{"id":"https://openalex.org/W1989893435","doi":"https://doi.org/10.1093/bioinformatics/btu582","title":"Limbform: a functional ontology-based database of limb regeneration experiments","display_name":"Limbform: a functional ontology-based database of limb regeneration experiments","publication_year":2014,"publication_date":"2014-08-27","ids":{"openalex":"https://openalex.org/W1989893435","doi":"https://doi.org/10.1093/bioinformatics/btu582","mag":"1989893435","pmid":"https://pubmed.ncbi.nlm.nih.gov/25170026"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btu582","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btu582","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/30/24/3598/48931629/bioinformatics_30_24_3598.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"public-domain","license_id":"https://openalex.org/licenses/public-domain","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/30/24/3598/48931629/bioinformatics_30_24_3598.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5021222550","display_name":"Daniel Lobo","orcid":"https://orcid.org/0000-0003-4666-6118"},"institutions":[{"id":"https://openalex.org/I121934306","display_name":"Tufts University","ror":"https://ror.org/05wvpxv85","country_code":"US","type":"education","lineage":["https://openalex.org/I121934306"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Daniel Lobo","raw_affiliation_strings":["Center for Regenerative and Developmental Biology, Department of Biology, Tufts University, 200 Boston Avenue, Suite 4600, Medford, MA 02155, USA"],"affiliations":[{"raw_affiliation_string":"Center for Regenerative and Developmental Biology, Department of Biology, Tufts University, 200 Boston Avenue, Suite 4600, Medford, MA 02155, USA","institution_ids":["https://openalex.org/I121934306"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5110765233","display_name":"Erica Feldman","orcid":null},"institutions":[{"id":"https://openalex.org/I121934306","display_name":"Tufts University","ror":"https://ror.org/05wvpxv85","country_code":"US","type":"education","lineage":["https://openalex.org/I121934306"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Erica B. Feldman","raw_affiliation_strings":["Center for Regenerative and Developmental Biology, Department of Biology, Tufts University, 200 Boston Avenue, Suite 4600, Medford, MA 02155, USA"],"affiliations":[{"raw_affiliation_string":"Center for Regenerative and Developmental Biology, Department of Biology, Tufts University, 200 Boston Avenue, Suite 4600, Medford, MA 02155, USA","institution_ids":["https://openalex.org/I121934306"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5025663634","display_name":"Michelle Shah","orcid":null},"institutions":[{"id":"https://openalex.org/I121934306","display_name":"Tufts University","ror":"https://ror.org/05wvpxv85","country_code":"US","type":"education","lineage":["https://openalex.org/I121934306"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Michelle Shah","raw_affiliation_strings":["Center for Regenerative and Developmental Biology, Department of Biology, Tufts University, 200 Boston Avenue, Suite 4600, Medford, MA 02155, USA"],"affiliations":[{"raw_affiliation_string":"Center for Regenerative and Developmental Biology, Department of Biology, Tufts University, 200 Boston Avenue, Suite 4600, Medford, MA 02155, USA","institution_ids":["https://openalex.org/I121934306"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5065188006","display_name":"Taylor J. Malone","orcid":"https://orcid.org/0000-0002-2358-4665"},"institutions":[{"id":"https://openalex.org/I121934306","display_name":"Tufts University","ror":"https://ror.org/05wvpxv85","country_code":"US","type":"education","lineage":["https://openalex.org/I121934306"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Taylor J. Malone","raw_affiliation_strings":["Center for Regenerative and Developmental Biology, Department of Biology, Tufts University, 200 Boston Avenue, Suite 4600, Medford, MA 02155, USA"],"affiliations":[{"raw_affiliation_string":"Center for Regenerative and Developmental Biology, Department of Biology, Tufts University, 200 Boston Avenue, Suite 4600, Medford, MA 02155, USA","institution_ids":["https://openalex.org/I121934306"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5085228887","display_name":"Michael Levin","orcid":"https://orcid.org/0000-0001-7292-8084"},"institutions":[{"id":"https://openalex.org/I121934306","display_name":"Tufts University","ror":"https://ror.org/05wvpxv85","country_code":"US","type":"education","lineage":["https://openalex.org/I121934306"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Michael