Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Search research articles

Related Experiment Videos

Mining literature for systems biology.

Phoebe M Roberts¹

¹Biogen Idec Inc., 14 Cambridge Center, Cambridge MA 02142, USA. Phoebe.Roberts@biogenidec.com

Briefings in Bioinformatics

|October 13, 2006

Summary

Systems biology utilizes literature through manual curation, derived concepts from ontologies and databases, and text mining. These methods aid in building biological models and analyzing complex biological data.

Related Concept Videos

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by

Same author

A CTD-Pfizer collaboration: manual curation of 88,000 scientific articles text mined for drug-disease and drug-phenotype interactions.

Database : the journal of biological databases and curation·2013

Same author

Cataloging the biomedical world of pain through semi-automated curation of molecular interactions.

Database : the journal of biological databases and curation·2013

Same author

BioCreative III interactive task: an overview.

BMC bioinformatics·2011

Same author

Identifying and classifying biomedical perturbations in text.

Nucleic acids research·2008

Same author

Information needs and the role of text mining in drug development.

Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing·2008

Same author

Advances in text analytics for drug discovery.

Current opinion in drug discovery & development·2005

Area of Science:

Systems biology
Bioinformatics
Computational biology

Background:

Literature is a crucial resource for systems biology research.
Current integration methods include manual curation, derived concepts, and text mining.
Efficiently leveraging literature is key for advancing biological understanding.

Purpose of the Study:

To discuss the integration of scientific literature in systems biology.
To outline three primary methods of literature utilization.
To highlight the role of text mining and ontologies in biological studies.

Main Methods:

Review of existing literature integration strategies in systems biology.
Discussion of manual pathway curation.
Analysis of derived data from ontologies (e.g., Gene Ontologies) and databases (e.g., protein-protein interaction databases).
Exploration of text mining techniques for information extraction.

Main Results:

Manual curation of pathways is a foundational method.
Derived concepts from ontologies and databases offer structured, computable representations of literature.
Text mining is increasingly viable for direct information extraction.

Conclusions:

Effective integration of literature is essential for systems biology.
A combination of manual curation, derived data, and text mining optimizes knowledge extraction.
Advancements in text analytics enhance the utility of literature for biological modeling and data analysis.

Related Experiment Videos