From c20e2441aec14c911b2c7d9e2f323ee40735db84 Mon Sep 17 00:00:00 2001 From: alhendrickson <159636032+alhendrickson@users.noreply.github.com.> Date: Thu, 7 Aug 2025 09:59:35 +0000 Subject: [PATCH 1/3] CU-8699mrvup docs: Update URLs to point to new cogstack-nlp repo --- README.md | 2 +- anoncat-demo-app/README.md | 4 +- anoncat-demo-app/app/frontend/src/App.vue | 2 +- medcat-trainer/docs/installation.md | 6 +- medcat-trainer/docs/maintenance.md | 2 +- medcat-trainer/docs/project_admin.md | 2 +- medcat-trainer/install.sh | 4 +- .../notebook_docs/API_Examples.ipynb | 2 +- .../notebook_docs/Generate_CUI_Filters.ipynb | 2 +- .../Processing_Annotations.ipynb | 4 +- .../webapp/scripts/load_examples.py | 3 +- medcat-v1/docs/main.md | 2 +- medcat-v2-tutorials/README.md | 14 +- .../3._Supervised_training_on_model.ipynb | 500 +++++++++--------- medcat-v2/README.md | 2 +- medcat-v2/docs/main.md | 6 +- medcat-v2/pyproject.toml | 2 +- 17 files changed, 280 insertions(+), 279 deletions(-) diff --git a/README.md b/README.md index a5285e05d..f8cab9a6d 100644 --- a/README.md +++ b/README.md @@ -2,7 +2,7 @@ [![Build Status](https://github.com/CogStack/cogstack-nlp/actions/workflows/medcat-v2_main.yml/badge.svg?branch=main)](https://github.com/CogStack/cogstack-nlp/actions/workflows/medcat-v2_main.yml/badge.svg?branch=main) [![Documentation Status](https://readthedocs.org/projects/cogstack-nlp/badge/?version=latest)](https://readthedocs.org/projects/cogstack-nlp/badge/?version=latest) -[![Latest release](https://img.shields.io/github/v/release/CogStack/MedCAT2)](https://github.com/CogStack/MedCAT2/releases/latest) +[![Latest release](https://img.shields.io/github/v/release/CogStack/cogstack-nlp?filter=medcat/*)](https://github.com/CogStack/cogstack-nlp/releases/latest) Cogstack Natural Language Processing is for analysing clinical data using AI to draw insights from text in or documents in an Electronic Health Records. diff --git a/anoncat-demo-app/README.md b/anoncat-demo-app/README.md index ba85699c1..d4ee545eb 100644 --- a/anoncat-demo-app/README.md +++ b/anoncat-demo-app/README.md @@ -1,6 +1,6 @@ # Deidentify app -Demo for AnonCAT. It uses [MedCAT](https://github.com/CogStack/MedCAT), an advanced natural language processing tool, to identify and classify sensitive information, such as names, addresses, and medical terms. +Demo for AnonCAT. It uses [MedCAT](https://github.com/CogStack/cogstack-nlp/tree/main/medcat-v1), an advanced natural language processing tool, to identify and classify sensitive information, such as names, addresses, and medical terms. ## Example @@ -22,7 +22,7 @@ MODEL_NAME = '' ### Build your own model -To build your own models please follow the tutorials outlined in [MedCATtutorials](https://github.com/CogStack/MedCATtutorials) +To build your own models please follow the tutorials outlined in [MedCATtutorials](https://github.com/CogStack/cogstack-nlp/tree/main/medcat-v1-tutorials) *__Note:__ This is currently under development* diff --git a/anoncat-demo-app/app/frontend/src/App.vue b/anoncat-demo-app/app/frontend/src/App.vue index 2cfb2f401..dfc028115 100644 --- a/anoncat-demo-app/app/frontend/src/App.vue +++ b/anoncat-demo-app/app/frontend/src/App.vue @@ -21,7 +21,7 @@

Please DO NOT test with any real sensitive PHI data.


