{"id":"https://openalex.org/W2095723013","doi":"https://doi.org/10.1186/2041-1480-5-12","title":"The zebrafish anatomy and stage ontologies: representing the anatomy and development of Danio rerio","display_name":"The zebrafish anatomy and stage ontologies: representing the anatomy and development of Danio rerio","publication_year":2014,"publication_date":"2014-01-01","ids":{"openalex":"https://openalex.org/W2095723013","doi":"https://doi.org/10.1186/2041-1480-5-12","mag":"2095723013","pmid":"https://pubmed.ncbi.nlm.nih.gov/24568621"},"language":"en","primary_location":{"id":"doi:10.1186/2041-1480-5-12","is_oa":true,"landing_page_url":"https://doi.org/10.1186/2041-1480-5-12","pdf_url":"https://jbiomedsem.biomedcentral.com/counter/pdf/10.1186/2041-1480-5-12","source":{"id":"https://openalex.org/S172276550","display_name":"Journal of Biomedical Semantics","issn_l":"2041-1480","issn":["2041-1480"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Biomedical Semantics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://jbiomedsem.biomedcentral.com/counter/pdf/10.1186/2041-1480-5-12","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5032460049","display_name":"Ceri E. Van Slyke","orcid":"https://orcid.org/0000-0002-2244-7917"},"institutions":[{"id":"https://openalex.org/I181233156","display_name":"University of Oregon","ror":"https://ror.org/0293rh119","country_code":"US","type":"education","lineage":["https://openalex.org/I181233156"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Ceri E Van Slyke","raw_affiliation_strings":["ZFIN, 5291 University of Oregon, Eugene, OR 97403-5291, USA. van_slyke@zfin.org","ZFIN, 5291 University of Oregon, Eugene, OR, 97403-5291, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"ZFIN, 5291 University of Oregon, Eugene, OR 97403-5291, USA. van_slyke@zfin.org","institution_ids":["https://openalex.org/I181233156"]},{"raw_affiliation_string":"ZFIN, 5291 University of Oregon, Eugene, OR, 97403-5291, USA","institution_ids":["https://openalex.org/I181233156"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5031573747","display_name":"Yvonne M. Bradford","orcid":"https://orcid.org/0000-0002-9900-7880"},"institutions":[{"id":"https://openalex.org/I181233156","display_name":"University of Oregon","ror":"https://ror.org/0293rh119","country_code":"US","type":"education","lineage":["https://openalex.org/I181233156"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Yvonne M Bradford","raw_affiliation_strings":["ZFIN, 5291 University of Oregon, Eugene, OR, 97403-5291, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"ZFIN, 5291 University of Oregon, Eugene, OR, 97403-5291, USA","institution_ids":["https://openalex.org/I181233156"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5055268752","display_name":"Monte Westerfield","orcid":"https://orcid.org/0000-0003-1187-7839"},"institutions":[{"id":"https://openalex.org/I181233156","display_name":"University of Oregon","ror":"https://ror.org/0293rh119","country_code":"US","type":"education","lineage":["https://openalex.org/I181233156"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Monte Westerfield","raw_affiliation_strings":["Institute of Neuroscience, 1254 University of Oregon, Eugene, OR, 97403-5291, USA","ZFIN, 5291 University of Oregon, Eugene, OR, 97403-5291, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Neuroscience, 1254 University of Oregon, Eugene, OR, 97403-5291, USA","institution_ids":["https://openalex.org/I181233156"]},{"raw_affiliation_string":"ZFIN, 5291 University of Oregon, Eugene, OR, 97403-5291, USA","institution_ids":["https://openalex.org/I181233156"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5064320417","display_name":"Melissa Haendel","orcid":"https://orcid.org/0000-0001-9114-8737"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Melissa A Haendel","raw_affiliation_strings":["Ontology Development Group, OHSU Library, 181 Southwest Sam Jackson Park Road, Portland, OR, 97239-3079, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Ontology Development Group, OHSU Library, 181 Southwest Sam Jackson Park Road, Portland, OR, 97239-3079, USA","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5031573747","https://openalex.org/A5032460049"],"corresponding_institution_ids":["https://openalex.org/I181233156"],"apc_list":{"value":1340,"currency":"USD","value_usd":1340},"apc_paid":{"value":1340,"currency":"USD","value_usd":1340},"fwci":3.3838,"has_fulltext":true,"cited_by_count":75,"citation_normalized_percentile":{"value":0.93359909,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":96,"max":99},"biblio":{"volume":"5","issue":"1","first_page":"12","last_page":"12"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.5052000284194946,"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/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.5052000284194946,"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"}},{"id":"https://openalex.org/T11685","display_name":"Zebrafish