{"id":"https://openalex.org/W2779457220","doi":"https://doi.org/10.1093/bioinformatics/btx815","title":"GRAM-CNN: a deep learning approach with local context for named entity recognition in biomedical text","display_name":"GRAM-CNN: a deep learning approach with local context for named entity recognition in biomedical text","publication_year":2017,"publication_date":"2017-12-19","ids":{"openalex":"https://openalex.org/W2779457220","doi":"https://doi.org/10.1093/bioinformatics/btx815","mag":"2779457220","pmid":"https://pubmed.ncbi.nlm.nih.gov/29272325"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btx815","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btx815","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/34/9/1547/25120965/btx815.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":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/34/9/1547/25120965/btx815.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5079869432","display_name":"Qile Zhu","orcid":"https://orcid.org/0000-0002-8703-7425"},"institutions":[{"id":"https://openalex.org/I1311060795","display_name":"U.S. National Science Foundation","ror":"https://ror.org/021nxhr62","country_code":"US","type":"government","lineage":["https://openalex.org/I1311060795"]},{"id":"https://openalex.org/I2802640032","display_name":"Foundation Center","ror":"https://ror.org/0377f6951","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I2802640032"]},{"id":"https://openalex.org/I33213144","display_name":"University of Florida","ror":"https://ror.org/02y3ad647","country_code":"US","type":"education","lineage":["https://openalex.org/I33213144"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Qile Zhu","raw_affiliation_strings":["Department of Computer & Information Science & Engineering, University of Florida, Gainesville, FL, USA","National Science Foundation Center for Big Learning, University of Florida, Gainesville, FL, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer & Information Science & Engineering, University of Florida, Gainesville, FL, USA","institution_ids":["https://openalex.org/I33213144"]},{"raw_affiliation_string":"National Science Foundation Center for Big Learning, University of Florida, Gainesville, FL, USA","institution_ids":["https://openalex.org/I1311060795","https://openalex.org/I2802640032","https://openalex.org/I33213144"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100353846","display_name":"Xiaolin Li","orcid":"https://orcid.org/0000-0002-3368-159X"},"institutions":[{"id":"https://openalex.org/I1311060795","display_name":"U.S. National Science Foundation","ror":"https://ror.org/021nxhr62","country_code":"US","type":"government","lineage":["https://openalex.org/I1311060795"]},{"id":"https://openalex.org/I2802640032","display_name":"Foundation Center","ror":"https://ror.org/0377f6951","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I2802640032"]},{"id":"https://openalex.org/I33213144","display_name":"University of Florida","ror":"https://ror.org/02y3ad647","country_code":"US","type":"education","lineage":["https://openalex.org/I33213144"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Xiaolin Li","raw_affiliation_strings":["Department of Electrical and Computer Engineering, University of Florida, Gainesville, FL, USA","National Science Foundation Center for Big Learning, University of Florida, Gainesville, FL, USA"],"affiliations":[{"raw_affiliation_string":"Department of Electrical and Computer Engineering, University of Florida, Gainesville, FL, USA","institution_ids":["https://openalex.org/I33213144"]},{"raw_affiliation_string":"National Science Foundation Center for Big Learning, University of Florida, Gainesville, FL, USA","institution_ids":["https://openalex.org/I1311060795","https://openalex.org/I2802640032","https://openalex.org/I33213144"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5002377126","display_name":"Ana Conesa","orcid":"https://orcid.org/0000-0001-9597-311X"},"institutions":[{"id":"https://openalex.org/I33213144","display_name":"University of Florida","ror":"https://ror.org/02y3ad647","country_code":"US","type":"education","lineage":["https://openalex.org/I33213144"]},{"id":"https://openalex.org/I4210165109","display_name":"Centro de Investigacion Principe Felipe","ror":"https://ror.org/05xr2yq54","country_code":"ES","type":"facility","lineage":["https://openalex.org/I4210165109"]}],"countries":["ES","US"],"is_corresponding":true,"raw_author_name":"Ana Conesa","raw_affiliation_strings":["Department of Microbiology and Cell Science, Institute for Food and Agricultural Sciences, University of Florida, Gainesville, FL, USA","Genomics of Gene Expression Laboratory, Centro de Investigaci\u00f3n Pr\u00edncipe Felipe, Valencia, Spain"],"affiliations":[{"raw_affiliation_string":"Department of Microbiology and Cell Science, Institute for Food and Agricultural Sciences, University of Florida, Gainesville, FL, USA","institution_ids":["https://openalex.org/I33213144"]},{"raw_affiliation_string":"Genomics of