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
- I agree to abide by pyOpenSci's Code of Conduct during the review process and in maintaining my package after should it be accepted.
- I have read and will commit to package maintenance after the review as per the pyOpenSci Policies Guidelines.
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.
- [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
If your package is associated with an existing community please check below:
- Pangeo
- My package adheres to the Pangeo standards listed in the pyOpenSci peer review guidebook
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.
To our knowledge pyOBIS is the only python package bridging the gap between the raw OBIS API and our target users.
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.
- Do you wish to automatically submit to the Journal of Open Source Software? If so:
JOSS Checks
- The package has an obvious research application according to JOSS's definition in their submission requirements. Be aware that completing the pyOpenSci review process does not guarantee acceptance to JOSS. Be sure to read their submission requirements (linked above) if you are interested in submitting to JOSS.
- The package is not a "minor utility" as defined by JOSS's submission requirements: "Minor ‘utility’ packages, including ‘thin’ API clients, are not acceptable." pyOpenSci welcomes these packages under "Data Retrieval", but JOSS has slightly different criteria.
- The package contains a
paper.mdmatching JOSS's requirements with a high-level description in the package root or ininst/. - The package is deposited in a long-term repository with the DOI:
Note: JOSS accepts our review as theirs. You will NOT need to go through another full review. JOSS will only review your paper.md file. Be sure to link to this pyOpenSci issue when a JOSS issue is opened for your package. Also be sure to tell the JOSS editor that this is a pyOpenSci reviewed package once you reach this step.
- Yes I am OK with reviewers submitting requested changes as issues to my repo. Reviewers will then link to the issues in their submitted review.
Confirm each of the following by checking the box.
- I have read the author guide.
- I expect to maintain this package for at least 2 years and can help find a replacement for the maintainer (team) if needed.
- Last but not least please fill out our pre-review survey. This helps us track submission and improve our peer review process. We will also ask our reviewers and editors to fill this out.
P.S. Have feedback/comments about our review process? Leave a comment here