{"id":"https://openalex.org/W2786912752","doi":"https://doi.org/10.1093/database/bax087","title":"Gold-standard ontology-based anatomical annotation in the CRAFT Corpus","display_name":"Gold-standard ontology-based anatomical annotation in the CRAFT Corpus","publication_year":2017,"publication_date":"2017-01-01","ids":{"openalex":"https://openalex.org/W2786912752","doi":"https://doi.org/10.1093/database/bax087","mag":"2786912752","pmid":"https://pubmed.ncbi.nlm.nih.gov/31725864"},"language":"en","primary_location":{"id":"doi:10.1093/database/bax087","is_oa":true,"landing_page_url":"https://doi.org/10.1093/database/bax087","pdf_url":"https://academic.oup.com/database/article-pdf/doi/10.1093/database/bax087/23119571/bax087.pdf","source":{"id":"https://openalex.org/S4210201630","display_name":"Database","issn_l":"1758-0463","issn":["1758-0463"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311647","host_organization_name":"University of Oxford","host_organization_lineage":["https://openalex.org/P4310311647"],"host_organization_lineage_names":["University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Database","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/database/article-pdf/doi/10.1093/database/bax087/23119571/bax087.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5083125835","display_name":"Michael Bada","orcid":"https://orcid.org/0000-0003-3366-4738"},"institutions":[{"id":"https://openalex.org/I51713134","display_name":"University of Colorado Anschutz Medical Campus","ror":"https://ror.org/03wmf1y16","country_code":"US","type":"education","lineage":["https://openalex.org/I51713134"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Michael Bada","raw_affiliation_strings":["School of Medicine, Department of Pharmacology, University of Colorado Anschutz Medical Campus, 12801 E. 17th Ave., P.O. Box 6511, MS 8303, Aurora, CO 80045-0511, USA"],"affiliations":[{"raw_affiliation_string":"School of Medicine, Department of Pharmacology, University of Colorado Anschutz Medical Campus, 12801 E. 17th Ave., P.O. Box 6511, MS 8303, Aurora, CO 80045-0511, USA","institution_ids":["https://openalex.org/I51713134"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5041814853","display_name":"Nicole Vasilevsky","orcid":"https://orcid.org/0000-0001-5208-3432"},"institutions":[{"id":"https://openalex.org/I165690674","display_name":"Oregon Health & Science University","ror":"https://ror.org/009avj582","country_code":"US","type":"education","lineage":["https://openalex.org/I165690674"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Nicole Vasilevsky","raw_affiliation_strings":["Ontology Development Group, Library, Oregon Health & Science University, 318 SW Sam Jackson, Park Road, Portland, OR 97239, USA"],"affiliations":[{"raw_affiliation_string":"Ontology Development Group, Library, Oregon Health & Science University, 318 SW Sam Jackson, Park Road, Portland, OR 97239, USA","institution_ids":["https://openalex.org/I165690674"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5030261399","display_name":"William A. Baumgartner","orcid":"https://orcid.org/0000-0001-6717-5313"},"institutions":[{"id":"https://openalex.org/I51713134","display_name":"University of Colorado Anschutz Medical Campus","ror":"https://ror.org/03wmf1y16","country_code":"US","type":"education","lineage":["https://openalex.org/I51713134"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"William A Baumgartner","raw_affiliation_strings":["School of Medicine, Department of Pharmacology, University of Colorado Anschutz Medical Campus, 12801 E. 17th Ave., P.O. Box 6511, MS 8303, Aurora, CO 80045-0511, USA"],"affiliations":[{"raw_affiliation_string":"School of Medicine, Department of Pharmacology, University of Colorado Anschutz Medical Campus, 12801 E. 17th Ave., P.O. Box 6511, MS 8303, Aurora, CO 80045-0511, USA","institution_ids":["https://openalex.org/I51713134"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5064320417","display_name":"Melissa Haendel","orcid":"https://orcid.org/0000-0001-9114-8737"},"institutions":[{"id":"https://openalex.org/I165690674","display_name":"Oregon Health & Science University","ror":"https://ror.org/009avj582","country_code":"US","type":"education","lineage":["https://openalex.org/I165690674"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Melissa Haendel","raw_affiliation_strings":["Ontology Development Group, Library, Oregon Health & Science University, 318 SW Sam Jackson, Park Road, Portland, OR 