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27 changes: 11 additions & 16 deletions medcat-v2/README.md
Original file line number Diff line number Diff line change
Expand Up @@ -10,21 +10,22 @@ Details on breaking are outlined [here](docs/breaking_changes.md).
<!-- [![pypi Version](https://img.shields.io/pypi/v/medcat.svg?style=flat-square&logo=pypi&logoColor=white)](https://pypi.org/project/medcat/) -->

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).
Original paper for v1 on [arXiv](https://arxiv.org/abs/2010.01165).
Original paper for v1 on [arXiv](https://arxiv.org/abs/2010.01165).

**Official Docs [here](https://cogstack-nlp.readthedocs.io/)**

**Discussion Forum [discourse](https://discourse.cogstack.org/)**

## Available Models

As MedCAT v2 is still in Beta, we do not currently have any models publically available.
As MedCAT v2 is still in early release, we do not currently have any models publically available.
You can still use models for v1, however (see the [README](https://github.com/CogStack/cogstack-nlp/blob/main/medcat-v2/README.md) there).

If you wish you can also convert the v1 models into the v2 format (see tutorial (TODO + link)).

## News
- **MedCAT v2 beta** \[1. April 2025\] MedCATv2 beta 0.1.5 was released 1. April 2025.
<!-- - **Paper** van Es, B., Reteig, L.C., Tan, S.C. et al. [Negation detection in Dutch clinical texts: an evaluation of rule-based and machine learning methods](https://doi.org/10.1186/s12859-022-05130-x). BMC Bioinformatics 24, 10 (2023).
- **MedCAT 2.0.0** was released 18. August 2025.
<!-- - **Paper** van Es, B., Reteig, L.C., Tan, S.C. et al. [Negation detection in Dutch clinical texts: an evaluation of rule-based and machine learning methods](https://doi.org/10.1186/s12859-022-05130-x). BMC Bioinformatics 24, 10 (2023).
- **New tool in the Cogstack ecosystem \[19. December 2022\]** [Foresight -- Deep Generative Modelling of Patient Timelines using Electronic Health Records](https://arxiv.org/abs/2212.08072)
- **New Paper using MedCAT \[21. October 2022\]**: [A New Public Corpus for Clinical Section Identification: MedSecId.](https://aclanthology.org/2022.coling-1.326.pdf)
- **Major Change to the Permissions of Use \[4. August 2022\]** MedCAT now uses the [Elastic License 2.0](https://github.com/CogStack/MedCAT/pull/271/commits/c9f4e86116ec751a97c618c97dadaa23e1feb6bc). For further information please click [here.](https://www.elastic.co/licensing/elastic-license)
Expand All @@ -42,27 +43,21 @@ If you wish you can also convert the v1 models into the v2 format (see tutorial

## Installation

Currently MedCAT v2 is in Beta.
As such, you need to explicitly specify the beta release.
MedCAT v2 has its first full release
```
pip install medcat~=2.0.0b
pip install medcat~=2.0.0
```
Do note that **this installs only the core MedCAT v2**.
**It does not necessary dependencies for `spacy`-based tokenizing or MetaCATs or DeID**.
However, all of those are supported as well.
You can install them as follows:
```
pip install medcat[spacy]~=2.0.0b # for spacy-based tokenizer
pip install medcat[meta-cat]~=2.0.0b # for MetaCAT
pip install medcat[deid]~=2.0.0b # for DeID models
pip install medcat[spacy,meta-cat,deid,rel-cat,dict-ner]~=2.0.0b # for all of the above
pip install "medcat[spacy]~=2.0.0" # for spacy-based tokenizer
pip install "medcat[meta-cat]~=2.0.0" # for MetaCAT
pip install "medcat[deid]~=2.0.0" # for DeID models
pip install "medcat[spacy,meta-cat,deid,rel-cat,dict-ner]~=2.0.0" # for all of the above
```

PS:
For in the above example, we're installing the MedCAT v2 BETA version of `v0.8.0`.
The README is unlikely to change after every new release.
If another version is available / required, substitute the version tag as appropriate.

## Demo

The MedCAT v2 demo web app is available [here](https://medcatv2.sites.er.kcl.ac.uk/).
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