-

Local validation and fine-tuning available via MedCATtrainer. +

Local validation and fine-tuning available via MedCATtrainer. Email us, contact@cogstack.org, to discuss model access, model performance, and your use case.


diff --git a/medcat-trainer/docs/installation.md b/medcat-trainer/docs/installation.md index 6b2c4c7cf..f9b0738e7 100644 --- a/medcat-trainer/docs/installation.md +++ b/medcat-trainer/docs/installation.md @@ -4,8 +4,8 @@ MedCATtrainer is a docker-compose packaged Django application. ## Download from Dockerhub Clone the repo, run the default docker-compose file and default env var: ```shell -$ git clone https://github.com/CogStack/MedCATtrainer -$ cd MedCATtrainer +$ git clone https://github.com/CogStack/cogstack-nlp +$ cd cogstack-nlp/medcat-trainer $ docker-compose up ``` @@ -61,7 +61,7 @@ Environment variables are used to configure the app: |Parameter|Description| |---------|-----------| -|MEDCAT_CONFIG_FILE|MedCAT config file as described [here](https://github.com/CogStack/MedCAT/blob/master/medcat/config.py)| +|MEDCAT_CONFIG_FILE|MedCAT config file as described [here](https://github.com/CogStack/cogstack-nlp/blob/main/medcat-v2/medcat/config/config.py)| |BEHIND_RP| If you're running MedCATtrainer, use 1, otherwise this defaults to 0 i.e. False| |MCTRAINER_PORT|The port to run the trainer app on| |EMAIL_USER|Email address which will be used to send users emails regarding password resets| diff --git a/medcat-trainer/docs/maintenance.md b/medcat-trainer/docs/maintenance.md index f3349ef09..b21af39b1 100644 --- a/medcat-trainer/docs/maintenance.md +++ b/medcat-trainer/docs/maintenance.md @@ -6,7 +6,7 @@ be upgrading to the latest release. The latest stable releases update the `docker-compose.yml` and `docker-compose-prod.yml` files. -To update these docker compose files, either copy them directly from the [repo](https://github.com/CogStack/MedCATtrainer) +To update these docker compose files, either copy them directly from the [repo](https://github.com/CogStack/cogstack-nlp/tree/main/medcat-trainer) or update the cloned files via: ```shell diff --git a/medcat-trainer/docs/project_admin.md b/medcat-trainer/docs/project_admin.md index 65023333a..19f1e30ab 100644 --- a/medcat-trainer/docs/project_admin.md +++ b/medcat-trainer/docs/project_admin.md @@ -69,7 +69,7 @@ Admin users have extra options on the home screen: 3. Save Model - Write the in memory model to disk - to save the current in memory model state. This option is generally not advised as full model training should be done outside the trainer instance ideally. ### Notes -- Example Concept and Vocab databses are freely available on MedCAT [github](https://github.com/CogStack/MedCAT). +- Example Concept and Vocab databses are freely available on MedCAT [github](https://github.com/CogStack/cogstack-nlp/tree/main/medcat-v2). Note. UMLS and SNOMED-CT are licensed products so only these smaller trained concept / vocab databases are made available currently. - More documentation on the creation of UMLS / SNOMED-CT CDBs from respective source data will be released soon. - Tasks allow for the creation of meta-annotations and their associated set of values an annotator can use. diff --git a/medcat-trainer/install.sh b/medcat-trainer/install.sh index 98af586f2..b7bbb2305 100644 --- a/medcat-trainer/install.sh +++ b/medcat-trainer/install.sh @@ -7,8 +7,8 @@ DOCKER_COMP_FILE=dc.yml ENV_FILE=/tmp/mc_trainer/envs/env echo "Downloading docker-compose.yml and default env vars" -curl https://cdn.githubraw.com/CogStack/MedCATtrainer/9fbd517e/docker-compose.yml > $DOCKER_COMP_FILE -curl