list of additional fields to be
returned for each retrieved list item. (See the Output format section for how the data for fields
is returned.) If you wish the keys in the returned data hash to be something
other than the field names, you can specify an alias for the field name by
separating it from its field name with a colon, e.g.,
"ef=field_name1:alias1,field2,field_name3:alias3,etc. Note that not
every field specified in the ef parameter needs to have an alias. The parameter "df" (see above) may also be used to specify the data fields to retrieve. The main difference is that the value of "df" is always a string (for display), while the value for "ef" could be a json object when the field value has a complex structure. |
Disease Name Field Descriptions
| Field | Field Description |
|---|---|
| DiseaseName | The disease name, taken from the DiseaseName column of the ClinVar disease names file. |
| ConceptID | An ID for the disease name, taken from the ConceptID column of the ClinVar disease names file. |
Output format
Output for an API query is an array of the following elements:
- The total number of results on the server, which can be more than the number of results returned. This reported total number of results may also be significantly less than the actual number of results and is limited to 10,000, which may significantly improve the service response time.
- An array of codes for the returned items. (This is the field specified with the cf query parameter above.)
- A hash of the "extra" data requested via the "ef" query parameter above. The keys on the hash are the fields (or their requested aliases) named in the "ef" parameter, and the value for a field is an array of that field's values in the same order as the returned codes.
- An array, with one element for each returned code, where each element is an array of the display strings specified with the "df" query parameter.
- An array, with one element for each returned code, where each element is the "code system" for the returned code. Note that only code-system aware APIs will return this array.
Sample API Queries
| Query | Result | Description |
|---|---|---|
| https://clinicaltables.nlm.nih.gov/api/disease_names/v3/search?terms=pleur | [11,["Abnormality of the pleura","DICER1-related pleuropulmonary blastoma cancer predisposition syndrome","Pleuropulmonary blastoma","Pleural effusion","Exudative pleural effusion","Transudative pleural effusion","Pleural empyema","Pleural lymphangiectasia","Pleural mesothelioma","Neoplasia of the pleura","Pleuritis"],null,[["Abnormality of the pleura"],["DICER1-related pleuropulmonary blastoma cancer predisposition syndrome"],["Pleuropulmonary blastoma"],["Pleural effusion"],["Exudative pleural effusion"],["Transudative pleural effusion"], ["Pleural empyema"],["Pleural lymphangiectasia"],["Pleural mesothelioma"],["Neoplasia of the pleura"],["Pleuritis"]]] | Returns a complete count of the 11 medical conditions that match the string "pleur", displaying all 11 terms. Because this dataset has no code field, the default term search returns the disease names in the code field as well. |