Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Experiment Videos

Representations of metabolic knowledge: pathways

P D Karp1, S M Paley

  • 1Artificial Intelligence Center, SRI International, Menlo Park, CA 94025, USA.

Proceedings. International Conference on Intelligent Systems for Molecular Biology
|January 1, 1994
PubMed
Summary
This summary is machine-generated.

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

MjCyc: Rediscovering the pathway-genome landscape of the first sequenced archaeon, <i>Methanocaldococcus (Methanococcus) jannaschii</i>.

iScience·2025
Same author

Many Genbank entries for complete microbial genomes violate the Genbank standard.

Comparative and functional genomics·2008
Same author

The outcomes of pathway database computations depend on pathway ontology.

Nucleic acids research·2006
Same author

Genome annotation errors in pathway databases due to semantic ambiguity in partial EC numbers.

Nucleic acids research·2005
Same author

An evidence ontology for use in pathway/genome databases.

Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing·2004
Same author

Using functional and organizational information to improve genome-wide computational prediction of transcription units on pathway-genome databases.

Bioinformatics (Oxford, England)·2004
Same journal

Proceedings of the 8th International Conference on Intelligent Systems for Molecular Biology (ISMB 2000). San Diego, California, USA. August 19-23, 2000.

Proceedings. International Conference on Intelligent Systems for Molecular Biology·2001
Same journal

Analysis of gene expression data with pathway scores.

Proceedings. International Conference on Intelligent Systems for Molecular Biology·2000
Same journal

Towards a complete map of the protein space based on a unified sequence and structure analysis of all known proteins.

Proceedings. International Conference on Intelligent Systems for Molecular Biology·2000
Same journal

Mining for putative regulatory elements in the yeast genome using gene expression data.

Proceedings. International Conference on Intelligent Systems for Molecular Biology·2000
Same journal

A multiple alignment algorithm for metabolic pathway analysis using enzyme hierarchy.

Proceedings. International Conference on Intelligent Systems for Molecular Biology·2000
Same journal

Sequence database search using jumping alignments.

Proceedings. International Conference on Intelligent Systems for Molecular Biology·2000
See all related articles

This study introduces a compact "predecessor list" for biochemical pathways, enabling efficient automatic generation of metabolic pathway drawings. This representation simplifies pathway data, improving computational analysis and visualization.

Area of Science:

  • Computational Biology
  • Bioinformatics
  • Systems Biology

Background:

  • Automatic generation of metabolic pathway drawings is complex due to data variability.
  • Existing representations can be redundant and lack compactness.

Purpose of the Study:

  • To develop a minimized representation for biochemical pathways.
  • To create inference procedures for converting this representation into a drawable graph.

Main Methods:

  • Introduced the "predecessor list" as a compact biochemical pathway representation.
  • Formulated conversion to a pathway-graph as constraint-satisfaction and logical inference problems.
  • Developed production rules and heuristics for reaction direction and compound importance inference.

Related Experiment Videos

Main Results:

  • The predecessor list offers compactness and reduced redundancy compared to pathway graphs.
  • Inference procedures successfully assigned directions and identified main compounds.
  • Heuristics effectively inferred the role of peripheral compounds.

Conclusions:

  • The predecessor list and associated inference methods provide an effective approach for metabolic pathway representation and drawing.
  • This work enhances computational analysis and visualization of metabolic networks.