title: Limbform: a functional ontology-based database of limb regeneration experiments.
abstract: The ability of certain organisms to completely regenerate lost limbs is a fascinating process, far from solved. Despite the extraordinary published efforts during the past centuries of scientists performing amputations, transplantations and molecular experiments, no mechanistic model exists yet that can completely explain patterning during the limb regeneration process. The lack of a centralized repository to enable the efficient mining of this huge dataset is hindering the discovery of comprehensive models of limb regeneration. Here, we introduce Limbform (Limb formalization), a centralized database of published limb regeneration experiments. 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 database represents an extraordinary resource for mining the existing knowledge of functional data in this field; furthermore, its mathematical nature based on a functional ontology will pave the way for artificial intelligence tools applied to the discovery of the sought-after comprehensive limb regeneration models.
authors.affiliation: Center for Regenerative and Developmental Biology, Department of Biology, Tufts University, 200 Boston Avenue, Suite 4600, Medford, MA 02155, USA.
authors.forename: Daniel
authors.initials: D
authors.lastname: Lobo
authors.affiliation: Center for Regenerative and Developmental Biology, Department of Biology, Tufts University, 200 Boston Avenue, Suite 4600, Medford, MA 02155, USA.
authors.forename: Erica B
authors.initials: EB
authors.lastname: Feldman
authors.affiliation: Center for Regenerative and Developmental Biology, Department of Biology, Tufts University, 200 Boston Avenue, Suite 4600, Medford, MA 02155, USA.
authors.forename: Michelle
authors.initials: M
authors.lastname: Shah
authors.affiliation: Center for Regenerative and Developmental Biology, Department of Biology, Tufts University, 200 Boston Avenue, Suite 4600, Medford, MA 02155, USA.
authors.forename: Taylor J
authors.initials: TJ
authors.lastname: Malone
authors.affiliation: Center for Regenerative and Developmental Biology, Department of Biology, Tufts University, 200 Boston Avenue, Suite 4600, Medford, MA 02155, USA.
authors.forename: Michael
authors.initials: M
authors.lastname: Levin
mesh_terms: D064229:Biological Ontologies; D016208:Databases, Factual; D005121:Extremities / Q000033:anatomy & histology / Q000502:physiology*; D010641:Phenotype; D012038:Regeneration