MedCAT | Medical Concept Annotation Tool | Natural Language Processing library

by CogStack Python Version: 1.11.0 License: Non-SPDX

X-Ray Key Features Code Snippets Community Discussions(4)Vulnerabilities Install Support

kandi X-RAY | MedCAT Summary

MedCAT is a Python library typically used in Artificial Intelligence, Natural Language Processing, Deep Learning applications. MedCAT has no bugs, it has no vulnerabilities, it has build file available and it has low support. However MedCAT has a Non-SPDX License. You can install using 'pip install MedCAT' or download it from GitHub, PyPI.

Medical Concept Annotation Tool

Support

Quality

Security

License

Reuse

Support

MedCAT has a low active ecosystem.

It has 331 star(s) with 86 fork(s). There are 19 watchers for this library.

There were 4 major release(s) in the last 6 months.

There are 1 open issues and 57 have been closed. On average issues are closed in 37 days. There are 3 open pull requests and 0 closed requests.

It has a neutral sentiment in the developer community.

The latest version of MedCAT is 1.11.0

Quality

MedCAT has 0 bugs and 0 code smells.

Security

MedCAT has no vulnerabilities reported, and its dependent libraries have no vulnerabilities reported.

MedCAT code analysis shows 0 unresolved vulnerabilities.

There are 0 security hotspots that need review.

License

MedCAT has a Non-SPDX License.

Non-SPDX licenses can be open source with a non SPDX compliant license, or non open source licenses, and you need to review them closely before use.

Reuse

MedCAT releases are available to install and integrate.

Deployable package is available in PyPI.

Build file is available. You can build the component from source.

Installation instructions, examples and code snippets are available.

It has 9515 lines of code, 591 functions and 109 files.

It has high code complexity. Code complexity directly impacts maintainability of the code.

Top functions reviewed by kandi - BETA

kandi has reviewed MedCAT and discovered the below as its top functions. This is intended to give you an instant insight into MedCAT implemented functionality, and help decide if they suit your requirements.

Validates the data in the numpy data file
Return the name for a given CUI
Return the value associated with key
Train the model
Encode category values
Prepare data from a JSON object
Check project differences
Count the number of annotations in a given project
Load data from a JSON file
Prepare cdb data
Convert original format to JSON
Unlink names from scores
Map SNOMED CTD CTD artifacts
Convert a relationshipcode to a json file
Load a MetaCAT
Maps SNOMED CT
Get all concepts from a patient
List all SNOMs in the data directory
Create models
Builds a vocab from a vocabulary
Convert a UML file to a dictionary
Encode the given examples
Combine double annotations
Convert snomed source file to csv
Runs a cdb using the cdb library
Generates a concept data file from the SNPs

Get all kandi verified functions for this library.

MedCAT Key Features

No Key Features are available at this moment for MedCAT.

MedCAT Examples and Code Snippets

No Code Snippets are available at this moment for MedCAT.

Community Discussions

Trending Discussions on MedCAT

Trying to use a tool but I get the following error KeyError: 'str'

Windows compatibility: Permissions?

Run Concept Annotation Tool (CAT) using Docker

Message: Undefined index: when getting column name (two table with the same column) Codeigniter

QUESTION

Trying to use a tool but I get the following error KeyError: 'str'

Asked 2019-Sep-08 at 03:53

I'm trying to use a Medical Concept Annotation tool. The documentation can be found here: https://github.com/CogStack/MedCAT

The med_ann_norm_dict.dat file was downloaded from github from this section:

...

ANSWER

Answered 2019-Sep-08 at 03:53

MedCat needs you to label your columns with a heading. You are required to have at least cui and str. See the example table at https://github.com/CogStack/MedCAT/blob/d1be623a380881a5c8e4e17622a884b9fb3cfa85/examples/simple_cdb.csv

Source https://stackoverflow.com/questions/56865907

QUESTION

Windows compatibility: Permissions?

Asked 2019-Jun-20 at 10:05

OS Windows 10, I am using Docker Engine version 18.09.2, the API version is 1.39

The website explaining the steps to run CAT is: https://libraries.io/pypi/medcat

I am building the medcat image locally. Output looks good until the end of the build process:

...

ANSWER

Answered 2019-Jun-20 at 05:16

This is because windows & linux has CR-LF & LF difference issue, meanwhile, permission need to be added for linux executable.
For your case, as you have got the source code, I think you have git installed on your windows. Then, you can open Git Bash, change the path to your source code directory, and execute next in it:

find . -type f | xargs dos2unix
chmod -R 777 *

Finally, rebuild it.

Update:

I try your code completely, it seems the issue is in cat/api/api.py, it misses a #!. So, into your sourcecode, edit cat/api/api.py, add next at the beginning of the sourcecode:

Source https://stackoverflow.com/questions/56663926

QUESTION

Run Concept Annotation Tool (CAT) using Docker

Asked 2019-Jun-19 at 08:41

I am trying to run CAT using docker. "If using docker the appropriate models will be automatically downloaded, you only need to run:"

...

ANSWER

Answered 2019-Jun-18 at 13:26

You have to clone the respective Git repository. Then run the command from there.

Source https://stackoverflow.com/questions/56650112

QUESTION

Message: Undefined index: when getting column name (two table with the same column) Codeigniter

Asked 2019-May-01 at 03:46

I want to get the data from two tables with the same column name. I already put some aliases in the column name. But it doesn't work.

Controller

...

ANSWER

Answered 2019-May-01 at 03:46

Try this,

CI select accepts only two params, you passed three

Source https://stackoverflow.com/questions/55931143

Community Discussions, Code Snippets contain sources that include Stack Exchange Network

Vulnerabilities

No vulnerabilities reported

Install MedCAT

Path to file containing UMLS concepts, including primary names, synonyms, types and source ontology. See examples and tests/model_creator/umls_sample.csv for format description and examples. Path to file containing text dataset used for spell checking and unsupervised training. Path to output directory for writing the CDB and vocab models. Path to optional config file for adjusting MedCAT properties, see configs, medcat/config.py and tests/model_creator/medcat.txt. Optional parameter for setting the initialization size of the unigram table in the vocab model. Default is 100000000, while for testing with a small unsupervised training data file a much smaller size could work.
Upgrade pip pip install --upgrade pip
Install MedCAT
For macOS/linux: pip install --upgrade medcat
For Windows (see PyTorch documentation): pip install --upgrade medcat -f https://download.pytorch.org/whl/torch_stable.html
Quickstart (MedCAT v1.2+):
Quick start with separate models: New Models (MedCAT v1.2+) need the spacy en_core_web_md while older ones use the scispacy models, install the one you need or all if not sure. If using model packs you do not need to download these models:
Quick start with to create CDB and vocab models using local data and a config file:

Support

For any new features, suggestions and bugs create an issue on GitHub. If you have any questions check and ask questions on community page Stack Overflow .

Find more information at: