-
-
Save rnaimehaom/a86d789e2aa9cdc614ec8b4bdc3ee083 to your computer and use it in GitHub Desktop.
Extract information from DrugBank xml file
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| DRUG | |
| ->drugbank-id | |
| ->drugbank-id | |
| ->drugbank-id | |
| ->name | |
| ->description | |
| ->cas-number (5) | |
| ->unii | |
| ->state | |
| ->groups | |
| ->group | |
| ->general-references | |
| ->articles | |
| ->article | |
| ->textbooks | |
| ->textbook | |
| ->links | |
| ->link | |
| ->attachments | |
| ->synthesis-reference (10) | |
| -> | |
| ->indication | |
| ->parmacodynamics | |
| ->mechanism-ofaction | |
| ->toxicity | |
| ->metabolism (15) | |
| ->absorption | |
| ->helf-life | |
| ->protein-binding | |
| -> | |
| ->route-of-elimination | |
| ->volume-of-distribution (20) | |
| ->clearance | |
| ->classification | |
| ->description | |
| ->direct-parent | |
| ->kingdom | |
| ->superclass | |
| ->class | |
| ->subclass | |
| ->salts | |
| -> | |
| ->synonyms | |
| ->synonym | |
| ->products (25) | |
| ->product | |
| ->name | |
| ->labeller | |
| ->ndc-id, | |
| ->ndc-product-code | |
| ->dpd-id | |
| ->ema-product-code | |
| ->ema-ma-number | |
| ->started-marketing-on | |
| ->ended-marketing-on | |
| ->dosage-form | |
| ->strength | |
| ->route | |
| ->fda-application-number | |
| ->generic | |
| ->over-the-counter | |
| ->approved | |
| ->country | |
| ->source | |
| ->international-brands | |
| -> | |
| ->mixtures | |
| ->mixture | |
| ->name | |
| ->ingredients | |
| ->packagers | |
| ->packager | |
| ->name | |
| ->url | |
| ->manufacturers | |
| ->manufacturer | |
| ->prices (30) | |
| ->price | |
| ->description | |
| ->cost | |
| ->unit | |
| ->categories | |
| ->category | |
| ->category | |
| ->mesh-id | |
| ->affected-organisms | |
| ->affected-organism | |
| ->dosages | |
| ->dosage | |
| ->form | |
| ->route | |
| ->strength | |
| ->atc-codes | |
| ->atc-code | |
| ->level | |
| ->ahfs-codes (35) | |
| ->ahfs-code | |
| ->pdb-entries | |
| ->pdb-entry | |
| ->fda-label | |
| ->msds | |
| ->patents | |
| ->patent | |
| ->number | |
| ->country | |
| ->approved | |
| ->expires | |
| ->pediatric-extension | |
| ->food-interactions (40) | |
| ->food-interaction | |
| ->drug-interactions | |
| ->drug-interaction | |
| ->drugbank-id | |
| ->name | |
| ->description | |
| ->sequences | |
| ->sequence | |
| ->experimental-properties | |
| ->property | |
| ->kind | |
| ->value | |
| ->source | |
| ->external-identifiers | |
| ->external-identifier | |
| ->resource (DPD, PubChem, KEGG Drug, PharmGKB, UniProtKB, Therapeutic Targets Database, Wikipedia, ChEMBL) | |
| ->identifier | |
| ->external-links (45) | |
| ->external-link | |
| ->resource (RxList, Drugs.com) | |
| ->identifier | |
| ->pathways | |
| ->pathway | |
| ->smpdb-id | |
| ->name | |
| ->category | |
| ->drugs | |
| ->drug | |
| ->drugbank-id | |
| ->name | |
| ->enzymes | |
| ->uniprot-id | |
| ->reactions | |
| ->reaction | |
| ->snp-effects | |
| ->snp-effect | |
| ->snp-adverse-drug-reactions | |
| ->snp-adverse-drug-reaction | |
| ->targets | |
| ->target | |
| ->id | |
| ->name | |
| ->organism | |
| ->actions | |
| ->action | |
| ->references | |
| ->articles | |
| ->article | |
| ->textbooks | |
