{"id":"https://openalex.org/W2808814008","doi":"https://doi.org/10.18653/v1/w18-2306","title":"Ontology alignment in the biomedical domain using entity definitions and context","display_name":"Ontology alignment in the biomedical domain using entity definitions and context","publication_year":2018,"publication_date":"2018-01-01","ids":{"openalex":"https://openalex.org/W2808814008","doi":"https://doi.org/10.18653/v1/w18-2306","mag":"2808814008"},"language":"en","primary_location":{"id":"doi:10.18653/v1/w18-2306","is_oa":true,"landing_page_url":"https://doi.org/10.18653/v1/w18-2306","pdf_url":"https://www.aclweb.org/anthology/W18-2306.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 BioNLP 2018 workshop","raw_type":"proceedings-article"},"type":"preprint","indexed_in":["arxiv","crossref","datacite"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://www.aclweb.org/anthology/W18-2306.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5001778694","display_name":"Lucy Lu Wang","orcid":"https://orcid.org/0000-0001-8752-6635"},"institutions":[{"id":"https://openalex.org/I2801852214","display_name":"University of Washington Medical Center","ror":"https://ror.org/00wbzw723","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I2801852214"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Lucy Wang","raw_affiliation_strings":["Department of Biomedical Informatics and Medical Education, University of Washington Seattle, Washington, USA"],"affiliations":[{"raw_affiliation_string":"Department of Biomedical Informatics and Medical Education, University of Washington Seattle, Washington, USA","institution_ids":["https://openalex.org/I2801852214"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5044250030","display_name":"Chandra Bhagavatula","orcid":"https://orcid.org/0000-0001-6264-0378"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Chandra Bhagavatula","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103695396","display_name":"Mark E Neumann","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Mark Neumann","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5066588555","display_name":"Kyle Lo","orcid":"https://orcid.org/0000-0002-1804-2853"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Kyle Lo","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5024910360","display_name":"Chris Wilhelm","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Chris Wilhelm","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5102948988","display_name":"Waleed Ammar","orcid":"https://orcid.org/0000-0003-3541-6981"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Waleed Ammar","raw_affiliation_strings":[],"affiliations":[]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5001778694"],"corresponding_institution_ids":["https://openalex.org/I2801852214"],"apc_list":null,"apc_paid":null,"fwci":0.3711,"has_fulltext":true,"cited_by_count":6,"citation_normalized_percentile":{"value":0.60226105,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":null,"issue":null,"first_page":"47","last_page":"55"},"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/T10028","display_name":"Topic Modeling","score":0.9990000128746033,"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/T10215","display_name":"Semantic Web and Ontologies","score":0.9958000183105469,"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/ontology-alignment","display_name":"Ontology alignment","score":0.8207593560218811},{"id":"https://openalex.org/keywords/ontology","display_name":"Ontology","score":0.8056426644325256},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7927629947662354},{"id":"https://openalex.org/keywords/snomed-ct","display_name":"SNOMED CT","score":0.7480472326278687},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.6635290384292603},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.641621470451355},{"id":"https://openalex.org/keywords/domain","display_name":"Domain (mathematical analysis)","score":0.5313501954078674},{"id":"https://openalex.org/keywords/ontology-based-data-integration","display_name":"Ontology-based data integration","score":0.5273388624191284},{"id":"https://openalex.org/keywords/process-ontology","display_name":"Process ontology","score":0.45489946007728577},{"id":"https://openalex.org/keywords/upper-ontology","display_name":"Upper ontology","score":0.45412176847457886},{"id":"https://openalex.org/keywords/task","display_name":"Task (project management)","score":0.45377403497695923},{"id":"https://openalex.org/keywords/open-biomedical-ontologies","display_name":"Open Biomedical Ontologies","score":0.4343729615211487},{"id":"https://openalex.org/keywords/natural-language-processing","display_name":"Natural language processing","score":0.3794482350349426},{"id":"https://openalex.org/keywords/terminology","display_name":"Terminology","score":0.22508791089057922},{"id":"https://openalex.org/keywords/semantic-web","display_name":"Semantic Web","score":0.18978416919708252},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.05773121118545532}],"concepts":[{"id":"https://openalex.org/C98893333","wikidata":"https://www.wikidata.org/wiki/Q4339878","display_name":"Ontology alignment","level":4,"score":0.8207593560218811},{"id":"https://openalex.org/C25810664","wikidata":"https://www.wikidata.org/wiki/Q44325","display_name":"Ontology","level":2,"score":0.8056426644325256},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7927629947662354},{"id":"https://openalex.org/C206497026","wikidata":"https://www.wikidata.org/wiki/Q1753883","display_name":"SNOMED CT","level":3,"score":0.7480472326278687},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.6635290384292603},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.641621470451355},{"id":"https://openalex.org/C36503486","wikidata":"https://www.wikidata.org/wiki/Q11235244","display_name":"Domain (mathematical analysis)","level":2,"score":0.5313501954078674},{"id":"https://openalex.org/C22550185","wikidata":"https://www.wikidata.org/wiki/Q7095047","display_name":"Ontology-based