DATA_PROVENANCE.md

Data Provenance & Ingestion Log

This document records all external data sources, exact URLs, versions, download dates, licensing, and processing rules used for building real ADR datasets and GTEx tissue profiles in EpiADR-Net.

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1. SIDER 4.1 Side Effect Resource

• Source Name: SIDER: Side Effect Resource (Version 4.1)
• Publisher / Organization: European Molecular Biology Laboratory (EMBL)
• URL: http://sideeffects.embl.de/media/download/meddra_all_se.tsv.gz
• Secondary Resource: SIDER Drug Names (http://sideeffects.embl.de/media/download/drug_names.tsv)
• Download Date: 2026-08-02
• License: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)
• MedDRA Target Mapping:
  • Hepatotoxicity -> MedDRA Concept / Preferred Term matching hepatic injury / liver disorders
  • Arrhythmia -> MedDRA Concept / Preferred Term matching cardiac arrhythmia
  • Seizure -> MedDRA Concept / Preferred Term matching seizure / convulsion
  • Nephrotoxicity -> MedDRA Concept / Preferred Term matching renal impairment / nephrotoxicity
  • Pneumonitis -> MedDRA Concept / Preferred Term matching pneumonitis / pulmonary toxicity
  • Nausea -> MedDRA Concept / Preferred Term matching nausea
  • Headache -> MedDRA Concept / Preferred Term matching headache
  • Dizziness -> MedDRA Concept / Preferred Term matching dizziness
  • Fatigue -> MedDRA Concept / Preferred Term matching fatigue
  • Rash -> MedDRA Concept / Preferred Term matching rash / dermatological reaction
• Compound Resolution: Drug identifiers / names resolved to canonical SMILES via PubChem REST PUG API (https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/). Unresolvable or invalid SMILES strings dropped and logged.
• Organ Assignment Rule: Organ targets (Liver, Heart, Brain, Kidney, Lung) mapped systematically using MedDRA System Organ Class (SOC) primary physiological organ targets and WHO ATC organ classification.

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2. GTEx Analysis Release V8 (RNA-Seq Transcriptomics)

• Source Name: Genotype-Tissue Expression (GTEx) Project (Analysis Release V8)
• Publisher / Organization: The Broad Institute of MIT and Harvard / NIH Common Fund
• URL: https://storage.googleapis.com/gtex_analysis_v8/rna_seq_data/GTEx_Analysis_2017-06-05_v8_RNASeQCv1.1.9_gene_median_tpm.gct.gz
• Download Date: 2026-08-02
• License: Open Access (GTEx Data Use Agreement / NIH Public Domain)
• Organ Granularity Aggregation:
  • Liver: Liver
  • Heart: Average of Heart - Atrial Appendage and Heart - Left Ventricle
  • Brain: Average of GTEx brain sub-region columns (Brain - Cortex, Brain - Cerebellum, Brain - Hippocampus, Brain - Caudate, Brain - Substantia nigra, Brain - Amygdala, Brain - Anterior cingulate cortex, Brain - Hypothalamus, Brain - Nucleus accumbens, Brain - Putamen, Brain - Spinal cord, Brain - Subthalamic nucleus)
  • Kidney: Kidney - Cortex
  • Lung: Lung
• Dimensionality Reduction: Scikit-Learn PCA(n_components=128, random_state=42) fitted across genes.