To run notebooks:
virtualenv -p python3 venv-CLOpenTree
source venv-CLOpenTree/bin/activate
pip install -r requirements.txt
pip install ipykernel
python -m ipykernel install --user --name=opentree
pip install jupyter
jupyter notebook
Directory bird_studies_translation contains all the bird trees in Phylesystem as of May 4, 2021.
In each subfolder (named for the study_id) Are at least 3 files - the full citation, a nexus tree, and a .csv mapping across the original label from upload, the label we currently have in opentree, and our best guess of the Clements (2019) label (or "unknown" if we don't even have a guess, and "not_a_bird" for outgroups). There will be a tree file and a .csv for each tree associated with the study.
If you open the nexus tree in figtree you can choose the tip labels to display, from the original labels that were on the upload, or the OpenTree labels, or the Clements best guess.
Jupyter script which generated these files found in notebooks/OTT_Clements_translator.ipynb Translation table used is taxonomy_info/combined_data.tsv