Levin","raw_affiliation_strings":["Center for Regenerative and Developmental Biology, Department of Biology, Tufts University, 200 Boston Avenue, Suite 4600, Medford, MA 02155, USA"],"affiliations":[{"raw_affiliation_string":"Center for Regenerative and Developmental Biology, Department of Biology, Tufts University, 200 Boston Avenue, Suite 4600, Medford, MA 02155, USA","institution_ids":["https://openalex.org/I121934306"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5021222550"],"corresponding_institution_ids":["https://openalex.org/I121934306"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.7116,"has_fulltext":false,"cited_by_count":16,"citation_normalized_percentile":{"value":0.69174528,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"30","issue":"24","first_page":"3598","last_page":"3600"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12789","display_name":"Planarian Biology and Electrostimulation","score":0.9986000061035156,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T12789","display_name":"Planarian Biology and Electrostimulation","score":0.9986000061035156,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/regeneration","display_name":"Regeneration (biology)","score":0.7079759836196899},{"id":"https://openalex.org/keywords/ontology","display_name":"Ontology","score":0.6872055530548096},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6856993436813354},{"id":"https://openalex.org/keywords/process","display_name":"Process (computing)","score":0.5937300324440002},{"id":"https://openalex.org/keywords/resource","display_name":"Resource (disambiguation)","score":0.49788355827331543},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.3759872317314148},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.3698223829269409},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.33099767565727234},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2487754225730896},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.08079385757446289}],"concepts":[{"id":"https://openalex.org/C171056886","wikidata":"https://www.wikidata.org/wiki/Q193119","display_name":"Regeneration (biology)","level":2,"score":0.7079759836196899},{"id":"https://openalex.org/C25810664","wikidata":"https://www.wikidata.org/wiki/Q44325","display_name":"Ontology","level":2,"score":0.6872055530548096},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6856993436813354},{"id":"https://openalex.org/C98045186","wikidata":"https://www.wikidata.org/wiki/Q205663","display_name":"Process (computing)","level":2,"score":0.5937300324440002},{"id":"https://openalex.org/C206345919","wikidata":"https://www.wikidata.org/wiki/Q20380951","display_name":"Resource (disambiguation)","level":2,"score":0.49788355827331543},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.3759872317314148},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.3698223829269409},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.33099767565727234},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2487754225730896},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.08079385757446289},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.0},{"id":"https://openalex.org/C95444343","wikidata":"https://www.wikidata.org/wiki/Q7141","display_name":"Cell biology","level":1,"score":0.0},{"id":"https://openalex.org/C31258907","wikidata":"https://www.wikidata.org/wiki/Q1301371","display_name":"Computer network","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D005121","descriptor_name":"Extremities","qualifier_ui":"Q000033","qualifier_name":"anatomy & histology","is_major_topic":false},{"descriptor_ui":"D005121","descriptor_name":"Extremities","qualifier_ui":"Q000033","qualifier_name":"anatomy & histology","is_major_topic":false},{"descriptor_ui":"D005121","descriptor_name":"Extremities","qualifier_ui":"Q000033","qualifier_name":"anatomy & histology","is_major_topic":false},{"descriptor_ui":"D005121","descriptor_name":"Extremities","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D005121","descriptor_name":"Extremities","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D005121","descriptor_name":"Extremities","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D010641","descriptor_name":"Phenotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010641","descriptor_name":"Phenotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010641","descriptor_name":"Phenotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012038","descriptor_name":"Regeneration","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012038","descriptor_name":"Regeneration","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012038","descriptor_name":"Regeneration","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D064229","descriptor_name":"Biological Ontologies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D064229","descriptor_name":"Biological Ontologies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D064229","descriptor_name":"Biological Ontologies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btu582","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btu582","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/30/24/3598/48931629/bioinformatics_30_24_3598.