| ->textbook | |
| ->links | |
| ->link | |
| ->attachments | |
| ->known-action (5) | |
| ->polypeptide | |
| ->name | |
| ->general-function | |
| ->specific-function | |
| ->gene-name | |
| ->locus | |
| ->cellular-location (5) | |
| ->transmembrane-regions | |
| -> | |
| ->signal-regions | |
| ->theoretical-pi | |
| ->molecular-weight | |
| ->chromosome-location (10) | |
| ->organism | |
| ->external-identifiers (HGNC,GenAtlas,GenBank Gene Database,GenBank Protein Database,Guide to Pharmacology,UniProtKB,UniProt Accession) | |
| ->external-identifier | |
| ->resource | |
| ->identifier | |
| ->synonyms | |
| ->synonym | |
| ->amino-acid-sequence | |
| ->gene-sequence (15) | |
| ->pfams | |
| ->pfam | |
| ->identifier | |
| ->name | |
| ->go-classifiers | |
| ->go-classifier | |
| ->category | |
| ->description | |
| ->enzymes | |
| ->enzyme | |
| ->carriers | |
| ->carrier | |
| ->transporters | |
| ->transporter |
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| """ | |
| TITLE :parsing_DrugBank | |
| AUTHOR : Hernansaiz Ballesteros, Rosa. | |
| rosa.hernansaiz@bioquant.uni-heidelberg.de | |
| DESCRIPTION : Parsing full database of DrugBank to extract information | |
| about drugs that affects a specific organism. | |
| Information retrieved: | |
| - name | |
| - synonyms | |
| - classification (kingdom and superfamily) | |
| - drug-interactions (with other drugs) | |
| - external-identifiers (to connect to other sources) | |
| - pathways | |
| - targets (if polypeptides) | |
| - target_name | |
| - target_uniprot | |
| - target_gene_name | |
| - action (of the drug over the target) | |
| - cell_loc (cell localitation) | |
| To get the tree structure of the xml file, | |
| see drugBank_tree_structure.txt | |
| LICENSE : GPL-v3 | |
| """ | |
| # Classes # | |
| class Drug: | |
| """ | |
| docstring for Drug. | |
| """ | |
| def __init__(self, features): | |
| self.id = features['id'] | |
| self.name = features['name'] | |
| self.synonyms = features['synm'] | |
| self.kingdom = features['kgd'] | |
| self.superclass = features['sclass'] | |
| self.interaction = features['itrc'] | |
| self.external_id = features['ext_id'] | |
| self.pathways = features['pathways'] | |
| self.target = [] | |
| def getDrugfeatures(self): | |
| drug_dict = {"dg_id":self.id, | |
| "dg_name":self.name, | |
| "dg_synm":self.synonyms, | |
| "dg_kingdom":self.kingdom, | |
| "dg_superclass":self.superclass, | |
| "dg_interactions":self.interaction, | |
| "dg_ext_id":self.external_id, | |
| "dg_pathways":self.pathways} | |
| return drug_dict | |
| def addTarget(self, feature_target): | |
| self.target.append(feature_target) | |
| # Parameters and required variables # | |
| dB_file = '../00-Drugs/drugBank_v515_20200103.xml' | |
| organism = 'Humans' | |
| saveFile = '../00-Drugs/drugBank_v515_targetExtracted.csv' | |
| # Main script # | |
| ''' | |
| Get targets from drugBank database for the drugs on the ic50 file | |
| ''' | |
| import xml.etree.ElementTree as ET | |
| import time | |
| from tqdm import tqdm | |
| import pandas as pd | |
| xtree = ET.parse(dB_file) | |
| xroot = xtree.getroot() | |
| drugs = list(xroot) | |
| drug_targets = [] | |
| for i in tqdm(range(len(drugs))): | |
| drug = drugs[i] | |
| idDB = drug[0].text # Drug Bank ID | |
| for idx,feature in enumerate(drug): | |
| if 'name' in str(feature): # drug name | |
| drug_name = drug[idx].text | |
| if 'synonyms' in str(feature): # drug's synonyms | |
| drug_synm = ';'.join([synm.text \ | |
| for synm in list(drug[idx])]) | |
| if 'classification' in str(feature): #type of drug | |
| drug_class_kingdom = list(drug[idx])[2].text | |
| drug_class_superclass = list(drug[idx])[3].text | |
| if 'drug-interactions' in str(feature): #interaction other drugs | |
| drug_interaction = ';'.join([di[0].text | |
| for di in list(drug[idx])]) | |
| if 'external-identifiers' in str(feature): #other drug's IDs | |
| aux = [ext_id[0].text + ":" + ext_id[1].text \ | |
| for ext_id in list(drug[idx])] | |
| drug_external_id = ';'.join(aux) | |
| if 'pathways' in str(feature): #related pathways | |
| drug_pathway = ';'.join([pathway[1].text \ | |
| for pathway in list(drug[idx])]) | |
| if 'targets' in str(feature): #if polypeptide, drug's targets | |
| targets = list(drug[idx]) | |
| # get all drug-related information in a dictionary | |
| drug_dict = {"id":idDB, | |
| "name":drug_name, | |
| "synm":drug_synm, | |
| "kgd":drug_class_kingdom, | |
| "sclass":drug_class_superclass, | |
| "itrc":drug_interaction, | |
| "ext_id":drug_external_id, | |
| "pathways":drug_pathway} | |
| drug = Drug(drug_dict) | |
| # get information of polypeptide targets | |
| if len(targets) > 0: | |
| for target in targets: | |
| idx_pep = None | |
| # get indexes | |
| for idx,feature in enumerate(target): # check features of targets | |
| if 'organism' in str(feature): | |
| idx_org = idx | |
| if 'name' in str(feature): | |
| idx_name = idx | |
| if 'actions' in str(feature): | |
| idx_act = idx | |
| if 'polypeptide' in str(feature): | |
| idx_pep = idx | |
| # Get information for polypeptide | |
| if target[idx_org].text == organism: | |
| target_name = target[idx_name].text | |
| actions = ';'.join([action.text | |
| for action in list(target[idx_act])]) | |
| # Get information for polypeptide | |
| if idx_pep is not None: #if there is polypeptide's info... | |
| for idx,feature in enumerate(target[idx_pep]): | |
| if 'gene-name' in str(feature): | |
| gene_name = target[idx_pep][idx].text | |
| if 'cellular-location' in str(feature): | |
| cell_loc = target[idx_pep][idx].text | |
| if 'external-identifiers' in str(feature): | |
| for ext_id in list(target[idx_pep][idx]): | |
| if ext_id[0].text == "UniProtKB": | |
| uniprot = ext_id[1].text | |
| else: | |
| gene_name = None | |
| action = None | |
| cell_loc = None | |
| uniprot = None | |
| row = { | |
| "dg_id":drug.id, | |
| "dg_name":drug.name, | |
| "dg_synm":drug.synonyms, | |
| "dg_kingdom":drug.kingdom, | |
| "dg_superclass":drug.superclass, | |
| "dg_interactions":drug.interaction, | |
| "dg_ext_id":drug.external_id, | |
| "dg_pathways":drug.pathways, | |
| "target_name":target_name, | |
| "target_uniprot":uniprot, | |
| "target_gene_name":gene_name, | |
| "action":actions, | |
| "cell_loc":cell_loc, | |
| } | |
| drug_targets.append(row) | |
| dt = pd.DataFrame.from_dict(drug_targets, orient='columns') | |
| dt.shape | |
| dt.to_csv(saveFile) |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment