{"id":"https://openalex.org/W2126067687","doi":"https://doi.org/10.1186/2041-1480-5-45","title":"Annotation of phenotypic diversity: decoupling data curation and ontology curation using Phenex","display_name":"Annotation of phenotypic diversity: decoupling data curation and ontology curation using Phenex","publication_year":2014,"publication_date":"2014-01-01","ids":{"openalex":"https://openalex.org/W2126067687","doi":"https://doi.org/10.1186/2041-1480-5-45","mag":"2126067687","pmid":"https://pubmed.ncbi.nlm.nih.gov/25411634"},"language":"en","primary_location":{"id":"doi:10.1186/2041-1480-5-45","is_oa":true,"landing_page_url":"https://doi.org/10.1186/2041-1480-5-45","pdf_url":"https://jbiomedsem.biomedcentral.com/counter/pdf/10.1186/2041-1480-5-45","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/10.1186/2041-1480-5-45","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5021056529","display_name":"James P. Balhoff","orcid":"https://orcid.org/0000-0002-8688-6599"},"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"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"James P Balhoff","raw_affiliation_strings":["National Evolutionary Synthesis Center, Durham, NC USA ; Department of Biology, University of North Carolina, Chapel Hill, NC USA","National Evolutionary Synthesis Center, Durham, NC, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"National Evolutionary Synthesis Center, Durham, NC USA ; Department of Biology, University of North Carolina, Chapel Hill, NC USA","institution_ids":[]},{"raw_affiliation_string":"National Evolutionary Synthesis Center, Durham, NC, USA","institution_ids":["https://openalex.org/I6002401"]}]},{"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/I189957204","display_name":"University of South Dakota","ror":"https://ror.org/0043h8f16","country_code":"US","type":"education","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, SD USA","Department of Biology, University of South Dakota, Vermillion, SD, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biology, University of South Dakota, Vermillion, SD USA","institution_ids":["https://openalex.org/I189957204"]},{"raw_affiliation_string":"Department of Biology, University of South Dakota, Vermillion, SD, USA","institution_ids":["https://openalex.org/I189957204"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5072721792","display_name":"T. Alexander Dececchi","orcid":"https://orcid.org/0000-0001-7972-3866"},"institutions":[{"id":"https://openalex.org/I189957204","display_name":"University of South Dakota","ror":"https://ror.org/0043h8f16","country_code":"US","type":"education","lineage":["https://openalex.org/I189957204"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"T Dececchi","raw_affiliation_strings":["Department of Biology, University of South Dakota, Vermillion, SD USA","Department of Biology, University of South Dakota, Vermillion, SD, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biology, University of South Dakota, Vermillion, SD USA","institution_ids":["https://openalex.org/I189957204"]},{"raw_affiliation_string":"Department of Biology, University of South Dakota, Vermillion, SD, USA","institution_ids":["https://openalex.org/I189957204"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5005484581","display_name":"Hilmar Lapp","orcid":"https://orcid.org/0000-0001-9107-0714"},"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"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Hilmar Lapp","raw_affiliation_strings":["National Evolutionary Synthesis Center, Durham, NC USA","National Evolutionary Synthesis Center, Durham, NC, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"National Evolutionary Synthesis Center, Durham, NC USA","institution_ids":["https://openalex.org/I6002401"]},{"raw_affiliation_string":"National Evolutionary Synthesis Center, Durham, NC, USA","institution_ids":["https://openalex.org/I6002401"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5020099887","display_name":"Paula Mabee","orcid":"https://orcid.org/0000-0002-8455-3213"},"institutions":[{"id":"https://openalex.org/I189957204","display_name":"University of South Dakota","ror":"https://ror.org/0043h8f16","country_code":"US","type":"education","lineage":["https://openalex.org/I189957204"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Paula M Mabee","raw_affiliation_strings":["Department of Biology, University of South Dakota, Vermillion, SD USA","Department of Biology, University of South Dakota, Vermillion, SD, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biology, University of South Dakota, Vermillion, SD USA","institution_ids":["https://openalex.org/I189957204"]},{"raw_affiliation_string":"Department of Biology, University of South Dakota, Vermillion, SD, USA","institution_ids":["https://openalex.org/I189957204"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5013911206","display_name":"Todd