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SeroTools

SeroTools: a Python package for Salmonella serotype data analysis - Published in JOSS (2020)

https://github.com/cfsan-biostatistics/serotools

Science Score: 93.0%

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    CITATION.cff file
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    DOI references
    Found 6 DOI reference(s) in README and JOSS metadata
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    Links to: joss.theoj.org
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    JOSS paper metadata
    Published in Journal of Open Source Software
Last synced: 6 months ago · JSON representation

Repository

A toolkit and repository for the White-Kauffmann-Le Minor scheme for Salmonella serotyping.

Basic Info
  • Host: GitHub
  • Owner: CFSAN-Biostatistics
  • License: other
  • Language: Python
  • Default Branch: master
  • Homepage:
  • Size: 789 KB
Statistics
  • Stars: 2
  • Watchers: 6
  • Forks: 1
  • Open Issues: 1
  • Releases: 4
Created over 6 years ago · Last pushed about 3 years ago
Metadata Files
Readme Changelog Contributing License Authors

README.rst 

===============================
SeroTools
===============================


.. Image showing the PyPI version badge - links to PyPI
.. image:: https://img.shields.io/pypi/v/serotools.svg
        :target: https://pypi.python.org/pypi/serotools

.. Image showing the Travis Continuous Integration test status, commented out for now
.. .. image:: https://img.shields.io/travis/CFSAN-Biostatistics/serotools.svg
..        :target: https://travis-ci.org/CFSAN-Biostatistics/serotools

.. Image showing the JOSS paper badge
.. image:: https://joss.theoj.org/papers/10.21105/joss.02556/status.svg
   :target: https://doi.org/10.21105/joss.02556

This package serves as a toolkit and repository for the White-Kauffmann-Le Minor scheme for *Salmonella* serotyping, which is made available in multiple formats, along with methods for querying and comparing serovar names and antigenic formulae, as well as determining the most abundant serovar for a cluster of isolates.

SeroTools was developed by the United States Food and Drug Administration, Center for Food 
Safety and Applied Nutrition.

* Free software
* Documentation: https://serotools.readthedocs.io
* Source Code: https://github.com/CFSAN-Biostatistics/serotools
* PyPI Distribution: https://pypi.python.org/pypi/serotools

Introduction
------------

*Salmonella* bacteria are major foodborne pathogens estimated by the U.S. Centers for Disease Control and Prevention to cause 1.35 million infections annually in the United States [1]_. Serological subtyping (serotyping) of *Salmonella* has historically been a critical component of characterization and successful outbreak identification and traceback efforts employed by public health researchers and regulatory agencies. The White-Kauffmann-Le Minor (WKL) *Salmonella* serotyping scheme specifies the commonly accepted naming and formatting conventions for *Salmonella* serotyping data and the antigenic factors (and other characteristics) which define each serovar. *Salmonella* serotyping data is routinely employed by a broad range of scientific researchers, physicians, public health professionals, food safety experts, etc.

SeroTools addresses multiple critical needs for the efficient analysis of *Salmonella* serotyping data. As technological advances continue to produce a range of high resolution subtyping options, including *in silico* serovar prediction based on whole genome sequencing, new tools are necessary for efficient method-comparison studies and quality control applied to increasingly large numbers of isolates. SeroTools serves as the only multiformat WKL repository accessible for software development and provides the only existing tools for querying the WKL scheme, comparing serovars for congruence, and predicting the most abundant serovar for clusters of isolates.

.. [1] The U.S. Centers for Disease Control and Prevention. .


Features
--------

* Query the White-Kauffmann-Le Minor *Salmonella* serotyping repository

* Compare serovar predictions for state of congruence

* Determine the most abundant serovar for a cluster of isolates


Citing SeroTools
--------------------------------------

If you use SeroTools, please cite the following publication:
   
Baugher, J. D., (2020). SeroTools: a Python package for Salmonella serotype data analysis. Journal of Open Source Software, 5(53), 2556, https://doi.org/10.21105/joss.02556.



License
-------

See the LICENSE file included in the SeroTools distribution.

Owner

  • Name: CFSAN (Center for Food Safety and Applied Nutrition)
  • Login: CFSAN-Biostatistics
  • Kind: organization

JOSS Publication

SeroTools: a Python package for Salmonella serotype data analysis
Published
September 05, 2020
DOI
Volume 5, Issue 53, Page 2556
Authors
Joseph D. Baugher, ORCID
Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration
Editor
Mark A. Jensen ORCID
Tags
Salmonella serotype serovar White-Kauffmann-Le Minor bioinformatics
View PDF Review Thread Software Archive

GitHub Events

Total
  • Fork event: 1
Last Year
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Committers

Last synced: 7 months ago

All Time
  • Total Commits: 82
  • Total Committers: 3
  • Avg Commits per committer: 27.333
  • Development Distribution Score (DDS): 0.11
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Joseph Baugher j****r 73
Joseph D. Baugher, Ph.D j****r@f****v 8
Baugher j****r@C****v 1
Committer Domains (Top 20 + Academic)
cfm5081560.fda.gov: 1 fda.hhs.gov: 1

Issues and Pull Requests

Last synced: 6 months ago

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  • Total issues: 1
  • Total pull requests: 1
  • Average time to close issues: 9 days
  • Average time to close pull requests: N/A
  • Total issue authors: 1
  • Total pull request authors: 1
  • Average comments per issue: 3.0
  • Average comments per pull request: 0.0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 1
Past Year
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  • Average time to close issues: N/A
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  • Average comments per issue: 0
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Top Authors
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  • amoeba (1)
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  • dependabot[bot] (1)
Top Labels
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dependencies (1)

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 8 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 1
  • Total versions: 4
  • Total maintainers: 1
pypi.org: serotools

This package serves as a toolkit and repository for the White-Kauffmann-Le Minor scheme for Salmonella serotyping, which defines nomenclature and antigenic factors for each recognized serovar. The scheme is made available in multiple formats, along with methods for querying and comparing serovar names and antigenic formulae, as well as determining the most abundant serovar for a cluster of isolates.

  • Versions: 4
  • Dependent Packages: 0
  • Dependent Repositories: 1
  • Downloads: 8 Last month
Rankings
Dependent packages count: 10.0%
Dependent repos count: 21.7%
Stargazers count: 27.8%
Average: 27.9%
Forks count: 29.8%
Downloads: 50.5%
Maintainers (1)
jdbaugher
Last synced: 6 months ago

Dependencies

requirements.txt pypi
  • wheel ==0.23.0