{"id":"https://openalex.org/W3114761096","doi":"https://doi.org/10.1186/s12859-020-03905-8","title":"Dependency parsing of biomedical text with BERT","display_name":"Dependency parsing of biomedical text with BERT","publication_year":2020,"publication_date":"2020-12-01","ids":{"openalex":"https://openalex.org/W3114761096","doi":"https://doi.org/10.1186/s12859-020-03905-8","mag":"3114761096","pmid":"https://pubmed.ncbi.nlm.nih.gov/33372589"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-020-03905-8","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-020-03905-8","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-020-03905-8","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"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":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-020-03905-8","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5048932608","display_name":"Jenna Kanerva","orcid":"https://orcid.org/0000-0003-4580-5366"},"institutions":[{"id":"https://openalex.org/I155660961","display_name":"University of Turku","ror":"https://ror.org/05vghhr25","country_code":"FI","type":"education","lineage":["https://openalex.org/I155660961"]}],"countries":["FI"],"is_corresponding":true,"raw_author_name":"Jenna Kanerva","raw_affiliation_strings":["TurkuNLP Group, University of Turku, Turku, Finland. jmnybl@utu.fi","TurkuNLP Group, University of Turku, Turku, Finland"],"raw_orcid":"https://orcid.org/0000-0003-4580-5366","affiliations":[{"raw_affiliation_string":"TurkuNLP Group, University of Turku, Turku, Finland. jmnybl@utu.fi","institution_ids":["https://openalex.org/I155660961"]},{"raw_affiliation_string":"TurkuNLP Group, University of Turku, Turku, Finland","institution_ids":["https://openalex.org/I155660961"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5019929457","display_name":"Filip Ginter","orcid":"https://orcid.org/0000-0002-5484-6103"},"institutions":[{"id":"https://openalex.org/I155660961","display_name":"University of Turku","ror":"https://ror.org/05vghhr25","country_code":"FI","type":"education","lineage":["https://openalex.org/I155660961"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"Filip Ginter","raw_affiliation_strings":["TurkuNLP Group, University of Turku, Turku, Finland"],"raw_orcid":"https://orcid.org/0000-0002-5484-6103","affiliations":[{"raw_affiliation_string":"TurkuNLP Group, University of Turku, Turku, Finland","institution_ids":["https://openalex.org/I155660961"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5066925770","display_name":"Sampo Pyysalo","orcid":"https://orcid.org/0000-0002-6279-5000"},"institutions":[{"id":"https://openalex.org/I155660961","display_name":"University of Turku","ror":"https://ror.org/05vghhr25","country_code":"FI","type":"education","lineage":["https://openalex.org/I155660961"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"Sampo Pyysalo","raw_affiliation_strings":["TurkuNLP Group, University of Turku, Turku, Finland"],"raw_orcid":"https://orcid.org/0000-0002-6279-5000","affiliations":[{"raw_affiliation_string":"TurkuNLP Group, University of Turku, Turku, Finland","institution_ids":["https://openalex.org/I155660961"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5048932608"],"corresponding_institution_ids":["https://openalex.org/I155660961"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":1.0741,"has_fulltext":true,"cited_by_count":10,"citation_normalized_percentile":{"value":0.8321351,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"21","issue":"S23","first_page":"580","last_page":"580"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10181","display_name":"Natural Language Processing Techniques","score":0.2651999890804291,"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"}},"topics":[{"id":"https://openalex.org/T10181","display_name":"Natural Language Processing Techniques","score":0.2651999890804291,"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":0.1624000072479248,"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/T13702","display_name":"Machine Learning in Healthcare","score":0.1412000060081482,"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/parsing","display_name":"Parsing","score":0.8908414840698242},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.862946629524231},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.756033182144165},{"id":"https://openalex.org/keywords/natural-language-processing","display_name":"Natural language processing","score":0.7244276404380798},{"id":"https://openalex.org/keywords/initialization","display_name":"Initialization","score":0.6325466632843018},{"id":"https://openalex.org/keywords/dependency-grammar","display_name":"Dependency grammar","score":0.6265201568603516},{"id":"https://openalex.org/keywords/task","display_name":"Task (project management)","score":0.5258815288543701},{"id":"https://openalex.org/keywords/bottom-up-parsing","display_name":"Bottom-up