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pycontextnlp

https://github.com/chapmanbe/pycontextnlp

Science Score: 20.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ○
    codemeta.json file
  • ○
    .zenodo.json file
  • ○
    DOI references
  • ✓
    Academic publication links
    Links to: pubmed.ncbi, ncbi.nlm.nih.gov, sciencedirect.com
  • ✓
    Committers with academic emails
    2 of 8 committers (25.0%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (12.6%) to scientific vocabulary
Last synced: 11 months ago · JSON representation

Repository

Basic Info
  • Host: GitHub
  • Owner: chapmanbe
  • Language: HTML
  • Default Branch: master
  • Size: 300 KB
Statistics
  • Stars: 98
  • Watchers: 14
  • Forks: 41
  • Open Issues: 11
  • Releases: 0
Created over 11 years ago · Last pushed about 3 years ago
Metadata Files
Readme

README.rst 

pyConTextNLP
============

This package has been in *de facto* retirement for many years. The direct successor to this project is `MedSpaCy `_.

This code has been validated using the included notebooks on Python v 3.7.2. Python 2.x is no longer supported.

pyConTextNLP is a Python implementation/extension/modification of the
ConText algorithm described in `"Context: An Algorithm for Determining Negation, Experiencer, and Temporal Status from Clinical Reports" `_ which is itself a
generalization of the NegEx algorithm described in `"A simple algorithm for identifying negated findings and diseases in discharge summaries" `_.

The package is maintained by Brian Chapman at the University of Utah.
Other active and past developers include:

-  Wendy W. Chapman
-  Glenn Dayton
-  Danielle Mowery

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

pyConTextNLP is a partial implementation of the ConText algorithm using
Python. The original description of pyConTextNLP was provided in Chapman
BE, Lee S, Kang HP, Chapman WW, "Document-level classification of CT
pulmonary angiography reports based on an extension of the ConText
algorithm." `J Biomed Inform. 2011
Oct;44(5):728-37 `__

Other publications/presentations based on pyConText include: \* Wilson
RA, et al. "Automated ancillary cancer history classification for
mesothelioma patients from free-text clinical reports." J Pathol Inform.
2010 Oct 11;1:24. \* Chapman BE, Lee S, Kang HP, Chapman WW. "Using
ConText to Identify Candidate Pulmonary Embolism Subjects Based on
Dictated Radiology Reports." (Presented at AMIA Clinical Research
Informatics Summit 2011) \* Wilson RA, Chapman WW, DeFries SJ, Becich
MJ, Chapman BE. "Identifying History of Ancillary Cancers in
Mesothelioma Patients from Free-Text Clinical Reports." (Presented at
AMIA 2010).

Note: we changed the package name from pyConText to pyConTextNLP because
of a name conflict on pypi.

Installation
------------

Latest Version
~~~~~~~~~~~~~~

The latest version of pyConTextNLP is available on [github](https://github.com/chapmanbe/pyConTextNLP). 
The package can be installed by either cloning the repository and running `python setup.py install`. 
Alternatively or by
.. code:: shell
    pip install git+https://github.com/chapmanbe/pyConTextNLP.git 

PyPi
~~~~~

pyConTextNLP is also available via the Python Package Index and can be installed via

.. code:: shell

    pip install pyConTextNLP

Dependencies include 

* networkx
* PyYAML


Tutorials
---------

See the `notebooks folder <./notebooks>`__ for a series of walkthroughs
demonstrating pyConTextNLP core concepts with example data.


How to Use
----------

I am working on improving the documentation and (hopefully) adding some
testing to the code.

Some preliminary comments:

-  pyConTextNLP works marks up text on a sentence by sentence level.
-  pyConTextNLP assumes the sentence is a string not a list of words
- Our preferred way to represent knowledge is now with YAML files rather than TSV files.

Owner

  • Name: Brian Chapman
  • Login: chapmanbe
  • Kind: user
  • Location: Melbourne, VIC, AU
  • Company: University of Melbourne

GitHub Events

Total
  • Watch event: 1
Last Year
  • Watch event: 1

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 172
  • Total Committers: 8
  • Avg Commits per committer: 21.5
  • Development Distribution Score (DDS): 0.349
Past Year
  • Commits: 5
  • Committers: 1
  • Avg Commits per committer: 5.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Brian Chapman b****n@u****u 112
chapmanbe@gmail.com c****e@g****m@8****c 30
chapmanbe c****e@8****c 14
Nathan Vonnahme n****n@c****m 11
Mathaeus Dejori m****i@s****m 2
a****5@L****n 1
Wendy Chapman w****n@u****u 1
abhishekl2625 a****6@g****m 1
Committer Domains (Top 20 + Academic)
utah.edu: 2 laptop-dp87l2hb.localdomain: 1 stansonhealth.com: 1 careevolution.com: 1

Issues and Pull Requests

Last synced: 12 months ago

All Time
  • Total issues: 9
  • Total pull requests: 9
  • Average time to close issues: 10 days
  • Average time to close pull requests: 8 days
  • Total issue authors: 8
  • Total pull request authors: 7
  • Average comments per issue: 0.44
  • Average comments per pull request: 0.0
  • Merged pull requests: 6
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • quzhouxiachuan (2)
  • jianlins (1)
  • vsoch (1)
  • apyrros (1)
  • Martijn-Sturm (1)
  • chapmanbe (1)
  • datduong (1)
  • dr00b (1)
Pull Request Authors
  • n8v (3)
  • caleb-lindgren (1)
  • jianlins (1)
  • Martijn-Sturm (1)
  • dejori (1)
  • abhishekl2625 (1)
  • wwchapman (1)
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 1,553 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 3
  • Total versions: 27
  • Total maintainers: 1
pypi.org: pycontextnlp

A Python implementation of the ConText algorithm

  • Versions: 27
  • Dependent Packages: 0
  • Dependent Repositories: 3
  • Downloads: 1,553 Last month
Rankings
Forks count: 6.3%
Stargazers count: 7.2%
Downloads: 8.1%
Average: 8.1%
Dependent repos count: 9.0%
Dependent packages count: 10.0%
Maintainers (1)
brchapman
Last synced: 12 months ago

Dependencies

requirements-py2.txt pypi
  • unicodecsv *
setup.py pypi
  • networkx *
  • pyyaml *