{"id":"https://openalex.org/W2512546630","doi":"https://doi.org/10.18653/v1/w16-2909","title":"Disambiguation of entities in MEDLINE abstracts by combining MeSH terms with knowledge","display_name":"Disambiguation of entities in MEDLINE abstracts by combining MeSH terms with knowledge","publication_year":2016,"publication_date":"2016-01-01","ids":{"openalex":"https://openalex.org/W2512546630","doi":"https://doi.org/10.18653/v1/w16-2909","mag":"2512546630"},"language":"en","primary_location":{"id":"doi:10.18653/v1/w16-2909","is_oa":true,"landing_page_url":"https://doi.org/10.18653/v1/w16-2909","pdf_url":"https://www.aclweb.org/anthology/W16-2909.pdf","source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 15th Workshop on Biomedical Natural Language Processing","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://www.aclweb.org/anthology/W16-2909.pdf","any_repository_has_fulltext":null},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5065988924","display_name":"Amy Siu","orcid":null},"institutions":[{"id":"https://openalex.org/I4210109712","display_name":"Max Planck Institute for Informatics","ror":"https://ror.org/01w19ak89","country_code":"DE","type":"facility","lineage":["https://openalex.org/I149899117","https://openalex.org/I4210109712"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Amy Siu","raw_affiliation_strings":["Max Planck Institute for Informatics 66123 Saarbrcken, Germany","Max Planck Institute for Informatics 66123 Saarbr\u00fccken, Germany"],"affiliations":[{"raw_affiliation_string":"Max Planck Institute for Informatics 66123 Saarbrcken, Germany","institution_ids":["https://openalex.org/I4210109712"]},{"raw_affiliation_string":"Max Planck Institute for Informatics 66123 Saarbr\u00fccken, Germany","institution_ids":["https://openalex.org/I4210109712"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5013361951","display_name":"Patrick Er\u00f1st","orcid":"https://orcid.org/0000-0001-6037-1856"},"institutions":[{"id":"https://openalex.org/I4210109712","display_name":"Max Planck Institute for Informatics","ror":"https://ror.org/01w19ak89","country_code":"DE","type":"facility","lineage":["https://openalex.org/I149899117","https://openalex.org/I4210109712"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Patrick Ernst","raw_affiliation_strings":["Max Planck Institute for Informatics 66123 Saarbrcken, Germany","Max Planck Institute for Informatics 66123 Saarbr\u00fccken, Germany"],"affiliations":[{"raw_affiliation_string":"Max Planck Institute for Informatics 66123 Saarbrcken, Germany","institution_ids":["https://openalex.org/I4210109712"]},{"raw_affiliation_string":"Max Planck Institute for Informatics 66123 Saarbr\u00fccken, Germany","institution_ids":["https://openalex.org/I4210109712"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5088135366","display_name":"Gerhard Weikum","orcid":"https://orcid.org/0000-0003-4959-6098"},"institutions":[{"id":"https://openalex.org/I4210109712","display_name":"Max Planck Institute for Informatics","ror":"https://ror.org/01w19ak89","country_code":"DE","type":"facility","lineage":["https://openalex.org/I149899117","https://openalex.org/I4210109712"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Gerhard Weikum","raw_affiliation_strings":["Max Planck Institute for Informatics 66123 Saarbrcken, Germany","Max Planck Institute for Informatics 66123 Saarbr\u00fccken, Germany"],"affiliations":[{"raw_affiliation_string":"Max Planck Institute for Informatics 66123 Saarbrcken, Germany","institution_ids":["https://openalex.org/I4210109712"]},{"raw_affiliation_string":"Max Planck Institute for Informatics 66123 Saarbr\u00fccken, Germany","institution_ids":["https://openalex.org/I4210109712"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5065988924"],"corresponding_institution_ids":["https://openalex.org/I4210109712"],"apc_list":null,"apc_paid":null,"fwci":0.6972,"has_fulltext":true,"cited_by_count":5,"citation_normalized_percentile":{"value":0.7463154,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":null,"issue":null,"first_page":"72","last_page":"76"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9994999766349792,"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":0.9994999766349792,"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":0.996399998664856,"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/T10028","display_name":"Topic