Vision","orcid":"https://orcid.org/0000-0002-6133-2581"},"institutions":[{"id":"https://openalex.org/I114027177","display_name":"University of North Carolina at Chapel Hill","ror":"https://ror.org/0130frc33","country_code":"US","type":"education","lineage":["https://openalex.org/I114027177"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Todd J Vision","raw_affiliation_strings":["National Evolutionary Synthesis Center, Durham, NC USA ; Department of Biology, University of North Carolina, Chapel Hill, NC USA","Department of Biology, University of North Carolina, Chapel Hill, NC, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"National Evolutionary Synthesis Center, Durham, NC USA ; Department of Biology, University of North Carolina, Chapel Hill, NC USA","institution_ids":[]},{"raw_affiliation_string":"Department of Biology, University of North Carolina, Chapel Hill, NC, USA","institution_ids":["https://openalex.org/I114027177"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5021056529"],"corresponding_institution_ids":["https://openalex.org/I6002401"],"apc_list":{"value":1190,"currency":"GBP","value_usd":1459},"apc_paid":{"value":1190,"currency":"GBP","value_usd":1459},"fwci":0.8537,"has_fulltext":true,"cited_by_count":20,"citation_normalized_percentile":{"value":0.73442031,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"5","issue":"1","first_page":"45","last_page":"45"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.7764000296592712,"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":0.7764000296592712,"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/T10215","display_name":"Semantic Web and Ontologies","score":0.04349999874830246,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.0357000008225441,"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/computer-science","display_name":"Computer science","score":0.846847653388977},{"id":"https://openalex.org/keywords/data-curation","display_name":"Data curation","score":0.7884973287582397},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.7476733326911926},{"id":"https://openalex.org/keywords/workflow","display_name":"Workflow","score":0.6349925994873047},{"id":"https://openalex.org/keywords/ontology","display_name":"Ontology","score":0.5885409116744995},{"id":"https://openalex.org/keywords/identifier","display_name":"Identifier","score":0.571155846118927},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.47079601883888245},{"id":"https://openalex.org/keywords/consistency","display_name":"Consistency (knowledge bases)","score":0.4659005105495453},{"id":"https://openalex.org/keywords/metadata","display_name":"Metadata","score":0.41611456871032715},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.4064151346683502},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.3054771423339844},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.09930729866027832}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.846847653388977},{"id":"https://openalex.org/C91632574","wikidata":"https://www.wikidata.org/wiki/Q15088675","display_name":"Data curation","level":2,"score":0.7884973287582397},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.7476733326911926},{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.6349925994873047},{"id":"https://openalex.org/C25810664","wikidata":"https://www.wikidata.org/wiki/Q44325","display_name":"Ontology","level":2,"score":0.5885409116744995},{"id":"https://openalex.org/C154504017","wikidata":"https://www.wikidata.org/wiki/Q853614","display_name":"Identifier","level":2,"score":0.571155846118927},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.47079601883888245},{"id":"https://openalex.org/C2776436953","wikidata":"https://www.wikidata.org/wiki/Q5163215","display_name":"Consistency (knowledge bases)","level":2,"score":0.4659005105495453},{"id":"https://openalex.org/C93518851","wikidata":"https://www.wikidata.org/wiki/Q180160","display_name":"Metadata","level":2,"score":0.41611456871032715},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.4064151346683502},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.3054771423339844},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.09930729866027832},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"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/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1186/2041-1480-5-45","is_oa":true,"landing_page_url":"https://doi.org/10.1186/2041-1480-5-45","pdf_url":"https://jbiomedsem.biomedcentral.com/counter/pdf/10.1186/2041-1480-5-45","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:25411634","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/25411634","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:pubmedcentral.nih.gov:4236444","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4236444","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:10.1186/2041-1480-5-45","is_oa":true,"landing_page_url":"https://doi.org/10.1186/2041-1480-5-45","pdf_url":"https://jbiomedsem.biomedcentral.com/counter/pdf/10.1186/2041-1480-5-45","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":[{"score":0.550000011920929,"id":"https://metadata.un.org/sdg/17","display_name":"Partnerships