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RelCAT tutorials v1 (CogStack/MedCATtutorials#31)
* RelCAT tutorials v1. * Updated RelCAT notebooks (incl html version). * Updated README.md * Workflow update to incl RelCAT. * Update MedCAT requirement to 1.16 * Allow nbmake>=1.4 for compatibility with pydantic 2. pydantic was dropped as a requirement in nbmake==1.4.3 * Make workflow run on ubuntu-24.04 * Bump all install targets to 1.16 * Updated RelCAT tutorial to include tutorial model links. * Allow later pandas versions * Revert "Allow later pandas versions" This reverts commit e794964. * Force usage of full path for model * Add some debug information regarding issues when loading model * Do archive unpack in pytho nrather than in a subprocess * Unpack model in part 6.2 to a distinct path * Undo debug output / exception handling * Make sure to use correct paths when downloading and unzipping * Remove unused import * Use relative paths again for downloaded model * Fix usage of undefined variable * Fix loadable model path * Add further information to exception * Specfiy unzip path explicitly --------- Co-authored-by: mart-r <[email protected]>
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‎medcat-v1-tutorials/.github/workflows/main.yml‎

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jobs:
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main:
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runs-on: macos-latest
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runs-on: ubuntu-24.04
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strategy:
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matrix:
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part: [
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introductory/Part_4_*.ipynb,
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introductory/Part_5_*.ipynb,
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introductory/Part_1_*.ipynb,
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introductory/Part_6_*.ipynb,
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specialised/Comparing_Models_with_RegressionSuite.ipynb # this should work still
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# specialised/*.ipynb # To make it run, the SnomedCT file needs to be mocked
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‎medcat-v1-tutorials/README.md‎

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| 4.2 | [Supervised training and fine-tuning + Meta-annotations](https://htmlpreview.github.io/?https://github.com/CogStack/MedCATtutorials/blob/main/notebooks/introductory/Part_4_2_Supervised_Training_and_Meta_annotations.html) | [![Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/CogStack/MedCATtutorials/blob/main/notebooks/introductory/Part_4_2_Supervised_Training_and_Meta_annotations.ipynb) | - |
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| 4.3 | [Annotating documents with the full MedCAT pipeline with MetaAnnotations](https://htmlpreview.github.io/?https://github.com/CogStack/MedCATtutorials/blob/main/notebooks/introductory/Part_4_3_Annotating_documents_with_the_full_MedCAT_pipeline_with_MetaAnnotations.html) | [![Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/CogStack/MedCATtutorials/blob/main/notebooks/introductory/Part_4_3_Annotating_documents_with_the_full_MedCAT_pipeline_with_MetaAnnotations.ipynb) | - |
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| 5 | [Analysing the results](https://htmlpreview.github.io/?https://github.com/CogStack/MedCATtutorials/blob/main/notebooks/introductory/Part_5_Prevalence_of_Physical_and_Mental_Diseases.html) | [![Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/CogStack/MedCATtutorials/blob/main/notebooks/introductory/Part_5_Prevalence_of_Physical_and_Mental_Diseases.ipynb) | [TDS](https://medium.com/@w_is_h/prevalence-of-physical-and-mental-diseases-450c0f4f5851) |
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| 6.1 | [Supervised training Relation-annotations](https://htmlpreview.github.io/?https://github.com/CogStack/MedCATtutorials/blob/rel_cat_tutorials/notebooks/introductory/Part_6_1_Supervised_Training_Relation_Extraction.html) | - | - |
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| 6.2 | [Infering relationships from annotations](https://htmlpreview.github.io/?https://github.com/CogStack/MedCATtutorials/blob/rel_cat_tutorials/notebooks/introductory/Part_6_2_Infering_relations_from_annotations_with_Relation_toolkit.html) | - | - |
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## Specialised tutorials
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‎medcat-v1-tutorials/notebooks/introductory/Part_1_1_OPTIONAL_Logging_With_MedCAT.html‎

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<div class=" highlight hl-ipython3"><pre><span></span><span class="c1"># Install medcat</span>
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<span class="o">!</span> pip install medcat~<span class="o">=</span><span class="m">1</span>.14.0
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<span class="o">!</span> pip install medcat~<span class="o">=</span><span class="m">1</span>.16.0
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‎medcat-v1-tutorials/notebooks/introductory/Part_1_1_OPTIONAL_Logging_With_MedCAT.ipynb‎

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‎medcat-v1-tutorials/notebooks/introductory/Part_3_1_Building_a_Concept_Database_and_Vocabulary.html‎

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‎medcat-v1-tutorials/notebooks/introductory/Part_3_1_Building_a_Concept_Database_and_Vocabulary.ipynb‎

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‎medcat-v1-tutorials/notebooks/introductory/Part_3_2_Extracting_Diseases_from_Electronic_Health_Records.html‎

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{"model_id": "05b18c97da9d4d05b9280df006a5fb82", "version_major": 2, "version_minor": 0}

‎medcat-v1-tutorials/notebooks/introductory/Part_3_2_Extracting_Diseases_from_Electronic_Health_Records.ipynb‎

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"vscode": {
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‎medcat-v1-tutorials/notebooks/introductory/Part_3_3_Model_technical_optimisations.html‎

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‎medcat-v1-tutorials/notebooks/introductory/Part_3_3_Model_technical_optimisations.ipynb‎

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