Ideally use Python 3.12.
Create a venv folder in the project directory using python -m venv venv. Then, activate the venv using venv\Scripts\activate. Install all libraries using pip install -r requirements.txt. Optional: run python -m ipykernel install --user --name=myenv --display-name="jupyter edds" to set a kernel for Jupyter. Then, just enter jupyter lab in the terminal to launch Jupter lab (make sure to have venv activated and select jupyter edds in Jupyter).
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Original data: https://dmice.ohsu.edu/hersh/ohsumed/
- Contains the original data
- Contains the judged.txt
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Link to the overleaf doc: https://www.overleaf.com/project/67683cb9765d4cd482e8e67e.
- This is the template they require us to use I think. It's quite messy with lots of unnecessary stuff in there.
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Link to the GitHub repo: https://github.com/shef-ski/edds-ex2
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Link to Zenodo community for the final submission: https://zenodo.org/uploads/new?community=tuw-exdds-ws24
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(Outdated) link to data: https://huggingface.co/datasets/community-datasets/ohsumed
- Since this a popular dataset, there exist multiple versions of it, but they are more or less the same.
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XML data from here (Used year 2019): https://www.nlm.nih.gov/databases/download/mesh.html
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MESH tree view: https://meshb.nlm.nih.gov/record/ui?ui=D052801
- Not very necessary, just for browsing the tree structure of MESH