https://raw.githubusercontent.com/CogStack/MedCATtrainer/9fbd517e/envs/env > $ENV_FILE +curl https://raw.githubusercontent.com/CogStack/cogstack-nlp/09e32429/medcat-trainer/docker-compose.yml > $DOCKER_COMP_FILE +curl https://raw.githubusercontent.com/CogStack/cogstack-nlp/09e32429/medcat-trainer/envs/env > $ENV_FILE trap 'rm -rf /tmp/mc_trainer && cd $CURR_LOC' EXIT echo "Starting MedCATtrainer containers" diff --git a/medcat-trainer/notebook_docs/API_Examples.ipynb b/medcat-trainer/notebook_docs/API_Examples.ipynb index feacc4d41..d4ceffc87 100644 --- a/medcat-trainer/notebook_docs/API_Examples.ipynb +++ b/medcat-trainer/notebook_docs/API_Examples.ipynb @@ -216,7 +216,7 @@ "### Create CDBs and Vocabularies\n", "The MedCAT models used by MedCATTrainer are output by MedCAT instances of classesmedcat.cdb.CDB, medcat.utils.vocab.Vocabulary. Calling save_dict('\\') will write a file that can be loaded in another instance of MedCAT (via load_dict()), or within MedCATTrainer.\n", "\n", - "Examples models are provided on the MedCAT Repository: https://github.com/CogStack/MedCAT" + "Examples models are provided on the MedCAT Repository: https://github.com/CogStack/cogstack-nlp/tree/main/medcat-v1" ] }, { diff --git a/medcat-trainer/notebook_docs/Generate_CUI_Filters.ipynb b/medcat-trainer/notebook_docs/Generate_CUI_Filters.ipynb index 01d69660e..6f4842e32 100644 --- a/medcat-trainer/notebook_docs/Generate_CUI_Filters.ipynb +++ b/medcat-trainer/notebook_docs/Generate_CUI_Filters.ipynb @@ -25,7 +25,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "Relation file from SNOMED-CT Preprocessing tutorial: https://github.com/CogStack/MedCATtutorials/blob/main/notebooks/specialised/Preprocessing_SNOMED_CT.ipynb, \n", + "Relation file from SNOMED-CT Preprocessing tutorial: https://github.com/CogStack/cogstack-nlp/blob/main/medcat-v1-tutorials/notebooks/specialised/Preprocessing_SNOMED_CT.ipynb, \n", "\n", "In section \"SNOMED Relationships\"\n" ] diff --git a/medcat-trainer/notebook_docs/Processing_Annotations.ipynb b/medcat-trainer/notebook_docs/Processing_Annotations.ipynb index a1fb73bc9..31c08bd0c 100644 --- a/medcat-trainer/notebook_docs/Processing_Annotations.ipynb +++ b/medcat-trainer/notebook_docs/Processing_Annotations.ipynb @@ -143,11 +143,11 @@ }, { "cell_type": "code", - "execution_count": 2, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ - "# Load the annotations downloaded - as described: https://github.com/CogStack/MedCATtrainer/blob/main/README.md#download-annos\n", + "# Load the annotations downloaded - as described: https://github.com/CogStack/cogstack-nlp/tree/main/medcat-trainer/blob/main/README.md#download-annos\n", "projs = json.load(open('example_data/MedCAT_Export_With_Text_2020-05-22_10_34_09.json'))['projects']" ] }, diff --git a/medcat-trainer/webapp/scripts/load_examples.py b/medcat-trainer/webapp/scripts/load_examples.py index ec0c1b7a9..e4031324c 100644 --- a/medcat-trainer/webapp/scripts/load_examples.py +++ b/medcat-trainer/webapp/scripts/load_examples.py @@ -61,7 +61,8 @@ def main(port=8000, with open(vocab_tmp_file, 'wb') as f: f.write(vocab_file.content) print("Downloading example dataset") - ds = requests.get('https://raw.githubusercontent.com/CogStack/MedCATtrainer/main/notebook_docs/example_data/ortho.csv') + ds = requests.get( + 'https://raw.githubusercontent.com/CogStack/cogstack-nlp/09e32429/medcat-trainer/notebook_docs/example_data/ortho.csvv') with open(dataset_tmp_file, 'w') as f: f.write(ds.text) diff --git a/medcat-v1/docs/main.md b/medcat-v1/docs/main.md index c4bd6dbd6..2e37b86bb 100644 --- a/medcat-v1/docs/main.md +++ b/medcat-v1/docs/main.md @@ -33,7 +33,7 @@ A demo application