Gene Expression Laboratory, Centro de Investigaci\u00f3n Pr\u00edncipe Felipe, Valencia, Spain","institution_ids":["https://openalex.org/I4210165109"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5091529220","display_name":"C\u00e9cile Pereira","orcid":"https://orcid.org/0000-0001-8050-3019"},"institutions":[{"id":"https://openalex.org/I33213144","display_name":"University of Florida","ror":"https://ror.org/02y3ad647","country_code":"US","type":"education","lineage":["https://openalex.org/I33213144"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"C\u00e9cile Pereira","raw_affiliation_strings":["Department of Microbiology and Cell Science, Institute for Food and Agricultural Sciences, University of Florida, Gainesville, FL, USA"],"affiliations":[{"raw_affiliation_string":"Department of Microbiology and Cell Science, Institute for Food and Agricultural Sciences, University of Florida, Gainesville, FL, USA","institution_ids":["https://openalex.org/I33213144"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5002377126","https://openalex.org/A5100353846"],"corresponding_institution_ids":["https://openalex.org/I1311060795","https://openalex.org/I2802640032","https://openalex.org/I33213144","https://openalex.org/I4210165109"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":12.0569,"has_fulltext":false,"cited_by_count":156,"citation_normalized_percentile":{"value":0.98783086,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":99,"max":100},"biblio":{"volume":"34","issue":"9","first_page":"1547","last_page":"1554"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10028","display_name":"Topic Modeling","score":0.9994000196456909,"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":0.9994000196456909,"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":0.9993000030517578,"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":0.9922000169754028,"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":0.8762577772140503},{"id":"https://openalex.org/keywords/named-entity-recognition","display_name":"Named-entity recognition","score":0.8009713888168335},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.7453784942626953},{"id":"https://openalex.org/keywords/convolutional-neural-network","display_name":"Convolutional neural network","score":0.7347086071968079},{"id":"https://openalex.org/keywords/feature-engineering","display_name":"Feature engineering","score":0.7143797874450684},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.6022882461547852},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.5795795917510986},{"id":"https://openalex.org/keywords/n-gram","display_name":"n-gram","score":0.5320003628730774},{"id":"https://openalex.org/keywords/task","display_name":"Task (project management)","score":0.53052818775177},{"id":"https://openalex.org/keywords/natural-language-processing","display_name":"Natural language processing","score":0.5264518857002258},{"id":"https://openalex.org/keywords/feature","display_name":"Feature (linguistics)","score":0.47767171263694763},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.43904614448547363},{"id":"https://openalex.org/keywords/word","display_name":"Word (group theory)","score":0.43241164088249207},{"id":"https://openalex.org/keywords/code","display_name":"Code (set theory)","score":0.42987877130508423},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.38140878081321716},{"id":"https://openalex.org/keywords/language-model","display_name":"Language model","score":0.3600797653198242}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8762577772140503},{"id":"https://openalex.org/C2779135771","wikidata":"https://www.wikidata.org/wiki/Q403574","display_name":"Named-entity recognition","level":3,"score":0.8009713888168335},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.7453784942626953},{"id":"https://openalex.org/C81363708","wikidata":"https://www.wikidata.org/wiki/Q17084460","display_name":"Convolutional neural network","level":2,"score":0.7347086071968079},{"id":"https://openalex.org/C2778827112","wikidata":"https://www.wikidata.org/wiki/Q22245680","display_name":"Feature engineering","level":3,"score":0.7143797874450684},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.6022882461547852},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.5795795917510986},{"id":"https://openalex.org/C117884012","wikidata":"https://www.wikidata.org/wiki/Q94489","display_name":"n-gram","level":3,"score":0.5320003628730774},{"id":"https://openalex.org/C2780451532","wikidata":"https://www.wikidata.org/wiki/Q759676","display_name":"Task (project management)","level":2,"score":0.53052818775177},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.5264518857002258},{"id":"https://openalex.org/C2776401178","wikidata":"https://www.wikidata.org/wiki/Q12050496","display_name":"Feature (linguistics)","level":2,"score":0.47767171263694763},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.43904614448547363},{"id":"https://openalex.org/C90805587","wikidata":"https://www.wikidata.org/wiki/Q10944557","display_name":"Word (group theory)","level":2,"score":0.43241164088249207},{"id":"https://openalex.org/C2776760102","wikidata":"https://www.wikidata.org/wiki/Q5139990","display_name":"Code (set theory)","level":3,"score":0.42987877130508423},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.38140878081321716},{"id":"https://openalex.org/C137293760","wikidata":"https://www.wikidata.org/wiki/Q3621696","display_name":"Language model","level":2,"score":0.3600797653198242},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"score":0.0},{"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/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.0},{"id":"https://openalex.org/C187736073","wikidata":"https://www.wikidata.org/wiki/Q2920921","display_name":"Management","level":1,"score":0.0},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","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}],"mesh":[{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","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":false},{"descriptor_ui":"D012984","descriptor_name":"Software","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":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btx815","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btx815","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/34/9/1547/25120965/btx815.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:29272325","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/29272325","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:europepmc.org:4855648","is_oa":true,"landing_page_url":"http://europepmc.org/pmc/articles/PMC5925775","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:5925775","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5925775","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":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btx815","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btx815","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/34/9/1547/25120965/btx815.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":[{"display_name":"Quality Education","id":"https://metadata.un.org/sdg/4","score":0.47999998927116394}],"awards":[{"id":"https://openalex.org/G5425734403","display_name":null,"funder_award_id":"2015-70016-23029","funder_id":"https://openalex.org/F4320321985","funder_display_name":"Department of Agriculture, Australian Government"},{"id":"https://openalex.org/G8503375817","display_name":null,"funder_award_id":"R01GM110240","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G8534810846","display_name":null,"funder_award_id":"ACI 1245880, ACI 1229576, CCF-1128805, CNS-1624782","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"},{"id":"https://openalex.org/F4320306114","display_name":"U.S. Department of Agriculture","ror":"https://ror.org/01na82s61"},{"id":"https://openalex.org/F4320321985","display_name":"Department of Agriculture, Australian Government","ror":"https://ror.org/030c92375"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320332299","display_name":"National Institute of Food and Agriculture","ror":"https://ror.org/05qx3fv49"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2779457220.pdf","grobid_xml":"https://content.openalex.org/works/W2779457220.grobid-xml"},"referenced_works_count":22,"referenced_works":["https://openalex.org/W1521626219","https://openalex.org/W1632114991","https://openalex.org/W2031868269","https://openalex.org/W2065963191","https://openalex.org/W2095705004","https://openalex.org/W2107005506","https://openalex.org/W2127008962","https://openalex.org/W2127479124","https://openalex.org/W2142016317","https://openalex.org/W2154142897","https://openalex.org/W2158899491","https://openalex.org/W2159640576","https://openalex.org/W2160815625","https://openalex.org/W2169099542","https://openalex.org/W2169918010","https://openalex.org/W2414378847","https://openalex.org/W2919115771","https://openalex.org/W2952230511","https://openalex.org/W4229756444","https://openalex.org/W6636649193","https://openalex.org/W6674330103","https://openalex.org/W6683738474"],"related_works":["https://openalex.org/W2250909759","https://openalex.org/W4387517132","https://openalex.org/W2532616038","https://openalex.org/W2787311093","https://openalex.org/W155946694","https://openalex.org/W1555968995","https://openalex.org/W4307474317","https://openalex.org/W2884705011","https://openalex.org/W2057384730","https://openalex.org/W2147879411"],"abstract_inverted_index":{"Supplementary":[0],"data":[1],"are":[2],"available":[3],"at":[4],"Bioinformatics":[5],"online.":[6]},"counts_by_year":[{"year":2026,"cited_by_count":4},{"year":2025,"cited_by_count":10},{"year":2024,"cited_by_count":17},{"year":2023,"cited_by_count":21},{"year":2022,"cited_by_count":24},{"year":2021,"cited_by_count":22},{"year":2020,"cited_by_count":24},{"year":2019,"cited_by_count":23},{"year":2018,"cited_by_count":11}],"updated_date":"2026-04-17T18:11:37.981687","created_date":"2025-10-10T00:00:00"}