97239, USA"],"affiliations":[{"raw_affiliation_string":"Ontology Development Group, Library, Oregon Health & Science University, 318 SW Sam Jackson, Park Road, Portland, OR 97239, USA","institution_ids":["https://openalex.org/I165690674"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5041860080","display_name":"Lawrence Hunter","orcid":"https://orcid.org/0000-0003-1455-3370"},"institutions":[{"id":"https://openalex.org/I51713134","display_name":"University of Colorado Anschutz Medical Campus","ror":"https://ror.org/03wmf1y16","country_code":"US","type":"education","lineage":["https://openalex.org/I51713134"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Lawrence E Hunter","raw_affiliation_strings":["School of Medicine, Department of Pharmacology, University of Colorado Anschutz Medical Campus, 12801 E. 17th Ave., P.O. Box 6511, MS 8303, Aurora, CO 80045-0511, USA"],"affiliations":[{"raw_affiliation_string":"School of Medicine, Department of Pharmacology, University of Colorado Anschutz Medical Campus, 12801 E. 17th Ave., P.O. Box 6511, MS 8303, Aurora, CO 80045-0511, USA","institution_ids":["https://openalex.org/I51713134"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5083125835"],"corresponding_institution_ids":["https://openalex.org/I51713134"],"apc_list":{"value":1415,"currency":"GBP","value_usd":1735},"apc_paid":{"value":1415,"currency":"GBP","value_usd":1735},"fwci":0.319,"has_fulltext":false,"cited_by_count":5,"citation_normalized_percentile":{"value":0.59506557,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"2017","issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9998000264167786,"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":0.9998000264167786,"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":0.967199981212616,"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/T10028","display_name":"Topic Modeling","score":0.954200029373169,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.8241087198257446},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.7535364627838135},{"id":"https://openalex.org/keywords/markup-language","display_name":"Markup language","score":0.6464248895645142},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.5254791378974915},{"id":"https://openalex.org/keywords/natural-language-processing","display_name":"Natural language processing","score":0.49650412797927856},{"id":"https://openalex.org/keywords/consistency","display_name":"Consistency (knowledge bases)","score":0.49122709035873413},{"id":"https://openalex.org/keywords/terminology","display_name":"Terminology","score":0.47223496437072754},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.43368443846702576},{"id":"https://openalex.org/keywords/ontology","display_name":"Ontology","score":0.4220591187477112},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.40772441029548645},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.39068537950515747},{"id":"https://openalex.org/keywords/xml","display_name":"XML","score":0.17645475268363953},{"id":"https://openalex.org/keywords/linguistics","display_name":"Linguistics","score":0.12036082148551941}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8241087198257446},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.7535364627838135},{"id":"https://openalex.org/C45874996","wikidata":"https://www.wikidata.org/wiki/Q37045","display_name":"Markup language","level":3,"score":0.6464248895645142},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.5254791378974915},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.49650412797927856},{"id":"https://openalex.org/C2776436953","wikidata":"https://www.wikidata.org/wiki/Q5163215","display_name":"Consistency (knowledge bases)","level":2,"score":0.49122709035873413},{"id":"https://openalex.org/C547195049","wikidata":"https://www.wikidata.org/wiki/Q1725664","display_name":"Terminology","level":2,"score":0.47223496437072754},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.43368443846702576},{"id":"https://openalex.org/C25810664","wikidata":"https://www.wikidata.org/wiki/Q44325","display_name":"Ontology","level":2,"score":0.4220591187477112},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.40772441029548645},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.39068537950515747},{"id":"https://openalex.org/C8797682","wikidata":"https://www.wikidata.org/wiki/Q2115","display_name":"XML","level":2,"score":0.17645475268363953},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"score":0.12036082148551941},{"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/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":3,"locations":[{"id":"doi:10.1093/database/bax087","is_oa":true,"landing_page_url":"https://doi.org/10.1093/database/bax087","pdf_url":"https://academic.oup.com/database/article-pdf/doi/10.1093/database/bax087/23119571/bax087.pdf","source":{"id":"https://openalex.org/S4210201630","display_name":"Database","issn_l":"1758-0463","issn":["1758-0463"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311647","host_organization_name":"University of Oxford","host_organization_lineage":["https://openalex.org/P4310311647"],"host_organization_lineage_names":["University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Database","raw_type":"journal-article"},{"id":"pmid:31725864","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31725864","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":"Database : the journal of biological databases and curation","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:7243923","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7243923","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Database (Oxford)","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/database/bax087","is_oa":true,"landing_page_url":"https://doi.org/10.1093/database/bax087","pdf_url":"https://academic.oup.com/database/article-pdf/doi/10.1093/database/bax087/23119571/bax087.pdf","source":{"id":"https://openalex.org/S4210201630","display_name":"Database","issn_l":"1758-0463","issn":["1758-0463"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311647","host_organization_name":"University of Oxford","host_organization_lineage":["https://openalex.org/P4310311647"],"host_organization_lineage_names":["University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Database","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.49000000953674316,"display_name":"Responsible consumption and production","id":"https://metadata.un.org/sdg/12"}],"awards":[{"id":"https://openalex.org/G6503315187","display_name":null,"funder_award_id":"5R01LM009254","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G7902908084","display_name":null,"funder_award_id":"5R01LM00811","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G8128167343","display_name":null,"funder_award_id":"DARPA-BAA-14-14","funder_id":"https://openalex.org/F4320332180","funder_display_name":"Defense Advanced Research Projects Agency"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320332180","display_name":"Defense Advanced Research Projects Agency","ror":"https://ror.org/02caytj08"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2786912752.pdf","grobid_xml":"https://content.openalex.org/works/W2786912752.grobid-xml"},"referenced_works_count":74,"referenced_works":["https://openalex.org/W70893897","https://openalex.org/W79139011","https://openalex.org/W90362830","https://openalex.org/W580573057","https://openalex.org/W819451571","https://openalex.org/W1118136420","https://openalex.org/W1410632286","https://openalex.org/W1473718842","https://openalex.org/W1505011908","https://openalex.org/W1561977250","https://openalex.org/W1679133234","https://openalex.org/W1757909678","https://openalex.org/W1786456657","https://openalex.org/W1859283887","https://openalex.org/W1878217576","https://openalex.org/W1958077162","https://openalex.org/W1972978393","https://openalex.org/W1974896839","https://openalex.org/W1981492645","https://openalex.org/W1984067176","https://openalex.org/W1992593537","https://openalex.org/W1995082001","https://openalex.org/W2033237963","https://openalex.org/W2033582794","https://openalex.org/W2040298461","https://openalex.org/W2055032581","https://openalex.org/W2058490165","https://openalex.org/W2072725120","https://openalex.org/W2073650115","https://openalex.org/W2077797310","https://openalex.org/W2094726706","https://openalex.org/W2096777607","https://openalex.org/W2098722636","https://openalex.org/W2103017472","https://openalex.org/W2113142309","https://openalex.org/W2116034137","https://openalex.org/W2117752917","https://openalex.org/W2120754707","https://openalex.org/W2128535227","https://openalex.org/W2134498732","https://openalex.org/W2134967412","https://openalex.org/W2143185181","https://openalex.org/W2147154106","https://openalex.org/W2148014577","https://openalex.org/W2149852578","https://openalex.org/W2150838562","https://openalex.org/W2159709123","https://openalex.org/W2160259754","https://openalex.org/W2161853863","https://openalex.org/W2162385209","https://openalex.org/W2