parsing","score":0.4499991834163666},{"id":"https://openalex.org/keywords/parser-combinator","display_name":"Parser combinator","score":0.4225311577320099},{"id":"https://openalex.org/keywords/top-down-parsing","display_name":"Top-down parsing","score":0.3284263610839844},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.208857923746109}],"concepts":[{"id":"https://openalex.org/C186644900","wikidata":"https://www.wikidata.org/wiki/Q194152","display_name":"Parsing","level":2,"score":0.8908414840698242},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.862946629524231},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.756033182144165},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.7244276404380798},{"id":"https://openalex.org/C114466953","wikidata":"https://www.wikidata.org/wiki/Q6034165","display_name":"Initialization","level":2,"score":0.6325466632843018},{"id":"https://openalex.org/C164883195","wikidata":"https://www.wikidata.org/wiki/Q674834","display_name":"Dependency grammar","level":3,"score":0.6265201568603516},{"id":"https://openalex.org/C2780451532","wikidata":"https://www.wikidata.org/wiki/Q759676","display_name":"Task (project management)","level":2,"score":0.5258815288543701},{"id":"https://openalex.org/C60690694","wikidata":"https://www.wikidata.org/wiki/Q894902","display_name":"Bottom-up parsing","level":4,"score":0.4499991834163666},{"id":"https://openalex.org/C118364021","wikidata":"https://www.wikidata.org/wiki/Q7139956","display_name":"Parser combinator","level":3,"score":0.4225311577320099},{"id":"https://openalex.org/C42560504","wikidata":"https://www.wikidata.org/wiki/Q15419395","display_name":"Top-down parsing","level":3,"score":0.3284263610839844},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.208857923746109},{"id":"https://openalex.org/C162324750","wikidata":"https://www.wikidata.org/wiki/Q8134","display_name":"Economics","level":0,"score":0.0},{"id":"https://openalex.org/C187736073","wikidata":"https://www.wikidata.org/wiki/Q2920921","display_name":"Management","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007802","descriptor_name":"Language","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007802","descriptor_name":"Language","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007802","descriptor_name":"Language","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009323","descriptor_name":"Natural Language Processing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009323","descriptor_name":"Natural Language Processing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009323","descriptor_name":"Natural Language Processing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D035843","descriptor_name":"Biomedical Research","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D035843","descriptor_name":"Biomedical Research","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D035843","descriptor_name":"Biomedical Research","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":5,"locations":[{"id":"doi:10.1186/s12859-020-03905-8","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-020-03905-8","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-020-03905-8","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"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":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:33372589","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/33372589","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:doaj.org/article:980e92cad093490ab14fb2d2b804c910","is_oa":true,"landing_page_url":"https://doaj.org/article/980e92cad093490ab14fb2d2b804c910","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 21, Iss S23, Pp 1-12 (2020)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:7771067","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7771067","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":"BMC Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:www.utupub.fi:10024/153256","is_oa":false,"landing_page_url":"https://www.utupub.fi/handle/10024/153256","pdf_url":null,"source":{"id":"https://openalex.org/S4306402470","display_name":"UTUPub (University of Turku)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I155660961","host_organization_name":"University of Turku","host_organization_lineage":["https://openalex.org/I155660961"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":""}],"best_oa_location":{"id":"doi:10.1186/s12859-020-03905-8","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-020-03905-8","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-020-03905-8","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"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":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Quality Education","score":0.8500000238418579,"id":"https://metadata.un.org/sdg/4"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320321108","display_name":"Academy of Finland","ror":"https://ror.org/05k73zm37"},{"id":"https://openalex.org/F4320322725","display_name":"China