{"id":"https://openalex.org/W2151949849","doi":"https://doi.org/10.1186/1471-2105-15-160","title":"A resource-saving collective approach to biomedical semantic role labeling","display_name":"A resource-saving collective approach to biomedical semantic role labeling","publication_year":2014,"publication_date":"2014-05-27","ids":{"openalex":"https://openalex.org/W2151949849","doi":"https://doi.org/10.1186/1471-2105-15-160","mag":"2151949849","pmid":"https://pubmed.ncbi.nlm.nih.gov/24884358"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-15-160","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-15-160","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-15-160","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","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":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-15-160","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5030771512","display_name":"Richard Tzong\u2010Han Tsai","orcid":"https://orcid.org/0000-0003-0513-107X"},"institutions":[{"id":"https://openalex.org/I22265921","display_name":"National Central University","ror":"https://ror.org/00944ve71","country_code":"TW","type":"education","lineage":["https://openalex.org/I22265921"]}],"countries":["TW"],"is_corresponding":true,"raw_author_name":"Richard Tzong-Han Tsai","raw_affiliation_strings":["Department of Computer Science and Information Engineering, National Central University, Taoyuan, Taiwan, Republic of China. thtsai@csie.ncu.edu.tw","Department of Computer Science and Information Engineering, National Central University, Taoyuan, Taiwan, Republic of China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Information Engineering, National Central University, Taoyuan, Taiwan, Republic of China. thtsai@csie.ncu.edu.tw","institution_ids":[]},{"raw_affiliation_string":"Department of Computer Science and Information Engineering, National Central University, Taoyuan, Taiwan, Republic of China","institution_ids":["https://openalex.org/I22265921"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5016587469","display_name":"Po\u2010Ting Lai","orcid":"https://orcid.org/0000-0003-2025-318X"},"institutions":[{"id":"https://openalex.org/I25846049","display_name":"National Tsing Hua University","ror":"https://ror.org/00zdnkx70","country_code":"TW","type":"education","lineage":["https://openalex.org/I25846049"]},{"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":"Po-Ting Lai","raw_affiliation_strings":["Department of Computer Science, National Tsing-Hua University, HsinChu, Taiwan, Republic of China","Institute of Information Science, Academia Sinica, Taipei, Taiwan, Republic of China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, National Tsing-Hua University, HsinChu, Taiwan, Republic of China","institution_ids":["https://openalex.org/I25846049"]},{"raw_affiliation_string":"Institute of Information Science, Academia Sinica, Taipei, Taiwan, Republic of China","institution_ids":["https://openalex.org/I4210098366"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5030771512"],"corresponding_institution_ids":["https://openalex.org/I22265921"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":0.2846,"has_fulltext":true,"cited_by_count":5,"citation_normalized_percentile":{"value":0.60945262,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":94},"biblio":{"volume":"15","issue":"1","first_page":"160","last_page":"160"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9261000156402588,"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":0.9261000156402588,"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":0.01730000041425228,"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":0.0142000000923872,"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":0.8411939144134521},{"id":"https://openalex.org/keywords/parsing","display_name":"Parsing","score":0.621170699596405},{"id":"https://openalex.org/keywords/tree","display_name":"Tree (set theory)","score":0.5962116122245789},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5698016881942749},{"id":"https://openalex.org/keywords/identifier","display_name":"Identifier","score":0.5195384621620178},{"id":"https://openalex.org/keywords/semantic-role-labeling","display_name":"Semantic role labeling","score":0.4970238506793976},{"id":"https://openalex.org/keywords/natural-language-processing","display_name":"Natural language processing","score":0.4680566191673279},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.46331122517585754},{"id":"https://openalex.org/keywords/parse-tree","display_name":"Parse tree","score":0.44537028670310974},{"id":"https://openalex.org/keywords/node","display_name":"Node (physics)","score":0.44043752551078796},{"id":"https://openalex.org/keywords/argument","display_name":"Argument (complex analysis)","score":0.4119876027107239}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8411939144134521},{"id":"https://openalex.org/C186644900","wikidata":"https://www.wikidata.org/wiki/Q194152","display_name":"Parsing","level":2,"score":0.621170699596405},{"id":"https://openalex.org/C113174947","wikidata":"https://www.wikidata.org/wiki/Q2859736","display_name":"Tree (set theory)","level":2,"score":0.5962116122245789},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5698016881942749},{"id":"https://openalex.org/C154504017","wikidata":"https://www.wikidata.org/wiki/Q853614","display_name":"Identifier","level":2,"score":0.5195384621620178},{"id":"https://openalex.org/C67277372","wikidata":"https://www.wikidata.org/wiki/Q7449085","display_name":"Semantic role labeling","level":3,"score":0.4970238506793976},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.4680566191673279},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.46331122517585754},{"id":"https://openalex.org/C2781466058","wikidata":"https://www.wikidata.org/wiki/Q627921","display_name":"Parse tree","level":3,"score":0.44537028670310974},{"id":"https://openalex.org/C62611344","wikidata":"https://www.wikidata.org/wiki/Q1062658","display_name":"Node (physics)","level":2,"score":0.44043752551078796},{"id":"https://openalex.org/C98184364","wikidata":"https://www.wikidata.org/wiki/Q1780131","display_name":"Argument (complex analysis)","level":2,"score":0.4119876027107239},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C66938386","wikidata":"https://www.wikidata.org/wiki/Q633538","display_name":"Structural engineering","level":1,"score":0.0},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"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/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.0},{"id":"https://openalex.org/C2777530160","wikidata":"https://www.wikidata.org/wiki/Q41796","display_name":"Sentence","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D008390","descriptor_name":"Markov Chains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008390","descriptor_name":"Markov Chains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008390","descriptor_name":"Markov Chains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012660","descriptor_name":"Semantics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012660","descriptor_name":"Semantics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012660","descriptor_name":"Semantics","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":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D035843","descriptor_name":"Biomedical Research","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D035843","descriptor_name":"Biomedical Research","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D035843","descriptor_name":"Biomedical Research","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1186/1471-2105-15-160","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-15-160","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-15-160","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","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":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:24884358","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/24884358","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:europepmc.org:3044249","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4062501","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":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/1471-2105-15-160","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-15-160","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-15-160","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","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":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.4300000071525574,"id":"https://metadata.un.org/sdg/8","display_name":"Decent work and economic growth"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320321040","display_name":"National Science Council","ror":"https://ror.org/02kv4zf79"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2151949849.pdf","grobid_xml":"https://content.openalex.org/works/W2151949849.grobid-xml"},"referenced_works_count":44,"referenced_works":["https://openalex.org/W12836875","https://openalex.org/W204260652","https://openalex.org/W595549847","https://openalex.org/W1484413656","https://openalex.org/W1506285740","https://openalex.org/W1507020546","https://openalex.org/W1535936886","https://openalex.org/W1538211826","https://openalex.org/W1898214464","https://openalex.org/W1908728294","https://openalex.org/W1975048439","https://openalex.org/W1977970897","https://openalex.org/W2007450471","https://openalex.org/W2051871732","https://openalex.org/W2060301741","https://openalex.org/W2067994019","https://openalex.org/W2078285016","https://openalex.org/W2101819947","https://openalex.org/W2113202266","https://openalex.org/W2121250409","https://openalex.org/W2122139846","https://openalex.org/W2126851059","https://openalex.org/W2137213923","https://openalex.org/W2138043057","https://openalex.org/W2145310422","https://openalex.org/W2151170651","https://openalex.org/W2160786602","https://openalex.org/W2161299591","https://openalex.org/W2163107094","https://openalex.org/W2166559705","https://openalex.org/W2167490942","https://openalex.org/W2171691447","https://openalex.org/W2250728538","https://openalex.org/W2265579607","https://openalex.org/W2556967238","https://openalex.org/W2626138915","https://openalex.org/W2912204212","https://openalex.org/W2914902904","https://openalex.org/W2962735828","https://openalex.org/W2998574808","https://openalex.org/W4285719527","https://openalex.org/W6600547426","https://openalex.org/W6678161993","https://openalex.org/W6691315532"],"related_works":["https://openalex.org/W2044479660","https://openalex.org/W4244615522","https://openalex.org/W1972256049","https://openalex.org/W2338828339","https://openalex.org/W2166677757","https://openalex.org/W2141288413","https://openalex.org/W2049995120","https://openalex.org/W3123688778","https://openalex.org/W1634973882","https://openalex.org/W2033808215"],"abstract_inverted_index":{"BACKGROUND:":[0],"Biomedical":[1],"semantic":[2,15],"role":[3],"labeling":[4],"(BioSRL)":[5],"is":[6,40,132,194,214,266,279],"a":[7,35,48,119,148,189],"natural":[8],"language":[9],"processing":[10],"technique":[11],"that":[12,41,206],"identifies":[13],"the":[14,18,66,99,135,140,156,169,215,224,304],"roles":[16],"of":[17,38,227,293],"words":[19],"or":[20],"phrases":[21],"in":[22,47,75,81,106,143,168,303],"sentences":[23],"describing":[24],"biological":[25],"processes":[26],"and":[27,102,112,159,235,274],"expresses":[28],"them":[29],"as":[30,197,229,287],"predicate-argument":[31],"structures":[32],"(PAS's).":[33],"Currently,":[34],"major":[36],"problem":[37],"BioSRL":[39,82,121,144,217,254],"most":[42],"systems":[43],"label":[44],"every":[45],"node":[46],"full":[49],"parse":[50,157,183],"tree":[51,158],"independently;":[52],"however,":[53],"some":[54],"nodes":[55,154,167],"always":[56],"exhibit":[57],"dependency.":[58],"In":[59],"general":[60],"SRL,":[61],"collective":[62,120,129,199],"approaches":[63],"based":[64,123],"on":[65,124,134,251,300],"Markov":[67],"logic":[68],"network":[69],"(MLN)":[70],"model":[71],"have":[72],"been":[73,88],"successful":[74],"dealing":[76],"with":[77],"this":[78],"problem.":[79],"However,":[80],"such":[83,286],"an":[84],"approach":[85],"has":[86],"not":[87,172,280],"attempted":[89],"because":[90],"it":[91,292],"would":[92],"require":[93],"more":[94,100,257],"training":[95,110,238,250,299],"data":[96],"to":[97,151,164,187,196,261,296],"recognize":[98],"specialized":[101],"diverse":[103],"terms":[104],"found":[105],"biomedical":[107,258,263],"literature,":[108],"increasing":[109],"time":[111],"computational":[113],"complexity.":[114],"RESULTS:":[115],"We":[116,290],"first":[117],"constructed":[118],"system":[122,210],"MLN.":[125],"This":[126,241],"system,":[127,192],"called":[128],"BIOSMILE":[130,200],"(CBIOSMILE),":[131],"trained":[133],"BioProp":[136,265],"corpus.":[137],"To":[138],"reduce":[139],"resources":[141],"used":[142,186],"training,":[145],"we":[146],"employ":[147],"tree-pruning":[149],"filter":[150],"remove":[152],"unlikely":[153],"from":[155],"four":[160],"argument":[161],"candidate":[162,166,176],"identifiers":[163],"retain":[165],"tree.":[170],"Nodes":[171],"recognized":[173],"by":[174],"any":[175],"identifier":[177],"are":[178,185],"discarded.":[179],"The":[180],"pruned":[181],"annotated":[182],"trees":[184],"train":[188],"resource-saving":[190,198],"MLN-based":[191],"which":[193,213],"referred":[195],"(RCBIOSMILE).":[201],"Our":[202],"experimental":[203],"results":[204],"show":[205],"our":[207,220],"proposed":[208,221],"CBIOSMILE":[209,230],"outperforms":[211],"BIOSMILE,":[212],"top":[216],"system.":[218],"Furthermore,":[219],"RCBIOSMILE":[222,246],"maintains":[223],"same":[225],"level":[226],"accuracy":[228],"using":[231],"92%":[232],"less":[233,237],"memory":[234],"57%":[236],"time.":[239],"CONCLUSIONS:":[240],"greatly":[242],"improved":[243],"efficiency":[244],"makes":[245],"potentially":[247],"suitable":[248],"for":[249,283],"much":[252],"larger":[253],"corpora":[255,302],"over":[256],"domains.":[259],"Compared":[260],"real-world":[262],"corpora,":[264],"relatively":[267],"small,":[268],"containing":[269],"only":[270],"445":[271],"MEDLINE":[272],"abstracts":[273],"30":[275],"event":[276],"triggers.":[277],"It":[278],"large":[281,301],"enough":[282],"practical":[284],"applications,":[285],"pathway":[288],"construction.":[289],"consider":[291],"primary":[294],"importance":[295],"pursue":[297],"SRL":[298],"future.":[305]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":1}],"updated_date":"2026-04-29T09:16:38.111599","created_date":"2025-10-10T00:00:00"}