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"public-domain","license_id":"https://openalex.org/licenses/public-domain","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:25170026","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/25170026","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:4253831","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4253831","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btu582","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btu582","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/30/24/3598/48931629/bioinformatics_30_24_3598.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"public-domain","license_id":"https://openalex.org/licenses/public-domain","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W1989893435.pdf","grobid_xml":"https://content.openalex.org/works/W1989893435.grobid-xml"},"referenced_works_count":8,"referenced_works":["https://openalex.org/W1581582012","https://openalex.org/W1992683617","https://openalex.org/W1996383859","https://openalex.org/W2086761179","https://openalex.org/W2125738657","https://openalex.org/W2155443781","https://openalex.org/W2158797557","https://openalex.org/W2167491747"],"related_works":["https://openalex.org/W2058795891","https://openalex.org/W2521179722","https://openalex.org/W572025462","https://openalex.org/W1981919236","https://openalex.org/W3001086633","https://openalex.org/W4353086860","https://openalex.org/W2461129609","https://openalex.org/W2003333417","https://openalex.org/W3173270574","https://openalex.org/W1984219920"],"abstract_inverted_index":{"The":[0,49,114,135],"ability":[1],"of":[2,26,51,60,68,71,83,146,173],"certain":[3],"organisms":[4],"to":[5,55,90,106,170],"completely":[6,41],"regenerate":[7],"lost":[8],"limbs":[9],"is":[10,64,97],"a":[11,52,80,100,158],"fascinating":[12],"process,":[13],"far":[14],"from":[15],"solved.":[16],"Despite":[17],"the":[18,23,45,57,66,143,163,171,174],"extraordinary":[19,139],"published":[20,84,120],"efforts":[21],"during":[22,44],"past":[24],"centuries":[25],"scientists":[27],"performing":[28],"amputations,":[29],"transplantations":[30],"and":[31,111,133],"molecular":[32],"experiments,":[33],"no":[34],"mechanistic":[35],"model":[36,126],"exists":[37],"yet":[38],"that":[39],"can":[40],"explain":[42],"patterning":[43],"limb":[46,72,85,109,121,177],"regeneration":[47,86,122,178],"process.":[48],"lack":[50],"centralized":[53,81,115],"repository":[54],"enable":[56],"efficient":[58],"mining":[59,142],"this":[61,150],"huge":[62],"dataset":[63],"hindering":[65],"discovery":[67,172],"comprehensive":[69,176],"models":[70],"regeneration.":[73],"Here,":[74],"we":[75],"introduce":[76],"Limbform":[77,96],"(Limb":[78],"formalization),":[79],"database":[82,116,136],"experiments.":[87],"In":[88],"contrast":[89],"natural":[91],"language":[92],"or":[93],"text-based":[94],"ontologies,":[95],"based":[98,156],"on":[99,157],"functional":[101,147,159],"ontology":[102,160],"using":[103],"mathematical":[104,154],"graphs":[105],"represent":[107],"unambiguously":[108],"phenotypes":[110],"manipulation":[112],"procedures.":[113],"currently":[117],"contains":[118],">800":[119],"experiments":[123],"comprising":[124],"many":[125],"organisms,":[127],"including":[128],"salamanders,":[129],"frogs,":[130],"insects,":[131],"crustaceans":[132],"arachnids.":[134],"represents":[137],"an":[138],"resource":[140],"for":[141,165],"existing":[144],"knowledge":[145],"data":[148],"in":[149],"field;":[151],"furthermore,":[152],"its":[153],"nature":[155],"will":[161],"pave":[162],"way":[164],"artificial":[166],"intelligence":[167],"tools":[168],"applied":[169],"sought-after":[175],"models.":[179]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":3},{"year":2018,"cited_by_count":1},{"year":2016,"cited_by_count":4},{"year":2015,"cited_by_count":1}],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2025-10-10T00:00:00"}