Biomedical Research Applications","score":0.28130000829696655,"subfield":{"id":"https://openalex.org/subfields/1307","display_name":"Cell 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"}},{"id":"https://openalex.org/T10268","display_name":"Developmental Biology and Gene Regulation","score":0.09030000120401382,"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/zebrafish","display_name":"Zebrafish","score":0.8609254956245422},{"id":"https://openalex.org/keywords/danio","display_name":"Danio","score":0.8135808706283569},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5911344289779663},{"id":"https://openalex.org/keywords/hierarchy","display_name":"Hierarchy","score":0.5098065733909607},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.49773934483528137},{"id":"https://openalex.org/keywords/phenotype","display_name":"Phenotype","score":0.465858519077301},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.3871385455131531},{"id":"https://openalex.org/keywords/anatomy","display_name":"Anatomy","score":0.3489551544189453},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.32998353242874146},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.23447132110595703}],"concepts":[{"id":"https://openalex.org/C2776878037","wikidata":"https://www.wikidata.org/wiki/Q169444","display_name":"Zebrafish","level":3,"score":0.8609254956245422},{"id":"https://openalex.org/C2780384893","wikidata":"https://www.wikidata.org/wiki/Q901804","display_name":"Danio","level":4,"score":0.8135808706283569},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5911344289779663},{"id":"https://openalex.org/C31170391","wikidata":"https://www.wikidata.org/wiki/Q188619","display_name":"Hierarchy","level":2,"score":0.5098065733909607},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.49773934483528137},{"id":"https://openalex.org/C127716648","wikidata":"https://www.wikidata.org/wiki/Q104053","display_name":"Phenotype","level":3,"score":0.465858519077301},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.3871385455131531},{"id":"https://openalex.org/C105702510","wikidata":"https://www.wikidata.org/wiki/Q514","display_name":"Anatomy","level":1,"score":0.3489551544189453},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.32998353242874146},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.23447132110595703},{"id":"https://openalex.org/C162324750","wikidata":"https://www.wikidata.org/wiki/Q8134","display_name":"Economics","level":0,"score":0.0},{"id":"https://openalex.org/C34447519","wikidata":"https://www.wikidata.org/wiki/Q179522","display_name":"Market economy","level":1,"score":0.0}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1186/2041-1480-5-12","is_oa":true,"landing_page_url":"https://doi.org/10.1186/2041-1480-5-12","pdf_url":"https://jbiomedsem.biomedcentral.com/counter/pdf/10.1186/2041-1480-5-12","source":{"id":"https://openalex.org/S172276550","display_name":"Journal of Biomedical Semantics","issn_l":"2041-1480","issn":["2041-1480"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Biomedical Semantics","raw_type":"journal-article"},{"id":"pmid:24568621","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/24568621","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":"Journal of biomedical semantics","raw_type":null},{"id":"pmh:oai:europepmc.org:2929917","is_oa":true,"landing_page_url":"http://europepmc.org/articles/PMC3944782","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:3944782","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3944782","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"J Biomed Semantics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/2041-1480-5-12","is_oa":true,"landing_page_url":"https://doi.org/10.1186/2041-1480-5-12","pdf_url":"https://jbiomedsem.biomedcentral.com/counter/pdf/10.1186/2041-1480-5-12","source":{"id":"https://openalex.org/S172276550","display_name":"Journal of Biomedical Semantics","issn_l":"2041-1480","issn":["2041-1480"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Biomedical Semantics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2656359811","display_name":"ZFIN: The Zebrafish Model Organism Database","funder_award_id":"5u24hg002659-20","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G3389655473","display_name":null,"funder_award_id":"P41HG002659","funder_id":"https://openalex.org/F4320337348","funder_display_name":"National Human Genome Research Institute"},{"id":"https://openalex.org/G3446960996","display_name":"Linking Evolution to Genomics Using Phenotype Ontologies","funder_award_id":"0641025","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G3750968026","display_name":"The Monarch Initiative: Linking Diseases to Model Organism