Hands-on Jupyter notebooks for the book Data and Text Processing for Health and Life Sciences.
Each notebook is a short tutorial on using the Unix shell to find, retrieve, and process biomedical data and text. The files of each tutorial are in the matching *-files.zip.
| # | Notebook | Topics |
|---|---|---|
| 01 | Unix shell | ls, pwd, head, cat, pipes |
| 02 | Data retrieval | curl, EBI APIs, UniProt downloads |
| 03 | Data extraction | grep, cut, filtering proteins |
| 04 | Task repetition | loops, xargs, parallel |
| 05 | XML processing | xmllint, XPath, PubMed IDs |
| 06 | Text retrieval | publication titles and abstracts |
| 07 | Text processing | patterns, regex, tokenization |
| 08 | Semantic processing | ontologies, synonyms, NER |
- Open Google Colab.
- Choose File → Open notebook → GitHub.
- Paste
https://github.com/lasigeBioTM/data-text-processing-notebooksand open a notebook.
Direct links:
- 01 Unix shell
- 02 Data retrieval
- 03 Data extraction
- 04 Task repetition
- 05 XML processing
- 06 Text retrieval
- 07 Text processing
- 08 Semantic processing
git clone [https://github.com/lasigeBioTM/data-text-processing-notebooks](https://github.com/lasigeBioTM/data-text-processing-notebooks)
cd data-text-processing-notebooks
unzip 01-unix-shell-files.zip
jupyter notebookUnzip the *-files.zip that matches the notebook you want to run.