From 9575ecbe3df2af9a8e989da2be0e3efd5abf9f10 Mon Sep 17 00:00:00 2001 From: alhendrickson Date: Fri, 24 Apr 2026 10:11:54 +0000 Subject: [PATCH 01/11] docs: Build Medcat Tutorials with Mkdocs --- .devcontainer/devcontainer.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json index c7fff090f..c662d0aa8 100644 --- a/.devcontainer/devcontainer.json +++ b/.devcontainer/devcontainer.json @@ -3,7 +3,7 @@ { "name": "Python 3", // Or use a Dockerfile or Docker Compose file. More info: https://containers.dev/guide/dockerfile - "image": "mcr.microsoft.com/devcontainers/python:1-3.12-bullseye", + "image": "mcr.microsoft.com/devcontainers/python:3.13-bookworm", "features": { "ghcr.io/devcontainers/features/docker-outside-of-docker:1": {}, "ghcr.io/va-h/devcontainers-features/uv:1": { From b32a7f60552dc3efab67ceb5974bf72c33542258 Mon Sep 17 00:00:00 2001 From: alhendrickson Date: Fri, 24 Apr 2026 10:12:06 +0000 Subject: [PATCH 02/11] docs: Build Medcat Tutorials with Mkdocs --- medcat-v2-tutorials/mkdocs.yml | 74 + medcat-v2-tutorials/notebooks/index.md | 52 + medcat-v2-tutorials/pyproject.toml | 20 + medcat-v2-tutorials/uv.lock | 1733 ++++++++++++++++++++++++ 4 files changed, 1879 insertions(+) create mode 100644 medcat-v2-tutorials/mkdocs.yml create mode 100644 medcat-v2-tutorials/notebooks/index.md create mode 100644 medcat-v2-tutorials/pyproject.toml create mode 100644 medcat-v2-tutorials/uv.lock diff --git a/medcat-v2-tutorials/mkdocs.yml b/medcat-v2-tutorials/mkdocs.yml new file mode 100644 index 000000000..e38880176 --- /dev/null +++ b/medcat-v2-tutorials/mkdocs.yml @@ -0,0 +1,74 @@ +# yaml-language-server: $schema=https://squidfunk.github.io/mkdocs-material/schema.json +site_name: MedCAT Tutorials +site_url: https://docs.cogstack.org/ + +theme: + name: material + favicon: _static/img/cat-logo.svg + logo: _static/img/cat-logo.svg + icon: + logo: _static/img/cat-logo.svg + palette: + primary: white + + features: + - navigation.tabs + - navigation.sections + - navigation.top + - navigation.indexes + - navigation.tracking + - navigation.footer + - header.autohide + - content.tooltips + - search.highlight + - search.share + - search.suggest + - toc.follow + - attr_list + +repo_url: https://github.com/CogStack/cogstack-nlp +repo_name: cogstack-nlp + +docs_dir: notebooks + +nav: + - Home: index.md + - Introductory Tutorials: + - Basic: + - README: introductory/basic/README.md + - 1. Build a Concept Database and a Vocabulary: introductory/basic/1._Build_a_Concept_Database_and_a_Vocabulary.ipynb + - 2. Unsupervised training on model: introductory/basic/2._Unsupervised_training_on_model.ipynb + - 3. Supervised training on model: introductory/basic/3._Supervised_training_on_model.ipynb + - 4. Evaluating performance on dataset: introductory/basic/4._Evaluating_performance_on_dataset.ipynb + - Custom: + - README: introductory/custom/README.md + - 1. Create Modelpack with 2step linker: introductory/custom/1._Create_Modelpack_with_2step_linker.ipynb + - MetaCAT: + - README: introductory/meta/README.md + - 1. Add a MetaCat to a Model: introductory/meta/1._Add_a_MetaCat_to_a_Model.ipynb + - Migration: + - README: introductory/migration/README.md + - 1. Migrate v1 model to v2: introductory/migration/1._Migrate_v1_model_to_v2.ipynb + - RelCAT: + - 1. Supervised Training Relation Extraction: introductory/relcat/1._Supervised_Training_Relation_Extraction.ipynb + - 2. Infering relations from annotations with Relation toolkit: introductory/relcat/2._Infering_relations_from_annotations_with_Relation_toolkit.ipynb + + - Advanced Tutorials: + - 1. Creating and using a custom tokenizer: advanced/1._Creating_and_using_a_custom_tokenizer.ipynb + - 2. Create and use component: advanced/2._Create_and_use_component.ipynb + +plugins: + - search + - termynal + - autorefs # Resolves cross-refs from mkdocstrings so type links work across pages + - mkdocs-jupyter: + ignore_h1_titles: True + +markdown_extensions: + - admonition + - attr_list + - pymdownx.details + - pymdownx.superfences + - pymdownx.emoji: + emoji_index: !!python/name:material.extensions.emoji.twemoji + emoji_generator: !!python/name:material.extensions.emoji.to_svg diff --git a/medcat-v2-tutorials/notebooks/index.md b/medcat-v2-tutorials/notebooks/index.md new file mode 100644 index 000000000..95efa1e1d --- /dev/null +++ b/medcat-v2-tutorials/notebooks/index.md @@ -0,0 +1,52 @@ +# MedCAT Tutorials + +The MedCAT Tutorials provide an interactive learning path for using MedCAT. + +NOTE: These tutorials are aimed at developers and / or people creating their own models. +For every day usage (e.g inference) the [medcat-scripts](https://github.com/CogStack/cogstack-nlp/tree/main/medcat-scripts) portion would probably be more useful. + +## Interactive Tutorials + +These tutorials are written as real, executable code in jupyter notebooks. The version on docs.cogstack.org is read only, but you could instead choose to follow along and run the code as you go. + +To get set up to run the tutorials interactively, clone the repo and install the tutorial dependencies. + +```bash +git clone https://github.com/CogStack/cogstack-nlp.git +cd cogstack-nlp/medcat-v2-tutorials + +python -m venv .venv +source .venv/bin/activate +pip install -r requirements.txt +``` +You can now open the notebook in vscode and run the tutorials. Alternatively you could use `pip install jupyter` and run `jupyter lab` to do this on the command line. + +## Introductory tutorials + +### Migration of v1 models + +| Part | Title | +| ---- |-----------------------------------------------------------------------------| +| 1. | [Migrate a v1 model to v2](notebooks/introductory/migration/1._Migrate_v1_model_to_v2.ipynb) | + +### Basic (regex-tokenizer) tutorials + +| Part | Title | +| ---- |-----------------------------------------------------------------------------| +| 1. | [Building a Concept Database and a Vocab](notebooks/introductory/basic/1._Build_a_Concept_Database_and_a_Vocabulary.ipynb) | +| 2. | [Unsupervised training on model](notebooks/introductory/basic/2._Unsupervised_training_on_model.ipynb) | +| 3. | [Supervised training on model](notebooks/introductory/basic/3._Supervised_training_on_model.ipynb) | +| 4. | [Evaluating perfromance on dataset](notebooks/introductory/basic/4._Evaluating_performance_on_dataset.ipynb) | + +### MetaCAT (meta-annotation) tutorials + +| Part | Title | +| ---- |-----------------------------------------------------------------------------| +| 1. | [Add a MetaCAT to a Model](notebooks/introductory/meta/1._Add_a_MetaCat_to_a_Model.ipynb) | + +## Advanced tutorials + +| Part | Title | +| ---- |-----------------------------------------------------------------------------| +| 1. | [Creating and using a custom tokenizer](notebooks/advanced/1._Creating_and_using_a_custom_tokenizer.ipynb) | +| 2. | [Create and use component](notebooks/advanced/2._Create_and_use_component.ipynb) | diff --git a/medcat-v2-tutorials/pyproject.toml b/medcat-v2-tutorials/pyproject.toml new file mode 100644 index 000000000..ed5643307 --- /dev/null +++ b/medcat-v2-tutorials/pyproject.toml @@ -0,0 +1,20 @@ +[project] +name = "medcat-v2-documentation" +version = "0.1.0" +description = "MedCAT v2 Documentation" +requires-python = ">=3.10" +dependencies = [ + "mkdocs-api-autonav>=0.4.0", + 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autorefs # Resolves cross-refs from mkdocstrings so type links work across pages - api-autonav: modules: ['medcat'] - + - monorepo + - mkdocs-jupyter: + ignore_h1_titles: True markdown_extensions: - admonition From 4452ead967f979eff0c483d7022b9ce131503e6e Mon Sep 17 00:00:00 2001 From: alhendrickson Date: Fri, 24 Apr 2026 10:37:47 +0000 Subject: [PATCH 04/11] docs(medcat): Add medcat tutorials into public documentation page --- medcat-v2/mkdocs.