Resources

Biomedical Knowledgebases (Public) -

1. Exposome Correlation and Interpretation Database (ECID) : www.ecidbase.org 

2. Blood Exposome Database - www.bloodexposome.org 

3. GeoSpace - www.gsbase.org 

Exposomic and Metabolomic Databases (In-House)-

1. IDSL-Spectral Database : A database of over 100,000 experimental and > 200 million in-silico spectra (ML, QC, LLM). 

2. IDSL-Reaction Database : A database of known and simulated biochemical reactions. 

3. IDSL-Chemical Annotation Database : A database of chemicals reported in human biomonitoring datasets (targeted and untargeted), with annotations including reaction, pathway, MESH, Gene-ontology, toxicity, chemical-class, sources. 

4. IDSL-Literature Database: A database of PubMed/PMC full text articles. We annotate each paper with biological concepts, chemicals and health outcomes to allow rapid literature screening and summarization using LLMs/AI. 

5. IDSL-Substance Database: A consolidated database of chemical substances listed in over 60 sources that are relevant for exposome and metabolome. Sources are from governmental and other public sector agencies/organizations. 

Software (online and local installation)

Mass Spectrometry Data Mining : 

1. mzView: An online reader for mzML data files ( www.mzview.org )

2. IDSL.IPA: Intrinsic Peak Analyzer, R package : ( https://cran.r-project.org/package=IDSL.IPA ), 

3. IDSL.UFA: United Formula Annotation , R package: (  https://cran.r-project.org/package=IDSL.UFA ) 

4. IDSL.CSA : Composite Spectra Analysis (https://cran.r-project.org/package=IDSL.CSA) 

5. IDSL_MINT: Deep learning framework for predicting molecular fingerprints from a spectra ( https://github.com/idslme/IDSL_MINT  ) 

Metabolic Bioinformatics: 

6. IDSL.GOA: (Gene Ontology Analysis) (www.goa.idsl.me)

7. ChemRICH for chemical set enrichment analysis : (https://chemrich.idsl.me/ )

8. MetaMapp for metabolic network mapping : https://github.com/barupal/metamapp 

9. In-Silico Transformation: https://github.com/idslme/in-silico-transformation 

Toxicology and Exposome:

10. Predictive Toxicology :  https://github.com/idslme/exposome-toxicity-prediction 

11. IARC Monographs Agent Prioritization :  (https://cancer.idsl.me/ )