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Related Concept Videos

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Genomics is the science of genomes: it is the study of all the genetic material of an organism. In humans, the genome consists of information carried in 23 pairs of chromosomes in the nucleus, as well as mitochondrial DNA. In genomics, both coding and non-coding DNA is sequenced and analyzed. Genomics allows a better understanding of all living things, their evolution, and their diversity. It has a myriad of uses: for example, to build phylogenetic trees, to improve productivity and...
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Genome-wide association studies or GWAS are used to identify whether common SNPs are associated with certain diseases. Suppose specific SNPs are more frequently observed in individuals with a particular disease than those without the disease. In that case, those SNPs are said to be associated with the disease. Chi-square analysis is performed to check the probability of the allele likely to be associated with the disease.
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Related Experiment Video

Updated: Jan 19, 2026

Performing Data Mining And Integrative Analysis Of Biomarker in Breast Cancer Using Multiple Publicly Accessible Databases
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Generating the Blood Exposome Database Using a Comprehensive Text Mining and Database Fusion Approach.

Dinesh Kumar Barupal1, Oliver Fiehn1

  • 1National Institutes of Health (NIH) West Coast Metabolomics Center, Genome Center, University of California, Davis, Davis, California, USA.

Environmental Health Perspectives
|September 27, 2019
PubMed
Summary

A new Blood Exposome Database was created by mining scientific literature, linking over 41,000 chemicals to more than 878,000 publications. This resource aids exposome research and metabolomics data interpretation.

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Area of Science:

  • Environmental Health Sciences
  • Computational Biology
  • Toxicology

Background:

  • Blood chemical analysis is crucial for disease diagnosis, risk assessment, and understanding treatment responses.
  • The PubMed database contains extensive literature on blood-related research, offering a valuable resource for data mining.
  • Existing databases lack a comprehensive catalog of endogenous and exogenous chemicals found in the mammalian circulatory system.

Purpose of the Study:

  • To develop a comprehensive Blood Exposome Database by integrating information on chemicals present in mammalian blood.
  • To utilize text mining and database fusion techniques for creating this novel resource.
  • To link identified chemicals to relevant scientific publications and other biological databases.

Main Methods:

  • Extensive text mining of PubMed abstracts and PMC open-access papers was performed.
  • PubChem chemical synonyms and compound identifiers were utilized for chemical association.
  • Data fusion from multiple sources, including NCBI resources and PubChem crowdsourcing, was employed.
  • A phrase pattern and compound exclusion list were used to refine results and remove false positives.

Main Results:

  • The study identified and linked 41,474 unique achiral chemical structures to 65,957 PubChem CIDs and over 878,966 PubMed articles.
  • These compounds were mapped to 50 diverse databases, including those for metabolites, pathways, toxicology, and pharmacology.
  • The resulting Blood Exposome Database significantly expands upon existing resources like the Human Metabolome Database (HMDB).

Conclusions:

  • The Blood Exposome Database provides a valuable resource for exposome research, enabling chemical prioritization for systematic reviews and assay development.
  • It facilitates compound identification in untargeted mass spectrometry and aids in the biological interpretation of metabolomics data.
  • The database is publicly accessible at http://bloodexposome.org, promoting further research and discovery.