Modeling","score":0.9945999979972839,"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":0.8498944640159607},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.7126932740211487},{"id":"https://openalex.org/keywords/heuristics","display_name":"Heuristics","score":0.6998535394668579},{"id":"https://openalex.org/keywords/task","display_name":"Task (project management)","score":0.6558166742324829},{"id":"https://openalex.org/keywords/exploit","display_name":"Exploit","score":0.6003750562667847},{"id":"https://openalex.org/keywords/unified-medical-language-system","display_name":"Unified Medical Language System","score":0.5916439890861511},{"id":"https://openalex.org/keywords/domain","display_name":"Domain (mathematical analysis)","score":0.5839000344276428},{"id":"https://openalex.org/keywords/computation","display_name":"Computation","score":0.49683406949043274},{"id":"https://openalex.org/keywords/domain-knowledge","display_name":"Domain knowledge","score":0.47636958956718445},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.4507163465023041},{"id":"https://openalex.org/keywords/quality","display_name":"Quality (philosophy)","score":0.44716840982437134},{"id":"https://openalex.org/keywords/natural-language-processing","display_name":"Natural language processing","score":0.4112752676010132},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3915681838989258},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.09814423322677612},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.07993730902671814}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8498944640159607},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.7126932740211487},{"id":"https://openalex.org/C127705205","wikidata":"https://www.wikidata.org/wiki/Q5748245","display_name":"Heuristics","level":2,"score":0.6998535394668579},{"id":"https://openalex.org/C2780451532","wikidata":"https://www.wikidata.org/wiki/Q759676","display_name":"Task (project management)","level":2,"score":0.6558166742324829},{"id":"https://openalex.org/C165696696","wikidata":"https://www.wikidata.org/wiki/Q11287","display_name":"Exploit","level":2,"score":0.6003750562667847},{"id":"https://openalex.org/C69505689","wikidata":"https://www.wikidata.org/wiki/Q455338","display_name":"Unified Medical Language System","level":2,"score":0.5916439890861511},{"id":"https://openalex.org/C36503486","wikidata":"https://www.wikidata.org/wiki/Q11235244","display_name":"Domain (mathematical analysis)","level":2,"score":0.5839000344276428},{"id":"https://openalex.org/C45374587","wikidata":"https://www.wikidata.org/wiki/Q12525525","display_name":"Computation","level":2,"score":0.49683406949043274},{"id":"https://openalex.org/C207685749","wikidata":"https://www.wikidata.org/wiki/Q2088941","display_name":"Domain knowledge","level":2,"score":0.47636958956718445},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.4507163465023041},{"id":"https://openalex.org/C2779530757","wikidata":"https://www.wikidata.org/wiki/Q1207505","display_name":"Quality (philosophy)","level":2,"score":0.44716840982437134},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.4112752676010132},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3915681838989258},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.09814423322677612},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.07993730902671814},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","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/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"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/C187736073","wikidata":"https://www.wikidata.org/wiki/Q2920921","display_name":"Management","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/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0},{"id":"https://openalex.org/C38652104","wikidata":"https://www.wikidata.org/wiki/Q3510521","display_name":"Computer