{"id":"https://openalex.org/W3122727957","doi":"https://doi.org/10.1145/3459930.3469524","title":"Low resource recognition and linking of biomedical concepts from a large ontology","display_name":"Low resource recognition and linking of biomedical concepts from a large ontology","publication_year":2021,"publication_date":"2021-07-30","ids":{"openalex":"https://openalex.org/W3122727957","doi":"https://doi.org/10.1145/3459930.3469524","mag":"3122727957"},"language":"en","primary_location":{"id":"doi:10.1145/3459930.3469524","is_oa":false,"landing_page_url":"https://doi.org/10.1145/3459930.3469524","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 12th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics","raw_type":"proceedings-article"},"type":"preprint","indexed_in":["arxiv","crossref"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://arxiv.org/pdf/2101.10587","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5110738569","display_name":"Sunil Mohan","orcid":null},"institutions":[{"id":"https://openalex.org/I4210121800","display_name":"Chan Zuckerberg Initiative (United States)","ror":"https://ror.org/02qenvm24","country_code":"US","type":"company","lineage":["https://openalex.org/I4210121800"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Sunil Mohan","raw_affiliation_strings":["Chan Zuckerberg Initiative"],"affiliations":[{"raw_affiliation_string":"Chan Zuckerberg Initiative","institution_ids":["https://openalex.org/I4210121800"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5047594082","display_name":"Rico Angell","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Rico Angell","raw_affiliation_strings":["University of Massachusetts"],"affiliations":[{"raw_affiliation_string":"University of Massachusetts","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5029504586","display_name":"Nicholas Monath","orcid":"https://orcid.org/0000-0002-5135-2423"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Nicholas Monath","raw_affiliation_strings":["University of Massachusetts"],"affiliations":[{"raw_affiliation_string":"University of Massachusetts","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5107835063","display_name":"Andrew McCallum","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Andrew McCallum","raw_affiliation_strings":["University of Massachusetts"],"affiliations":[{"raw_affiliation_string":"University of Massachusetts","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5110738569"],"corresponding_institution_ids":["https://openalex.org/I4210121800"],"apc_list":null,"apc_paid":null,"fwci":0.7319,"has_fulltext":false,"cited_by_count":11,"citation_normalized_percentile":{"value":0.68148895,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":null,"issue":null,"first_page":"1","last_page":"10"},"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":0.9994999766349792,"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":0.9980000257492065,"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/unified-medical-language-system","display_name":"Unified Medical Language System","score":0.83589106798172},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7805876731872559},{"id":"https://openalex.org/keywords/ontology","display_name":"Ontology","score":0.764198362827301},{"id":"https://openalex.org/keywords/search-engine-indexing","display_name":"Search engine indexing","score":0.7144761085510254},{"id":"https://openalex.org/keywords/biomedicine","display_name":"Biomedicine","score":0.6890708804130554},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.6138443946838379},{"id":"https://openalex.org/keywords/open-biomedical-ontologies","display_name":"Open Biomedical Ontologies","score":0.5560657978057861},{"id":"https://openalex.org/keywords/resource","display_name":"Resource (disambiguation)","score":0.46092814207077026},{"id":"https://openalex.org/keywords/upper-ontology","display_name":"Upper ontology","score":0.4496769905090332},{"id":"https://openalex.org/keywords/semantics","display_name":"Semantics (computer science)","score":0.4275043308734894},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.3889584243297577},{"id":"https://openalex.org/keywords/semantic-web","display_name":"Semantic