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Related Concept Videos

Proteomics01:33

Proteomics

A proteome is the entire set of proteins that a cell type produces. We can study proteomes using the knowledge of genomes because genes code for mRNAs, and the mRNAs encode proteins. Although mRNA analysis is a step in the right direction, not all mRNAs are translated into proteins.
Proteomics is the study of proteomes' function. It involves the large-scale systematic study of the proteome to denote the protein complement expressed by a genome. Scientist Mark Wilkins coined the term proteomics...
Protein Networks02:26

Protein Networks

An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
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Protein-protein Interfaces02:04

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Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a polypeptide...
Ribosome Profiling02:24

Ribosome Profiling

Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
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The technique helps...

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Related Experiment Video

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Biosensor-based High Throughput Biopanning and Bioinformatics Analysis Strategy for the Global Validation of Drug-protein Interactions
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BioProber: software system for biomedical relation discovery from PubMed.

Hyunchul Jang1, Jaesoo Lim, Joon-Ho Lim

  • 1Bioinformatics Team, Electron. & Telecommun. Res. Inst., Daejeon, Korea.

Conference Proceedings : ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual Conference
|October 20, 2007
PubMed
Summary

This study introduces a novel system for automatic information extraction from biomedical literature. It discovers and visualizes relationships between diverse biomedical entities, overcoming limitations of traditional information retrieval.

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Area of Science:

  • Biomedical Informatics
  • Text Mining
  • Information Retrieval

Background:

  • The rapid growth of scientific literature presents challenges for knowledge acquisition.
  • Existing information retrieval methods struggle with large volumes of data and specific entity extraction.
  • Much valuable information remains locked in unstructured biomedical text.

Purpose of the Study:

  • To develop a system for discovering relations between various categories of biomedical entities.
  • To address the limitations of current text mining and information extraction techniques in handling vast datasets.
  • To facilitate automated knowledge discovery from biomedical literature.

Main Methods:

  • Collecting abstracts from PubMed using topic-specific queries.
  • Employing automatic information extraction techniques to identify entity relationships.
  • Developing a system to visualize discovered relationships.

Main Results:

  • The system successfully extracts and visualizes relationships between different biomedical entities.
  • Demonstrated the capability to handle large collections of abstracts.
  • Overcame the limitations of traditional search methods for extensive literature sets.

Conclusions:

  • The developed system offers an effective approach for automated knowledge discovery in the biomedical domain.
  • It enhances the ability to extract and understand complex relationships from unstructured text.
  • This method provides a valuable tool for researchers navigating the expanding body of scientific publications.