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Related Concept Videos

Protein-protein Interfaces02:04

Protein-protein Interfaces

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...
Protein-Protein Interfaces02:04

Protein-Protein Interfaces

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...
Ligand Binding Sites02:40

Ligand Binding Sites

Proteins are dynamic macromolecules that carry out a wide variety of essential processes; however, the activities of most proteins depend on their interactions with other molecules or ions, known as ligands.
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...
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.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
Noncovalent Attractions in Biomolecules02:35

Noncovalent Attractions in Biomolecules

Noncovalent attractions are associations within and between molecules that influence the shape and structural stability of complexes. These interactions differ from covalent bonding in that they do not involve sharing of electrons.
Four types of noncovalent interactions are hydrogen bonds, van der Waals forces, ionic bonds, and hydrophobic interactions.
Hydrogen bonding results from the electrostatic attraction of a hydrogen atom covalently bonded to a strong-electronegative atom like oxygen,...
Noncovalent Attractions in Biomolecules02:35

Noncovalent Attractions in Biomolecules

Noncovalent attractions are associations within and between molecules that influence the shape and structural stability of complexes. These interactions differ from covalent bonding in that they do not involve sharing of electrons.
Four types of noncovalent interactions are hydrogen bonds, van der Waals forces, ionic bonds, and hydrophobic interactions.
Hydrogen bonding results from the electrostatic attraction of a hydrogen atom covalently bonded to a strong-electronegative atom like oxygen,...

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Challenges for automatically extracting molecular interactions from full-text articles.

Tara McIntosh1, James R Curran

  • 1School of Information Technology, Faculty of Engineering and IT, University of Sydney, Sydney, Australia. tara@it.usyd.edu.au

BMC Bioinformatics
|September 26, 2009
PubMed
Summary
This summary is machine-generated.

A new corpus of full-text biomedical articles enables better information extraction. This resource aids in developing tools to process complex scientific texts and understand molecular interactions.

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Area of Science:

  • Biomedical Informatics
  • Computational Biology
  • Natural Language Processing

Background:

  • Current biomedical information retrieval and extraction tools primarily process article abstracts.
  • Limited availability of full-text corpora hinders the development of advanced tools for knowledge extraction.
  • There is a need to explore the advantages of full-text document structure and associated processing challenges.

Purpose of the Study:

  • To create a corpus of manually annotated full-text biomedical articles for Molecular Interaction Map (MIM) summarization.
  • To capture the process of fact identification, factual dependencies, and the resolution of negated and coreference expressions.
  • To provide a gold-standard evaluation set for full-text information retrieval and extraction tasks.

Main Methods:

  • Manual annotation of passages from full-text articles describing interactions for MIM summarization.
  • Development of guidelines for identifying relevant passages and dependencies.
  • Creation of a corpus comprising 2162 sentences from 78 full-text articles.

Main Results:

  • Corpus analysis confirms the necessity of full-text processing for comprehensive biomedical knowledge extraction.
  • Identified key article sections where interaction statements are most frequently located.
  • Quantified the proportion of interaction statements requiring coherent dependencies, synonym identification, and negation resolution.

Conclusions:

  • Introduction of the MIM corpus, a novel resource linking interaction facts to annotated full-text passages.
  • The MIM corpus serves as a valuable case study for guiding the development of biomedical information retrieval and extraction systems.
  • The corpus is suitable for use as a gold-standard evaluation set for full-text information retrieval tasks.