/clinvitae

Technical Assessment for Invitae - invitae.com

Primary LanguagePython

Ben Kremer - Technical Application

Clinvitae

Running live at: https://ben-kremer-clinvitae.herokuapp.com/

Clinvitae is a genomic variant web application that allows a user to search for genomic variants based on a gene name and display the results in a table.

To run this project locally

  1. Clone repo
  2. which python3
  3. mkvirtualenv ben_kremer_clinvitae --python=<result from step 2>
  4. cd ben_kremer_clinvitae
  5. pip install -r requirements.txt
  6. python3 manage.py migrate
  7. Download variant_results.tsv file and place in management/data directory http://clinvitae.invitae.com/download
  8. python3 manage.py loadtsvdata genomic_variants/management/data/variant_results.tsv
  9. python3 manage.py runserver

Features

There are two components to the Clinvitae application, web UI access and API access (described below).

Clinvitae API V1 WIKI

The Clinvitae REST API provides simple access to read data in JSON format via HTTP GET/POST requests over http(s).

Endpoints

URL Description HTTP
api/v1/variants/ Genomic Variant List GET
api/v1/variants/:variant_id Genomic Variant Details by Variant Id GET
api/v1/gene/suggest/ Suggested Autocomplete search based on name argument GET/POST

Genomic Variant List [GET]

Example: Genomic Variant List [GET]

https://ben-kremer-clinvitae.herokuapp.com/api/v1/variants/

Response

Paginated list of Genomic Variants, as described below

Genomic Variant Detail [GET]

Response

Single Genomic Variant object with the following properties:

Name Type Description
gene integer ID of related Gene.
id integer ID of Genomic Variant.
nucleotide_change string nucleotide change.
protein_change string protein change.
other_mappings string additional mappings.
alias string alias.
transcripts string transcripts.
region string region.
reported_classification string reported classification.
inferred_classification string inferred classification.
source string source.
last_evaluated datetime last evaluated datetime.
last_updated datetime last updated datetime.
url string html url.
submitter_comment string submitter comment.
assembly string assembly.
chr string chr.
genomic_start string genomic start.
genomic_stop string genomic stop.
ref string ref.
alt string alt.
accession string accession.
reported_ref string reported ref.
reported_alt string reported alt.

Example: Genomic Variant Detail [GET]

https://ben-kremer-clinvitae.herokuapp.com/api/v1/variants/2/

{
    id: 2,
    gene: 2
    nucleotide_change: "NM_000018.3:c.1182+1G>A",
    protein_change: "",
    other_mappings: "NM_000018.3:c.1182+1G>A,NG_007975.1:g.8405G>A,NC_000017.11:g.7223238G>A,NC_000017.10:g.7126557G>A,NM_000018.2:c.1182+1G>A",
    alias: "",
    transcripts: "NM_000018.3,NG_007975.1,NC_000017.11,NC_000017.10,NM_000018.2",
    region: "NM_000018.3:IVS11",
    reported_classification: "Pathogenic",
    inferred_classification: "Pathogenic",
    source: "ClinVar",
    last_evaluated: "2014-05-15T00:00:00Z",
    last_updated: "2017-09-14T00:00:00Z",
    url: "https://www.ncbi.nlm.nih.gov/clinvar/RCV000077901",
    submitter_comment: "",
    assembly: "GRCh37",
    chr: "17",
    genomic_start: "7126556",
    genomic_stop: "7126557",
    ref: "G",
    alt: "A",
    accession: "NC_000017.10",
    reported_ref: "G",
    reported_alt: "A",
}

Gene Name suggests [GET]

Request Query Parameters

Name Format Description
name string Retrieve Gene's beginning with this string

Example: Suggested Gene names [GET]

https://ben-kremer-clinvitae.herokuapp.com/api/v1/gene/suggest/?name=a

{
    results: [{
            id: "3142",
            text: "A1BG-AS1"
        },
        {
            id: "2927",
            text: "A1CF"
        },
        {
            id: "44",
            text: "AADAC"
        },
        {
            id: "2914",
            text: "AADACL2-AS1"
        },
    ],
    pagination: {
        more: true
    }
}