pyopensci.md

Submitting Author: Kozo Nishida (@kozo2) All current maintainers: (@kozo2) Package Name: pywikipathways One-Line Description of Package: Python Client Package for the WikiPathways API Repository Link: https://github.com/kozo2/pywikipathways Version submitted: 0.0.2 Editor: TBD
Reviewer 1: TBD
Reviewer 2: TBD
Archive: TBD
Version accepted: TBD Date accepted (month/day/year): TBD

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Description

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Use this package to interface with the WikiPathways API. It provides programmatic access to WikiPathways content.

This is a Python port of rWikiPathways R (Bioconductor) package. The names of functions and their arguments are unified between the two. (However, there is a difference between a camel case and a snake case.)

This project is inspired by py4cytoscape for RCy3. Just as py4cytoscape ports RCy3 and function specifications to Python, pywikipathways also ports rWikiPathways functions to Python.

Scope

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  • Data retrieval
  • Data extraction
  • Data processing/munging
  • Data deposition
  • Data validation and testing
  • Data visualization¹
  • Workflow automation
  • Citation management and bibliometrics
  • Scientific software wrappers
  • Database interoperability

Domain Specific & Community Partnerships

• Geospatial
• Education
• Pangeo

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• Pangeo
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• For all submissions, explain how the and why the package falls under the categories you indicated above. In your explanation, please address the following points (briefly, 1-2 sentences for each):

  • Who is the target audience and what are scientific applications of this package? The target audience consists of biological pathway analysts. The scientific application involves acquiring pathway data and mapping molecular IDs between user data and WikiPathways.

  • Are there other Python packages that accomplish the same thing? If so, how does yours differ? No other Python package does the same thing.

  • If you made a pre-submission enquiry, please paste the link to the corresponding issue, forum post, or other discussion, or @tag the editor you contacted: I did not make a pre-submission enquiry.

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Footnotes

1. Please fill out a pre-submission inquiry before submitting a data visualization package. ↩