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Notebook","category":"Biosphere","sub_category":"Biodiversity Data Access and Management","monthly_downloads":218,"total_dependent_repos":3,"total_dependent_packages":0,"readme":"# pyobis\n\n[![pypi](https://img.shields.io/pypi/v/pyobis.svg)](https://pypi.python.org/pypi/pyobis)\n[![Conda Version](https://img.shields.io/conda/vn/conda-forge/pyobis.svg)](https://anaconda.org/conda-forge/pyobis)\n[![docs](https://github.com/iobis/pyobis/actions/workflows/deploy-docs.yml/badge.svg)](https://iobis.github.ic/pyobis)\n[![tests](https://github.com/iobis/pyobis/actions/workflows/tests.yml/badge.svg)](https://github.com/iobis/pyobis/actions/workflows/tests.yml)\n\nPython client for the [OBIS API](https://api.obis.org/).\n\n[Source on GitHub at iobis/pyobis](https://github.com/iobis/pyobis)\n\nTry it out:\n\n[![Open In Collab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/iobis/pyobis)\n\n\n## What is it?\nPyobis is an interesting python package that helps users fetch data from OBIS API which\nharvests occurrence records from thousands of datasets and makes them available as a\nsingle integrated dataset.\n\n[The Ocean Biodiversity Information System (OBIS)](https://obis.org) is a global open-access data and\ninformation clearing-house on marine biodiversity for science, conservation, and sustainable\ndevelopment, maintained by IOOS.\n\nOther OBIS clients:\n\n+ R: `robis`, [iobis/robis](https://github.com/iobis/robis)\n\n## Main Features\nHere are just a few of things pyOBIS can do:\n\n+ Easy handling of OBIS data, easy fetching without handling the raw API response directly.\n+ Built-in functions for `occurrence`, `taxon`, `node`, `checklist` and `dataset` endpoints of OBIS API.\n+ Provides easy export of data to `Pandas` DataFrame, and helps researchers focus more on analysis rather than data mining.\n\nFor examples of how to use this repo, see the jupyter notebooks in the `/notebooks/` directory.\nNOTE: 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.\n\n## Installation\n\n### Install from PyPI\n\n```bash\npip install pyobis\n```\n### Install from conda-forge\n\nInstalling pyobis from the conda-forge channel can be achieved by adding conda-forge to your channels with:\n\n```bash\nconda install pyobis --channel conda-forge\n```\n[More information here](https://github.com/conda-forge/pyobis-feedstock)\n\n## Usage\n\n```python\nfrom pyobis import occurrences\n\n# Search for occurrences\nquery = occurrences.search(scientificname=\"Mola mola\")\ndata = query.execute()\n\n# Get occurrence by ID\nquery = occurrences.get(id=\"00003cf7-f2fc-4c53-98a6-7d846e70f5d1\")\ndata = query.execute()\n```\n\n## Documentation\n\nFor more information, see the [documentation](https://pyobis.readthedocs.io/).\n\n## License\n\nThis project is licensed under the MIT License - see the [LICENSE](LICENSE) file for details.\n\n## Contributing\n\nPlease read [CONTRIBUTING.md](CONTRIBUTING.md) for details on our code of conduct and the process for submitting pull requests.\n\n## Library API\n\n`pyobis` is split up into modules for each of the groups of API methods.\n\n+ `checklist` - Checklist. Generate a checklist of species under a taxa, IUCN Red List, or most recently added species.\n+ `dataset` - Dataset. Get metadata of datasets (including `datasetid`, `owner`, `institution`, `number of records`, etc) for a queried spatiotemporal region or taxa.\n+ `nodes` - Nodes. Get records or activities for an OBIS node.\n+ `occurrences` - Occurrence. Fetch occurrence records, geopoints, lookup for a `scientificname`, extensions (e.g. DNADerivedData, MeasurementOrFacts, etc.)\n+ `taxa` - Taxonomic names. Get taxon records with `taxonid` or `scientificname`, and scientific name annotations by the WoRMS team.\n\nYou can import the entire library, or each module individually as needed.\n\n## Usage Guide\n\nFor a detailed usage guide with information about inputs, output and module functions please read the [Usage Guide](notebooks/usage_guide.ipynb)\n\n## Sample analysis\n\nSome Jupyter Notebook based sample analysis and visualization of data grabbed through `pyobis` have been made available through `/notebooks/` directory.\nTo 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.)\n\n## Meta\n\n* License: MIT, see [LICENSE file](LICENSE)\n* Help make this project even more useful! Please read the [Contributing Guide](CONTRIBUTING.md).\n* Please note that this project is released with a [Contributor Code of Conduct](CONDUCT.md). By participating in this project you agree to abide by its terms.\n\n## Further Reading\n\n* In case you face data quality issues, please look at [OBIS QC repo](https://github.com/iobis/obis-qc)\n* For issues with the package itself, feel free to open an issue here!\n","funding_links":[],"readme_doi_urls":[],"works":{},"citation_counts":{},"total_citations":0,"keywords_from_contributors":["climate","marine-biology"],"project_url":"https://ost.ecosyste.ms/api/v1/projects/347728","html_url":"https://ost.ecosyste.ms/projects/347728"}