{"id":"https://openalex.org/W2914601452","doi":"https://doi.org/10.1109/bibm.2018.8621564","title":"Extended Analysis of Topological-Pattern-Based Ontology Enrichment","display_name":"Extended Analysis of Topological-Pattern-Based Ontology Enrichment","publication_year":2018,"publication_date":"2018-12-01","ids":{"openalex":"https://openalex.org/W2914601452","doi":"https://doi.org/10.1109/bibm.2018.8621564","mag":"2914601452","pmid":"https://pubmed.ncbi.nlm.nih.gov/30854243"},"language":"en","primary_location":{"id":"doi:10.1109/bibm.2018.8621564","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm.2018.8621564","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2018 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5047567293","display_name":"Zhe He","orcid":"https://orcid.org/0000-0003-3608-0244"},"institutions":[{"id":"https://openalex.org/I103163165","display_name":"Florida State University","ror":"https://ror.org/05g3dte14","country_code":"US","type":"education","lineage":["https://openalex.org/I103163165"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Zhe He","raw_affiliation_strings":["School of Information, Florida State University Tallahassee, Florida USA zhe.he@cci.fsu.edu","School of Information, Florida State University, Tallahassee, Florida, USA"],"affiliations":[{"raw_affiliation_string":"School of Information, Florida State University Tallahassee, Florida USA zhe.he@cci.fsu.edu","institution_ids":[]},{"raw_affiliation_string":"School of Information, Florida State University, Tallahassee, Florida, USA","institution_ids":["https://openalex.org/I103163165"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5080240865","display_name":"Vipina K. Keloth","orcid":"https://orcid.org/0000-0001-6919-1122"},"institutions":[{"id":"https://openalex.org/I118118575","display_name":"New Jersey Institute of Technology","ror":"https://ror.org/05e74xb87","country_code":"US","type":"education","lineage":["https://openalex.org/I118118575"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Vipina Kuttichi Keloth","raw_affiliation_strings":["Department of Computer Science, New Jersey Institute of Technology, Newark, NJ USA, vk396@nijt.edu","Department of Computer Science, New Jersey Institute of Technology, Newark, NJ, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, New Jersey Institute of Technology, Newark, NJ USA, vk396@nijt.edu","institution_ids":[]},{"raw_affiliation_string":"Department of Computer Science, New Jersey Institute of Technology, Newark, NJ, USA","institution_ids":["https://openalex.org/I118118575"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100378184","display_name":"Yan Chen","orcid":"https://orcid.org/0009-0009-1387-4165"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Yan Chen","raw_affiliation_strings":["Department of Computer Inforamtion Systems, BMCC, CUNY, New York, NY USA, yan.chen222@gmail.com","Department of Computer Inforamtion Systems, BMCC CUNY, New York, NJ, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer Inforamtion Systems, BMCC, CUNY, New York, NY USA, yan.chen222@gmail.com","institution_ids":[]},{"raw_affiliation_string":"Department of Computer Inforamtion Systems, BMCC CUNY, New York, NJ, USA","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5070654032","display_name":"James Geller","orcid":"https://orcid.org/0000-0002-9120-525X"},"institutions":[{"id":"https://openalex.org/I103163165","display_name":"Florida State University","ror":"https://ror.org/05g3dte14","country_code":"US","type":"education","lineage":["https://openalex.org/I103163165"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"James Geller","raw_affiliation_strings":["Department of Computer Science, New Jersey Institute of Technology, Newark, NJ USA, james.geller@njit.edu","School of Information, Florida State University, Tallahassee, Florida, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, New Jersey Institute of Technology, Newark, NJ USA, james.geller@njit.edu","institution_ids":[]},{"raw_affiliation_string":"School of Information, Florida State University, Tallahassee, Florida, USA","institution_ids":["https://openalex.org/I103163165"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5047567293"],"corresponding_institution_ids":["https://openalex.org/I103163165"],"apc_list":null,"apc_paid":null,"fwci":0.4639,"has_fulltext":false,"cited_by_count":7,"citation_normalized_percentile":{"value":0.64530118,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"9","issue":null,"first_page":"1641","last_page":"1648"},"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/T10215","display_name":"Semantic Web and Ontologies","score":0.9993000030517578,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.95169997215271,"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/ontology","display_name":"Ontology","score":0.6975497603416443},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6358846426010132},{"id":"https://openalex.org/keywords/topology","display_name":"Topology (electrical circuits)","score":0.47260600328445435},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.13057881593704224},{"id":"https://openalex.org/keywords/electrical-engineering","display_name":"Electrical engineering","score":0.06782916188240051},{"id":"https://openalex.org/keywords/epistemology","display_name":"Epistemology","score":0.05968412756919861}],"concepts":[{"id":"https://openalex.org/C25810664","wikidata":"https://www.wikidata.org/wiki/Q44325","display_name":"Ontology","level":2,"score":0.6975497603416443},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6358846426010132},{"id":"https://openalex.org/C184720557","wikidata":"https://www.wikidata.org/wiki/Q7825049","display_name":"Topology (electrical circuits)","level":2,"score":0.47260600328445435},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.13057881593704224},{"id":"https://openalex.org/C119599485","wikidata":"https://www.wikidata.org/wiki/Q43035","display_name":"Electrical engineering","level":1,"score":0.06782916188240051},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.05968412756919861},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1109/bibm.2018.8621564","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm.2018.8621564","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2018 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"},{"id":"pmid:30854243","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/30854243","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":"Proceedings. IEEE International Conference on Bioinformatics and Biomedicine","raw_type":null},{"id":"pmh:oai:europepmc.org:5391136","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6402505","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320310094","display_name":"University of Washington","ror":"https://ror.org/00cvxb145"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337351","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":49,"referenced_works":["https://openalex.org/W35340939","https://openalex.org/W46109541","https://openalex.org/W117186093","https://openalex.org/W136147141","https://openalex.org/W166276185","https://openalex.org/W1509392121","https://openalex.org/W1772637012","https://openalex.org/W1881304685","https://openalex.org/W1972390403","https://openalex.org/W1978023536","https://openalex.org/W2004119291","https://openalex.org/W2008857142","https://openalex.org/W2022609434","https://openalex.org/W2029596088","https://openalex.org/W2037625543","https://openalex.org/W2057475448","https://openalex.org/W2087204000","https://openalex.org/W2104139434","https://openalex.org/W2121877672","https://openalex.org/W2132610455","https://openalex.org/W2139144616","https://openalex.org/W2150771407","https://openalex.org/W2151423112","https://openalex.org/W2156997379","https://openalex.org/W2159151673","https://openalex.org/W2159583324","https://openalex.org/W2159946338","https://openalex.org/W2318583686","https://openalex.org/W2411162957","https://openalex.org/W2473349478","https://openalex.org/W2515576947","https://openalex.org/W2518614434","https://openalex.org/W2576606657","https://openalex.org/W2599664447","https://openalex.org/W2620729021","https://openalex.org/W2729275743","https://openalex.org/W2785873424","https://openalex.org/W2941084384","https://openalex.org/W6604804359","https://openalex.org/W6606844211","https://openalex.org/W6639432686","https://openalex.org/W6675653202","https://openalex.org/W6680539400","https://openalex.org/W6683627992","https://openalex.org/W6699844393","https://openalex.org/W6715003298","https://openalex.org/W6739085955","https://openalex.org/W6748281016","https://openalex.org/W6761959423"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W2358668433","https://openalex.org/W4396701345","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W4396696052","https://openalex.org/W4402327032","https://openalex.org/W2382290278"],"abstract_inverted_index":{"Maintenance":[0],"of":[1,18,28,42,90,103,106,109,129,152,192],"biomedical":[2],"ontologies":[3,39,193],"is":[4,176],"difficult.":[5],"We":[6,97],"have":[7],"previously":[8],"developed":[9],"a":[10,22,33,80,100,113,116,126,161],"topological-pattern-based":[11],"method":[12,50],"to":[13,76,134,160,189],"deal":[14],"with":[15,61,194],"the":[16,43,49,55,65,69,88,104,138,149,177,184,198],"problem":[17],"identifying":[19],"concepts":[20,63,111,156],"in":[21,94,112,115,142],"reference":[23,66,110],"ontology":[24,57,175],"that":[25,37],"could":[26,58],"be":[27,59,77,135,187],"interest":[29],"for":[30,120,137],"insertion":[31],"into":[32],"target":[34,56,117,174],"ontology.":[35,67],"Assuming":[36],"both":[38],"are":[40],"parts":[41],"Unified":[44],"Medical":[45],"Language":[46],"System":[47],"(UMLS),":[48],"suggests":[51],"approximate":[52],"locations":[53],"where":[54,154],"extended":[60],"new":[62,121],"from":[64,197],"However,":[68,183],"final":[70],"decision":[71],"about":[72],"each":[73],"concept":[74],"has":[75],"made":[78],"by":[79],"human":[81],"expert.":[82],"In":[83,166],"this":[84,146,167,171],"paper,":[85,168],"we":[86,169],"describe":[87],"universe":[89],"cross-ontology":[91,122],"topological":[92],"patterns":[93],"quantitative":[95],"terms.":[96],"then":[98],"present":[99],"theoretical":[101],"analysis":[102],"number":[105],"potential":[107],"placements":[108],"path":[114],"ontology,":[118],"allowing":[119],"synonyms.":[123],"This":[124],"provides":[125],"rough":[127],"estimate":[128],"what":[130],"expert":[131],"resources":[132],"need":[133],"allocated":[136],"task.":[139],"One":[140],"insight":[141],"previous":[143],"work":[144],"on":[145],"topic":[147],"was":[148,157],"large":[150],"percentage":[151],"cases":[153],"importing":[155],"impossible,":[158],"due":[159],"configuration":[162],"called":[163],"\"alternative":[164],"classification.\"":[165],"confirm":[170],"observation.":[172],"Our":[173],"National":[178],"Cancer":[179],"Institute":[180],"thesaurus":[181],"(NCIt).":[182],"methods":[185],"can":[186],"applied":[188],"other":[190],"pairs":[191],"hierarchical":[195],"relationships":[196],"UMLS.":[199]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":3},{"year":2019,"cited_by_count":1}],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2025-10-10T00:00:00"}