{"id":"https://openalex.org/W2984274159","doi":"https://doi.org/10.18653/v1/d19-5728","title":"Neural Dependency Parsing of Biomedical Text: TurkuNLP entry in the CRAFT Structural Annotation Task","display_name":"Neural Dependency Parsing of Biomedical Text: TurkuNLP entry in the CRAFT Structural Annotation Task","publication_year":2019,"publication_date":"2019-01-01","ids":{"openalex":"https://openalex.org/W2984274159","doi":"https://doi.org/10.18653/v1/d19-5728","mag":"2984274159"},"language":"en","primary_location":{"id":"doi:10.18653/v1/d19-5728","is_oa":true,"landing_page_url":"https://doi.org/10.18653/v1/d19-5728","pdf_url":"https://www.aclweb.org/anthology/D19-5728.pdf","source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of The 5th Workshop on BioNLP Open Shared Tasks","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://www.aclweb.org/anthology/D19-5728.pdf","any_repository_has_fulltext":null},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5074738893","display_name":"Thang Minh Ngo","orcid":null},"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":"Thang Minh Ngo","raw_affiliation_strings":["Turku NLP Group, Department of Future Technologies, University of Turku, Finland"],"affiliations":[{"raw_affiliation_string":"Turku NLP Group, Department of Future Technologies, University of Turku, Finland","institution_ids":["https://openalex.org/I155660961"]}]},{"author_position":"middle","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":false,"raw_author_name":"Jenna Kanerva","raw_affiliation_strings":["Turku NLP Group, Department of Future Technologies, University of Turku, Finland"],"affiliations":[{"raw_affiliation_string":"Turku NLP Group, Department of Future Technologies, University of 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":["Turku NLP Group, Department of Future Technologies, University of Turku, Finland"],"affiliations":[{"raw_affiliation_string":"Turku NLP Group, Department of Future Technologies, University of 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":["Turku NLP Group, Department of Future Technologies, University of Turku, Finland"],"affiliations":[{"raw_affiliation_string":"Turku NLP Group, Department of Future Technologies, University of Turku, Finland","institution_ids":["https://openalex.org/I155660961"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5074738893"],"corresponding_institution_ids":["https://openalex.org/I155660961"],"apc_list":null,"apc_paid":null,"fwci":0.28,"has_fulltext":true,"cited_by_count":3,"citation_normalized_percentile":{"value":0.66561289,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":96},"biblio":{"volume":null,"issue":null,"first_page":"206","last_page":"215"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10028","display_name":"Topic Modeling","score":0.9991999864578247,"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/T10028","display_name":"Topic Modeling","score":0.9991999864578247,"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/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9991999864578247,"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/T10181","display_name":"Natural Language Processing Techniques","score":0.9975000023841858,"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":0.8895502090454102},{"id":"https://openalex.org/keywords/dependency-grammar","display_name":"Dependency grammar","score":0.8744984865188599},{"id":"https://openalex.org/keywords/parsing","display_name":"Parsing","score":0.8605944514274597},{"id":"https://openalex.org/keywords/task","display_name":"Task (project management)","score":0.768919825553894},{"id":"https://openalex.org/keywords/natural-language-processing","display_name":"Natural language processing","score":0.760985255241394},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.735225260257721},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.6977589726448059},{"id":"https://openalex.org/keywords/dependency","display_name":"Dependency (UML)","score":0.6658783555030823},{"id":"https://openalex.org/keywords/domain","display_name":"Domain (mathematical analysis)","score":0.5475713014602661},{"id":"https://openalex.org/keywords/word","display_name":"Word (group theory)","score":0.4215776324272156},{"id":"https://openalex.org/keywords/linguistics","display_name":"Linguistics","score":0.06172466278076172}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8895502090454102},{"id":"https://openalex.org/C164883195","wikidata":"https://www.wikidata.org/wiki/Q674834","display_name":"Dependency grammar","level":3,"score":0.8744984865188599},{"id":"https://openalex.org/C186644900","wikidata":"https://www.wikidata.org/wiki/Q194152","display_name":"Parsing","level":2,"score":0.8605944514274597},{"id":"https://openalex.org/C2780451532","wikidata":"https://www.wikidata.org/wiki/Q759676","display_name":"Task (project