for the goals"}],"awards":[{"id":"https://openalex.org/G2993633737","display_name":null,"funder_award_id":"DBI-1062404","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G4105349646","display_name":null,"funder_award_id":"DBI-1062542","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G5429225240","display_name":null,"funder_award_id":"1062404","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G5768129421","display_name":null,"funder_award_id":"1062542","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2126067687.pdf","grobid_xml":"https://content.openalex.org/works/W2126067687.grobid-xml"},"referenced_works_count":12,"referenced_works":["https://openalex.org/W1541298030","https://openalex.org/W1544291342","https://openalex.org/W1994474588","https://openalex.org/W2001291669","https://openalex.org/W2007859640","https://openalex.org/W2022451103","https://openalex.org/W2096704019","https://openalex.org/W2123152121","https://openalex.org/W2124991490","https://openalex.org/W2131555431","https://openalex.org/W2165625764","https://openalex.org/W2170041483"],"related_works":["https://openalex.org/W2392768766","https://openalex.org/W2058118494","https://openalex.org/W2361861616","https://openalex.org/W2095118173","https://openalex.org/W2382021449","https://openalex.org/W2104269053","https://openalex.org/W2263699433","https://openalex.org/W2106424170","https://openalex.org/W2082577974","https://openalex.org/W2169425537"],"abstract_inverted_index":{"BACKGROUND:":[0],"Phenex":[1,163,193,208],"(http://phenex.phenoscape.org/)":[2],"is":[3,130],"a":[4,58,108,124,137,211],"desktop":[5],"application":[6],"for":[7,80,111,151],"semantically":[8],"annotating":[9],"the":[10,34,37,44,76,104,116,128,149,160,180,189],"phenotypic":[11],"character":[12],"matrix":[13],"datasets":[14],"common":[15,145],"in":[16,33,113,187],"evolutionary":[17],"biology.":[18],"Since":[19],"its":[20],"initial":[21],"publication,":[22],"we":[23],"have":[24,195,209],"added":[25,131,136],"new":[26,184],"features":[27],"that":[28,52],"address":[29],"several":[30],"major":[31],"bottlenecks":[32],"efficiency":[35],"of":[36,78,139,162,182],"phenotype":[38],"curation":[39,46,146],"process:":[40],"allowing":[41],"curators":[42,206],"during":[43],"data":[45,87,114,203],"phase":[47],"to":[48,67,106,132,143,198],"provisionally":[49],"request":[50,107],"terms":[51],"are":[53],"not":[54],"yet":[55],"available":[56],"from":[57,89,219],"relevant":[59],"ontology;":[60],"supporting":[61],"quality":[62],"control":[63],"against":[64],"annotation":[65,88,140,213],"guidelines":[66],"reduce":[68],"later":[69,152],"manual":[70],"review":[71],"and":[72,74,175,186,222],"revision;":[73],"enabling":[75],"sharing":[77,169],"files":[79],"collaboration":[81],"among":[82],"curators.":[83],"RESULTS:":[84],"We":[85,135,154],"decoupled":[86],"ontology":[90,220],"development":[91],"by":[92,158],"creating":[93],"an":[94,133],"Ontology":[95,190],"Request":[96,191],"Broker":[97],"(ORB)":[98],"within":[99],"Phenex.":[100],"Curators":[101],"can":[102,119],"use":[103,112],"ORB":[105],"provisional":[109,117],"term":[110,118,129],"annotation;":[115],"be":[120],"automatically":[121],"replaced":[122],"with":[123,166,215],"permanent":[125],"identifier":[126],"once":[127],"ontology.":[134],"set":[138],"consistency":[141],"checks":[142],"prevent":[144],"errors,":[147],"reducing":[148],"need":[150],"correction.":[153],"facilitated":[155],"collaborative":[156],"editing":[157],"improving":[159],"reliability":[161],"when":[164],"used":[165],"online":[167],"folder":[168],"services,":[170],"via":[171],"file":[172,223],"change":[173],"monitoring":[174],"continual":[176],"autosave.":[177],"CONCLUSIONS:":[178],"With":[179],"addition":[181],"these":[183],"features,":[185],"particular":[188],"Broker,":[192],"users":[194],"been":[196],"able":[197],"focus":[199],"more":[200],"effectively":[201],"on":[202],"annotation.":[204],"Phenoscape":[205],"using":[207],"reported":[210],"smoother":[212],"workflow,":[214],"much":[216],"reduced":[217],"interruptions":[218],"maintenance":[221],"management":[224],"issues.":[225]},"counts_by_year":[{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":1},{"year":2019,"cited_by_count":3},{"year":2018,"cited_by_count":4},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":5}],"updated_date":"2026-04-29T09:16:38.111599","created_date":"2025-10-10T00:00:00"}