is available at [MedCAT](https://medcat.sites.er.kcl.ac.uk). A guide on how to use MedCAT is available at [MedCAT Tutorials](https://github.com/CogStack/MedCATtutorials). Read more about MedCAT on [Towards Data Science](https://towardsdatascience.com/medcat-introduction-analyzing-electronic-health-records-e1c420afa13a). ## Related Projects -- [MedCATtrainer](https://github.com/CogStack/MedCATtrainer/) - an interface for building, improving and customising a given Named Entity Recognition and Linking (NER+L) model (MedCAT) for biomedical domain text. +- [MedCATtrainer](https://github.com/CogStack/cogstack-nlp/tree/main/medcat-trainer/) - an interface for building, improving and customising a given Named Entity Recognition and Linking (NER+L) model (MedCAT) for biomedical domain text. - [MedCATservice](https://github.com/CogStack/MedCATservice) - implements the MedCAT NLP application as a service behind a REST API. - [iCAT](https://github.com/CogStack/iCAT) - A docker container for CogStack/MedCAT/HuggingFace development in isolated environments. diff --git a/medcat-v2-tutorials/README.md b/medcat-v2-tutorials/README.md index 45bb02914..0c734ccde 100644 --- a/medcat-v2-tutorials/README.md +++ b/medcat-v2-tutorials/README.md @@ -6,25 +6,25 @@ | Part | Title | | ---- |-----------------------------------------------------------------------------| -| 1. | [Migrate a v1 model to v2](https://github.com/CogStack/MedCATv2tutorials/blob/main/notebooks/introductory/migration/1._Migrate_v1_model_to_v2.ipynb) | +| 1. | [Migrate a v1 model to v2](https://github.com/CogStack/cogstack-nlp/blob/main/notebooks/introductory/migration/1._Migrate_v1_model_to_v2.ipynb) | ### Basic (regex-tokenizer) tutorials | Part | Title | | ---- |-----------------------------------------------------------------------------| -| 1. | [Building a Concept Database and a Vocab](https://github.com/CogStack/MedCATv2tutorials/blob/main/notebooks/introductory/basic/1._Build_a_Concept_Database_and_a_Vocabulary.ipynb) | -| 2. | [Unsupervised training on model](https://github.com/CogStack/MedCATv2tutorials/blob/main/notebooks/introductory/basic/2._Unsupervised_training_on_model.ipynb) | -| 3. | [Supervised training on model](https://github.com/CogStack/MedCATv2tutorials/blob/main/notebooks/introductory/basic/3._Supervised_training_on_model.ipynb) | +| 1. | [Building a Concept Database and a Vocab](https://github.com/CogStack/cogstack-nlp/blob/main/notebooks/introductory/basic/1._Build_a_Concept_Database_and_a_Vocabulary.ipynb) | +| 2. | [Unsupervised training on model](https://github.com/CogStack/cogstack-nlp/blob/main/notebooks/introductory/basic/2._Unsupervised_training_on_model.ipynb) | +| 3. | [Supervised training on model](https://github.com/CogStack/cogstack-nlp/blob/main/notebooks/introductory/basic/3._Supervised_training_on_model.ipynb) | ### MetaCAT (meta-annotation) tutorials | Part | Title | | ---- |-----------------------------------------------------------------------------| -| 1. | [Add a MetaCAT to a Model](https://github.com/CogStack/MedCATv2tutorials/blob/main/notebooks/introductory/meta/1._Add_a_MetaCat_to_a_Model.ipynb) | +| 1. | [Add a MetaCAT to a Model](https://github.com/CogStack/cogstack-nlp/blob/main/notebooks/introductory/meta/1._Add_a_MetaCat_to_a_Model.ipynb) | ## Advanced tutorials | Part | Title | | ---- |-----------------------------------------------------------------------------| -| 1. | [Creating and using a custom tokenizer](https://github.com/CogStack/MedCATv2tutorials/blob/main/notebooks/advanced/1._Creating_and_using_a_custom_tokenizer.ipynb) | -| 2. | [Create and use