NERO-nlp

NERO-nlp is a biomedical Named Entity (Recognition) Ontology.

Using NERO-nlp, we annotated a large biomedical corpus to enable a broad spectrum of natural language processing and biomedical machine learning tasks.

NERO-nlp is a wrapper around this corpus.

Sample usage:

In [3]: from NERO.corpus import corpus

# Directly access basic dataframe attributes
In [4]: corpus.columns 

In [5]: corpus.shape

# access to the whole dataframe
In [6]: corpus._data

# Having directly access to columns by calling them as an attribute
In [7]: corpus.semantic_class_actionType

In [8]:                                                                                                                                                                                                     

# Using documentation 
In [8]: corpus.procset_topic_bd.__doc__                                                                                                                                                        

# other generic and multipurpose functions
In [9]: corpus.procset_topic_bd('aut')                                                                                                                                                               

In [10]: corpus.plot_protein_domain_entity() 

Installation:

For running the NERO-nlp you need to have python3.7+ and pandas installed. For installation you can use pip or pip3.

# Install
sudo pip3 install NERO-nlp
# or
sudo python3 -m pip install NERO-nlp
# Upgrade
sudo pip3 install NERO-nlp --upgrade

Contact

You are welcome to:

• submit suggestions and bug-reports at: https://github.com/Bohdan-Khomtchouk/NERO-nlp/issues
• send a pull request on: https://github.com/Bohdan-Khomtchouk/NERO-nlp
• compose an e-mail to: bohdan@uchicago.edu

Code of conduct

Please note that this project is released with a Contributor Code of Conduct. By participating in this project you agree to abide by its terms.