{"id":"https://openalex.org/W2105731904","doi":"https://doi.org/10.1186/2041-1480-4-31","title":"Enhanced XAO: the ontology of Xenopus anatomy and development underpins more accurate annotation of gene expression and queries on Xenbase","display_name":"Enhanced XAO: the ontology of Xenopus anatomy and development underpins more accurate annotation of gene expression and queries on Xenbase","publication_year":2013,"publication_date":"2013-01-01","ids":{"openalex":"https://openalex.org/W2105731904","doi":"https://doi.org/10.1186/2041-1480-4-31","mag":"2105731904","pmid":"https://pubmed.ncbi.nlm.nih.gov/24139024","pmcid":"https://www.ncbi.nlm.nih.gov/pmc/articles/3816597"},"language":"en","primary_location":{"is_oa":true,"landing_page_url":"https://doi.org/10.1186/2041-1480-4-31","pdf_url":"https://jbiomedsem.biomedcentral.com/counter/pdf/10.1186/2041-1480-4-31","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_indexed_in_scopus":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310319965","https://openalex.org/P4310320256"],"host_organization_lineage_names":["Springer Nature","BioMed Central"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true},"type":"article","type_crossref":"journal-article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://jbiomedsem.biomedcentral.com/counter/pdf/10.1186/2041-1480-4-31","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5007833252","display_name":"Erik Segerdell","orcid":"https://orcid.org/0000-0002-9611-1279"},"institutions":[{"id":"https://openalex.org/I165690674","display_name":"Oregon Health & Science University","ror":"https://ror.org/009avj582","country_code":"US","type":"funder","lineage":["https://openalex.org/I165690674"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Erik Segerdell","raw_affiliation_strings":["Knight Cancer Institute, Oregon Health and Science University, Portland, USA"],"affiliations":[{"raw_affiliation_string":"Knight Cancer Institute, Oregon Health and Science University, Portland, USA","institution_ids":["https://openalex.org/I165690674"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5046489815","display_name":"Virgilio G. Ponferrada","orcid":"https://orcid.org/0000-0002-8590-7183"},"institutions":[{"id":"https://openalex.org/I1285204247","display_name":"Cincinnati Children's Hospital Medical Center","ror":"https://ror.org/01hcyya48","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1285204247"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Virgilio G Ponferrada","raw_affiliation_strings":["Division of Developmental Biology, Cincinnati Children\u2019s Research Foundation, Cincinnati, USA"],"affiliations":[{"raw_affiliation_string":"Division of Developmental Biology, Cincinnati Children\u2019s Research Foundation, Cincinnati, USA","institution_ids":["https://openalex.org/I1285204247"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5046907178","display_name":"Christina James\u2010Zorn","orcid":"https://orcid.org/0000-0001-5495-4588"},"institutions":[{"id":"https://openalex.org/I1285204247","display_name":"Cincinnati Children's Hospital Medical Center","ror":"https://ror.org/01hcyya48","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1285204247"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Christina James-Zorn","raw_affiliation_strings":["Division of Developmental Biology, Cincinnati Children\u2019s Research Foundation, Cincinnati, USA"],"affiliations":[{"raw_affiliation_string":"Division of Developmental Biology, Cincinnati Children\u2019s Research Foundation, Cincinnati, USA","institution_ids":["https://openalex.org/I1285204247"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5005917511","display_name":"Kevin A. Burns","orcid":"https://orcid.org/0009-0003-6587-4809"},"institutions":[{"id":"https://openalex.org/I1285204247","display_name":"Cincinnati Children's Hospital Medical Center","ror":"https://ror.org/01hcyya48","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1285204247"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Kevin A Burns","raw_affiliation_strings":["Division of Developmental Biology, Cincinnati Children\u2019s Research Foundation, Cincinnati, USA"],"affiliations":[{"raw_affiliation_string":"Division of Developmental Biology, Cincinnati