163107094","https://openalex.org/W2163685645","https://openalex.org/W2199670077","https://openalex.org/W2236252949","https://openalex.org/W2239231358","https://openalex.org/W2412320574","https://openalex.org/W2415021352","https://openalex.org/W2490083709","https://openalex.org/W2499659094","https://openalex.org/W2517579954","https://openalex.org/W2557110550","https://openalex.org/W2558643140","https://openalex.org/W2588331448","https://openalex.org/W2604748391","https://openalex.org/W2977393556","https://openalex.org/W4233863423","https://openalex.org/W6603694148","https://openalex.org/W6623146473","https://openalex.org/W6628421016","https://openalex.org/W6638185459","https://openalex.org/W6639190232","https://openalex.org/W6683586573","https://openalex.org/W6687463490","https://openalex.org/W6733396110"],"related_works":["https://openalex.org/W2350593162","https://openalex.org/W2390350206","https://openalex.org/W1969477129","https://openalex.org/W2921208823","https://openalex.org/W2353483812","https://openalex.org/W2131808775","https://openalex.org/W2130038259","https://openalex.org/W2360756181","https://openalex.org/W2374093222","https://openalex.org/W4289346578"],"abstract_inverted_index":{"Gold-standard":[0],"annotated":[1],"corpora":[2],"have":[3,108],"become":[4],"important":[5],"resources":[6],"for":[7,164,236],"the":[8,38,43,110,167,172,183,195,237],"training":[9],"and":[10,21,30,64,70,96,98,130,151,181,222],"testing":[11],"of":[12,41,52,86,92,117,133,142,148,158,166,177,190,197,209,240],"natural-language-processing":[13],"(NLP)":[14],"systems":[15,87],"designed":[16],"to":[17,26,83,203,220,231],"support":[18],"biocuration":[19],"efforts,":[20],"ontologies":[22],"are":[23],"increasingly":[24],"used":[25,79],"facilitate":[27],"curational":[28],"consistency":[29],"semantic":[31,65,97,120],"integration":[32],"across":[33,136],"disparate":[34],"resources.":[35],"Bringing":[36],"together":[37],"respective":[39],"power":[40],"these,":[42],"Colorado":[44],"Richly":[45],"Annotated":[46],"Full-Text":[47],"(CRAFT)":[48],"Corpus,":[49],"a":[50,90,114,206,233,247,257],"collection":[51,176],"full-length,":[53],"open-access":[54],"biomedical":[55,191,244],"journal":[56],"articles":[57],"with":[58,113,205,256],"extensive":[59],"manually":[60,118],"created":[61,69,119,156],"syntactic,":[62],"formatting":[63],"markup,":[66],"was":[67],"previously":[68],"released.":[71],"This":[72,154],"initial":[73],"public":[74],"release":[75],"has":[76,161],"already":[77],"been":[78,162],"in":[80,146,215,243],"multiple":[81],"projects":[82],"drive":[84],"development":[85],"focused":[88],"on":[89,103,123,194],"variety":[91],"biocuration,":[93],"search,":[94],"visualization,":[95],"syntactic":[99],"NLP":[100],"tasks.":[101],"Building":[102],"its":[104],"demonstrated":[105],"utility,":[106],"we":[107,228],"expanded":[109],"CRAFT":[111],"Corpus":[112],"large":[115],"set":[116,157],"annotations":[121],"relying":[122,193],"Uberon,":[124],"an":[125,198],"ontology":[126],"representing":[127],"anatomical":[128,179,199,211,241],"entities":[129],"life-cycle":[131,149],"stages":[132],"multicellular":[134,143],"organisms":[135,144],"species":[137],"as":[138,140,201,213],"well":[139],"types":[141],"defined":[145],"terms":[147],"stage":[150],"sexual":[152],"characteristics.":[153],"newly":[155,225],"annotations,":[159],"which":[160],"added":[163],"v2.1":[165],"corpus,":[168,254],"is":[169,182],"by":[170],"far":[171],"largest":[173],"publicly":[174],"available":[175,226],"gold-standard":[178],"markup":[180,189],"first":[184],"large-scale":[185],"effort":[186],"at":[187],"manual":[188],"text":[192,245],"entirety":[196],"terminology,":[200],"opposed":[202],"annotation":[204,239],"small":[207],"number":[208],"high-level":[210],"categories,":[212],"performed":[214],"previous":[216],"corpora.":[217],"In":[218],"addition":[219],"presenting":[221],"discussing":[223],"this":[224],"resource,":[227],"apply":[229],"it":[230],"provide":[232],"performance":[234],"baseline":[235],"automatic":[238],"concepts":[242],"using":[246],"prominent":[248],"concept":[249],"recognition":[250],"system.":[251],"The":[252],"full":[253],"released":[255],"CC":[258],"BY":[259],"3.0":[260],"license,":[261],"may":[262],"be":[263],"downloaded":[264],"from":[265],"http://bionlp-corpora.sourceforge.net/CRAFT/index.shtml.":[266,269],"Database":[267],"URL:":[268]},"counts_by_year":[{"year":2023,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2019,"cited_by_count":3}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