data integration","level":3,"score":0.5273388624191284},{"id":"https://openalex.org/C137003198","wikidata":"https://www.wikidata.org/wiki/Q7247296","display_name":"Process ontology","level":3,"score":0.45489946007728577},{"id":"https://openalex.org/C78726541","wikidata":"https://www.wikidata.org/wiki/Q3882785","display_name":"Upper ontology","level":3,"score":0.45412176847457886},{"id":"https://openalex.org/C2780451532","wikidata":"https://www.wikidata.org/wiki/Q759676","display_name":"Task (project management)","level":2,"score":0.45377403497695923},{"id":"https://openalex.org/C137982476","wikidata":"https://www.wikidata.org/wiki/Q7072326","display_name":"Open Biomedical Ontologies","level":5,"score":0.4343729615211487},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.3794482350349426},{"id":"https://openalex.org/C547195049","wikidata":"https://www.wikidata.org/wiki/Q1725664","display_name":"Terminology","level":2,"score":0.22508791089057922},{"id":"https://openalex.org/C2129575","wikidata":"https://www.wikidata.org/wiki/Q54837","display_name":"Semantic Web","level":2,"score":0.18978416919708252},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.05773121118545532},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","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/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.0},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"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/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"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/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.18653/v1/w18-2306","is_oa":true,"landing_page_url":"https://doi.org/10.18653/v1/w18-2306","pdf_url":"https://www.aclweb.org/anthology/W18-2306.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 BioNLP 2018 workshop","raw_type":"proceedings-article"},{"id":"pmh:oai:arXiv.org:1806.07976","is_oa":true,"landing_page_url":"http://arxiv.org/abs/1806.07976","pdf_url":"https://arxiv.org/pdf/1806.07976","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"},{"id":"mag:2808814008","is_oa":true,"landing_page_url":"http://export.arxiv.org/pdf/1806.07976","pdf_url":null,"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":"arXiv (Cornell University)","raw_type":null},{"id":"doi:10.48550/arxiv.1806.07976","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.1806.07976","pdf_url":null,"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":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"article"}],"best_oa_location":{"id":"doi:10.18653/v1/w18-2306","is_oa":true,"landing_page_url":"https://doi.org/10.18653/v1/w18-2306","pdf_url":"https://www.aclweb.org/anthology/W18-2306.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 BioNLP 2018 workshop","raw_type":"proceedings-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320317052","display_name":"Allen Institute for Artificial Intelligence","ror":"https://ror.org/05w520734"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2808814008.pdf","grobid_xml":"https://content.openalex.org/works/W2808814008.grobid-xml"},"referenced_works_count":20,"referenced_works":["https://openalex.org/W102861580","https://openalex.org/W1554891152","https://openalex.org/W1984978840","https://openalex.org/W2013093146","https://openalex.org/W2037783154","https://openalex.org/W2095705004","https://openalex.org/W2107598941","https://openalex.org/W2117446654","https://openalex.org/W2118100588","https://openalex.org/W2159583324","https://openalex.org/W2164508904","https://openalex.org/W2165957204","https://openalex.org/W2188545607","https://openalex.org/W2406695577","https://openalex.org/W2507905585","https://openalex.org/W2509019445","https://openalex.org/W2605047533","https://openalex.org/W2621032966","https://openalex.org/W2952867657","https://openalex.org/W4381304672"],"related_works":["https://openalex.org/W2963104256","https://openalex.org/W2294500000","https://openalex.org/W2047043514","https://openalex.org/W2123593707","https://openalex.org/W3184550427","https://openalex.org/W1972578349","https://openalex.org/W2038511337","https://openalex.org/W2098243473","https://openalex.org/W2774226075","https://openalex.org/W2964478958","https://openalex.org/W199960160","https://openalex.org/W1982540051","https://openalex.org/W1971322864","https://openalex.org/W3088084723","https://openalex.org/W2026816491","https://openalex.org/W1706063366","https://openalex.org/W1184841501","https://openalex.org/W2127001182","https://openalex.org/W1751732855","https://openalex.org/W1995689060"],"abstract_inverted_index":{"Ontology":[0,86],"alignment":[1],"is":[2],"the":[3,20,65,73,85,96],"task":[4],"of":[5,19,63,75,82],"identifying":[6],"semantically":[7],"equivalent":[8],"entities":[9,29,39],"from":[10],"two":[11],"given":[12],"ontologies.":[13,32],"Different":[14],"ontologies":[15],"have":[16],"different":[17],"representations":[18],"same":[21],"entity,":[22],"resulting":[23],"in":[24,40,79,99],"a":[25,35,59,100],"need":[26],"to":[27],"de-duplicate":[28],"when":[30,68],"merging":[31],"We":[33,57],"propose":[34],"method":[36],"for":[37,54],"enriching":[38],"an":[41,80],"ontology":[42,55],"with":[43,95],"external":[44,76],"definition":[45],"and":[46,49,70],"context":[47],"information,":[48],"use":[50],"this":[51],"additional":[52,66],"information":[53,67],"alignment.":[56],"develop":[58],"neural":[60],"architecture":[61],"capable":[62],"encoding":[64],"available,":[69],"show":[71],"that":[72],"addition":[74],"data":[77],"results":[78],"F1-score":[81],"0.69":[83],"on":[84],"Alignment":[87],"Evaluation":[88],"Initiative":[89],"(OAEI)":[90],"largebio":[91],"SNOMED-NCI":[92],"subtask,":[93],"comparable":[94],"entitylevel":[97],"matchers":[98],"SOTA":[101],"system.":[102]},"counts_by_year":[{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":1}],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2025-10-10T00:00:00"}
