Dataset information

degree=1 has freq =454

degree=2 has freq =162

degree=3 has freq =76

degree=4 has freq =29

degree=5 has freq =18

degree=6 has freq =13

degree=7 has freq =1

degree=8 has freq =6

degree=9 has freq =1

degree=10 has freq =1

degree=11 has freq =4

degree=14 has freq =1

degree=17 has freq =1

degree=18 has freq =1

degree=20 has freq =1

degree=21 has freq =1

degree=31 has freq =1

degree=67 has freq =1

degree=103 has freq =1

degree=109 has freq =1

degree=336 has freq =1

degree=406 has freq =1

Steps to generate copd_label.txt (the file that generate copd bipartite graph)

• all_gene_disease_pmid_associations.py
• create generated_dataset/gene_disease_uniq.txt
• gene_disease_uniq.txt
• :contains :contains uniq value from each col of disease_gene.tsv. Therefore, number of uniq value in each col are not the same.

• map_umls.py
• :create gene_disease_uniq_DO_mapping.txt
• gene_disease_uniq_DO_mapping.txt
• :use generated_dataset/gene_dsease_uniq.txt to map cuis and doid in disease_gene.tsv
• :contains diseaseId, code where diseaseId = cuis contains in disease_gene.tsv code = doid contains in disease_gene.tsv

• manually select copd commobidities to as label by refering to well known research papers
• :such as Network.medicine.analysis.of.COPD, COPD.Comorbidities.network and more.

• copd_terminology_extract.py
• :create copd_comorbidities_label.txt,copd_uniq_cuis_label_mapping.txt
• copd_comorbidities_label.txt
• :contains doid,label where doid = doid of children of label doid in DISEASE ONTOLOGY label = doid of the chosen labels
• copd_uniq_cuis_label_mapping.txt
• :use copd_comorbidities_label.txt to create mapping to cuis in gene_disease_uniq_DO_mapping.txt
• :contains diseaseId, code where diseaseId = cuis code = doid of the chosen labels

• all_gene_disease_pmid_associations.py
• :create copd_label.txt
• copd_label.txt
• :contains diseasid, geneid and edges(rows) are extracted from disease_gene.tsv