management)","level":2,"score":0.768919825553894},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.760985255241394},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.735225260257721},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.6977589726448059},{"id":"https://openalex.org/C19768560","wikidata":"https://www.wikidata.org/wiki/Q320727","display_name":"Dependency (UML)","level":2,"score":0.6658783555030823},{"id":"https://openalex.org/C36503486","wikidata":"https://www.wikidata.org/wiki/Q11235244","display_name":"Domain (mathematical analysis)","level":2,"score":0.5475713014602661},{"id":"https://openalex.org/C90805587","wikidata":"https://www.wikidata.org/wiki/Q10944557","display_name":"Word (group theory)","level":2,"score":0.4215776324272156},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"score":0.06172466278076172},{"id":"https://openalex.org/C187736073","wikidata":"https://www.wikidata.org/wiki/Q2920921","display_name":"Management","level":1,"score":0.0},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.0},{"id":"https://openalex.org/C162324750","wikidata":"https://www.wikidata.org/wiki/Q8134","display_name":"Economics","level":0,"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":1,"locations":[{"id":"doi:10.18653/v1/d19-5728","is_oa":true,"landing_page_url":"https://doi.org/10.18653/v1/d19-5728","pdf_url":"https://www.aclweb.org/anthology/D19-5728.pdf","source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of The 5th Workshop on BioNLP Open Shared Tasks","raw_type":"proceedings-article"}],"best_oa_location":{"id":"doi:10.18653/v1/d19-5728","is_oa":true,"landing_page_url":"https://doi.org/10.18653/v1/d19-5728","pdf_url":"https://www.aclweb.org/anthology/D19-5728.pdf","source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of The 5th Workshop on BioNLP Open Shared Tasks","raw_type":"proceedings-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"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/W2984274159.pdf","grobid_xml":"https://content.openalex.org/works/W2984274159.grobid-xml"},"referenced_works_count":34,"referenced_works":["https://openalex.org/W102233799","https://openalex.org/W1614298861","https://openalex.org/W1632114991","https://openalex.org/W1934889228","https://openalex.org/W2027979924","https://openalex.org/W2048679005","https://openalex.org/W2055032581","https://openalex.org/W2064299012","https://openalex.org/W2075655036","https://openalex.org/W2094061585","https://openalex.org/W2096489769","https://openalex.org/W2116159459","https://openalex.org/W2123442489","https://openalex.org/W2127147316","https://openalex.org/W2140526624","https://openalex.org/W2163568299","https://openalex.org/W2166111585","https://openalex.org/W2252979829","https://openalex.org/W2493916176","https://openalex.org/W2515248967","https://openalex.org/W2527896214","https://openalex.org/W2569308312","https://openalex.org/W2579343286","https://openalex.org/W2673116624","https://openalex.org/W2739827909","https://openalex.org/W2740840489","https://openalex.org/W2741029840","https://openalex.org/W2775952680","https://openalex.org/W2802199653","https://openalex.org/W2898796642","https://openalex.org/W2950577311","https://openalex.org/W2963626623","https://openalex.org/W2988304195","https://openalex.org/W3029683630"],"related_works":["https://openalex.org/W2251084681","https://openalex.org/W2098784136","https://openalex.org/W287510790","https://openalex.org/W3117798239","https://openalex.org/W4241489294","https://openalex.org/W2250721602","https://openalex.org/W2968543375","https://openalex.org/W4288558800","https://openalex.org/W2888625260","https://openalex.org/W2953770453"],"abstract_inverted_index":{"We":[0,85],"present":[1],"the":[2,6,10,26,37,40,50,53,65,77,93],"approach":[3,22],"taken":[4],"by":[5],"TurkuNLP":[7],"group":[8],"in":[9,39],"CRAFT":[11],"Structural":[12],"Annotation":[13],"task,":[14],"a":[15,30,60,87],"shared":[16],"task":[17,97],"on":[18,25,44],"dependency":[19,32],"parsing.":[20],"Our":[21],"builds":[23],"primarily":[24],"Turku":[27],"neural":[28],"parser,":[29],"native":[31],"parser":[33,51],"that":[34],"ranked":[35],"among":[36,96],"best":[38,94],"recent":[41],"CoNLL":[42],"tasks":[43],"parsing":[45],"Universal":[46],"Dependencies.":[47],"To":[48],"adapt":[49],"to":[52],"biomedical":[54],"domain,":[55],"we":[56],"considered":[57],"and":[58,76],"evaluated":[59],"number":[61],"of":[62,67,79,91],"approaches,":[63],"including":[64],"generation":[66],"custom":[68],"word":[69],"embeddings,":[70],"combination":[71],"with":[72],"other":[73],"in-domain":[74],"resources,":[75],"incorporation":[78],"information":[80],"from":[81],"named":[82],"entity":[83],"recognition.":[84],"achieved":[86],"labeled":[88],"attachment":[89],"score":[90],"89.7%,":[92],"result":[95],"participants.":[98]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2020,"cited_by_count":2}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
