API for RefSeqs

This API provides access to information about RefSeqs for assembly GRCh37 of the human genome, taken from NCBI's Genome dataset.

Source file: ref_GRCh37.p5_top_level.gff3.gz

This processed data includes RefSeqs with prefixes NM, NR, NP, NC, and NG. NM, NR, and NP RefSeqs will have an associated NC RefSeq (in the field NC_RefSeq) and a gene symbol if present in the source file. NM RefSeqs will also have an associated NP RefSeq in the NP_RefSeq field.

API Demo

The following demo shows how this API might be used with an autocompleter we've developed. (Example: Try typing NM.)

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/refseqs/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 NameDefault ValueDescription
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 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.
qAn 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.
dfRefSeq, gene, NP_RefSeq, NC_RefSeqA comma-separated list of display fields (from the fields section below) which are intended for the user to see when looking at the results.
sfAll fieldsA comma-separated list of fields to be searched.
cfRefSeqA field to regard as the "code" for the returned item data.
efA 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.

RefSeqs Field Descriptions

FieldField Description
RefSeqThe RefSeq accession number.
geneThe symbol of a gene (if any) associated with the RefSeq.
NP_RefSeqIf the RefSeq has an NM prefix, this will be the associated NP RefSeq.
NC_RefSeqIf the RefSeq has an NM prefix, this will be the associated NC RefSeq.

Output format

Output for an API query is an array of the following elements:

  1. The total number of results on the server (which can be more than the number returned). For APIs in which there are millions of records, this number might be a lower bound due to early termination if there are more than a hundred thousand results.
  2. An array of codes for the returned items. (This is the field specified with the cf query parameter above.)
  3. 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.
  4. 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.
  5. 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

QueryResultDescription
https://clinicaltables.nlm.nih.gov/api/refseqs/v3/search?terms=MTX1 [2,["NM_002455.3","NM_198883.2"],null,[["NM_002455.3","MTX1","NC_000001.10"], ["NM_198883.2","MTX1","NC_000001.10"]]] Finds two NM RefSeqs for gene MTX1. The RefSeqs are returned as code fields, no extra data was requested ("ef" was not specified in the URL), and finally the three (default) display fields for each record are returned.