{"id":"https://openalex.org/W3049032230","doi":"https://doi.org/10.1093/bioinformatics/btab042","title":"HunFlair: an easy-to-use tool for state-of-the-art biomedical named entity recognition","display_name":"HunFlair: an easy-to-use tool for state-of-the-art biomedical named entity recognition","publication_year":2021,"publication_date":"2021-01-20","ids":{"openalex":"https://openalex.org/W3049032230","doi":"https://doi.org/10.1093/bioinformatics/btab042","mag":"3049032230","pmid":"https://pubmed.ncbi.nlm.nih.gov/33508086"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btab042","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab042","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/37/17/2792/40342596/btab042.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","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":"Bioinformatics","raw_type":"journal-article"},"type":"preprint","indexed_in":["arxiv","crossref","datacite","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/37/17/2792/40342596/btab042.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5041680406","display_name":"Leon Weber","orcid":"https://orcid.org/0000-0002-2499-472X"},"institutions":[{"id":"https://openalex.org/I205582932","display_name":"Max Delbr\u00fcck Center","ror":"https://ror.org/04p5ggc03","country_code":"DE","type":"facility","lineage":["https://openalex.org/I1305996414","https://openalex.org/I205582932"]},{"id":"https://openalex.org/I39343248","display_name":"Humboldt-Universit\u00e4t zu Berlin","ror":"https://ror.org/01hcx6992","country_code":"DE","type":"education","lineage":["https://openalex.org/I39343248"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Leon Weber","raw_affiliation_strings":["Computer Science Department, Humboldt-Universit\u00e4t zu Berlin , Berlin 10099, Germany","Group Mathematical Modelling of Cellular Processes, Max Delbr\u00fcck Center for Molecular Medicine in the Helmholtz Association , Berlin 13125, Germany","Computer Science Department, Humboldt-Universit\u00e4t zu Berlin, Berlin 10099, Germany","Group Mathematical Modelling of Cellular Processes, Max Delbr\u00fcck Center for Molecular Medicine in the Helmholtz Association, Berlin 13125, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computer Science Department, Humboldt-Universit\u00e4t zu Berlin , Berlin 10099, Germany","institution_ids":["https://openalex.org/I39343248"]},{"raw_affiliation_string":"Group Mathematical Modelling of Cellular Processes, Max Delbr\u00fcck Center for Molecular Medicine in the Helmholtz Association , Berlin 13125, Germany","institution_ids":["https://openalex.org/I205582932"]},{"raw_affiliation_string":"Computer Science Department, Humboldt-Universit\u00e4t zu Berlin, Berlin 10099, Germany","institution_ids":["https://openalex.org/I39343248"]},{"raw_affiliation_string":"Group Mathematical Modelling of Cellular Processes, Max Delbr\u00fcck Center for Molecular Medicine in the Helmholtz Association, Berlin 13125, Germany","institution_ids":["https://openalex.org/I205582932"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5017484078","display_name":"Mario S\u00e4nger","orcid":"https://orcid.org/0000-0002-2950-2587"},"institutions":[{"id":"https://openalex.org/I39343248","display_name":"Humboldt-Universit\u00e4t zu Berlin","ror":"https://ror.org/01hcx6992","country_code":"DE","type":"education","lineage":["https://openalex.org/I39343248"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Mario S\u00e4nger","raw_affiliation_strings":["Computer Science Department, Humboldt-Universit\u00e4t zu Berlin , Berlin 10099, Germany","Computer Science Department, Humboldt-Universit\u00e4t zu Berlin, Berlin, 10099, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computer Science Department, Humboldt-Universit\u00e4t zu Berlin , Berlin 10099, Germany","institution_ids":["https://openalex.org/I39343248"]},{"raw_affiliation_string":"Computer Science Department, Humboldt-Universit\u00e4t zu Berlin, Berlin, 10099, Germany","institution_ids":["https://openalex.org/I39343248"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5070254031","display_name":"Jannes M\u00fcnchmeyer","orcid":"https://orcid.org/0000-0002-4006-9673"},"institutions":[{"id":"https://openalex.org/I39343248","display_name":"Humboldt-Universit\u00e4t