Submitting Author: Name (@github_handle)
All current maintainers: (@ayushanand18, @7yl4r)
Package Name: pyOBIS
One-Line Description of Package: OBIS python client.
Repository Link: https://github.com/iobis/pyobis
Version submitted: 1.4.0
Editor: TBD
Reviewer 1: TBD
Reviewer 2: TBD
Archive: TBD
Version accepted: TBD Date accepted (month/day/year): TBD

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Description

The pyOBIS python package provides easy access to marine taxonomic occurrence records harvested from thousands of datasets. The package uses the API from the Ocean Biodiversity Information System (OBIS), a global open-access data and information clearinghouse on marine data for biodiversity for science, conservation, and sustainable development. As of 2023, OBIS had more than 107 million occurrence records availibile, but accesibility remains a major challenge for oceanographic researchers. pyOBIS solves the challenge by providing built-in functions for accessing data on occurrences, taxons, nodes, checklists, and dataset metadata. Users can download, visualize, segment, process and export data to any format of your choice with its built-in tools or rich ecosystem of libraries in python. Coupled together with other libraries like pyDwcViz, it forms an ecosystem of tools for analyzing Darwin-Core-standardized data with super of ease through built-in functions.

Scope

- [X] Data retrieval
- [X] Data extraction
- [X] Data processing/munging
- [ ] Data deposition
- [ ] Data validation and testing
- [ ] Data visualization[^1]
- [ ] Workflow automation
- [ ] Citation management and bibliometrics
- [ ] Scientific software wrappers
- [ ] Database interoperability

Domain Specific & Community Partnerships

- [X] Geospatial
- [ ] Education
- [ ] Pangeo

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• Pangeo
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explaination of scope

target audience and scientific applications

This package targets scientific python users seeking to use taxonomic occurrence data for research and data visualization purposes. The package and accompanying jupyter notebooks establish a broad foundation upon which more rigorous scientific research can be done.

related python packages

To our knowledge pyOBIS is the only python package bridging the gap between the raw OBIS API and our target users.

Technical checks

This package:

• does not violate the Terms of Service of any service it interacts with.
• uses an OSI approved license.
• contains a README with instructions for installing the development version.
• includes documentation with examples for all functions.
• contains a tutorial with examples of its essential functions and uses.
• has a test suite.
• has continuous integration setup, such as GitHub Actions CircleCI, and/or others.

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