NegBio

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When loading NegBioParser() the session crashes

1

I have learnt about NegBio from Coursera and tried to run the code on Colab. I have installed NegBio with pip and imported the required modules including NegBioParser(). However, when...

pythonista0801

Bumps [numpy](https://github.com/numpy/numpy) from 1.21.0 to 1.22.0. Release notes Sourced from numpy's releases. v1.22.0 NumPy 1.22.0 Release Notes NumPy 1.22.0 is a big release featuring the work of 153 contributors spread...

dependabot[bot]

strange error occur, when I run python negbio/main_chexpert.py text --output=examples/test.neg.xml examples/00019248.txt examples/00000086.txt

1

{'--bllip-model': '~/.local/share/bllipparser/GENIA+PubMed', '--mention_phrases_dir': 'negbio/chexpert/phrases/mention', '--neg-patterns': 'negbio/chexpert/patterns/negation.txt', '--newline_is_sentence_break': False, '--output': 'examples/test.neg.xml', '--post-negation-uncertainty-patterns': 'negbio/chexpert/patterns/post_negation_uncertainty.txt', '--pre-negation-uncertainty-patterns': 'negbio/chexpert/patterns/pre_negation_uncertainty.txt', '--split-document': False, '--unmention_phrases_dir': 'negbio/chexpert/phrases/unmention', '--verbose': False, 'SOURCE': None, 'SOURCES': ['examples/00019248.txt', 'examples/00000086.txt'], 'bioc': False, 'text': True} /home/bo/.local/lib/python3.6/site-packages...

bliu62

Install Error

2

ERROR: Could not find a version that satisfies the requirement negbio (from versions: none) ERROR: No matching distribution found for negbio I have tried different versions Ubuntu system, all get...

binerone

``` (base) mghenis@penguin:~/NegBio$ conda env create -f environment3.7.yml ``` Produces this warning: >Warning: you have pip-installed dependencies in your environment file, but you do not list pip itself as one...

MaxGhenis

JPype1 has released version 0.7 as mentioned in https://github.com/jpype-project/jpype/releases For the issue: https://github.com/ncbi-nlp/NegBio/issues/27 it was [mentioned](https://github.com/jpype-project/jpype/issues/395#issuecomment-502723967) that JPype1 version: 0.7 would resolve the issue I tried testing(in usual way by...

kaushikacharya

Detecting negation for one CUI but failing to detect negation for other CUIs

2

Environment: Using MetaMap 2016v2 Sentence: > There is no spinal canal hematoma. Among other CUIs, these are the ones I am focusing on: ``` Hematoma patf C0018944 MetaMap hematoma spinal...

kaushikacharya

1. if the code could not parse the sentence, it would return `None`, but should return `None, None` to be consistent 2. Using a `pathlib2` path for model_dir throws an...

alistairewj

"pip install negbio" doesn't work

3

The installation instructions say ``` pip install negbio ``` but I get ``` ERROR: Could not find a version that satisfies the requirement negbio (from versions: none) ERROR: No matching...

abisee

Bumps [future](https://github.com/PythonCharmers/python-future) from 0.16.0 to 0.18.3. Release notes Sourced from future's releases. v0.18.3 This is a minor bug-fix release containing a number of fixes: Backport fix for bpo-38804 (c91d70b) Fix...

dependabot[bot]