zu Berlin","ror":"https://ror.org/01hcx6992","country_code":"DE","type":"education","lineage":["https://openalex.org/I39343248"]},{"id":"https://openalex.org/I4210152878","display_name":"GFZ Helmholtz Centre for Geosciences","ror":"https://ror.org/04z8jg394","country_code":"DE","type":"facility","lineage":["https://openalex.org/I1305996414","https://openalex.org/I4210152878"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Jannes M\u00fcnchmeyer","raw_affiliation_strings":["Computer Science Department, Humboldt-Universit\u00e4t zu Berlin , Berlin 10099, Germany","Section Seismology, GFZ German Research Centre for Geosciences , Potsdam 14473, Germany","Computer Science Department, Humboldt-Universit\u00e4t zu Berlin, Berlin 10099, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computer Science Department, Humboldt-Universit\u00e4t zu Berlin , Berlin 10099, Germany","institution_ids":["https://openalex.org/I39343248"]},{"raw_affiliation_string":"Section Seismology, GFZ German Research Centre for Geosciences , Potsdam 14473, Germany","institution_ids":["https://openalex.org/I4210152878"]},{"raw_affiliation_string":"Computer Science Department, Humboldt-Universit\u00e4t zu Berlin, Berlin 10099, Germany","institution_ids":["https://openalex.org/I39343248"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5086385635","display_name":"Maryam Habibi","orcid":"https://orcid.org/0000-0002-3237-5080"},"institutions":[{"id":"https://openalex.org/I39343248","display_name":"Humboldt-Universit\u00e4t zu Berlin","ror":"https://ror.org/01hcx6992","country_code":"DE","type":"education","lineage":["https://openalex.org/I39343248"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Maryam Habibi","raw_affiliation_strings":["Computer Science Department, Humboldt-Universit\u00e4t zu Berlin , Berlin 10099, Germany","Computer Science Department, Humboldt-Universit\u00e4t zu Berlin, Berlin, 10099, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computer Science Department, Humboldt-Universit\u00e4t zu Berlin , Berlin 10099, Germany","institution_ids":["https://openalex.org/I39343248"]},{"raw_affiliation_string":"Computer Science Department, Humboldt-Universit\u00e4t zu Berlin, Berlin, 10099, Germany","institution_ids":["https://openalex.org/I39343248"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5055236937","display_name":"Ulf Leser","orcid":"https://orcid.org/0000-0003-2166-9582"},"institutions":[{"id":"https://openalex.org/I39343248","display_name":"Humboldt-Universit\u00e4t zu Berlin","ror":"https://ror.org/01hcx6992","country_code":"DE","type":"education","lineage":["https://openalex.org/I39343248"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Ulf Leser","raw_affiliation_strings":["Computer Science Department, Humboldt-Universit\u00e4t zu Berlin , Berlin 10099, Germany","Computer Science Department, Humboldt-Universit\u00e4t zu Berlin, Berlin, 10099, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computer Science Department, Humboldt-Universit\u00e4t zu Berlin , Berlin 10099, Germany","institution_ids":["https://openalex.org/I39343248"]},{"raw_affiliation_string":"Computer Science Department, Humboldt-Universit\u00e4t zu Berlin, Berlin, 10099, Germany","institution_ids":["https://openalex.org/I39343248"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5032877157","display_name":"Alan Akbik","orcid":null},"institutions":[{"id":"https://openalex.org/I39343248","display_name":"Humboldt-Universit\u00e4t zu Berlin","ror":"https://ror.org/01hcx6992","country_code":"DE","type":"education","lineage":["https://openalex.org/I39343248"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Alan Akbik","raw_affiliation_strings":["Computer Science Department, Humboldt-Universit\u00e4t zu Berlin , Berlin 10099, Germany","Computer Science Department, Humboldt-Universit\u00e4t zu Berlin, Berlin, 10099, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computer Science Department, Humboldt-Universit\u00e4t zu Berlin , Berlin 10099, Germany","institution_ids":["https://openalex.org/I39343248"]},{"raw_affiliation_string":"Computer Science Department, Humboldt-Universit\u00e4t zu Berlin, Berlin, 