{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,11]],"date-time":"2025-11-11T22:11:06Z","timestamp":1762899066147},"reference-count":8,"publisher":"Oxford University Press (OUP)","issue":"24","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2014,12,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: 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 &amp;gt;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.<\/jats:p>\n               <jats:p>Availability and implementaion: The Limbform database is freely available at http:\/\/limbform.daniel-lobo.com .<\/jats:p>\n               <jats:p>Contact: \u00a0michael.levin@tufts.edu<\/jats:p>","DOI":"10.1093\/bioinformatics\/btu582","type":"journal-article","created":{"date-parts":[[2014,8,29]],"date-time":"2014-08-29T00:22:23Z","timestamp":1409271743000},"page":"3598-3600","source":"Crossref","is-referenced-by-count":14,"title":["Limbform: a functional ontology-based database of limb regeneration experiments"],"prefix":"10.1093","volume":"30","author":[{"given":"Daniel","family":"Lobo","sequence":"first","affiliation":[{"name":"Center for Regenerative and Developmental Biology, Department of Biology, Tufts University, 200 Boston Avenue, Suite 4600, Medford, MA 02155, USA"}]},{"given":"Erica B.","family":"Feldman","sequence":"additional","affiliation":[{"name":"Center for Regenerative and Developmental Biology, Department of Biology, Tufts University, 200 Boston Avenue, Suite 4600, Medford, MA 02155, USA"}]},{"given":"Michelle","family":"Shah","sequence":"additional","affiliation":[{"name":"Center for Regenerative and Developmental Biology, Department of Biology, Tufts University, 200 Boston Avenue, Suite 4600, Medford, MA 02155, USA"}]},{"given":"Taylor J.","family":"Malone","sequence":"additional","affiliation":[{"name":"Center for Regenerative and Developmental Biology, Department of Biology, Tufts University, 200 Boston Avenue, Suite 4600, Medford, MA 02155, USA"}]},{"given":"Michael","family":"Levin","sequence":"additional","affiliation":[{"name":"Center for Regenerative and Developmental Biology, Department of Biology, Tufts University, 200 Boston Avenue, Suite 4600, Medford, MA 02155, USA"}]}],"member":"286","published-online":{"date-parts":[[2014,8,27]]},"reference":[{"key":"2023012712051741100_btu582-B1","doi-asserted-by":"crossref","first-page":"525","DOI":"10.1146\/annurev.cellbio.24.110707.175336","article-title":"Comparative aspects of animal regeneration","volume":"24","author":"Brockes","year":"2008","journal-title":"Annu. Rev. Cell. Dev. Biol."},{"key":"2023012712051741100_btu582-B2","doi-asserted-by":"crossref","first-page":"37","DOI":"10.1002\/reg2.13","article-title":"A bioinformatics expert system linking functional data to anatomical outcomes in limb regeneration","volume":"1","author":"Lobo","year":"2014","journal-title":"Regeneration"},{"key":"2023012712051741100_btu582-B3","doi-asserted-by":"crossref","first-page":"20130918","DOI":"10.1098\/rsif.2013.0918","article-title":"A linear-encoding model explains the variability of the target morphology in regeneration","volume":"11","author":"Lobo","year":"2014","journal-title":"J. R. Soc. Interface"},{"key":"2023012712051741100_btu582-B4","doi-asserted-by":"crossref","first-page":"6101","DOI":"10.1016\/j.tcs.2011.07.004","article-title":"Graph grammars with string-regulated rewriting","volume":"412","author":"Lobo","year":"2011","journal-title":"Theor. Comp. Sci."},{"key":"2023012712051741100_btu582-B5","doi-asserted-by":"crossref","first-page":"1098","DOI":"10.1093\/bioinformatics\/btt088","article-title":"Planform: an application and database of graph-encoded planarian regenerative experiments","volume":"29","author":"Lobo","year":"2013","journal-title":"Bioinformatics"},{"key":"2023012712051741100_btu582-B6","doi-asserted-by":"crossref","first-page":"156","DOI":"10.1242\/bio.20123400","article-title":"Towards a bioinformatics of patterning: a computational approach to understanding regulative morphogenesis","volume":"2","author":"Lobo","year":"2013","journal-title":"Biol. Open"},{"key":"2023012712051741100_btu582-B7","doi-asserted-by":"crossref","first-page":"409","DOI":"10.1146\/annurev-cellbio-092910-154115","article-title":"Limb regeneration: a new development?","volume":"27","author":"Nacu","year":"2011","journal-title":"Annu. Rev. Cell. Dev. Biol."},{"key":"2023012712051741100_btu582-B8","doi-asserted-by":"crossref","first-page":"e1004268","DOI":"10.1371\/journal.pgen.1004268","article-title":"Phenotype Ontologies and Cross-Species Analysis for Translational Research","volume":"10","author":"Robinson","year":"2014","journal-title":"PLoS Genet."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/30\/24\/3598\/48931629\/bioinformatics_30_24_3598.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/30\/24\/3598\/48931629\/bioinformatics_30_24_3598.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,27]],"date-time":"2023-01-27T13:03:42Z","timestamp":1674824622000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/30\/24\/3598\/2422217"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2014,8,27]]},"references-count":8,"journal-issue":{"issue":"24","published-print":{"date-parts":[[2014,12,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btu582","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2014,12,15]]},"published":{"date-parts":[[2014,8,27]]}}}