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Guide to Implementing a dataset

Pre-Requisites

Please make a github account prior to implementing a dataset; you can follow instructions to install git here.

You will also need at least Python 3.6+. If you are installing python, we recommend downloading anaconda to curate a python environment with necessary packages. We strongly recommend Python 3.8+ for stability.

Optional Setup your GitHub account with SSH (instructions here.)

1. Setup a local version of the bigscience-biomed repo

Fork the bigscience-biomed dataset repository to your local github account. To do this, click the link to the repository and click "fork" in the upper-right corner. You should get an option to fork to your account, provided you are signed into Github.

After you fork, clone the repository locally. You can do so as follows:

git clone [email protected]:<your_github_username>/biomedical.git
cd biomedical  # enter the directory

Next, you want to set your upstream location to enable you to push/pull (add or receive updates). You can do so as follows:

git remote add upstream [email protected]:bigscience-workshop/biomedical.git

You can optionally check that this was set properly by running the following command:

git remote -v

The output of this command should look as follows:

origin  [email protected]:<your_github_username>/biomedical.git(fetch)
origin  [email protected]:<your_github_username>/biomedical.git (push)
upstream    [email protected]:bigscience-workshop/biomedical.git (fetch)
upstream    [email protected]:bigscience-workshop/biomedical.git (push)

If you do NOT have an origin for whatever reason, then run:

git remote add origin [email protected]:<your_github_username>/biomedical.git

The goal of upstream is to keep your repository up-to-date to any changes that are made officially to the datasets library. You can do this as follows by running the following commands:

git fetch upstream
git pull

Provided you have no merge conflicts, this will ensure the library stays up-to-date as you make changes. However, before you make changes, you should make a custom branch to implement your changes.

You can make a new branch as such:

git checkout -b <dataset_name>

Please do not make changes on the master branch!

Always make sure you're on the right branch with the following command:

git branch

The correct branch will have a asterisk * in front of it.

2. Create a development environment

You can make an environment in any way you choose to. We highlight two possible options:

2a) Create a conda environment

The following instructions will create an Anaconda bigscience-biomedical environment.

  • Install anaconda for your appropriate operating system.
  • Run the following command while in the biomedical folder (you can pick your python version):
conda env create -f conda.yml  # Creates a conda env
conda activate bigscience-biomedical  # Activate your conda environment

You can deactivate your environment at any time by either exiting your terminal or using conda deactivate.

2b) Create a venv environment

Python 3.3+ has venv automatically installed; official information is found here.

python3 -m venv <your_env_name_here>
source <your_env_name_here>/bin/activate  # activate environment
pip install -r requirements.txt # Install this while in the datasets folder

Make sure your pip package points to your environment's source.

3. Implement your dataset

Make a new directory within the biomedical/bigbio/biodatasets directory:

mkdir bigbio/biodatasets/<dataset_name>

Add an __init__.py file to this directory:

touch bigbio/biodatasets/<dataset_name>/__init__.py

Please use lowercase letters and underscores when choosing a <dataset_name>. To implement your dataset, there are three key methods that are important:

  • _info: Specifies the schema of the expected dataloader
  • _split_generators: Downloads and extracts data for each split (e.g. train/val/test) or associate local data with each split.
  • _generate_examples: Create examples from data that conform to each schema defined in _info.

To start, copy templates/template.py to your biomedical/bigbio/biodatasets/<dataset_name> directory with the name <dataset_name>.py. Within this file, fill out all the TODOs.

cp templates/template.py bigbio/biodatasets/<dataset_name>/<dataset_name>.py

For the _info_ function, you will need to define features for your DatasetInfo object. For the bigbio config, choose the right schema from our list of examples. You can find a description of these in the Task Schemas Document. You can find the actual schemas in the schemas directory.

You will use this schema in the _generate_examples return value.

Populate the information in the dataset according to this schema; some fields may be empty.

To enable quality control, please add the following line in your file before the class definition:

from bigbio.utils.constants import Tasks
_SUPPORTED_TASKS = [Tasks.NAMED_ENTITY_RECOGNITION, Tasks.RELATION_EXTRACTION]

If your dataset is in a standard format, please use a recommended parser if available:

If the recommended parser does not work for you dataset, please alert us in Discord, Slack or the github issue.

Example scripts:

To help you implement a dataset, we offer example scripts.

Running & Debugging:

You can run your data loader script during development by appending the following statement to your code (templates/template.py already includes this):

if __name__ == "__main__":
    datasets.load_dataset(__file__)

If you want to use an interactive debugger during development, you will have to use breakpoint() instead of setting breakpoints directly in your IDE. Most IDEs will recognize the breakpoint() statement and pause there during debugging. If your prefered IDE doesn't support this, you can always run the script in your terminal and debug with pdb.

4. Check if your dataloader works

Make sure your dataset is implemented correctly by checking in python the following commands:

from datasets import load_dataset

data = load_dataset("bigbio/biodatasets/<dataset_name>/<dataset_name>.py", name="<dataset_name>_bigbio_<schema>")

Run these commands from the top level of the biomedical repo (i.e. the same directory that contains the requirements.txt file).

Once this is done, please also check if your dataloader satisfies our unit tests as follows by using this command in the terminal:

python -m tests.test_bigbio bigbio/biodatasets/<dataset_name>/<dataset_name>.py [--data_dir /path/to/local/data]

Your particular dataset may require use of some of the other command line args in the test script. To view full usage instructions you can use the --help command,

python -m tests.test_bigbio --help

5. Format your code

From the main directory, run the Makefile via the following command:

make check_file=bigbio/biodatasets/<dataset_name>/<dataset_name>.py

This runs the black formatter, isort, and lints to ensure that the code is readable and looks nice. Flake8 linting errors may require manual changes.

6. Commit your changes

First, commit your changes to the branch to "add" the work:

git add bigbio/biodatasets/<dataset_name>/<dataset_name>.py
git commit -m "A message describing your commits"

Then, run the following commands to incorporate any new changes in the master branch of datasets as follows:

git fetch upstream
git rebase upstream/master

Run these commands in your custom branch.

Push these changes to your fork with the following command:

git push -u origin <dataset_name>

7. Make a pull request

Make a Pull Request to implement your changes on the main repository here. To do so, click "New Pull Request". Then, choose your branch from your fork to push into "base:master".

When opening a PR, please link the issue corresponding to your dataset using closing keywords in the PR's description, e.g. resolves #17.