component](https://github.com/CogStack/MedCATv2tutorials/blob/main/notebooks/advanced/2._Create_and_use_component.ipynb) | +| 1. | [Creating and using a custom tokenizer](https://github.com/CogStack/cogstack-nlp/blob/main/notebooks/advanced/1._Creating_and_using_a_custom_tokenizer.ipynb) | +| 2. | [Create and use component](https://github.com/CogStack/cogstack-nlp/blob/main/notebooks/advanced/2._Create_and_use_component.ipynb) | diff --git a/medcat-v2-tutorials/notebooks/introductory/basic/3._Supervised_training_on_model.ipynb b/medcat-v2-tutorials/notebooks/introductory/basic/3._Supervised_training_on_model.ipynb index 0df598396..886f12670 100644 --- a/medcat-v2-tutorials/notebooks/introductory/basic/3._Supervised_training_on_model.ipynb +++ b/medcat-v2-tutorials/notebooks/introductory/basic/3._Supervised_training_on_model.ipynb @@ -1,252 +1,252 @@ { - "cells": [ - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "# Supervised training on a model\n", - "\n", - "Not everything can be learned in a self-supervised manner.\n", - "As a trivial exmaple, if there were two concepts - both only known by the same name, the unsupervised training approach won't be able to distinguish between them.\n", - "\n", - "For instance `abscess` could regfer either to a body structure (`44132006`) or a clinical finding (`128477000`) depending on conext.\n", - "And if there's no unique name that refers to either term, they cannot be disambiguated using only self-supervised methods.\n", - "In reality, these terms can also be known by names that are distinct from oneanother (e.g `abscess morphology` for `44132006` and `abscess disorder` for `128477000`).\n", - "But even this would require training data that actually uses these distinct terms.\n", - "\n", - "In any case, supervised training also has the added benefit of having a humans curate the names and linked concepts.\n", - "While this may be achieved in many different ways, when using MedCAT, we like to use a tool called [MedCATtrainer](https://github.com/CogStack/MedCATtrainer).\n", - "\n", - "First things first - we load the existing model." - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "import os\n", - "\n", - "from medcat.cat import CAT\n", - "\n", - "model_path = os.path.join(\"models\", \"unsup_trained_model.zip\")\n", - "\n", - "cat = CAT.load_model_pack(model_path)" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "Now that we have the model, we add the two new concepts.\n", - "We employ the help of the `CDBMaker` again.\n", - "Though this is not strictly speaking necessary this time around since the `CAT` instance has created its own tokenizer anyway." - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "DF:\n", - " name cui\n", - "0 abscess 44132006\n", - "1 abscess 128477000\n", - "CUIs: [('73211009', 'Diabetes Mellitus Diagnosed'), ('396230008', 'Wagner Unverricht Syndrome'), ('44132006', 'Abscess'), ('128477000', 'Abscess')]\n" - ] - } - ], - "source": [ - "import pandas as pd\n", - "from medcat.model_creation.cdb_maker import CDBMaker\n", - "\n", - "cdb_maker = CDBMaker(cat.config, cat.cdb)\n", - "\n", - "df = pd.DataFrame({\"name\": 'abscess', \"cui\": ['44132006', '128477000']})\n", - "print(\"DF:\\n\", df)\n", - "\n", - "cdb_maker.prepare_csvs([df])\n", - "\n", - "print(\"CUIs:\", [(cui, cat.cdb.get_name(cui)) for cui in cat.cdb.cui2info.keys()])" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "Now we have the concepts that we're trying to disambiguate.\n", - "All we need now is a dataset where a human has gone through the mentions and annotated them for the correct type.\n", - "And then we can use that for supervised training.