{"id":"https://openalex.org/W2611597380","doi":"https://doi.org/10.1186/s13637-017-0060-6","title":"BCC-NER: bidirectional, contextual clues named entity tagger for gene/protein mention recognition","display_name":"BCC-NER: bidirectional, contextual clues named entity tagger for gene/protein mention recognition","publication_year":2017,"publication_date":"2017-05-05","ids":{"openalex":"https://openalex.org/W2611597380","doi":"https://doi.org/10.1186/s13637-017-0060-6","mag":"2611597380","pmid":"https://pubmed.ncbi.nlm.nih.gov/28477208"},"language":"en","primary_location":{"id":"doi:10.1186/s13637-017-0060-6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13637-017-0060-6","pdf_url":"https://bsb-eurasipjournals.springeropen.com/track/pdf/10.1186/s13637-017-0060-6","source":{"id":"https://openalex.org/S22696228","display_name":"EURASIP Journal on Bioinformatics and Systems Biology","issn_l":"1687-4145","issn":["1687-4145","1687-4153"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","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":"EURASIP Journal on Bioinformatics and Systems Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://bsb-eurasipjournals.springeropen.com/track/pdf/10.1186/s13637-017-0060-6","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5088185255","display_name":"Gurusamy Murugesan","orcid":"https://orcid.org/0000-0003-1812-5218"},"institutions":[{"id":"https://openalex.org/I111575329","display_name":"Bharathiar University","ror":"https://ror.org/04fht8c22","country_code":"IN","type":"education","lineage":["https://openalex.org/I111575329"]}],"countries":["IN"],"is_corresponding":false,"raw_author_name":"Gurusamy Murugesan","raw_affiliation_strings":["Data Mining and Text Mining Lab, Department of Bioinformatics, Bharathiar University, Coimbatore, Tamilnadu, 641046, India","Data Mining and Text Mining Lab, Department of Bioinformatics, Bharathiar University, Coimbatore, India"],"affiliations":[{"raw_affiliation_string":"Data Mining and Text Mining Lab, Department of Bioinformatics, Bharathiar University, Coimbatore, Tamilnadu, 641046, India","institution_ids":["https://openalex.org/I111575329"]},{"raw_affiliation_string":"Data Mining and Text Mining Lab, Department of Bioinformatics, Bharathiar University, Coimbatore, India","institution_ids":["https://openalex.org/I111575329"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5075012683","display_name":"Sabenabanu Abdulkadhar","orcid":"https://orcid.org/0000-0002-7347-0930"},"institutions":[{"id":"https://openalex.org/I111575329","display_name":"Bharathiar University","ror":"https://ror.org/04fht8c22","country_code":"IN","type":"education","lineage":["https://openalex.org/I111575329"]}],"countries":["IN"],"is_corresponding":false,"raw_author_name":"Sabenabanu Abdulkadhar","raw_affiliation_strings":["Data Mining and Text Mining Lab, Department of Bioinformatics, Bharathiar University, Coimbatore, Tamilnadu, 641046, India","Data Mining and Text Mining Lab, Department of Bioinformatics, Bharathiar University, Coimbatore, India"],"affiliations":[{"raw_affiliation_string":"Data Mining and Text Mining Lab, Department of Bioinformatics, Bharathiar University, Coimbatore, Tamilnadu, 641046, India","institution_ids":["https://openalex.org/I111575329"]},{"raw_affiliation_string":"Data Mining and Text Mining Lab, Department of Bioinformatics, Bharathiar University, Coimbatore, India","institution_ids":["https://openalex.org/I111575329"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5050726436","display_name":"Balu Bhasuran","orcid":"https://orcid.org/0000-0002-9890-4627"},"institutions":[{"id":"https://openalex.org/I111575329","display_name":"Bharathiar University","ror":"https://ror.org/04fht8c22","country_code":"IN","type":"education","lineage":["https://openalex.org/I111575329"]}],"countries":["IN"],"is_corresponding":false,"raw_author_name":"Balu Bhasuran","raw_affiliation_strings":["Center for Computational Biology, DRDO-BU Center for Life Sciences, Bharathiar University, Coimbatore, Tamilnadu, 641046, India","Center for Computational Biology, DRDO-BU Center for Life Sciences, Bharathiar University, Coimbatore, India"],"affiliations":[{"raw_affiliation_string":"Center for Computational Biology, DRDO-BU Center for Life Sciences, Bharathiar University, Coimbatore, Tamilnadu, 641046, India","institution_ids":["https://openalex.org/I111575329"]},{"raw_affiliation_string":"Center for Computational Biology, DRDO-BU Center for Life Sciences, Bharathiar University, Coimbatore, India","institution_ids":["https://openalex.org/I111575329"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5077365599","display_name":"Jeyakumar Natarajan","orcid":"https://orcid.org/0000-0003-3981-619X"},"institutions":[{"id":"https://openalex.org/I111575329","display_name":"Bharathiar University","ror":"https://ror.org/04fht8c22","country_code":"IN","type":"education","lineage":["https://openalex.org/I111575329"]}],"countries":["IN"],"is_corresponding":true,"raw_author_name":"Jeyakumar