10099, Germany","institution_ids":["https://openalex.org/I39343248"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.3961,"has_fulltext":true,"cited_by_count":6,"citation_normalized_percentile":{"value":0.56562756,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"37","issue":"17","first_page":"2792","last_page":"2794"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.8547999858856201,"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":0.8547999858856201,"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/T10028","display_name":"Topic Modeling","score":0.11620000004768372,"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/T10181","display_name":"Natural Language Processing Techniques","score":0.003599999938160181,"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/named-entity-recognition","display_name":"Named-entity recognition","score":0.8784803152084351},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7941395044326782},{"id":"https://openalex.org/keywords/mit-license","display_name":"MIT License","score":0.6457111835479736},{"id":"https://openalex.org/keywords/natural-language-processing","display_name":"Natural language processing","score":0.5216060876846313},{"id":"https://openalex.org/keywords/code","display_name":"Code (set theory)","score":0.5153505206108093},{"id":"https://openalex.org/keywords/named-entity","display_name":"Named entity","score":0.5098940134048462},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4829965829849243},{"id":"https://openalex.org/keywords/state","display_name":"State (computer science)","score":0.45311036705970764},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.4318467080593109},{"id":"https://openalex.org/keywords/cover","display_name":"Cover (algebra)","score":0.4106597900390625},{"id":"https://openalex.org/keywords/license","display_name":"License","score":0.3947034776210785},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.23657891154289246},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.08590778708457947},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.07583823800086975},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.07028013467788696}],"concepts":[{"id":"https://openalex.org/C2779135771","wikidata":"https://www.wikidata.org/wiki/Q403574","display_name":"Named-entity recognition","level":3,"score":0.8784803152084351},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7941395044326782},{"id":"https://openalex.org/C174183944","wikidata":"https://www.wikidata.org/wiki/Q334661","display_name":"MIT License","level":3,"score":0.6457111835479736},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.5216060876846313},{"id":"https://openalex.org/C2776760102","wikidata":"https://www.wikidata.org/wiki/Q5139990","display_name":"Code (set theory)","level":3,"score":0.5153505206108093},{"id":"https://openalex.org/C2777889803","wikidata":"https://www.wikidata.org/wiki/Q25047676","display_name":"Named entity","level":2,"score":0.5098940134048462},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4829965829849243},{"id":"https://openalex.org/C48103436","wikidata":"https://www.wikidata.org/wiki/Q599031","display_name":"State (computer science)","level":2,"score":0.45311036705970764},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.4318467080593109},{"id":"https://openalex.org/C2780428219","wikidata":"https://www.wikidata.org/wiki/Q16952335","display_name":"Cover (algebra)","level":2,"score":0.4106597900390625},{"id":"https://openalex.org/C2780560020","wikidata":"https://www.wikidata.org/wiki/Q79719","display_name":"License","level":2,"score":0.3947034776210785},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.23657891154289246},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.08590778708457947},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.07583823800086975},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.07028013467788696},{"id":"https://openalex.org/C2780451532","wikidata":"https://www.wikidata.org/wiki/Q759676","display_name":"Task (project management)","level":2,"score":0.0},{"id":"https://openalex.org/C78519656","wikidata":"https://www.wikidata.org/wiki/Q101333","display_name":"Mechanical engineering","level":1,"score":0.0},{"id":"https://openalex.org/C201995342","wikidata":"https://www.wikidata.org/wiki/Q682496","display_name":"Systems engineering","level":1,"score":0.0}],"mesh":[],"locations_count":11,"locations":[{"id":"doi:10.1093/bioinformatics/btab042","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab042","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/37/17/2792/40342596/btab042.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","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":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:33508086","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/33508086","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:8428609","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8428609","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":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:edoc.mdc-berlin.de:19923","is_oa":false,"landing_page_url":null,"pdf_url":null,"source":{"id":"https://openalex.org/S4306400224","display_name":"MDC Repository (Max-Delbrueck-Center for Molecular Medicine)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I149899117","host_organization_name":"Max Planck Society","host_organization_lineage":["https://openalex.org/I149899117"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"","raw_type":"Article"},{"id":"pmh:oai:arXiv.org:2008.07347","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2008.07347","pdf_url":"https://arxiv.org/pdf/2008.07347","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"text"},{"id":"mag:3049032230","is_oa":true,"landing_page_url":"https://arxiv.org/pdf/2008.07347v2","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"arXiv (Cornell University)","raw_type":null},{"id":"pmh:oai:europepmc.org:7322597","is_oa":true,"landing_page_url":"http://europepmc.org/pmc/articles/PMC8428609","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":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":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Text"},{"id":"pmh:oai:gfzpublic.gfz-potsdam.de:item_5005588","is_oa":true,"landing_page_url":"https://gfzpublic.gfz-potsdam.de/pubman/item/item_5005588","pdf_url":null,"source":{"id":"https://openalex.org/S4306401313","display_name":"Publication Database GFZ (GFZ German Research Centre for Geosciences)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210152878","host_organization_name":"GFZ Helmholtz Centre for Geosciences","host_organization_lineage":["https://openalex.org/I4210152878"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:gfzpublic.gfz.de:item_5005588","is_oa":true,"landing_page_url":"https://gfzpublic.gfz.de/pubman/item/item_5005588","pdf_url":null,"source":{"id":"https://openalex.org/S4306401313","display_name":"Publication Database GFZ (GFZ German Research Centre for Geosciences)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210152878","host_organization_name":"GFZ Helmholtz Centre for Geosciences","host_organization_lineage":["https://openalex.org/I4210152878"],"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":"Bioinformatics","raw_type":"info:eu-repo/semantics/article"},{"id":"doi:10.48550/arxiv.2008.07347","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2008.07347","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"Preprint"},{"id":"doi:10.18452/33518","is_oa":true,"landing_page_url":"https://doi.org/10.18452/33518","pdf_url":null,"source":{"id":"https://openalex.org/S4306400923","display_name":"edoc Publication server (Humboldt University of Berlin)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I39343248","host_organization_name":"Humboldt-Universit\u00e4t zu Berlin","host_organization_lineage":["https://openalex.org/I39343248"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"article-journal"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btab042","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab042","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/37/17/2792/40342596/btab042.