security","level":1,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.18653/v1/w16-2909","is_oa":true,"landing_page_url":"https://doi.org/10.18653/v1/w16-2909","pdf_url":"https://www.aclweb.org/anthology/W16-2909.pdf","source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 15th Workshop on Biomedical Natural Language Processing","raw_type":"proceedings-article"},{"id":"pmh:oai:pure.mpg.de:item_2375398","is_oa":false,"landing_page_url":"http://hdl.handle.net/11858/00-001M-0000-002C-2040-3","pdf_url":null,"source":{"id":"https://openalex.org/S4306400654","display_name":"MPG.PuRe (Max Planck Society)","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Proceedings of the 15th Workshop on Biomedical Natural Language Processing","raw_type":"info:eu-repo/semantics/conferenceObject"}],"best_oa_location":{"id":"doi:10.18653/v1/w16-2909","is_oa":true,"landing_page_url":"https://doi.org/10.18653/v1/w16-2909","pdf_url":"https://www.aclweb.org/anthology/W16-2909.pdf","source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 15th Workshop on Biomedical Natural Language Processing","raw_type":"proceedings-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2512546630.pdf","grobid_xml":"https://content.openalex.org/works/W2512546630.grobid-xml"},"referenced_works_count":23,"referenced_works":["https://openalex.org/W1532254950","https://openalex.org/W1561787084","https://openalex.org/W1973031260","https://openalex.org/W1985104050","https://openalex.org/W1993068388","https://openalex.org/W2011365423","https://openalex.org/W2027049622","https://openalex.org/W2028102159","https://openalex.org/W2040298461","https://openalex.org/W2045016337","https://openalex.org/W2074838152","https://openalex.org/W2096150094","https://openalex.org/W2097678794","https://openalex.org/W2101680936","https://openalex.org/W2122402213","https://openalex.org/W2132079307","https://openalex.org/W2154439800","https://openalex.org/W2163141833","https://openalex.org/W2169491861","https://openalex.org/W2251636905","https://openalex.org/W2252174377","https://openalex.org/W2252205136","https://openalex.org/W2338971035"],"related_works":["https://openalex.org/W17155033","https://openalex.org/W3207760230","https://openalex.org/W1496222301","https://openalex.org/W4312814274","https://openalex.org/W1590307681","https://openalex.org/W2536018345","https://openalex.org/W4285370786","https://openalex.org/W2296488620","https://openalex.org/W2358353312","https://openalex.org/W2353836703"],"abstract_inverted_index":{"Entity":[0],"disambiguation":[1],"in":[2,10,21,40,65,114],"the":[3],"biomedical":[4],"domain":[5],"is":[6,85,104],"an":[7,44],"essential":[8],"task":[9],"any":[11],"text":[12],"mining":[13],"pipeline.":[14],"Much":[15],"existing":[16],"work":[17],"shares":[18],"one":[19,105],"limitation,":[20],"that":[22,48,82],"their":[23],"model":[24],"training":[25],"prerequisite":[26],"and/or":[27],"runtime":[28],"computation":[29],"are":[30],"too":[31],"expensive":[32],"to":[33,36,67,99],"be":[34],"applied":[35],"all":[37],"ambiguous":[38],"entities":[39,77],"real-time.":[41],"We":[42],"propose":[43],"automatic,":[45],"light-weight":[46],"method":[47,59,84,103],"processes":[49],"MEDLINE":[50],"abstracts":[51],"at":[52],"largescale":[53],"and":[54,63,73,87,92],"with":[55,110],"high-quality":[56],"output.":[57],"Our":[58],"exploits":[60],"MeSH":[61],"terms":[62],"knowledge":[64],"UMLS":[66],"first":[68],"identify":[69],"unambiguous":[70],"anchor":[71],"entities,":[72],"then":[74],"disambiguate":[75],"remaining":[76],"via":[78],"heuristics.":[79],"Experiments":[80],"showed":[81],"our":[83,102],"79.6%":[86],"87.7%":[88],"accurate":[89],"under":[90],"strict":[91],"relaxed":[93],"rating":[94],"schemes,":[95],"respectively.":[96],"When":[97],"compared":[98],"MetaMap's":[100],"disambiguation,":[101],"order":[106],"of":[107],"magnitude":[108],"faster":[109],"a":[111],"slight":[112],"advantage":[113],"accuracy.":[115]},"counts_by_year":[{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2017,"cited_by_count":3}],"updated_date":"2026-04-04T16:13:02.066488","created_date":"2025-10-10T00:00:00"}