\n", - "\n", - "First, we will verify that we cannot detect abscess before training." - ] - }, - { - "cell_type": "code", - "execution_count": 3, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "0 : {}\n", - "1 : {}\n" - ] - } - ], - "source": [ - "abscess_text_morph = \"\"\"Histopathology reveals a well-encapsulated abscess with central necrosis and neutrophilic infiltration.\"\"\"\n", - "abscess_text_disorder = \"\"\"An abscess is a disorder, which is a clinical condition characterized by the formation of a painful and inflamed mass containing purulent material\"\"\"\n", - "\n", - "# for reuse later\n", - "def find_texts():\n", - " for text_num, text in enumerate([abscess_text_morph, abscess_text_disorder]):\n", - " ents = cat.get_entities(text)['entities']\n", - " print(text_num, \":\", ents)\n", - "find_texts()\n" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "Now that it's clear that we can't, we're sure to need some supervised training.\n", - "Let's then do that." - ] - }, - { - "cell_type": "code", - "execution_count": 4, - "metadata": {}, - "outputs": [ - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Epoch: 0%| | 0/1 [00:00 MedCAT can be used to extract information from Electronic Health Records (EHRs) and link it to biomedical ontologies like SNOMED-CT, UMLS, or HPO (and potentially other ontologies). diff --git a/medcat-v2/docs/main.md b/medcat-v2/docs/main.md index 91862c4a8..96b7d875d 100644 --- a/medcat-v2/docs/main.md +++ b/medcat-v2/docs/main.md @@ -5,7 +5,7 @@ Details are outlined [here](breaking_changes.md). [![Build Status](https://github.com/CogStack/cogstack-nlp/actions/workflows/medcat-v2_main.yml)](https://github.com/CogStack/cogstack-nlp/actions/workflows/medcat-v2_main.yml) [![Documentation Status](https://readthedocs.org/projects/cogstack-nlp/badge/?version=latest)](https://readthedocs.org/projects/cogstack-nlp/badge/?version=latest) -[![Latest release](https://img.shields.io/github/v/release/CogStack/MedCAT2)](https://github.com/CogStack/MedCAT2/releases/latest) +[![Latest release](https://img.shields.io/github/v/release/CogStack/cogstack-nlp?filter=medcat/*)](https://github.com/CogStack/cogstack-nlp/releases/latest) [![pypi Version](https://img.shields.io/pypi/v/medcat.svg?style=flat-square&logo=pypi&logoColor=white)](https://pypi.org/project/medcat/) MedCAT(*v2*) can be used to extract information from Electronic Health Records (EHRs) and link it to biomedical ontologies like SNOMED-CT and UMLS. Paper on [arXiv](https://arxiv.org/abs/2010.01165). @@ -34,11 +34,11 @@ MedCAT(*v2*) can be used to extract information from Electronic Health Records ( A demo application is available [here](https://medcatv2.rosalind.kcl.ac.uk). ## Tutorials -Some guides on how to use MedCAT v2 are available at [MedCAT Tutorials](https://github.com/CogStack/MedCATv2tutorials). +Some guides on how to use MedCAT v2 are available at [MedCAT Tutorials](https://github.com/CogStack/cogstack-nlp/tree/main/medcat-v2-tutorials). ## Related Projects - [MedCAT](https://github.com/CogStack/cogstack-nlp/blob/main/medcat-v2/) - the original version of MedCAT that this v2 is based one. -- [MedCATtrainer](https://github.com/CogStack/MedCATtrainer/) - an interface for building, improving and customising a given Named Entity Recognition and Linking (NER+L) model (MedCAT) for biomedical domain text. +- [MedCATtrainer](https://github.com/CogStack/cogstack-nlp/tree/main/medcat-trainer/) - an interface for building, improving and customising a given Named Entity Recognition and Linking (NER+L) model (MedCAT) for biomedical domain text. - [MedCATservice](https://github.com/CogStack/cogstack-nlp/blob/main/medcat-service/) - implements