ArticleBioinformatics (Oxford, England)2014
Limbform: a functional ontology-based database of limb regeneration experiments.
Article in Bioinformatics (Oxford, England), 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
10 citing papers in PubMed, 16 citations in OpenAlex.
- Regeneration Roadmap: database resources for regenerative biology.Nucleic acids research · 2022Article
- Computational Systems Biology of Morphogenesis.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Formalizing Phenotypes of Regeneration.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Fluxer: a web application to compute, analyze and visualize genome-scale metabolic flux networks.Nucleic acids research · 2020Article
- Continuous Dynamic Modeling of Regulated Cell Adhesion: Sorting, Intercalation, and Involution.Biophysical journal · 2019Article
- EDEn-Electroceutical Design Environment: Ion Channel Tissue Expression Database with Small Molecule Modulators.iScience · 2019Article
- Physiological controls of large-scale patterning in planarian regeneration: a molecular and computational perspective on growth and form.Regeneration (Oxford, England) · 2016Article
- REGene: a literature-based knowledgebase of animal regeneration that bridge tissue regeneration and cancer.Scientific reports · 2016Article
- RegenBase: a knowledge base of spinal cord injury biology for translational research.Database : the journal of biological databases and curation · 2016Article
- Inferring regulatory networks from experimental morphological phenotypes: a computational method reverse-engineers planarian regeneration.PLoS computational biology · 2015Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors at 1 institution in 1 country.
Funding
Abstract
summaryThe 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.
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What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.