API Reference

Below is the class and function reference for the MMDB class. Please note that the package is under active development, and some features may not be stable yet.

MMDB

The MMDB class is a tool for interacting with a data repository. It provides functions for retrieving dataset information, downloading datasets, and listing datasets based on specific criteria.

# Class Definition
MMDB(storage_path=None)

  • storage_path: The path for storing the downloaded data.

Methods

# Method
mmdb.list_species() -> None

  • Lists all available species.

# Method
mmdb.list_tissue() -> None

  • Lists all available tissue types.

# Method
mmdb.list_disease() -> None

  • Lists all available diseases.

# Method
mmdb.list_technology_type() -> None

  • Lists all available technology types.

# Method
mmdb.list_technology() -> None

  • Lists all available technologies.

# Method
mmdb.list_dataset(species=None, tissue=None, disease=None, technology_type=None) -> pandas.DataFrame

  • species: Filters datasets by species.

  • tissue: Filters datasets by tissue type.

  • disease: Filters datasets by disease.

  • technology_type: Filters datasets by technology type.

  • Returns a DataFrame containing the filtered datasets.

# Method
mmdb.load_dataset(dataset_id) -> dict

  • dataset_id: The unique identifier of the dataset.

  • Downloads and loads the dataset identified by the given dataset ID.

  • Returns a dictionary where keys are data types and values are the corresponding data.

Example

from mmdb import MMDB

# Create an instance of MMDB
mmdb = MMDB(storage_path="path/to/storage")

# List available species
mmdb.list_species()

# Retrieve dataset information
datasets = mmdb.list_dataset(species="Homo sapiens")

# Load a specific dataset
dataset = mmdb.load_dataset("[Dataset_ID]")