the MedCAT NLP application as a service behind a REST API. ## Install using PIP (Requires Python 3.9+) diff --git a/medcat-v2/pyproject.toml b/medcat-v2/pyproject.toml index 1c555fe50..556a76993 100644 --- a/medcat-v2/pyproject.toml +++ b/medcat-v2/pyproject.toml @@ -114,7 +114,7 @@ test = [] # TODO - list [project.urls] "Homepage" = "https://cogstack.org/" "Bug Reports" = "https://discourse.cogstack.org/" -"Source" = "https://github.com/CogStack/MedCAT/" +"Source" = "https://github.com/CogStack/cogstack-nlp/" [build-system] # These are the assumed default build requirements from pip: From e20cc51226371c785978f4c22cdd32e2d9768976 Mon Sep 17 00:00:00 2001 From: alhendrickson <159636032+alhendrickson@users.noreply.github.com.> Date: Thu, 7 Aug 2025 10:02:34 +0000 Subject: [PATCH 2/3] CU-8699mrvup docs: Update URLs to point to new cogstack-nlp repo --- medcat-trainer/README.md | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/medcat-trainer/README.md b/medcat-trainer/README.md index 73005ae57..13b7ef260 100644 --- a/medcat-trainer/README.md +++ b/medcat-trainer/README.md @@ -1,10 +1,9 @@ # Medical oncept Annotation Tool Trainer -[![Build Status](https://github.com/CogStack/cogstack-nlp/actions/workflows/medcat-trainer_ci.yml/badge.svg?branch=main)](https://github.com/CogStack/cogstack-nlp/actions/workflows/medcat-trainer_ci.yml?query=branch%3Amain) [![Build Status](https://github.com/CogStack/cogstack-nlp/actions/workflows/medcat-trainer_qa.yml/badge.svg?branch=main)](https://github.com/CogStack/cogstack-nlp/actions/workflows/medcat-trainer_qa.yml?query=branch%3Amain) [![Build Status](https://github.com/CogStack/cogstack-nlp/actions/workflows/medcat-trainer_release.yml/badge.svg)](https://github.com/CogStack/cogstack-nlp/actions/workflows/medcat-trainer_release.yml) [![Documentation Status](https://readthedocs.org/projects/cogstack-nlp-medcat-trainer/badge/?version=latest)](https://readthedocs.org/projects/cogstack-nlp-medcat-trainer/badge/?version=latest) -[![Latest release](https://img.shields.io/github/v/release/CogStack/cogstack-nlp)](https://github.com/CogStack/cogstack-nlp/releases/latest) +[![Latest release](https://img.shields.io/github/v/release/CogStack/cogstack-nlp?filter=medcat-trainer/*)](https://github.com/CogStack/cogstack-nlp/releases/latest) MedCATTrainer is an interface for building, improving and customising a given Named Entity Recognition and Linking (NER+L) model (MedCAT) for biomedical domain text. From 39ac95ff4f33766f3902db6c9c9130a5b375503f Mon Sep 17 00:00:00 2001 From: alhendrickson <159636032+alhendrickson@users.noreply.github.com.> Date: Thu, 7 Aug 2025 10:05:31 +0000 Subject: [PATCH 3/3] CU-8699mrvup docs: Update URLs to point to new cogstack-nlp repo --- medcat-trainer/notebook_docs/Processing_Annotations.ipynb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/medcat-trainer/notebook_docs/Processing_Annotations.ipynb b/medcat-trainer/notebook_docs/Processing_Annotations.ipynb index 31c08bd0c..4ef56ec1d 100644 --- a/medcat-trainer/notebook_docs/Processing_Annotations.ipynb +++ b/medcat-trainer/notebook_docs/Processing_Annotations.ipynb @@ -147,7 +147,7 @@ "metadata": {}, "outputs": [], "source": [ - "# Load the annotations downloaded - as described: https://github.com/CogStack/cogstack-nlp/tree/main/medcat-trainer/blob/main/README.md#download-annos\n", + "# Load the annotations downloaded - as described: https://docs.cogstack.org/projects/medcat-trainer/en/latest/project_admin.html#downloading-annotations\n", "projs = json.load(open('example_data/MedCAT_Export_With_Text_2020-05-22_10_34_09.json'))['projects']" ] },