Blood Exposome Database

Blood Exposome Database catalogs endogenous and exogenous chemicals associated with the mammalian circulatory system by integrating PubMed literature, PubChem chemical synonyms and identifiers, and PMC supplementary metabolomics data to map compounds to publications and external databases.

Key Features:

• Literature corpus: Analysis of over 1.1 million blood-related publications retrieved from PubMed.
• Text mining: Matching approximately 15 million synonyms from over 6.5 million PubChem chemicals against all identified publications.
• Synonym-based associations: Association of 37,514 chemicals with 851,999 publication records derived from synonym matches.
• CID mapping: Mapping of PubChem Compound Identifiers (CIDs) to PubMed entries linking 49,940 unique chemicals to 676,643 papers.
• PMC metabolomics extraction: Analysis of open-access metabolomics studies in PMC identifying an additional 4,039 compounds across 204 papers.
• Consolidated dataset: Compilation of 41,474 achiral structures connected to over 878,966 PubMed articles and 65,957 PubChem CIDs.
• Cross-database mapping: Mapping of identified compounds to 50 databases covering metabolites, pathways, governmental and toxicological resources, pharmacology references, and bioassay repositories.
• Resource comparison: Expanded coverage relative to the Human Metabolome Database (HMDB), which links 1,075 compounds to blood-related publications.

Scientific Applications:

• Chemical prioritization: Prioritizing chemicals for systematic reviews and exposome-focused investigations.
• Assay development: Informing development of targeted assays for exposome research.
• Compound identification: Supporting identification of compounds in untargeted mass spectrometry studies.
• Biological interpretation: Facilitating biological interpretation of metabolomics datasets via literature-linked compound annotations.

Methodology:

Retrieval of >1.1 million blood-related PubMed publications; text mining that matches ~15 million PubChem synonyms from >6.5 million chemicals against publications; integration of PubChem synonyms and identifiers with PMC supplementary tables; mapping PubChem CIDs to PubMed entries; analysis of open-access PMC metabolomics studies; and mapping identified compounds to 50 external databases.