medcat workflow

Author: antsh3k

medcat/ReadMe.md

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+# Medical <img src="../data/media/medcat_logo.png" width=45>oncept Annotation Tool
+
+This directory contains information on retrieving data and creating models
+All details regarding creating, building and running the NLP model are stored here.
+
+## Locations for storing data:
+
+- The [data](data) directory stores textual content. 
+Methods for retrieving data should be stored in the [retrieve_data](search) folder.
+
+- The [MedCAT models](data/medcat_models) directory holds models.
+
+## Order of processing steps
+
+#### [__Step 1__](medcat/1_create_model): Create the model
+
+Each of the model components are found [here.](medcat/1_create_model)
+This directory contains all the components required to initialise a model pack.
+
+All models should be stored [here.](data/medcat_models)
+
+
+#### [__Step 2__](medcat/2_train_model): Perform training
+
+- [__Step 2.1__](medcat/2_train_model/1_unsupervised_training): Unsupervised training
+
+    The unsupervised training steps can be found within unsupervised_training folder.
+
+
+ - [__Step 2.2__](medcat/2_train_model/2_supervised_training): Supervised training
+
+    After providing supervised labels with MedCATtrainer.
+    The supervised training steps can be found within supervised_training folder.
+ 
+#### [__Step 3__](medcat/3_run_model): Run model
+
+Run model on your corpus of documents and write to csv/sql db.
+Instructions on how to do this can be found within [run_model](medcat/3_run_model/run_model.ipynb)
+
+
+