A database based on a functional ontology system that unambiguously centralize the knowledge of limb regeneration experiments in a diverse set of model organisms, enabling the unambiguous description, centralize storage and manual and automated mining of this vast dataset. In contrast to natural language or text-based ontologies, Limbform is based on a functional ontology using mathematical graphs to represent unambiguously limb phenotypes and manipulation procedures. The centralized database currently contains >800 published limb regeneration experiments comprising many model organisms, including salamanders, frogs, insects, crustaceans and arachnids. The Limbform database of limb regeneration experiment represents an invaluable resource for the community and establishes the first necessary steps of a new bioinformatics of shape.

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Limbform classification

  • Animals

Limbform specifications

Software type:
Standalone
Restrictions to use:
None
Programming languages:
C++
Computer skills:
Medium
Interface:
Graphical user interface
Operating system:
Unix/Linux, Mac OS, Windows
Database support:
Yes
Stability:
Stable

Publications

  • (Lobo et al., 2014) Limbform: a functional ontology-based database of limb regeneration experiments. Bioinformatics.
    PMID: 25170026

Limbform support

Maintainer

Credits

Institution(s)

Center for Regenerative and Developmental Biology, Department of Biology, Tufts University, 200 Boston Avenue, Suite 4600, Medford, MA 02155, USA

Funding source(s)

National Science Foundation (EF-1124651), National Institutes of Health (GM078484), W. M. Keck Foundation and G. Harold and Leila Y. Mathers Charitable Foundation

Link to literature

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