# Using DISNET towards COVID-19 drug repositioning This repository is structured as follows: >``` >disnet_covid_paper >├── counts >│ ├── count_dbc_path4.tsv >│ ├── count_dpc_path2.tsv >│ ├── count_drugs_path1.tsv >│ ├── count_drugs_path2.tsv >│ ├── count_drugs_path3.tsv >│ ├── count_drugs_path4.tsv >│ └── count_drugs_path5.tsv >├── paths >│ ├── covid_genes.tsv >│ ├── covid_symptoms.tsv >│ ├── diseases_bio_covid.tsv >│ ├── diseases_pheno_covid.tsv >│ ├── genes_dpc.tsv >│ ├── targets_gc.tsv >│ └── targets_dpc.tsv >├── results >│ ├── drugs_allpaths.tsv >│ ├── drugs_path1.tsv >│ ├── drugs_path2.tsv >│ ├── drugs_path3.tsv >│ ├── drugs_path4.tsv >│ └── drugs_path5.tsv >├── paths-pipeline.svg >└── README.md >``` Two important concepts to clarify: - **dpc**: stands for those diseases phenotypically related to COVID-19, that is, that have common symptoms. - **dbc**: stands for those diseases biologically related to COVID-19, that is, that have related genes in common. ## counts Files with different counts along the five paths of information. - **count_dbc_path4.tsv** | disease_id|disease_name|count_genes| |:-:|:-:|:-:| |Identifiers of diseases that have biological resemblance with COVID-19 (dbc), i.e. that have genes in common|Names of the diseases|Number of shared genes between diseases (dbc) and COVID-19| - **count_dpc_path2.tsv** |disease_name|count_symptoms| |:-:|:-:| |Names of diseases that have phenotypical resemblance with COVID-19 (dpc), i.e. that have symptoms in common|Number of shared symptoms between diseases (dpc) and COVID-19| - **count_drugs_path1.tsv** |drug_id|drug_name|count_symptoms| |:-:|:-:|:-:| |Identifiers of drugs potentially repurposable for COVID-19|Names of the drugs|Number of COVID related symptoms to which drugs are indicated for| - **count_drugs_path2.tsv** |drug_id|drug_name|count_dpc| |:-:|:-:|:-:| |Identifiers of drugs potentially repurposable for COVID-19|Names of the drugs|Number of diseases (dpc) that are associated to the drugs| - **count_drugs_path3.tsv** |drug_id|drug_name|count_targets| |:-:|:-:|:-:| |Identifiers of drugs potentially repurposable for COVID-19|Names of the drugs|Number of targets associated to each drug that are related to diseases that have phenotypical resemblance with COVID-19 (dpc)| - **count_drugs_path4.tsv** |drug_id|drug_name|count_dbc| |:-:|:-:|:-:| |Identifiers of drugs potentially repurposable for COVID-19|Names of the drugs|Number of diseases (dbc) that are associated to the drugs| - **count_drugs_path5.tsv** |drug_id|drug_name|count_targets| |:-:|:-:|:-:| |Identifiers of drugs potentially repurposable for COVID-19|Names of the drugs|Number of targets related to COVID-19 genes that are associated to each drug| ## paths Files with different data obtained in the paths of information. - **covid_genes.tsv** : genes that are related to COVID-19 |gene_id|gene_symbol|gene_name| |:-:|:-:|:-:| |NCBI identifiers of genes|Symbols of the genes|Complete name of the genes| - **covid_symptoms.tsv** : symptoms that are related to COVID-19 |symptom_cui|symptom_name|source| |:-:|:-:|:-:| |UMLS CUIs identifying COVID-19 symptoms|Names of the symptoms|Textual source from which the symptoms have been extracted| - **diseases_bio_covid.tsv** : (dbc) diseases that have a biological resemblance to COVID-19, that is, that have common related genes with COVID-19. |disease_cui|disease_name| |:-:|:-:| |UMLS CUIs identifying diseases (dbc)|Names of the diseases| - **diseases_pheno_covid.tsv**: (dpc) diseases that have a phenotypical resemblance to COVID-19, that is, that have common related symptoms with COVID-19. |disease_name| |:-:| |Names of the diseases (dpc)| - **genes_dpc.tsv**: genes related to diseases dpc and that are associated to targets and drugs potentially repurposable for COVID-19. |gene_id|gene_symbol|gene_name| |:-:|:-:|:-:| |NCBI identifiers of genes|Symbols of the genes|Complete name of the genes| - **targets_gc.tsv**: targets related to COVID associated genes, and that are also related to drugs potentially repurposable for COVID-19. |chembl_id|uniprot_id| |:-:|:-:| |Targets identified by CHEMBL identifiers|Targets identified by UniProt accession numbers| - **targets_dpc.tsv**: targets related to dpc associated genes, that are also related to drugs potentially repurposable for COVID-19. |chembl_id|uniprot_id| |:-:|:-:| |Targets identified by CHEMBL identifiers|Targets identified by UniProt accession numbers| ## results Files with lists of drugs derived from the different paths of information. - **drugs_allpaths.tsv**: drugs in all paths with the list of related targets (represented with the gene symbol). |drug_id|drug_name|covid_symptoms_path1|dpc_path2|dpc_genes_path3|dbc_path4|covid_genes_path5| |:-:|:-:|:-:|:-:|:-:|:-:|:-:| |Drug CHEMBL identifier|Drug name|COVID-19 symptom(s) to which the drug is indicated for|Disease(s) (dpc) phenotypically similar to COVID-19 related to the drug [Number of shared symptoms between COVID-19 and the disease]|Targets (represented with NCBI gene symbols) related to diseases (dbc) that are associated to the drug [Number of diseases (dpc) phenotypically similar to COVID-19 that are related to the target]|Diseases (dbc) biologically similar to COVID-19 related to the drug [Number of shared genes between COVID-19 and the disease]|Target(s) (represented with NCBI gene symbols) related to COVID-19 associated to the drug| - **drugs_path1.tsv**: list of drugs derived from Path 1. |drug_id|drug_name| |:-:|:-:| |Drug CHEMBL identifier|Drug name| - **drugs_path2.tsv**: list of drugs derived from Path 2. |drug_id|drug_name| |:-:|:-:| |Drug CHEMBL identifier|Drug name| - **drugs_path3.tsv**: list of drugs derived from Path 3. |drug_id|drug_name| |:-:|:-:| |Drug CHEMBL identifier|Drug name| - **drugs_path4.tsv**: list of drugs derived from Path 4. |drug_id|drug_name| |:-:|:-:| |Drug CHEMBL identifier|Drug name| - **drugs_path5.tsv**: list of drugs derived from Path 5. |drug_id|drug_name| |:-:|:-:| |Drug CHEMBL identifier|Drug name| ## paths-pipeline.svg Graphical representation of the different paths of information followed.