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/medcat-v2/mkdocs.yml b/medcat-v2/mkdocs.yml index 20533141e..6c8028a94 100644 --- a/medcat-v2/mkdocs.yml +++ b/medcat-v2/mkdocs.yml @@ -35,7 +35,7 @@ nav: - Home: index.md - Architecture: architecture.md - Tutorials: '!include ../medcat-v2-tutorials/mkdocs.yml' - - Upgrading + - Upgrading: - Migration guide (v2): migration_guide_v2.md - Breaking changes: breaking_changes.md From c9cfa424aa0445b07f48e160c3282f3b125ec283 Mon Sep 17 00:00:00 2001 From: alhendrickson Date: Fri, 24 Apr 2026 11:03:34 +0000 Subject: [PATCH 05/11] docs(medcat): Add medcat tutorials into public documentation page - fix link --- medcat-v2-tutorials/notebooks/index.md | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/medcat-v2-tutorials/notebooks/index.md b/medcat-v2-tutorials/notebooks/index.md index 95efa1e1d..3cb924ce1 100644 --- a/medcat-v2-tutorials/notebooks/index.md +++ b/medcat-v2-tutorials/notebooks/index.md @@ -27,26 +27,26 @@ You can now open the notebook in vscode and run the tutorials. Alternatively you | Part | Title | | ---- |-----------------------------------------------------------------------------| -| 1. | [Migrate a v1 model to v2](notebooks/introductory/migration/1._Migrate_v1_model_to_v2.ipynb) | +| 1. | [Migrate a v1 model to v2](introductory/migration/1._Migrate_v1_model_to_v2/) | ### Basic (regex-tokenizer) tutorials | Part | Title | | ---- |-----------------------------------------------------------------------------| -| 1. | [Building a Concept Database and a Vocab](notebooks/introductory/basic/1._Build_a_Concept_Database_and_a_Vocabulary.ipynb) | -| 2. | [Unsupervised training on model](notebooks/introductory/basic/2._Unsupervised_training_on_model.ipynb) | -| 3. | [Supervised training on model](notebooks/introductory/basic/3._Supervised_training_on_model.ipynb) | -| 4. | [Evaluating perfromance on dataset](notebooks/introductory/basic/4._Evaluating_performance_on_dataset.ipynb) | +| 1. | [Building a Concept Database and a Vocab](introductory/basic/1._Build_a_Concept_Database_and_a_Vocabulary/) | +| 2. | [Unsupervised training on model](introductory/basic/2._Unsupervised_training_on_model/) | +| 3. | [Supervised training on model](introductory/basic/3._Supervised_training_on_model/) | +| 4. | [Evaluating perfromance on dataset](introductory/basic/4._Evaluating_performance_on_dataset/) | ### MetaCAT (meta-annotation) tutorials | Part | Title | | ---- |-----------------------------------------------------------------------------| -| 1. | [Add a MetaCAT to a Model](notebooks/introductory/meta/1._Add_a_MetaCat_to_a_Model.ipynb) | +| 1. | [Add a MetaCAT to a Model](introductory/meta/1._Add_a_MetaCat_to_a_Model/) | ## Advanced tutorials | Part | Title | | ---- |-----------------------------------------------------------------------------| -| 1. | [Creating and using a custom tokenizer](notebooks/advanced/1._Creating_and_using_a_custom_tokenizer.ipynb) | -| 2. | [Create and use component](notebooks/advanced/2._Create_and_use_component.ipynb) | +| 1. | [Creating and using a custom tokenizer](advanced/1._Creating_and_using_a_custom_tokenizer/) | +| 2. | [Create and use component](advanced/2._Create_and_use_component/) | From bc72c55ae995bd3de84aba0b7af827ebb9497378 Mon Sep 17 00:00:00 2001 From: alhendrickson Date: Fri, 24 Apr 2026 11:35:21 +0000 Subject: [PATCH 06/11] docs(medcat-tutorial): Remove readme duplication --- medcat-v2-tutorials/README.md | 40 ++++++++++++++--------------------- 1 file changed, 16 insertions(+), 24 deletions(-) diff --git a/medcat-v2-tutorials/README.md b/medcat-v2-tutorials/README.md index e8b0d2bff..16b1fe59d 100644 --- a/medcat-v2-tutorials/README.md +++ b/medcat-v2-tutorials/README.md @@ -2,35 +2,27 @@ The MedCAT Tutorials provide an interactive learning path for using MedCAT. -NOTE: These tutorials are aimed at developers and / or people creating their own models. -For every day usage (e.g inference) the [medcat-scripts](../medcat-scripts) portion would probably be more useful. +*See the documentation on [index.md](notebooks/index.md) to get started with these tutorials.