Natarajan","raw_affiliation_strings":["Data Mining and Text Mining Lab, Department of Bioinformatics, Bharathiar University, Coimbatore, Tamilnadu, 641046, India. n.jeyakumar@yahoo.co.in","Data Mining and Text Mining Lab, Department of Bioinformatics, Bharathiar University, Coimbatore, India"],"affiliations":[{"raw_affiliation_string":"Data Mining and Text Mining Lab, Department of Bioinformatics, Bharathiar University, Coimbatore, Tamilnadu, 641046, India. n.jeyakumar@yahoo.co.in","institution_ids":[]},{"raw_affiliation_string":"Data Mining and Text Mining Lab, Department of Bioinformatics, Bharathiar University, Coimbatore, India","institution_ids":["https://openalex.org/I111575329"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5077365599"],"corresponding_institution_ids":["https://openalex.org/I111575329"],"apc_list":null,"apc_paid":null,"fwci":1.0105,"has_fulltext":true,"cited_by_count":22,"citation_normalized_percentile":{"value":0.75201359,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":"2017","issue":"1","first_page":"7","last_page":"7"},"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/T10028","display_name":"Topic Modeling","score":0.9958999752998352,"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":0.9940000176429749,"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":0.8637523651123047},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.8481249809265137},{"id":"https://openalex.org/keywords/conditional-random-field","display_name":"Conditional random field","score":0.8072501420974731},{"id":"https://openalex.org/keywords/natural-language-processing","display_name":"Natural language processing","score":0.6706663966178894},{"id":"https://openalex.org/keywords/parsing","display_name":"Parsing","score":0.6437878012657166},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.6004437208175659},{"id":"https://openalex.org/keywords/margin","display_name":"Margin (machine learning)","score":0.47218361496925354},{"id":"https://openalex.org/keywords/precision-and-recall","display_name":"Precision and recall","score":0.4596547484397888},{"id":"https://openalex.org/keywords/feature","display_name":"Feature (linguistics)","score":0.4516914188861847},{"id":"https://openalex.org/keywords/f1-score","display_name":"F1 score","score":0.41631758213043213},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.3221897482872009},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.2058369517326355},{"id":"https://openalex.org/keywords/task","display_name":"Task (project management)","score":0.13668647408485413}],"concepts":[{"id":"https://openalex.org/C2779135771","wikidata":"https://www.wikidata.org/wiki/Q403574","display_name":"Named-entity recognition","level":3,"score":0.8637523651123047},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8481249809265137},{"id":"https://openalex.org/C152565575","wikidata":"https://www.wikidata.org/wiki/Q1124538","display_name":"Conditional random field","level":2,"score":0.8072501420974731},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.6706663966178894},{"id":"https://openalex.org/C186644900","wikidata":"https://www.wikidata.org/wiki/Q194152","display_name":"Parsing","level":2,"score":0.6437878012657166},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.6004437208175659},{"id":"https://openalex.org/C774472","wikidata":"https://www.wikidata.org/wiki/Q6760393","display_name":"Margin (machine learning)","level":2,"score":0.47218361496925354},{"id":"https://openalex.org/C81669768","wikidata":"https://www.wikidata.org/wiki/Q2359161","display_name":"Precision and recall","level":2,"score":0.4596547484397888},{"id":"https://openalex.org/C2776401178","wikidata":"https://www.wikidata.org/wiki/Q12050496","display_name":"Feature (linguistics)","level":2,"score":0.4516914188861847},{"id":"https://openalex.org/C148524875","wikidata":"https://www.wikidata.org/wiki/Q6975395","display_name":"F1 score","level":2,"score":0.41631758213043213},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.3221897482872009},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.2058369517326355},{"id":"https://openalex.org/C2780451532","wikidata":"https://www.wikidata.org/wiki/Q759676","display_name":"Task (project management)","level":2,"score":0.13668647408485413},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"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/C187736073","wikidata":"https://www.wikidata.org/wiki/Q2920921","display_name":"Management","level":1,"score":0.0}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1186/s13637-017-0060-6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13637-017-0060-6","pdf_url":"https://bsb-eurasipjournals.springeropen.com/track/pdf/10.1186/s13637-017-0060-6","source":{"id":"https://openalex.org/S22696228","display_name":"EURASIP Journal on Bioinformatics and Systems Biology","issn_l":"1687-4145","issn":["1687-4145","1687-4153"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","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":"EURASIP