Resources","funder_award_id":"7r24od011883-13","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G483165192","display_name":null,"funder_award_id":"U41-HG002659","funder_id":"https://openalex.org/F4320337348","funder_display_name":"National Human Genome Research Institute"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337348","display_name":"National Human Genome Research Institute","ror":"https://ror.org/00baak391"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2095723013.pdf","grobid_xml":"https://content.openalex.org/works/W2095723013.grobid-xml"},"referenced_works_count":42,"referenced_works":["https://openalex.org/W63642558","https://openalex.org/W594823730","https://openalex.org/W1857560941","https://openalex.org/W1932653761","https://openalex.org/W1976391205","https://openalex.org/W1994474588","https://openalex.org/W1997058260","https://openalex.org/W1998756807","https://openalex.org/W2002306043","https://openalex.org/W2002507929","https://openalex.org/W2030197114","https://openalex.org/W2033561781","https://openalex.org/W2034175439","https://openalex.org/W2035415061","https://openalex.org/W2037382435","https://openalex.org/W2040712196","https://openalex.org/W2042317619","https://openalex.org/W2044252882","https://openalex.org/W2048024098","https://openalex.org/W2074442006","https://openalex.org/W2079432590","https://openalex.org/W2087264052","https://openalex.org/W2090486853","https://openalex.org/W2094108329","https://openalex.org/W2096704019","https://openalex.org/W2103017472","https://openalex.org/W2113142309","https://openalex.org/W2115591173","https://openalex.org/W2116034137","https://openalex.org/W2121557186","https://openalex.org/W2125349610","https://openalex.org/W2133045719","https://openalex.org/W2142139243","https://openalex.org/W2146466835","https://openalex.org/W2150791531","https://openalex.org/W2157079123","https://openalex.org/W2157217189","https://openalex.org/W2159907330","https://openalex.org/W2162385209","https://openalex.org/W2178026535","https://openalex.org/W2409949659","https://openalex.org/W4236241609"],"related_works":["https://openalex.org/W4237600267","https://openalex.org/W4245153001","https://openalex.org/W1992684640","https://openalex.org/W2938575486","https://openalex.org/W4253352342","https://openalex.org/W4388158194","https://openalex.org/W2947128474","https://openalex.org/W2922730069","https://openalex.org/W3109425268","https://openalex.org/W3025909797"],"abstract_inverted_index":{"BACKGROUND:":[0],"The":[1,42,70,102,118,140,158],"Zebrafish":[2,18],"Anatomy":[3],"Ontology":[4,20],"(ZFA)":[5],"is":[6,12],"an":[7],"OBO":[8,109],"Foundry":[9,110],"ontology":[10,159],"that":[11,92],"used":[13,165],"in":[14],"conjunction":[15],"with":[16,76,87],"the":[17,24,32,49,61,90,94,149,161],"Stage":[19],"(ZFS)":[21],"to":[22,40,53,89,112,169],"describe":[23],"gross":[25],"and":[26,29,51,56,64,74,82,86,104,116,133,145,155,160,176,186],"cellular":[27],"anatomy":[28,73,144],"development":[30,75,146],"of":[31,126,137,151,173,188],"zebrafish,":[33],"Danio":[34],"rerio,":[35],"from":[36,60,65,129,134],"single":[37],"cell":[38],"zygote":[39],"adult.":[41],"zebrafish":[43,143],"model":[44],"organism":[45],"database":[46],"(ZFIN)":[47],"uses":[48],"ZFA":[50,71,103,119,141],"ZFS":[52,91,105],"annotate":[54],"phenotype":[55,177],"gene":[57,153,174],"expression":[58,154,175],"data":[59,67,162],"primary":[62],"literature":[63],"contributed":[66],"sets.":[68],"RESULTS:":[69],"models":[72,187],"a":[77,80,83,124],"subclass":[78],"hierarchy,":[79],"partonomy,":[81],"developmental":[84],"hierarchy":[85],"relationships":[88],"define":[93],"stages":[95,136],"during":[96],"which":[97],"each":[98],"anatomical":[99,127,131,156],"entity":[100],"exists.":[101],"are":[106],"developed":[107],"utilizing":[108],"principles":[111],"ensure":[113],"orthogonality,":[114],"accessibility,":[115],"interoperability.":[117],"has":[120],"2860":[121],"classes":[122],"representing":[123],"diversity":[125],"structures":[128],"different":[130,135],"systems":[132],"development.":[138],"CONCLUSIONS:":[139],"describes":[142],"semantically":[147],"for":[148],"purposes":[150],"annotating":[152],"phenotypes.":[157],"have":[163],"been":[164],"by":[166],"other":[167],"resources":[168],"perform":[170],"cross-species":[171],"queries":[172],"data,":[178],"providing":[179],"insights":[180],"into":[181],"genetic":[182],"relationships,":[183],"morphological":[184],"evolution,":[185],"human":[189],"disease.":[190]},"counts_by_year":[{"year":2026,"cited_by_count":4},{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":7},{"year":2023,"cited_by_count":3},{"year":2022,"cited_by_count":6},{"year":2021,"cited_by_count":7},{"year":2020,"cited_by_count":10},{"year":2019,"cited_by_count":4},{"year":2018,"cited_by_count":5},{"year":2017,"cited_by_count":9},{"year":2016,"cited_by_count":8},{"year":2015,"cited_by_count":6},{"year":2014,"cited_by_count":3}],"updated_date":"2026-08-06T08:24:18.245995","created_date":"2025-10-10T00:00:00"}