* -## Introductory tutorials +## Developer Readme +The following readmes are around the setup of the tutorials themselves aimed at a tutorial author. -### Migration of v1 models +### Documentation Build -| Part | Title | -| ---- |-----------------------------------------------------------------------------| -| 1. | [Migrate a v1 model to v2](notebooks/introductory/migration/1._Migrate_v1_model_to_v2.ipynb) | +The `medcat-v2` documentation site imports this project’s MkDocs navigation file directly. The relevant plugins are the mkdocs-monorepo-plugin and the mkdocs-jupyter pluign. -### Basic (regex-tokenizer) tutorials +In `medcat-v2/mkdocs.yml` the `Tutorials` section is wired in via an include: -| Part | Title | -| ---- |-----------------------------------------------------------------------------| -| 1. | [Building a Concept Database and a Vocab](notebooks/introductory/basic/1._Build_a_Concept_Database_and_a_Vocabulary.ipynb) | -| 2. | [Unsupervised training on model](notebooks/introductory/basic/2._Unsupervised_training_on_model.ipynb) | -| 3. | [Supervised training on model](notebooks/introductory/basic/3._Supervised_training_on_model.ipynb) | -| 4. | [Evaluating perfromance on dataset](notebooks/introductory/basic/4._Evaluating_performance_on_dataset.ipynb) | +```yaml +nav: + - Tutorials: '!include ../medcat-v2-tutorials/mkdocs.yml' +``` -### MetaCAT (meta-annotation) tutorials +#### Run the docs locally (rendered site) -| Part | Title | -| ---- |-----------------------------------------------------------------------------| -| 1. | [Add a MetaCAT to a Model](notebooks/introductory/meta/1._Add_a_MetaCat_to_a_Model.ipynb) | +To preview the rendered docs site locally: -## Advanced tutorials - -| Part | Title | -| ---- |-----------------------------------------------------------------------------| -| 1. | [Creating and using a custom tokenizer](notebooks/advanced/1._Creating_and_using_a_custom_tokenizer.ipynb) | -| 2. | [Create and use component](notebooks/advanced/2._Create_and_use_component.ipynb) | +```bash +cd cogstack-nlp/medcat-v2-tutorials +uv run mkdocs serve +``` From b098f2798175f96c3486d3eb67edfa14f6158767 Mon Sep 17 00:00:00 2001 From: alhendrickson Date: Fri, 24 Apr 2026 11:44:38 +0000 Subject: [PATCH 07/11] docs(medcat-tutorial): Remove readme duplication --- medcat-v2-tutorials/notebooks/index.md | 46 ++++++++------------------ 1 file changed, 13 insertions(+), 33 deletions(-) diff --git a/medcat-v2-tutorials/notebooks/index.md b/medcat-v2-tutorials/notebooks/index.md index 3cb924ce1..483c2ea73 100644 --- a/medcat-v2-tutorials/notebooks/index.md +++ b/medcat-v2-tutorials/notebooks/index.md @@ -2,12 +2,22 @@ The MedCAT Tutorials provide an interactive learning path for using MedCAT. -NOTE: These tutorials are aimed at developers and / or people creating their own models. +These tutorials are aimed at developers and / or people creating their own models. For every day usage (e.g inference) the [medcat-scripts](https://github.com/CogStack/cogstack-nlp/tree/main/medcat-scripts) portion would probably be more useful. -## Interactive Tutorials +## Learning Path -These tutorials are written as real, executable code in jupyter notebooks. The version on docs.cogstack.org is read only, but you could instead choose to follow along and run the code as you go. +Get started by going to the [basic tutorials](introductory/basic/). Here you will learn about Concept Databases, Vocabularies, and perform supervised and unsupervised training. + +After that you can continue to see the other features of medcat, such as configuring MetaCAT, RelCAT and other features of medcat. + +Finally you can look at advanced tutorials where you will configure the internals of MedCAT. + +## Interactive Usage + +!!! tip + + These tutorials are written as real, executable code in jupyter notebooks. The version on docs.cogstack.org is read only, but you could instead choose to follow along and run the code as you go. To get set up to run the tutorials interactively, clone the repo and install the tutorial dependencies. @@ -20,33 +30,3 @@ source .venv/bin/activate pip install -r requirements.txt ``` You can now open the notebook in vscode and run the tutorials. Alternatively you could use `pip install jupyter` and run `jupyter lab` to do this on the command line. - -## Introductory tutorials - -### Migration of v1 models - -| Part | Title | -| ---- |-----------------------------------------------------------------------------| -| 1. | [Migrate a v1 model to v2](introductory/migration/1._Migrate_v1_model_to_v2/) | - -### Basic (regex-tokenizer) tutorials - -| Part | Title | -| ---- |-----------------------------------------------------------------------------| -| 1. | [Building a Concept Database and a Vocab](introductory/basic/1._Build_a_Concept_Database_and_a_Vocabulary/) | -| 2. | [Unsupervised training on model](introductory/basic/2._Unsupervised_training_on_model/) | -| 3. | [Supervised training on model](introductory/basic/3._Supervised_training_on_model/) | -| 4. | [Evaluating perfromance on dataset](introductory/basic/4._Evaluating_performance_on_dataset/) | - -### MetaCAT (meta-annotation) tutorials - -| Part | Title | -| ---- |-----------------------------------------------------------------------------| -| 1. | [Add a MetaCAT to a Model](introductory/meta/1._Add_a_MetaCat_to_a_Model/) | - -## Advanced tutorials - -| Part | Title | -| ---- |-----------------------------------------------------------------------------| -| 1. | [Creating and using a custom tokenizer](advanced/1._Creating_and_using_a_custom_tokenizer/) | -| 2. | [Create and use component](advanced/2._Create_and_use_component/) | From ddc409abba9dc7debd54c05882e6e660326cd158 Mon Sep 17 00:00:00 2001 From: alhendrickson Date: Fri, 24 Apr 2026 11:48:47 +0000 Subject: [PATCH 08/11] docs(medcat-tutorial): Refactor nav --- medcat-v2-tutorials/mkdocs.yml | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/medcat-v2-tutorials/mkdocs.yml b/medcat-v2-tutorials/mkdocs.yml index e38880176..43d8b4a3b 100644 --- a/medcat-v2-tutorials/mkdocs.yml +++ b/medcat-v2-tutorials/mkdocs.yml @@ -40,15 +40,9 @@ nav: - 2. Unsupervised training on model: introductory/basic/2._Unsupervised_training_on_model.ipynb - 3. Supervised training on model: introductory/basic/3._Supervised_training_on_model.ipynb - 4. Evaluating performance on dataset: introductory/basic/4._Evaluating_performance_on_dataset.ipynb - - Custom: - - README: introductory/custom/README.md - - 1. Create Modelpack with 2step linker: introductory/custom/1._Create_Modelpack_with_2step_linker.ipynb - MetaCAT: - README: introductory/meta/README.md - 1. Add a MetaCat to a Model: introductory/meta/1._Add_a_MetaCat_to_a_Model.ipynb - - Migration: - - README: introductory/migration/README.md - - 1. Migrate v1 model to v2: introductory/migration/1._Migrate_v1_model_to_v2.ipynb - RelCAT: - 1. Supervised Training Relation Extraction: introductory/relcat/1._Supervised_Training_Relation_Extraction.ipynb - 2. Infering relations from annotations with Relation toolkit: introductory/relcat/2._Infering_relations_from_annotations_with_Relation_toolkit.ipynb @@ -56,6 +50,12 @@ nav: - Advanced Tutorials: - 1. Creating and using a custom tokenizer: advanced/1._Creating_and_using_a_custom_tokenizer.ipynb - 2. Create and use component: advanced/2._Create_and_use_component.ipynb + - Custom Components: + - README: introductory/custom/README.md + - 1. Create Modelpack with 2step linker: introductory/custom/1._Create_Modelpack_with_2step_linker.ipynb + - Migration: + - README: introductory/migration/README.md + - 1. Migrate v1 model to v2: introductory/migration/1._Migrate_v1_model_to_v2.ipynb plugins: - search From 5f389196e9fde553c136c882c2c0b6ac898010ed Mon Sep 17 00:00:00 2001 From: alhendrickson Date: Fri, 24 Apr 2026 11:50:20 +0000 Subject: [PATCH 09/11] docs(medcat-tutorial): Refactor doc --- medcat-v2-tutorials/notebooks/index.