Children\u2019s Research Foundation, Cincinnati, USA","institution_ids":["https://openalex.org/I1285204247"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5046773761","display_name":"Joshua D. Fortriede","orcid":"https://orcid.org/0000-0002-3293-5463"},"institutions":[{"id":"https://openalex.org/I1285204247","display_name":"Cincinnati Children's Hospital Medical Center","ror":"https://ror.org/01hcyya48","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1285204247"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Joshua D Fortriede","raw_affiliation_strings":["Division of Developmental Biology, Cincinnati Children\u2019s Research Foundation, Cincinnati, USA"],"affiliations":[{"raw_affiliation_string":"Division of Developmental Biology, Cincinnati Children\u2019s Research Foundation, Cincinnati, USA","institution_ids":["https://openalex.org/I1285204247"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5037935786","display_name":"Wasila Dahdul","orcid":"https://orcid.org/0000-0003-3162-7490"},"institutions":[{"id":"https://openalex.org/I6002401","display_name":"National Evolutionary Synthesis Center","ror":"https://ror.org/001ykb961","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I6002401"]},{"id":"https://openalex.org/I189957204","display_name":"University of South Dakota","ror":"https://ror.org/0043h8f16","country_code":"US","type":"funder","lineage":["https://openalex.org/I189957204"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Wasila M Dahdul","raw_affiliation_strings":["Department of Biology, University of South Dakota, Vermillion, USA","National Evolutionary Synthesis Center, Durham, USA"],"affiliations":[{"raw_affiliation_string":"National Evolutionary Synthesis Center, Durham, USA","institution_ids":["https://openalex.org/I6002401"]},{"raw_affiliation_string":"Department of Biology, University of South Dakota, Vermillion, USA","institution_ids":["https://openalex.org/I189957204"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5064576180","display_name":"Peter D. Vize","orcid":"https://orcid.org/0000-0001-8026-0424"},"institutions":[{"id":"https://openalex.org/I168635309","display_name":"University of Calgary","ror":"https://ror.org/03yjb2x39","country_code":"CA","type":"funder","lineage":["https://openalex.org/I168635309"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Peter D Vize","raw_affiliation_strings":["Department of Biological Science, University of Calgary, Calgary, Canada"],"affiliations":[{"raw_affiliation_string":"Department of Biological Science, University of Calgary, Calgary, Canada","institution_ids":["https://openalex.org/I168635309"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5003793915","display_name":"Aaron M. Zorn","orcid":"https://orcid.org/0000-0003-3217-3590"},"institutions":[{"id":"https://openalex.org/I1285204247","display_name":"Cincinnati Children's Hospital Medical Center","ror":"https://ror.org/01hcyya48","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1285204247"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Aaron M Zorn","raw_affiliation_strings":["Division of Developmental Biology, Cincinnati Children\u2019s Research Foundation, Cincinnati, USA"],"affiliations":[{"raw_affiliation_string":"Division of Developmental Biology, Cincinnati Children\u2019s Research Foundation, Cincinnati, USA","institution_ids":["https://openalex.org/I1285204247"]}]}],"institution_assertions":[],"countries_distinct_count":2,"institutions_distinct_count":5,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":1190,"currency":"GBP","value_usd":1459},"apc_paid":{"value":1190,"currency":"GBP","value_usd":1459},"fwci":1.549,"has_fulltext":true,"fulltext_origin":"pdf","cited_by_count":39,"citation_normalized_percentile":{"value":0.820233,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":95},"biblio":{"volume":"4","issue":"1","first_page":"31","last_page":"31"},"is_retracted":false,"is_paratext":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9996,"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":0.9996,"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/T11642","display_name":"Genomics and Rare