Scholarship Council","ror":"https://ror.org/04atp4p48"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3114761096.pdf","grobid_xml":"https://content.openalex.org/works/W3114761096.grobid-xml"},"referenced_works_count":56,"referenced_works":["https://openalex.org/W95553785","https://openalex.org/W1535015163","https://openalex.org/W1566289585","https://openalex.org/W1741471566","https://openalex.org/W1877040722","https://openalex.org/W1962622193","https://openalex.org/W2015238682","https://openalex.org/W2040298461","https://openalex.org/W2055032581","https://openalex.org/W2094061585","https://openalex.org/W2097606805","https://openalex.org/W2103320915","https://openalex.org/W2114887620","https://openalex.org/W2116410915","https://openalex.org/W2124861326","https://openalex.org/W2125712079","https://openalex.org/W2134036914","https://openalex.org/W2138627627","https://openalex.org/W2189472871","https://openalex.org/W2229162816","https://openalex.org/W2250539671","https://openalex.org/W2250861254","https://openalex.org/W2511500211","https://openalex.org/W2515248967","https://openalex.org/W2527896214","https://openalex.org/W2552110825","https://openalex.org/W2579343286","https://openalex.org/W2739827909","https://openalex.org/W2740840489","https://openalex.org/W2741029840","https://openalex.org/W2752392399","https://openalex.org/W2833383446","https://openalex.org/W2898796642","https://openalex.org/W2911489562","https://openalex.org/W2923014074","https://openalex.org/W2934757881","https://openalex.org/W2950577311","https://openalex.org/W2951675429","https://openalex.org/W2962739339","https://openalex.org/W2963026768","https://openalex.org/W2963341956","https://openalex.org/W2963572611","https://openalex.org/W2970771982","https://openalex.org/W2984274159","https://openalex.org/W2985913541","https://openalex.org/W2996428491","https://openalex.org/W3018647120","https://openalex.org/W3029683630","https://openalex.org/W3037482111","https://openalex.org/W3037988398","https://openalex.org/W3148040514","https://openalex.org/W4210956481","https://openalex.org/W4232564286","https://openalex.org/W6600424091","https://openalex.org/W6691431627","https://openalex.org/W7081587516"],"related_works":["https://openalex.org/W3088470625","https://openalex.org/W3035970863","https://openalex.org/W2389755172","https://openalex.org/W2250574586","https://openalex.org/W2058621701","https://openalex.org/W2152451097","https://openalex.org/W1500431650","https://openalex.org/W2914096745","https://openalex.org/W4212887236","https://openalex.org/W2047121637"],"abstract_inverted_index":{"BACKGROUND:":[0],":":[1,74,150],"Syntactic":[2],"analysis,":[3],"or":[4],"parsing,":[5,57],"is":[6,159,197],"a":[7,15,39,134,188],"key":[8,198],"task":[9,94,98,107],"in":[10,55,176],"natural":[11],"language":[12],"processing":[13],"and":[14,104,118],"required":[16],"component":[17],"for":[18,35,145],"many":[19],"text":[20,87,147],"mining":[21],"approaches.":[22],"In":[23],"recent":[24,42,105],"years,":[25],"Universal":[26],"Dependencies":[27],"(UD)":[28],"has":[29,59],"emerged":[30],"as":[31,71],"the":[32,50,53,77,89,101,113,123,128,172,177,201,204],"leading":[33],"formalism":[34],"dependency":[36,82],"parsing.":[37],"While":[38],"number":[40],"of":[41,52,64,79,130,137,161,166,203],"tasks":[43],"centering":[44],"on":[45,171,194],"UD":[46,102,106],"have":[47],"substantially":[48,169],"advanced":[49],"state":[51],"art":[54],"multilingual":[56],"there":[58],"been":[60],"only":[61],"little":[62],"study":[63],"parsing":[65,83,157,205],"texts":[66,196],"from":[67],"specialized":[68],"domains":[69],"such":[70],"biomedicine.":[72],"METHODS:":[73],"We":[75,125,151,182],"explore":[76],"application":[78],"state-of-the-art":[80],"neural":[81,120,156],"methods":[84],"to":[85,111,122,199],"biomedical":[86,146,167],"using":[88,133,187],"recently":[90,154],"introduced":[91,155],"CRAFT-SA":[92,97,179],"shared":[93,180],"dataset.":[95],"The":[96],"broadly":[99],"follows":[100],"representation":[103],"conventions,":[108],"allowing":[109],"us":[110],"fine-tune":[112],"UD-compatible":[114],"Turku":[115],"Neural":[116],"Parser":[117],"UDify":[119],"parsers":[121],"task.":[124,181],"further":[126],"evaluate":[127],"effect":[129],"transfer":[131,190],"learning":[132,191],"broad":[135],"selection":[136],"BERT":[138],"models,":[139],"including":[140],"several":[141],"models":[142],"pre-trained":[143,193],"specifically":[144],"processing.":[148],"RESULTS:":[149],"find":[152,184],"that":[153,185],"technology":[158],"capable":[160],"generating":[162],"highly":[163],"accurate":[164],"analyses":[165],"text,":[168],"improving":[170],"best":[173],"performance":[174,202],"reported":[175],"original":[178],"also":[183],"initialization":[186],"deep":[189],"model":[192],"in-domain":[195],"maximizing":[200],"methods.":[206]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":5}],"updated_date":"2026-07-15T18:14:33.161393","created_date":"2025-10-10T00:00:00"}