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/medcat-v2-tutorials/notebooks/index.md b/medcat-v2-tutorials/notebooks/index.md index 483c2ea73..426bbedf9 100644 --- a/medcat-v2-tutorials/notebooks/index.md +++ b/medcat-v2-tutorials/notebooks/index.md @@ -9,9 +9,9 @@ For every day usage (e.g inference) the [medcat-scripts](https://github.com/CogS Get started by going to the [basic tutorials](introductory/basic/). Here you will learn about Concept Databases, Vocabularies, and perform supervised and unsupervised training. -After that you can continue to see the other features of medcat, such as configuring MetaCAT, RelCAT and other features of medcat. +After that you can continue to see the other features of medcat, such as configuring MetaCAT and RelCAT. -Finally you can look at advanced tutorials where you will configure the internals of MedCAT. +Finally you can look at advanced tutorials where you will dig into the internals of MedCAT. ## Interactive Usage From 1891543ad121244beed755231fa9fdcb1473ca2e Mon Sep 17 00:00:00 2001 From: alhendrickson Date: Fri, 24 Apr 2026 13:25:54 +0000 Subject: [PATCH 10/11] docs: Add links to the tutorials on medcat --- medcat-v2-tutorials/README.md | 2 +- medcat-v2/README.md | 4 +--- medcat-v2/docs/index.md | 2 +- 3 files changed, 3 insertions(+), 5 deletions(-) diff --git a/medcat-v2-tutorials/README.md b/medcat-v2-tutorials/README.md index 16b1fe59d..8a6101f8b 100644 --- a/medcat-v2-tutorials/README.md +++ b/medcat-v2-tutorials/README.md @@ -2,7 +2,7 @@ The MedCAT Tutorials provide an interactive learning path for using MedCAT. -*See the documentation on [index.md](notebooks/index.md) to get started with these tutorials.* +See the cogstack documentation site to view these tutorials and all the documentation on [docs.cogstack.org](https://docs.cogstack.org) ## Developer Readme The following readmes are around the setup of the tutorials themselves aimed at a tutorial author. diff --git a/medcat-v2/README.md b/medcat-v2/README.md index e491a77c9..2c8484ed9 100644 --- a/medcat-v2/README.md +++ b/medcat-v2/README.md @@ -149,9 +149,7 @@ The MedCAT v2 demo web app is available [here](https://medcat.sites.er.kcl.ac.uk See [Architecture Documentation](docs/architecture.md) for detailed information. ## Tutorials -A guide on how to use MedCAT v2 is available at [MedCATv2 Tutorials](../medcat-v2-tutorials). -However, the tutorials are a bit of a work in progress at this point in time. - +A guide on how to use MedCAT v2 is available at on the medcat documentation page on [docs.cogstack.org](https://docs.cogstack.org) ## Acknowledgements Entity extraction was trained on [MedMentions](https://github.com/chanzuckerberg/MedMentions) In total it has ~ 35K entites from UMLS diff --git a/medcat-v2/docs/index.md b/medcat-v2/docs/index.md index 0a6ffac4c..2808c9cbc 100644 --- a/medcat-v2/docs/index.md +++ b/medcat-v2/docs/index.md @@ -34,7 +34,7 @@ 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/cogstack-nlp/tree/main/medcat-v2-tutorials). +See the tutorials page for guides on how to use medcat on [MedCAT Tutorials](medcat-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. From baf8aefbde54da4bde1ac624aee2eafa443b7ab8 Mon Sep 17 00:00:00 2001 From: alhendrickson Date: Fri, 24 Apr 2026 13:33:10 +0000 Subject: [PATCH 11/11] docs: Add links to the tutorials on medcat - fix typo --- medcat-v2-tutorials/README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/medcat-v2-tutorials/README.md b/medcat-v2-tutorials/README.md index 8a6101f8b..771b05229 100644 --- a/medcat-v2-tutorials/README.md +++ b/medcat-v2-tutorials/README.md @@ -9,7 +9,7 @@ The following readmes are around the setup of the tutorials themselves aimed at ### Documentation Build -The `medcat-v2` documentation site imports this project’s MkDocs navigation file directly. The relevant plugins are the mkdocs-monorepo-plugin and the mkdocs-jupyter pluign. +The `medcat-v2` documentation site imports this project’s MkDocs navigation file directly. The relevant plugins are the mkdocs-monorepo-plugin and the mkdocs-jupyter plugin. In `medcat-v2/mkdocs.yml` the `Tutorials` section is wired in via an include: