{"id":"https://openalex.org/W2809129309","doi":"https://doi.org/10.1093/database/bay048","title":"SPRENO: a BioC module for identifying organism terms in figure captions","display_name":"SPRENO: a BioC module for identifying organism terms in figure captions","publication_year":2018,"publication_date":"2018-01-01","ids":{"openalex":"https://openalex.org/W2809129309","doi":"https://doi.org/10.1093/database/bay048","mag":"2809129309","pmid":"https://pubmed.ncbi.nlm.nih.gov/29873706"},"language":"en","primary_location":{"id":"doi:10.1093/database/bay048","is_oa":true,"landing_page_url":"https://doi.org/10.1093/database/bay048","pdf_url":"https://academic.oup.com/database/article-pdf/doi/10.1093/database/bay048/27438230/bay048.pdf","source":{"id":"https://openalex.org/S4210201630","display_name":"Database","issn_l":"1758-0463","issn":["1758-0463"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311647","host_organization_name":"University of Oxford","host_organization_lineage":["https://openalex.org/P4310311647"],"host_organization_lineage_names":["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":"Database","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/database/article-pdf/doi/10.1093/database/bay048/27438230/bay048.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5037362113","display_name":"Hong-Jie Dai","orcid":"https://orcid.org/0000-0002-1516-7255"},"institutions":[{"id":"https://openalex.org/I178613991","display_name":"National Taitung University","ror":"https://ror.org/05j9d8v51","country_code":"TW","type":"education","lineage":["https://openalex.org/I178613991"]}],"countries":["TW"],"is_corresponding":true,"raw_author_name":"Hong-Jie Dai","raw_affiliation_strings":["Department of Computer Science and Information Engineering, National Taitung University, 369, Sec. 2, University Rd., Taitung, Taiwan, R.O.C","Interdisciplinary Program of Green and Information Technology, National Taitung University, 369, Sec. 2, University Rd., Taitung, Taiwan, R.O.C"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Information Engineering, National Taitung University, 369, Sec. 2, University Rd., Taitung, Taiwan, R.O.C","institution_ids":["https://openalex.org/I178613991"]},{"raw_affiliation_string":"Interdisciplinary Program of Green and Information Technology, National Taitung University, 369, Sec. 2, University Rd., Taitung, Taiwan, R.O.C","institution_ids":["https://openalex.org/I178613991"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5030603764","display_name":"Onkar Singh","orcid":"https://orcid.org/0000-0002-4745-1584"},"institutions":[{"id":"https://openalex.org/I148366613","display_name":"National Yang Ming Chiao Tung University","ror":"https://ror.org/00se2k293","country_code":"TW","type":"education","lineage":["https://openalex.org/I148366613"]},{"id":"https://openalex.org/I4210098366","display_name":"Institute of Information Science, Academia Sinica","ror":"https://ror.org/00z83z196","country_code":"TW","type":"facility","lineage":["https://openalex.org/I4210098366","https://openalex.org/I84653119"]}],"countries":["TW"],"is_corresponding":false,"raw_author_name":"Onkar Singh","raw_affiliation_strings":["Bioinformatics Program, Taiwan International Graduate Program, Institute of Information Science, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei, Taiwan, R.O.C","Institute of Biomedical Informatics, National Yang-Ming University, No. 155, Sec. 2, Linong Street, Taipei, 112 Taiwan, R.O.C"],"affiliations":[{"raw_affiliation_string":"Bioinformatics Program, Taiwan International Graduate Program, Institute of Information Science, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei, Taiwan, R.O.C","institution_ids":["https://openalex.org/I4210098366"]},{"raw_affiliation_string":"Institute of Biomedical Informatics, National Yang-Ming University, No. 155, Sec. 2, Linong Street, Taipei, 112 Taiwan, R.O.C","institution_ids":["https://openalex.org/I148366613"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5037362113"],"corresponding_institution_ids":["https://openalex.org/I178613991"],"apc_list":{"value":1415,"currency":"GBP","value_usd":1735},"apc_paid":{"value":1415,"currency":"GBP","value_usd":1735},"fwci":0.2793,"has_fulltext":true,"cited_by_count":4,"citation_normalized_percentile":{"value":0.57108258,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":95},"biblio":{"volume":"2018","issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9995999932289124,"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":0.9995999932289124,"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/T10215","display_name":"Semantic Web and Ontologies","score":0.9632999897003174,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9610999822616577,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6705437898635864},{"id":"https://openalex.org/keywords/natural-language-processing","display_name":"Natural language processing","score":0.5452665686607361},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.5220499038696289},{"id":"https://openalex.org/keywords/organism","display_name":"Organism","score":0.5203872919082642},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.41398075222969055},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.358600914478302},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.24326109886169434},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.15100014209747314}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6705437898635864},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.5452665686607361},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.5220499038696289},{"id":"https://openalex.org/C137858568","wikidata":"https://www.wikidata.org/wiki/Q7239","display_name":"Organism","level":2,"score":0.5203872919082642},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.41398075222969055},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.358600914478302},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.24326109886169434},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.15100014209747314}],"mesh":[{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002965","descriptor_name":"Classification","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D002965","descriptor_name":"Classification","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D002965","descriptor_name":"Classification","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D004331","descriptor_name":"Drosophila melanogaster","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004331","descriptor_name":"Drosophila melanogaster","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004331","descriptor_name":"Drosophila melanogaster","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005814","descriptor_name":"Genes, Viral","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005814","descriptor_name":"Genes, Viral","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005814","descriptor_name":"Genes, Viral","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012845","descriptor_name":"Sindbis Virus","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012845","descriptor_name":"Sindbis Virus","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012845","descriptor_name":"Sindbis Virus","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012845","descriptor_name":"Sindbis Virus","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012845","descriptor_name":"Sindbis Virus","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012845","descriptor_name":"Sindbis Virus","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017344","descriptor_name":"Genes, Insect","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017344","descriptor_name":"Genes, Insect","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017344","descriptor_name":"Genes, Insect","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1093/database/bay048","is_oa":true,"landing_page_url":"https://doi.org/10.1093/database/bay048","pdf_url":"https://academic.oup.com/database/article-pdf/doi/10.1093/database/bay048/27438230/bay048.pdf","source":{"id":"https://openalex.org/S4210201630","display_name":"Database","issn_l":"1758-0463","issn":["1758-0463"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311647","host_organization_name":"University of Oxford","host_organization_lineage":["https://openalex.org/P4310311647"],"host_organization_lineage_names":["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":"Database","raw_type":"journal-article"},{"id":"pmid:29873706","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/29873706","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":"Database : the journal of biological databases and curation","raw_type":null},{"id":"pmh:oai:europepmc.org:4965970","is_oa":true,"landing_page_url":"http://europepmc.org/pmc/articles/PMC6007219","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:6007219","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6007219","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":"Database (Oxford)","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/database/bay048","is_oa":true,"landing_page_url":"https://doi.org/10.1093/database/bay048","pdf_url":"https://academic.oup.com/database/article-pdf/doi/10.1093/database/bay048/27438230/bay048.pdf","source":{"id":"https://openalex.org/S4210201630","display_name":"Database","issn_l":"1758-0463","issn":["1758-0463"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311647","host_organization_name":"University of Oxford","host_organization_lineage":["https://openalex.org/P4310311647"],"host_organization_lineage_names":["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":"Database","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G5563719332","display_name":null,"funder_award_id":"106-2221-E-","funder_id":"https://openalex.org/F4320322795","funder_display_name":"Ministry of Science and Technology, Taiwan"},{"id":"https://openalex.org/G5787228634","display_name":null,"funder_award_id":"MOST-106-2221-E-143-007-MY3","funder_id":"https://openalex.org/F4320322795","funder_display_name":"Ministry of Science and Technology, Taiwan"},{"id":"https://openalex.org/G6105676603","display_name":null,"funder_award_id":"MOST-105-2221-E-143-003","funder_id":"https://openalex.org/F4320322795","funder_display_name":"Ministry of Science and Technology, Taiwan"},{"id":"https://openalex.org/G7160539585","display_name":null,"funder_award_id":"Technology","funder_id":"https://openalex.org/F4320322795","funder_display_name":"Ministry of Science and Technology, Taiwan"},{"id":"https://openalex.org/G951433114","display_name":null,"funder_award_id":"007-MY3","funder_id":"https://openalex.org/F4320322795","funder_display_name":"Ministry of Science and Technology, Taiwan"}],"funders":[{"id":"https://openalex.org/F4320322795","display_name":"Ministry of Science and Technology, Taiwan","ror":"https://ror.org/02kv4zf79"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2809129309.pdf","grobid_xml":"https://content.openalex.org/works/W2809129309.grobid-xml"},"referenced_works_count":14,"referenced_works":["https://openalex.org/W102787101","https://openalex.org/W1991154713","https://openalex.org/W2007450471","https://openalex.org/W2022484638","https://openalex.org/W2071879021","https://openalex.org/W2124176947","https://openalex.org/W2124714582","https://openalex.org/W2166468803","https://openalex.org/W2171691447","https://openalex.org/W2489896305","https://openalex.org/W2509885322","https://openalex.org/W2573117738","https://openalex.org/W2952465807","https://openalex.org/W6652118667"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W24843447","https://openalex.org/W94193318","https://openalex.org/W2073808674","https://openalex.org/W2173289516","https://openalex.org/W322176015","https://openalex.org/W20947408","https://openalex.org/W2028140658","https://openalex.org/W2073011570","https://openalex.org/W3204019825"],"abstract_inverted_index":{"Recent":[0],"advances":[1],"in":[2,38,43,56,75,83,123,140,144,169,269],"biological":[3,18,24,60,125],"research":[4],"reveal":[5],"that":[6,50,220],"the":[7,10,17,32,39,73,76,102,120,131,145,176,182,187,191,197,213,218,243,246,250,259,266,270,288,294],"majority":[8,214,260],"of":[9,16,31,41,59,80,133,199,249,265,279],"experiments":[11],"strive":[12],"for":[13,98,164,305],"comprehensive":[14],"exploration":[15],"system":[19,256],"rather":[20],"than":[21],"targeting":[22],"specific":[23],"entities.":[25],"The":[26,87,230],"qualitative":[27],"and":[28,62,159,172,190,245,275,283,302],"quantitative":[29],"findings":[30,52],"investigations":[33],"are":[34],"often":[35],"exclusively":[36],"available":[37,311],"form":[40],"figures":[42],"published":[44],"papers.":[45],"There":[46],"is":[47,68,162,210,232,309],"no":[48],"denying":[49],"such":[51,67,92],"have":[53,206],"been":[54,207,222],"instrumental":[55],"intensive":[57],"understanding":[58],"processes":[61],"pathways.":[63],"However,":[64],"data":[65],"as":[66,72,94],"unacknowledged":[69],"by":[70,116,180,240],"machines":[71],"descriptions":[74],"figure":[77,170,188],"captions":[78,171],"comprise":[79],"sumptuous":[81],"information":[82,184,248],"an":[84],"ambiguous":[85,200],"manner.":[86],"abbreviated":[88],"term":[89],"'SIN'":[90],"exemplifies":[91],"issue":[93],"it":[95],"may":[96],"stand":[97],"Sindbis":[99],"virus":[100],"or":[101],"sex-lethal":[103],"interactor":[104],"gene":[105],"(Drosophila":[106],"melanogaster).":[107],"To":[108,195],"overcome":[109],"this":[110,148],"ambiguity,":[111],"entities":[112,143],"should":[113],"be":[114],"identified":[115],"linking":[117,173],"them":[118,174],"to":[119,175,216,225],"respective":[121],"entries":[122],"notable":[124],"databases.":[126],"Among":[127],"all":[128],"entity":[129,306],"types,":[130],"task":[132],"identifying":[134],"species":[135,153],"plays":[136],"a":[137,233,255],"pivotal":[138],"role":[139],"disambiguating":[141],"related":[142],"text.":[146,194],"In":[147],"study,":[149],"we":[150],"present":[151],"our":[152],"identification":[154],"tool":[155],"SPRENO":[156,262,308],"(Species":[157],"Recognition":[158],"Normalization),":[160],"which":[161],"established":[163],"recognizing":[165],"organism":[166,201,228,252],"terms":[167],"mentioned":[168,227],"NCBI":[177],"taxonomy":[178],"database":[179],"exploiting":[181],"contextual":[183],"from":[185],"both":[186,242],"caption":[189],"corresponding":[192],"full":[193],"determine":[196],"ID":[198,219],"mentions,":[202],"two":[203],"disambiguation":[204],"methods":[205],"developed.":[208],"One":[209],"based":[211,257],"on":[212,258,287],"rule":[215],"select":[217],"has":[221],"successfully":[223],"linked":[224],"previously":[226],"terms.":[229],"other":[231],"convolutional":[234],"neural":[235],"network":[236],"(CNN)":[237],"model":[238],"trained":[239],"learning":[241],"context":[244],"distance":[247],"target":[251],"mention.":[253],"As":[254],"rule,":[261],"was":[263],"one":[264],"top-ranked":[267],"systems":[268],"BioCreative":[271],"VI":[272],"BioID":[273],"track":[274],"achieved":[276],"micro":[277],"F-scores":[278,303],"0.776":[280],"(entity":[281,285],"recognition)":[282],"0.755":[284],"normalization)":[286],"official":[289],"test":[290],"set,":[291],"respectively.":[292],"Additionally,":[293],"SPRENO-CNN":[295],"exhibited":[296],"better":[297],"precisions":[298],"with":[299],"lower":[300],"recalls":[301],"(0.720/0.711":[304],"recognition/normalization).":[307],"freely":[310],"at":[312],"https://bigodatamining.github.io/software/201801/.Database":[313],"URL:":[314],"https://bigodatamining.github.io/software/201801/.":[315]},"counts_by_year":[{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":2},{"year":2018,"cited_by_count":1}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}
