sgd-rest 0.1.4

Saccharomyces Genome Database (SGD) REST API wrapper

sgd-rest

Saccharomyces Genome Database (SGD) REST API wrapper. Refer to the SGD REST page for information about API usage and terms of service.

Installation

pip install sgd-rest --upgrade

Quick start

Get GO (gene ontology) details for gene ARO1.

import sgd

aro1 = sgd.gene("ARO1")
aro1.go_details.json()

# >>> [{'id': 9761727, 'annotation_type': 'computational', 'date_created': '2024-10-14', 'qualifier': 'enables', 'locus': {'display_name': 'ARO1', 'link': '/locus/S000002534', 'id': 1284912, 'format_name': 'YDR127W'}, 'go': {'display_name': 'lyase activity', 'link': '/go/GO:0016829', 'go_id': 'GO:0016829', 'go_aspect': 'molecular function', 'id': 291052}, ...]

Background

Easily navigate the SGD REST API with Python.

Classes

Class	Description	Example
locus	Query SGD REST using locus ID.	locus("S000002534")
gene	Query SGD REST using gene name.	gene("ARO1")
phenotype	Query SGD REST using phenotype name.	phenotype("increased_chemical_compound_accumulation")
go	Query SGD REST using GO ID.	go("GO:0000001")

Instantiate the SGD class prior to working with subclasses:

import sgd

aro1 = sgd.gene("ARO1")

Subclasses

Use the endpoints attribute to display subclasses of a class:

import sgd

print(sgd.gene.endpoints)

Class	Subclass	Description
locus & gene	details	Gets basic information about a locus.
locus & gene	go_details	Gets GO (gene ontology) annotations and the references used to make them.
locus & gene	interaction_details	Gets interaction annotations and the references used to make them.
locus & gene	literature_details	Gets references which refer to a gene, organized by subject of relevance.
locus & gene	neighbor_sequence_details	Gets get sequences for neighboring loci in the strains for which they are available.
locus & gene	phenotype_details	Gets phenotype annotations and the references used to make them.
locus & gene	posttranslational_details	Gets posttranslational protein data.
locus & gene	protein_domain_details	Gets protein domains, their sources, and their positions relative to protein sequence.
locus & gene	protein_experiment_details	Gets metadata and data values for protein experiments.
locus & gene	regulation_details	Gets regulation annotations and the references used to make them.
locus & gene	sequence_details	Gets sequence for genomic, coding, protein, and +/- 1KB sequence.
phenotype	details	Gets basic information about a phenotype.
phenotype	locus_details	Gets a list of genes annotated to a phenotype with some information about the experiment and strain background.
go	details	Gets basic information about a GO term.
go	locus_details	Gets a list of genes annotated to a GO term.

Use a subclass to retrieve the endpoint's response. This library utilizes the requests library, returning a requests.models.Response instance. Use this instance to define how the REST API content should be processed.

For example, for gene ARO1, get GO details as JSON and literature details as text:

import sgd

aro1 = sgd.gene("ARO1")
aro1.go_details.json()
aro1.literature_details.text

Advanced

Just like a subclass returns a requests.models.Response instance, the user can pass keyword arguments directly to the requests.get method during class instantiation. For example, you can add a header to prevent server-side caching and parse the locus details response as text:

import sgd

go_0000001 = sgd.go("GO:0000001", headers={"Cache-Control": "no-cache", "Pragma": "no-cache"})
go_0000001.locus_details.text

Additional attributes

• url: Gets the endpoint's URL. Available for all classes.
• locus_id: Gets the endpoint's locus ID. Avaialble for locus and gene classes.

import sgd

tor2 = sgd.gene("TOR2")

# 1 
print(tor2.url)
# >>> 'https://www.yeastgenome.org/backend/locus/S000001686'

# 2
print(tor2.locus_id)
# >>> 'S000001686'

Exceptions

• InvalidGene: An invalid gene was queried.

import sgd
from sgd.exceptions import InvalidGene

try:
    bad_gene = sgd.gene("BadGene")
except InvalidGene:
    print("Whoops, an invalid gene was queried.")

Contribute

• Issues Tracker
• Source Code

Support

If you are having issues or would like to propose a new feature, please use the issues tracker.

License

This project is licensed under the MIT license.