Diseases","score":0.9864,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9848,"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":[],"concepts":[{"id":"https://openalex.org/C2779535977","wikidata":"https://www.wikidata.org/wiki/Q1342298","display_name":"Xenopus","level":3,"score":0.9492988},{"id":"https://openalex.org/C25810664","wikidata":"https://www.wikidata.org/wiki/Q44325","display_name":"Ontology","level":2,"score":0.6181733},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.61387557},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.53583026},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5178295},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.436935},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.37072584},{"id":"https://openalex.org/C169760540","wikidata":"https://www.wikidata.org/wiki/Q207011","display_name":"Neuroscience","level":1,"score":0.3520201},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.34255093},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.2953363},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.23976251},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.18086132},{"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}],"mesh":[],"locations_count":4,"locations":[{"is_oa":true,"landing_page_url":"https://doi.org/10.1186/2041-1480-4-31","pdf_url":"https://jbiomedsem.biomedcentral.com/counter/pdf/10.1186/2041-1480-4-31","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_indexed_in_scopus":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310319965","https://openalex.org/P4310320256"],"host_organization_lineage_names":["Springer Nature","BioMed Central"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true},{"is_oa":true,"landing_page_url":"https://europepmc.org/articles/pmc3816597","pdf_url":"https://europepmc.org/articles/pmc3816597?pdf=render","source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_indexed_in_scopus":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":["European Bioinformatics Institute"],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true},{"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3816597","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_indexed_in_scopus":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":["National Institutes of Health"],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true},{"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/24139024","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_indexed_in_scopus":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":["National Institutes of Health"],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false}],"best_oa_location":{"is_oa":true,"landing_page_url":"https://doi.org/10.1186/2041-1480-4-31","pdf_url":"https://jbiomedsem.biomedcentral.com/counter/pdf/10.1186/2041-1480-4-31","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_indexed_in_scopus":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310319965","https://openalex.org/P4310320256"],"host_organization_lineage_names":["Springer Nature","BioMed Central"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true},"sustainable_development_goals":[],"grants":[],"datasets":[],"versions":[],"referenced_works_count":37,"referenced_works":["https://openalex.org/W1501546233","https://openalex.org/W1541298030","https://openalex.org/W1565566882","https://openalex.org/W1966406774","https://openalex.org/W1970867422","https://openalex.org/W1987083115","https://openalex.org/W1997058260","https://openalex.org/W2010584894","https://openalex.org/W2016604946","https://openalex.org/W2024770693","https://openalex.org/W2037382435","https://openalex.org/W2044182000","https://openalex.org/W2059224185","https://openalex.org/W2061884320","https://openalex.org/W206379991","https://openalex.org/W2065275598","https://openalex.org/W2069748812","https://openalex.org/W2097860814","https://openalex.org/W2098076011","https://openalex.org/W2103017472","https://openalex.org/W2110769241","https://openalex.org/W2113142309","https://openalex.org/W2115047895","https://openalex.org/W2116034137","https://openalex.org/W2131071295","https://openalex.org/W2131660156","https://openalex.org/W2131969186","https://openalex.org/W2153482276","https://openalex.org/W2154264935","https://openalex.org/W2156895335","https://openalex.org