Python client for the OBIS API.
Source on GitHub at iobis/pyobis
Pyobis is an interesting python package that helps users fetch data from OBIS API which holds a great amount of ocean open-data, with ease.
The Ocean Biodiversity Information System (OBIS), a global open-access data and information clearing-house on marine biodiversity for science, conservation, and sustainable development, maintained by IOOS, harvests occurrence records from thousands of datasets and makes them available as a single integrated dataset via various services including the OBIS API.
Other OBIS clients:
- R: robis, iobis/robis
Here are just a few of things pyOBIS can do:
- Easy handling of OBIS data, easy fetching without handling the raw API response directly.
- Built-in functions for
occurrence,taxon,node,checklistanddatasetendpoints of OBIS API. - Provides easy export of data to
PandasDataFrame, and helps researchers focus more on analysis rather than data mining.
For examples of how to use this repo, see the jupyter notebooks in the /notebooks/ directory.
NOTE: GitHub's jupyter notebook display does not show interactive plots; open the notebooks in a jupyter hub (eg colab, binder, etc) for the full experience.
Install from pypi
pip install pyobisInstall latest dev version from github
pip install git+git://github.com/iobis/pyobis.git#egg=pyobisInstall editable dev version from github for local development. System prerequisites: python3, conda
# fetch code
git clone [email protected]:iobis/pyobis.git
cd pyobis
# install
python -m pip install -r requirements.txt
python -m pip install -r requirements-dev.txt
python -m pip install -e .
# test your installation
python -m pytest
# test and generate a coverage report
python -m pytest -rxs --cov=pyobis testsThe official documentation is hosted on GitHub Pages https://iobis.github.io/pyobis.
pyobis is split up into modules for each of the groups of API methods.
taxa- Taxonomic namesoccurrences- Occurrence searchdataset- Datasetnodes- Nodeschecklist- Checklist
You can import the entire library, or each module individually as needed.
For a detailed usage guide with information about inputs, output and module functions please read the Usage Guide
Some Jupyter Notebook based sample analysis and visualization of data grabbed through pyobis have been made available through /notebooks/ directory.
To get full experience of the interactive plots (eg. geoplots, etc) please open notebooks in a Jupyter Hub (eg. through Google Colab, Binder, local installation, etc.)
- License: MIT, see LICENSE file
- Help make this project even more useful! Please read the Contributing Guide.
- Please note that this project is released with a Contributor Code of Conduct. By participating in this project you agree to abide by its terms.
- In case you face data quality issues, please look at OBIS QC repo
- For issues with the package itself, feel free to open an issue here!