Inflammatory bowel disease (IBD)

Ontologies

• To get the ontologies first get pytag from https://github.com/KociOrges/pytag
• Follow the installation guide
• It is necessary to pay attention on the bibtexparser library, its necessary to get the exact version 0.6.2.
• Go to Pubmed https://www.ncbi.nlm.nih.gov/pubmed/
• Find the Advanced Search and enter the disease on the first textbox, on the second enter for example "Food".
• At the top there is a Send To link, find Citation Manager and export the results.
• Enter on EndNote and import the File, add the Accession Number and export to bibtex.
• Go to the terminal and enter:

 pytag --input_dir ~/yourbibtexfolder --onto_types all --out_file outputfile.tsv

• For more detailed information on using pytag go to https://github.com/KociOrges/pytag

• To run the statistics the result file needs two more columns: The first describing the Pubmed filter (Diet, Food, Intolerance, Nutrition and Probiotics) and the second with the disease.

• Save it to csv and import on WEKA. Run the cluster and get the statistics results.

Paper:

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6064635/

Local:

Weka project [All.Diseases.arff] (https://github.com/Trindad/digestive-diseases/blob/master/ontologies/Results/All.Diseases.arff)

CSV for Weka analysis [All.Diseases.csv] (https://github.com/Trindad/digestive-diseases/blob/master/ontologies/Results/All.Diseases.csv)

Complex Network

Dataset:

Nhanes 2007-2008: https://wwwn.cdc.gov/nchs/nhanes/continuousnhanes/default.aspx?BeginYear=2007

Nhanes 2009-2010: https://wwwn.cdc.gov/nchs/nhanes/continuousnhanes/default.aspx?BeginYear=2009

Local:

CSV generation: python -m xport .XPT > .csv

Database generation: python create_database.py

Queries: python correlation.py

File:

network.ipynb

Dependency:

To run locally, you need to install all dependencies listed in requirements.txt

Jupyter:

Machine Learning

Dataset:

Paper: https://www.nature.com/articles/s41598-017-02606-2.pdf

Instructions:

Look at the machine-leaning branch.

Statistics

The statistics are inside the jupyter notebook used for the complex network.