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Related Concept Videos

Genomics02:02

Genomics

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...
Genetic Screens02:46

Genetic Screens

Genetic screens are tools used to identify genes and mutations responsible for phenotypes of interest. Genetic screens help identify individuals or a group of people at risk of developing  genetic diseases and help them with early intervention, targeted therapy, and reproductive options.
Forward genetic screens
Forward or “classical” genetic screens involve creating random mutations in an organism’s DNA using radiation, mutagens, or insertion of additional bases, which result in visible changes...
Toxicity Testing in Animals01:23

Toxicity Testing in Animals

Toxicity tests in animals are grounded on two main assumptions: first, the effects observed in laboratory animals can be extrapolated to humans, especially when adjusted for body surface area; second, high-dose exposure in animals is essential to identify potential human hazards from lower doses. This is based on the quantal dose-response concept, which faces the challenge of extrapolating results from relatively few test animals to much larger human populations. For example, a 0.01% incidence...

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Related Experiment Video

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Selecting Multiple Biomarker Subsets with Similarly Effective Binary Classification Performances
07:35

Selecting Multiple Biomarker Subsets with Similarly Effective Binary Classification Performances

Published on: October 11, 2018

Using binary classification to prioritize and curate articles for the Comparative Toxicogenomics Database.

Dina Vishnyakova1, Emilie Pasche, Patrick Ruch

  • 1Bibliomics and Text Mining Group, Geneva, Switzerland. dina.vishnyakova@hcuge.ch

Database : the Journal of Biological Databases and Curation
|December 11, 2012
PubMed
Summary
This summary is machine-generated.

We developed ToxiCat, an automated system for classifying biomedical documents to accelerate the Comparative Toxicogenomics Database (CTD) curation. This pipeline prioritizes articles using machine learning, improving toxicogenomics data accessibility.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Toxicogenomics

Background:

  • The Comparative Toxicogenomics Database (CTD) requires efficient curation of vast biomedical literature.
  • Automated methods are needed to classify and prioritize documents for toxicogenomics research.

Purpose of the Study:

  • To develop and integrate an automated text categorization pipeline, ToxiCat, for biomedical document classification and prioritization.
  • To accelerate the curation process for the Comparative Toxicogenomics Database (CTD).

Main Methods:

  • ToxiCat employs a binary classification task using a Support Vector Machine (SVM) for ranking articles.
  • The SVM integrates an information retrieval engine (EAGLi), a gene normalization service (NormaGene), and entity recognition for diseases and chemicals.
  • Components of a question-answering system are utilized for extracting CTD-specific annotations.

Main Results:

  • Successful integration of ToxiCat pipeline for automated biomedical document classification and prioritization.
  • Demonstrated acceleration of the CTD curation process through efficient article ranking and annotation extraction.
  • Developed a publicly available web application and web services for the ToxiCat pipeline.

Conclusions:

  • ToxiCat significantly enhances the efficiency of biomedical literature curation for toxicogenomics.
  • The pipeline provides a valuable tool for researchers by prioritizing relevant articles and extracting key annotations.
  • Public availability of ToxiCat promotes wider adoption and contribution to toxicogenomics research.