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","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":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3049032230.pdf","grobid_xml":"https://content.openalex.org/works/W3049032230.grobid-xml"},"referenced_works_count":33,"referenced_works":["https://openalex.org/W39864132","https://openalex.org/W77347155","https://openalex.org/W1830777114","https://openalex.org/W1850865022","https://openalex.org/W2005058680","https://openalex.org/W2040298461","https://openalex.org/W2071879021","https://openalex.org/W2097678794","https://openalex.org/W2100627415","https://openalex.org/W2124767801","https://openalex.org/W2142016317","https://openalex.org/W2143521828","https://openalex.org/W2149369282","https://openalex.org/W2151025545","https://openalex.org/W2162442688","https://openalex.org/W2169099542","https://openalex.org/W2169491861","https://openalex.org/W2169974160","https://openalex.org/W2229453122","https://openalex.org/W2346452181","https://openalex.org/W2775645290","https://openalex.org/W2807245502","https://openalex.org/W2890830728","https://openalex.org/W2911489562","https://openalex.org/W2954075147","https://openalex.org/W2970771982","https://openalex.org/W2970998014","https://openalex.org/W3104059174","https://openalex.org/W3105491236","https://openalex.org/W3106224367","https://openalex.org/W6636556141","https://openalex.org/W6640362995","https://openalex.org/W6723250868"],"related_works":["https://openalex.org/W3125468681","https://openalex.org/W2136038431","https://openalex.org/W2514317811","https://openalex.org/W1666916593","https://openalex.org/W2804913846","https://openalex.org/W2053299703","https://openalex.org/W3005759282","https://openalex.org/W1664780981","https://openalex.org/W3107803095","https://openalex.org/W2033999403","https://openalex.org/W3164761369","https://openalex.org/W5053386","https://openalex.org/W2129086443","https://openalex.org/W3100463027","https://openalex.org/W2342853654","https://openalex.org/W2886100554","https://openalex.org/W3198660441","https://openalex.org/W2078589894","https://openalex.org/W2115562276","https://openalex.org/W2995936835"],"abstract_inverted_index":{"SUMMARY:":[0],"Named":[1],"entity":[2,24,61],"recognition":[3],"(NER)":[4],"is":[5,49,76,148,158,186],"an":[6,113,182],"important":[7],"step":[8],"in":[9,34,78,124,136],"biomedical":[10,60,98,109,165],"information":[11],"extraction":[12],"pipelines.":[13],"Tools":[14],"for":[15],"NER":[16,43,110,166],"should":[17],"be":[18,26,30,141],"easy":[19],"to":[20,82],"use,":[21],"cover":[22],"multiple":[23],"types,":[25,62],"highly":[27],"accurate":[28],"and":[29,37,75,100,128,147,185],"robust":[31],"toward":[32],"variations":[33],"text":[35],"genre":[36],"style.":[38],"We":[39],"present":[40],"HunFlair,":[41],"a":[42,69,79,89,125,144],"tagger":[44],"fulfilling":[45],"these":[46],"requirements.":[47],"HunFlair":[48,139,171],"integrated":[50],"into":[51],"the":[52,120,176],"widely":[53],"used":[54],"NLP":[55,178],"framework":[56,179],"Flair,":[57],"recognizes":[58],"five":[59],"reaches":[63],"or":[64],"overcomes":[65],"state-of-the-art":[66,133],"performance":[67],"on":[68,94],"wide":[70],"set":[71],"of":[72,116,154,163],"evaluation":[73],"corpora,":[74],"trained":[77],"cross-corpus":[80,126],"setting":[81,127],"avoid":[83],"corpus-specific":[84],"bias.":[85],"Technically,":[86],"it":[87,157],"uses":[88],"character-level":[90],"language":[91],"model":[92],"pretrained":[93],"roughly":[95],"24":[96],"million":[97,102],"abstracts":[99],"three":[101],"full":[103],"texts.":[104],"It":[105],"outperforms":[106],"other":[107],"off-the-shelf":[108],"tools":[111],"with":[112,132,143,150,188],"average":[114],"gain":[115],"7.26":[117],"pp":[118],"over":[119],"next":[121],"best":[122],"tool":[123],"achieves":[129],"on-par":[130],"results":[131],"research":[134],"prototypes":[135],"in-corpus":[137],"experiments.":[138],"can":[140],"installed":[142],"single":[145],"command":[146],"applied":[149],"only":[151],"four":[152],"lines":[153],"code.":[155],"Furthermore,":[156],"accompanied":[159],"by":[160],"harmonized":[161],"versions":[162],"23":[164],"corpora.":[167],"AVAILABILITY":[168],"AND":[169],"IMPLEMENTATION:":[170],"ist":[172],"freely":[173],"available":[174,198],"through":[175],"Flair":[177],"(https://github.com/flairNLP/flair)":[180],"under":[181],"MIT":[183],"license":[184],"compatible":[187],"all":[189],"major":[190],"operating":[191],"systems.":[192],"SUPPLEMENTARY":[193],"INFORMATION:":[194],"Supplementary":[195],"data":[196],"are":[197],"at":[199],"Bioinformatics":[200],"online.":[201]},"counts_by_year":[{"year":2024,"cited_by_count":4},{"year":2023,"cited_by_count":1},{"year":2020,"cited_by_count":1}],"updated_date":"2026-07-03T08:13:44.112507","created_date":"2025-10-10T00:00:00"}
