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Ensembl Services Platform

Introduction

This guide provides a brief overview of the Ensembl Services Platform, which implements the genes endpoint. It describes the endpoint's use, including accepted parameters.

Genes Endpoint

The putative "Ensembl Services Platform" allows users to search for a gene by its name. One web REST service is available on this platform to get all gene names corresponding to a pattern. The entry point accepts a string as parameter and return the list of matching genes in our database.

For example, if the user submit brc a list of suggested gene names may be:

  • BRCA1
  • BRCA2
  • BRCC3
  • BRCC3P1

Filtering on the gene's species is also available.

Genes Endpoint Request Example

/genes/lookup/hel?species=homo_sapiens

  • "hel" is a mandatory gene lookup example query, passed as a path parameter
  • "homo_sapiens" is an optional example query parameter to filter on species

Example Response

[
    {
        "display_label": "HELB",
        "location": "12:66302545-66347645",
        "stable_id": "ENSG00000127311",
        "species": "homo_sapiens"
    },
    {
        "display_label": "HELLPAR",
        "location": "12:102197585-102402596",
        "stable_id": "ENSG00000281344",
        "species": "homo_sapiens"
    },
    {
        "display_label": "HELLS",
        "location": "10:94501434-94613905",
        "stable_id": "ENSG00000119969",
        "species": "homo_sapiens"
    },
    {
        "display_label": "HELQ",
        "location": "4:83407343-83455855",
        "stable_id": "ENSG00000163312",
        "species": "homo_sapiens"
    },
    {
        "display_label": "HELT",
        "location": "4:185018841-185020804",
        "stable_id": "ENSG00000187821",
        "species": "homo_sapiens"
    },
    {
        "display_label": "HELZ",
        "location": "17:67070444-67245989",
        "stable_id": "ENSG00000198265",
        "species": "homo_sapiens"
    },
    {
        "display_label": "HELZ2",
        "location": "20:63558086-63574239",
        "stable_id": "ENSG00000130589",
        "species": "homo_sapiens"
    }
]

Endpoint usage limitations

  • The gene lookup path parameter is mandatory.
  • All parameters must be at least three characters long (if provided).
  • Only GET requests are accepted.
  • The lookup parameter matching is case insensitive.
  • The species parameter matching is exact.

Postman collection

A Postman Collection has been published to assist with querying the API. The collection can be accessed from the following link: https://www.getpostman.com/collections/ab2e10897deb4d350c43

Implementation Notes

This REST API endpoint was created using Django and Django Rest Framework.

A Django project named ensembl_services_platform contains a rest_endpoint app. The rest_endpoint app contains the implementation of the genes endpoint. All files were automatically generated using inbuilt commands, and unused stubs were retained (including comments with instructions).

The data source of the application is the publicly available Ensembl MySQL Database. The Django utility inspectdb was used to generate models automatically for all tables in this Database for use with this project. A database router was defined to ensure all operations of the GeneAutocomplete model are piped to the ensembl_website_97 database.

A serializer was defined to assist in creating the appropriate JSON representation of the GeneAutocomplete model instance objects which match the provided criteria.

Setting up the environment

The following notes will assist a user in setting up the endpoint on a MacOS computer for testing purposes.

A requirements.txt file is available for easy setup of a site specific Python virtual environment.

mysql, openssl and mysql-connector-c need to be installed via Homebrew.

mysql-connector-c currently has a bug when used on MacOS. The settings file needs to be modified, as described in this link: https://pypi.org/project/mysqlclient/

The following additional commands need to be typed into bash to set up OpenSSL on MacOS Mojave onwards:

export CPPFLAGS="-I/usr/local/opt/openssl/include"
export LDFLAGS="-L/usr/local/opt/openssl/lib"
export PATH="/usr/local/opt/openssl/bin:$PATH"

Issues and assumptions

  1. display_name field was not found in the gene_autocomplete table, so display_label was used instead.
  2. stable_id was manually set as the primary key of the model GeneAutocomplete. Other models had primary keys automatically denoted by the inspectdb command.
  3. It is assumed that both parameters need to be at least three characters long.
  4. Species parameter was assumed to be an exact match only.
  5. Assumption that a list of JSON objects is an appropriate response format.
  6. The response fields returned were not renamed in any way (e.g. display_label field was not renamed to "gene names").

References

  1. Setting up Django project and Apps: https://www.django-rest-framework.org/tutorial/quickstart/
  2. Connecting Django with a remote MySQL DB: https://gist.github.com/nathanielove/c51f5c4ee1d79045ffa629237e835157
  3. Using Django with an existing legacy database: https://datascience.blog.wzb.eu/2017/03/21/using-django-with-an-existinglegacy-database/