/W2163109444","https://openalex.org/W2164587543","https://openalex.org/W2178026535","https://openalex.org/W2328269288","https://openalex.org/W2495004097","https://openalex.org/W63642558","https://openalex.org/W638789088"],"related_works":["https://openalex.org/W97368944","https://openalex.org/W4293692464","https://openalex.org/W4248442972","https://openalex.org/W414781085","https://openalex.org/W2888806461","https://openalex.org/W2282195027","https://openalex.org/W2084483306","https://openalex.org/W2014201996","https://openalex.org/W1485043520","https://openalex.org/W1427873156"],"abstract_inverted_index":{"The":[0,29,42,78,169,233,242],"African":[1],"clawed":[2],"frogs":[3],"Xenopus":[4,7,14,30,91,228,251],"laevis":[5],"and":[6,23,37,116,129,165,176,186,190,201,208,222,230,237,244,254,261,267,271],"tropicalis":[8],"are":[9,135],"prominent":[10],"animal":[11],"model":[12,92,220],"organisms.":[13],"research":[15,252],"contributes":[16],"to":[17,51,69,82,204,215,239,277],"the":[18,35,72,83,90,98,101,137,155,205],"understanding":[19],"of":[20,40,59,85,218,250,263],"genetic,":[21],"developmental":[22,146,177],"molecular":[24],"mechanisms":[25,256],"underlying":[26],"human":[27,286],"disease.":[28],"Anatomy":[31],"Ontology":[32],"(XAO)":[33],"reflects":[34],"anatomy":[36,187,216],"embryological":[38],"development":[39],"Xenopus.":[41],"XAO":[43,79,99,206,246],"provides":[44,157],"consistent":[45],"terminology":[46],"that":[47,61,160],"can":[48,131],"be":[49,132],"applied":[50],"anatomical":[52,65,108,143,153,175,209],"feature":[53],"descriptions":[54],"along":[55],"with":[56,172,183],"a":[57,124,225],"set":[58],"relationships":[60,111],"indicate":[62],"how":[63],"each":[64],"entity":[66],"is":[67,80,235],"related":[68],"others":[70],"in":[71,100],"embryo,":[73],"tadpole,":[74],"or":[75],"adult":[76],"frog.":[77],"integral":[81],"functionality":[84],"Xenbase":[86,184],"(":[87],"http://www.xenbase.org":[88],"),":[89],"organism":[93],"database.":[94],"We":[95],"significantly":[96],"expanded":[97,243],"last":[102],"five":[103],"years":[104],"by":[105],"adding":[106],"612":[107],"terms,":[109,179],"2934":[110],"between":[112,194,227],"them,":[113],"640":[114],"synonyms,":[115],"547":[117],"ontology":[118,156,234],"cross-references.":[119],"Each":[120],"term":[121,139,188],"now":[122,149,171],"has":[123,180],"definition,":[125],"so":[126],"database":[127],"users":[128],"curators":[130],"certain":[133],"they":[134],"selecting":[136],"correct":[138],"when":[140],"specifying":[141],"an":[142],"entity.":[144],"With":[145],"timing":[147],"information":[148],"asserted":[150],"for":[151,257,285],"every":[152],"term,":[154],"internal":[158],"checks":[159],"ensure":[161],"high-quality":[162],"gene":[163,264],"expression":[164,185],"phenotype":[166],"data":[167,196,229,253,284],"annotation.":[168],"XAO,":[170],"1313":[173],"defined":[174],"stage":[178],"been":[181],"integrated":[182],"searches":[189],"it":[191],"enables":[192],"links":[193],"various":[195],"types":[197],"including":[198],"images,":[199],"clones,":[200],"publications.":[202],"Improvements":[203],"structure":[207],"definitions":[210],"have":[211],"also":[212],"enhanced":[213,248],"cross-references":[214],"ontologies":[217,278],"other":[219,231],"organisms":[221],"humans,":[223],"providing":[224],"bridge":[226],"vertebrates.":[232],"free":[236],"open":[238],"all":[240],"users.":[241],"improved":[245],"allows":[247],"capture":[249],"aids":[255],"performing":[258],"complex":[259],"retrieval":[260],"analysis":[262],"expression,":[265],"phenotypes,":[266],"antibodies":[268],"through":[269],"text-matching":[270],"manual":[272],"curation.":[273],"Its":[274],"comprehensive":[275],"references":[276],"across":[279],"taxa":[280],"help":[281],"integrate":[282],"these":[283],"disease":[287],"modeling.":[288]},"abstract_inverted_index_v3":null,"cited_by_api_url":"https://api.openalex.org/works?filter=cites:W2105731904","counts_by_year":[{"year":2024,"cited_by_count":6},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":6},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":5},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":6},{"year":2014,"cited_by_count":5}],"updated_date":"2025-02-18T07:56:14.728554","created_date":"2016-06-24"}