Journal on Bioinformatics and Systems Biology","raw_type":"journal-article"},{"id":"pmid:28477208","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/28477208","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":"EURASIP journal on bioinformatics & systems biology","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:5419958","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5419958","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":"EURASIP J Bioinform Syst Biol","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s13637-017-0060-6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13637-017-0060-6","pdf_url":"https://bsb-eurasipjournals.springeropen.com/track/pdf/10.1186/s13637-017-0060-6","source":{"id":"https://openalex.org/S22696228","display_name":"EURASIP Journal on Bioinformatics and Systems Biology","issn_l":"1687-4145","issn":["1687-4145","1687-4153"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","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":"EURASIP Journal on Bioinformatics and Systems Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2611597380.pdf","grobid_xml":"https://content.openalex.org/works/W2611597380.grobid-xml"},"referenced_works_count":32,"referenced_works":["https://openalex.org/W87493133","https://openalex.org/W180267634","https://openalex.org/W632578100","https://openalex.org/W1409617254","https://openalex.org/W1666916593","https://openalex.org/W1975568433","https://openalex.org/W2007200954","https://openalex.org/W2027913322","https://openalex.org/W2048140075","https://openalex.org/W2061478295","https://openalex.org/W2064199746","https://openalex.org/W2065963191","https://openalex.org/W2104148262","https://openalex.org/W2107005506","https://openalex.org/W2116410915","https://openalex.org/W2117243442","https://openalex.org/W2127008962","https://openalex.org/W2129564276","https://openalex.org/W2134967412","https://openalex.org/W2141615766","https://openalex.org/W2147880316","https://openalex.org/W2163922914","https://openalex.org/W2169918010","https://openalex.org/W2552843868","https://openalex.org/W2760736243","https://openalex.org/W2912915691","https://openalex.org/W2913550731","https://openalex.org/W4250397231","https://openalex.org/W4285719527","https://openalex.org/W6600286444","https://openalex.org/W6601454032","https://openalex.org/W6611894875"],"related_works":["https://openalex.org/W4250494529","https://openalex.org/W1964783010","https://openalex.org/W2399696375","https://openalex.org/W45206245","https://openalex.org/W2211396092","https://openalex.org/W2061834489","https://openalex.org/W3088215229","https://openalex.org/W2078793151","https://openalex.org/W3047727388","https://openalex.org/W3201257042"],"abstract_inverted_index":{"Tagging":[0],"biomedical":[1,19],"entities":[2],"such":[3],"as":[4],"gene,":[5],"protein,":[6],"cell,":[7],"and":[8,14,65,74,91,93,97,108,126,149],"cell-line":[9],"is":[10,46,54,71,111,155],"the":[11,85,95,158],"first":[12,52],"step":[13],"an":[15],"important":[16],"pre-requisite":[17],"in":[18,87],"literature":[20],"mining.":[21],"In":[22],"this":[23],"paper,":[24],"we":[25],"describe":[26],"our":[27],"hybrid":[28],"named":[29,38],"entity":[30,39],"tagging":[31],"approach":[32],"namely":[33],"BCC-NER":[34,45,140],"(bidirectional,":[35],"contextual":[36],"clues":[37],"tagger":[40],"for":[41,55,72,112],"gene/protein":[42],"mention":[43],"recognition).":[44],"deployed":[47],"with":[48,77],"three":[49],"modules.":[50],"The":[51,68,106,130],"module":[53,70,110],"text":[56,86,122],"processing":[57],"which":[58,119,154],"includes":[59,120],"basic":[60],"NLP":[61],"pre-processing,":[62],"feature":[63,66],"extraction,":[64],"selection.":[67],"second":[69],"training":[73],"model":[75],"building":[76],"bidirectional":[78],"conditional":[79],"random":[80],"fields":[81],"(CRF)":[82],"to":[83,114],"parse":[84],"both":[88],"directions":[89],"(forward":[90],"backward)":[92],"integrate":[94],"backward":[96],"forward":[98],"trained":[99],"models":[100],"using":[101],"margin-infused":[102],"relaxed":[103],"algorithm":[104],"(MIRA).":[105],"third":[107],"final":[109],"post-processing":[113],"achieve":[115,141],"a":[116,142],"better":[117],"performance,":[118],"surrounding":[121],"features,":[123],"parenthesis":[124],"mismatching,":[125],"two-tier":[127],"abbreviation":[128],"algorithm.":[129],"evaluation":[131],"results":[132],"on":[133],"BioCreative":[134],"II":[135],"GM":[136],"test":[137],"corpus":[138],"of":[139,144,147,152],"precision":[143],"89.95,":[145],"recall":[146],"84.15":[148],"overall":[150],"F-score":[151],"86.95,":[153],"higher":[156],"than":[157],"other":[159],"currently":[160],"available":[161],"open":[162],"source":[163],"taggers.":[164]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":4},{"year":2022,"cited_by_count":4},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":2},{"year":2018,"cited_by_count":5},{"year":2017,"cited_by_count":2}],"updated_date":"2026-04-21T08:09:41.155169","created_date":"2025-10-10T00:00:00"}
