Genomics API
You need to apply an API token if you want to access the data in your programs.
The API token is unique for each user. It will be allocated by CMDB and should not be shared with others. The API token will be used to validate the requests are legal or not.
Requests to the CMDB Genomics API for variant data must be accompanied by an identifier, which can just be the API token. It will return 403 if the token is not right or empty.
Overview
The CMDB Genomics API is created to enable researchers to better access CMDB variants data across remote sites. For example, instead of searching variants one by one in the website, the API allows retrieval of variants’ information. CMDB Genomics API currently supports access to variant information via position or RSID.
For more information please see this manual.
Schemas and formats
The CMDB Genomics API is created to enable researchers to better access CMDB variants data across remote sites. For example, instead of searching variants one by one in the website, the API allows retrieval of variants’ information. CMDB Genomics API currently supports access to variant information via position or RSID.
For more information please see this manual.
On the wire, the CMDB Genomics API takes the form of a client and a server exchanging JSON-serialized objects over HTTPS.
Getting Start
Here shows how to request a single variant by API token.
Query Parameters
| Parameter | Description |
|---|---|
| variant | The objects used to represent variant information. |
| type | The type of data. |
| query | Requests for data |
| token=$key | API token |
Supporing endpoints for CMDB entities
| CMDB Entitity | Base Path |
|---|---|
| position | api/v1.0/variant?type=position |
| rs | api/v1.0/variant?type=rs |
Example
Http Request
https://cmdb.bgi.com/cmdb/api/v1.0/variant?type=position&query=chr22-36955161&token=$key
https://cmdb.bgi.com/cmdb/api/v1.0/variant?type=rs&query=rs148755828&token=$key`
Running the query returns
Here is a serialized variant in JSON:
[
{
"allele_count": 27,
"allele_freq": 0.00218,
"allele_num": 10589,
"alt": "A",
"chrom": "4",
"filter_status": "PASS",
"genes": [
"ENSG00000131127"
],
"pos": 370328,
"ref": "T",
"rsid": "rs189432301",
"site_quality": 30.12,
"transcripts": [
"ENST00000240499"
],
"variant_id": "4-370328-T-A",
"xstart": 4000370328,
"xstop": 4000370328
}
]Entry Reference Data
| Parameter | Description |
|---|---|
| variant_id | chr:pos variant’s position consist of chromosomal id and position |
| rsid | dbSNP RSID |
| filter_status | Whether the variants passed QC or not. |
| chrom | Chromosome (e.g.chr20 or X) |
| allele_count | Alternate allele count |
| allele_num | Total number of alleles(i.e. Total read count in CMDB) |
| allele_freq | Alternate allele frenquencyin CMDB.The graphic displays allele frequency on a discrete:<2/1000,<5/1000,<1%,<5%,<10%,<50%,>50% |
| site_quality | Phred-scaled quality score for the assertion made in ALT. |
| xstop | End position of the variant described in this record. |
| genes | reference genes. |
| alt | List of alternate non-reference alleles. |
| ref | Reference base.Each base must be one of A,C,G,T (case insensitive). |
| xStart | The reference position, with the first base having position 1. |
| transcripts | A transcript is the operational unit of a gene. In a genomic context, transcripts consist of one or more exons, with adjoining exons being separated by introns. The exons/introns are transcribed and then the introns spliced out. Transcripts may or may not encode a protein. |
| Feature_type | Feature that is annotated by this region. |
Return Code Description
| Return Code | Error code description | Descrition |
|---|---|---|
| 404 | Unauthorized | query not found |
| 403 | Bad Request | malformed request syntax,invalid request |