Web","score":0.37830811738967896},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3654768168926239},{"id":"https://openalex.org/keywords/natural-language-processing","display_name":"Natural language processing","score":0.32039982080459595},{"id":"https://openalex.org/keywords/suggested-upper-merged-ontology","display_name":"Suggested Upper Merged Ontology","score":0.22842851281166077},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.1581631600856781}],"concepts":[{"id":"https://openalex.org/C69505689","wikidata":"https://www.wikidata.org/wiki/Q455338","display_name":"Unified Medical Language System","level":2,"score":0.83589106798172},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7805876731872559},{"id":"https://openalex.org/C25810664","wikidata":"https://www.wikidata.org/wiki/Q44325","display_name":"Ontology","level":2,"score":0.764198362827301},{"id":"https://openalex.org/C75165309","wikidata":"https://www.wikidata.org/wiki/Q2258979","display_name":"Search engine indexing","level":2,"score":0.7144761085510254},{"id":"https://openalex.org/C66782513","wikidata":"https://www.wikidata.org/wiki/Q864601","display_name":"Biomedicine","level":2,"score":0.6890708804130554},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.6138443946838379},{"id":"https://openalex.org/C137982476","wikidata":"https://www.wikidata.org/wiki/Q7072326","display_name":"Open Biomedical Ontologies","level":5,"score":0.5560657978057861},{"id":"https://openalex.org/C206345919","wikidata":"https://www.wikidata.org/wiki/Q20380951","display_name":"Resource (disambiguation)","level":2,"score":0.46092814207077026},{"id":"https://openalex.org/C78726541","wikidata":"https://www.wikidata.org/wiki/Q3882785","display_name":"Upper ontology","level":3,"score":0.4496769905090332},{"id":"https://openalex.org/C184337299","wikidata":"https://www.wikidata.org/wiki/Q1437428","display_name":"Semantics (computer science)","level":2,"score":0.4275043308734894},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.3889584243297577},{"id":"https://openalex.org/C2129575","wikidata":"https://www.wikidata.org/wiki/Q54837","display_name":"Semantic Web","level":2,"score":0.37830811738967896},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3654768168926239},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.32039982080459595},{"id":"https://openalex.org/C50971890","wikidata":"https://www.wikidata.org/wiki/Q7635093","display_name":"Suggested Upper Merged Ontology","level":4,"score":0.22842851281166077},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.1581631600856781},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","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/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.0},{"id":"https://openalex.org/C31258907","wikidata":"https://www.wikidata.org/wiki/Q1301371","display_name":"Computer network","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}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1145/3459930.3469524","is_oa":false,"landing_page_url":"https://doi.org/10.1145/3459930.3469524","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 12th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics","raw_type":"proceedings-article"},{"id":"pmh:oai:arXiv.org:2101.10587","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2101.10587","pdf_url":"https://arxiv.org/pdf/2101.10587","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"text"}],"best_oa_location":{"id":"pmh:oai:arXiv.org:2101.10587","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2101.10587","pdf_url":"https://arxiv.org/pdf/2101.10587","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"text"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":54,"referenced_works":["https://openalex.org/W86887328","https://openalex.org/W90362830","https://openalex.org/W1713614699","https://openalex.org/W1940872118","https://openalex.org/W1982488716","https://openalex.org/W2004763266","https://openalex.org/W2008830554","https://openalex.org/W2061167720","https://openalex.org/W2100341149","https://openalex.org/W2123442489","https://openalex.org/W2144578941","https://openalex.org/W2151048449","https://openalex.org/W2159583324","https://openalex.org/W2205981794","https://openalex.org/W2296283641","https://openalex.org/W2346452181","https://openalex.org/W2414378847","https://openalex.org/W2428528690","https://openalex.org/W2479527281","https://openalex.org/W2525579820","https://openalex.org/W2757369719","https://openalex.org/W2770431247","https://openalex.org/W2785888191","https://openalex.org/W2798442412","https://openalex.org/W2887593177","https://openalex.org/W2888236192","https://openalex.org/W2896457183","https://openalex.org/W2911489562","https://openalex.org/W2915623326","https://openalex.org/W2917650994","https://openalex.org/W2920882081","https://openalex.org/W2948909602","https://openalex.org/W2951299559","https://openalex.org/W2952087486","https://openalex.org/W2952826391","https://openalex.org/W2963184844","https://openalex.org/W2963403868","https://openalex.org/W2963709490","https://openalex.org/W2964075320","https://openalex.org/W2977393556","https://openalex.org/W2983608826","https://openalex.org/W2997303394","https://openalex.org/W3015646487","https://openalex.org/W3020786614","https://openalex.org/W3029976717","https://openalex.org/W3035763680","https://openalex.org/W3106224367","https://openalex.org/W3170280676","https://openalex.org/W3170822064","https://openalex.org/W4360982002","https://openalex.org/W4385245566","https://openalex.org/W6600654476","https://openalex.org/W6603694148","https://openalex.org/W6926259797"],"related_works":["https://openalex.org/W2064177607","https://openalex.org/W1801798365","https://openalex.org/W2157272674","https://openalex.org/W2103987857","https://openalex.org/W72173000","https://openalex.org/W4298842574","https://openalex.org/W1506177826","https://openalex.org/W26549824","https://openalex.org/W991275336","https://openalex.org/W2068800403"],"abstract_inverted_index":{"Tools":[0],"to":[1,29,56,80,118,164],"explore":[2],"scientific":[3,86],"literature":[4],"are":[5,18,125],"essential":[6],"for":[7,31,65,186],"scientists,":[8],"especially":[9],"in":[10,41,110,190],"biomedicine,":[11],"where":[12,122],"about":[13],"a":[14,129,143,154],"million":[15],"new":[16,66,155,183],"papers":[17,71],"published":[19],"every":[20],"year.":[21],"Many":[22],"such":[23],"tools":[24],"provide":[25],"users":[26],"the":[27,44,82,92,102,123,147,176,187],"ability":[28],"search":[30],"specific":[32],"entities":[33,165],"(e.g.":[34],"proteins,":[35],"diseases)":[36],"by":[37,161],"tracking":[38],"their":[39,89,119],"mentions":[40],"papers.":[42,87],"PubMed,":[43],"most":[45,135],"well":[46,198],"known":[47],"database":[48],"of":[49,85,96,104,131,146],"biomedical":[50,97],"papers,":[51,67],"relies":[52],"on":[53,91],"human":[54],"curators":[55],"add":[57],"these":[58,159],"annotations.":[59],"This":[60],"can":[61,140],"take":[62],"several":[63],"weeks":[64],"and":[68,137,170],"not":[69,100],"all":[70],"get":[72],"tagged.":[73],"Machine":[74],"learning":[75],"models":[76],"have":[77],"been":[78],"developed":[79],"facilitate":[81],"semantic":[83,200],"indexing":[84],"However":[88],"performance":[90],"more":[93],"comprehensive":[94],"ontologies":[95,124],"concepts":[98],"does":[99],"reach":[101],"levels":[103],"typical":[105],"entity":[106],"recognition":[107],"problems":[108],"studied":[109],"NLP.":[111],"In":[112,149],"large":[113],"part":[114],"this":[115,150],"is":[116,128],"due":[117],"low":[120],"resources,":[121],"large,":[126],"there":[127],"lack":[130],"descriptive":[132],"text":[133],"defining":[134],"entities,":[136],"labeled":[138],"data":[139],"only":[141],"cover":[142],"small":[144],"portion":[145],"ontology.":[148],"paper,":[151],"we":[152],"develop":[153],"model":[156],"that":[157],"overcomes":[158],"challenges":[160],"(1)":[162],"generalizing":[163],"unseen":[166],"at":[167],"training":[168],"time,":[169],"(2)":[171],"incorporating":[172],"linking":[173],"predictions":[174],"into":[175],"mention":[177],"segmentation":[178],"decisions.":[179],"Our":[180],"approach":[181],"achieves":[182],"state-of-the-art":[184],"results":[185],"UMLS":[188],"ontology":[189],"both":[191],"traditional":[192],"recognition/linking":[193],"(+8":[194],"F1":[195,204],"pts)":[196],"as":[197,199],"indexing-based":[201],"evaluation":[202],"(+10":[203],"pts).":[205]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":6}],"updated_date":"2026-04-05T17:49:38.594831","created_date":"2021-02-01T00:00:00"}
