{"id":"https://openalex.org/W4313525566","doi":"https://doi.org/10.1109/bibm55620.2022.9995644","title":"Integration of Gene Regulatory Pathways Found in the Literature in a Graph Database","display_name":"Integration of Gene Regulatory Pathways Found in the Literature in a Graph Database","publication_year":2022,"publication_date":"2022-12-06","ids":{"openalex":"https://openalex.org/W4313525566","doi":"https://doi.org/10.1109/bibm55620.2022.9995644"},"language":"en","primary_location":{"id":"doi:10.1109/bibm55620.2022.9995644","is_oa":false,"landing_page_url":"http://dx.doi.org/10.1109/bibm55620.2022.9995644","pdf_url":null,"source":{"id":"https://openalex.org/S4363607730","display_name":"2022 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"conference"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2022 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"},"type":"conference-paper","indexed_in":["crossref"],"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/A5100722130","display_name":"Yibo Chen","orcid":"https://orcid.org/0000-0002-7391-8790"},"institutions":[{"id":"https://openalex.org/I76835614","display_name":"University of Missouri","ror":"https://ror.org/02ymw8z06","country_code":"US","type":"education","lineage":["https://openalex.org/I76835614"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yibo Chen","raw_affiliation_strings":["Institute for Data Science and Informatics University of Missouri-Columbia,Columbia,MO,USA","Institute for Data Science and Informatics University of Missouri-Columbia, Columbia, MO, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute for Data Science and Informatics University of Missouri-Columbia,Columbia,MO,USA","institution_ids":["https://openalex.org/I76835614"]},{"raw_affiliation_string":"Institute for Data Science and Informatics University of Missouri-Columbia, Columbia, MO, USA","institution_ids":["https://openalex.org/I76835614"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5082428303","display_name":"Dong Xu","orcid":"https://orcid.org/0000-0002-4809-0514"},"institutions":[{"id":"https://openalex.org/I76835614","display_name":"University of Missouri","ror":"https://ror.org/02ymw8z06","country_code":"US","type":"education","lineage":["https://openalex.org/I76835614"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Dong Xu","raw_affiliation_strings":["University of Missouri-Columbia,Department of Electrical Engineering and Computer Science,Columbia,MO,USA","Department of Electrical Engineering and Computer Science, University of Missouri-Columbia, Columbia, MO, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Missouri-Columbia,Department of Electrical Engineering and Computer Science,Columbia,MO,USA","institution_ids":["https://openalex.org/I76835614"]},{"raw_affiliation_string":"Department of Electrical Engineering and Computer Science, University of Missouri-Columbia, Columbia, MO, USA","institution_ids":["https://openalex.org/I76835614"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5060329217","display_name":"Mihail Popescu","orcid":"https://orcid.org/0000-0002-6145-8096"},"institutions":[{"id":"https://openalex.org/I76835614","display_name":"University of Missouri","ror":"https://ror.org/02ymw8z06","country_code":"US","type":"education","lineage":["https://openalex.org/I76835614"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Mihail Popescu","raw_affiliation_strings":["University of Missouri-Columbia,School of Medicines,Columbia,MO,USA","School of Medicines, University of Missouri-Columbia, Columbia, MO, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Missouri-Columbia,School of Medicines,Columbia,MO,USA","institution_ids":["https://openalex.org/I76835614"]},{"raw_affiliation_string":"School of Medicines, University of Missouri-Columbia, Columbia, MO, USA","institution_ids":["https://openalex.org/I76835614"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I76835614"],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":2,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":"18","issue":null,"first_page":"3791","last_page":"3793"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9993000030517578,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9993000030517578,"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9954000115394592,"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/T10885","display_name":"Gene expression and cancer classification","score":0.9947999715805054,"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/computer-science","display_name":"Computer science","score":0.6086644530296326},{"id":"https://openalex.org/keywords/graph-database","display_name":"Graph database","score":0.5904321670532227},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.4804946184158325},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.33922284841537476},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.3358559012413025},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.3259497284889221},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.22213459014892578},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.16354379057884216}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6086644530296326},{"id":"https://openalex.org/C176225458","wikidata":"https://www.wikidata.org/wiki/Q595971","display_name":"Graph database","level":3,"score":0.5904321670532227},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.4804946184158325},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.33922284841537476},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.3358559012413025},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.3259497284889221},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.22213459014892578},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.16354379057884216}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/bibm55620.2022.9995644","is_oa":false,"landing_page_url":"http://dx.doi.org/10.1109/bibm55620.2022.9995644","pdf_url":null,"source":{"id":"https://openalex.org/S4363607730","display_name":"2022 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"conference"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2022 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/3","score":0.5199999809265137,"display_name":"Good health and well-being"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320338440","display_name":"HORIZON EUROPE Health","ror":null}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":12,"referenced_works":["https://openalex.org/W2078126475","https://openalex.org/W2172226195","https://openalex.org/W2182274437","https://openalex.org/W2336774614","https://openalex.org/W2496792076","https://openalex.org/W2786122698","https://openalex.org/W2808743742","https://openalex.org/W2915769855","https://openalex.org/W4210706440","https://openalex.org/W4294216483","https://openalex.org/W6685787327","https://openalex.org/W6766989317"],"related_works":["https://openalex.org/W2003932708","https://openalex.org/W1967424056","https://openalex.org/W2284877871","https://openalex.org/W2138102289","https://openalex.org/W978295669","https://openalex.org/W868043274","https://openalex.org/W2513523087","https://openalex.org/W1187916458","https://openalex.org/W3115442681","https://openalex.org/W2391000461"],"abstract_inverted_index":{"Gene":[0],"regulatory":[1,66],"pathways":[2,11,34,61,102,156],"plays":[3],"a":[4,28,160],"significant":[5],"role":[6],"in":[7,77],"personalized":[8,192],"medicine.":[9,193],"Because":[10],"often":[12],"branch":[13],"or":[14,95,132],"converge,":[15],"graphs":[16],"are":[17],"better":[18],"at":[19],"describing":[20],"them.":[21],"In":[22],"this":[23],"work,":[24],"we":[25,149],"introduced":[26],"Neo4j,":[27],"graph":[29,57,152],"database,":[30],"to":[31,64],"represent":[32],"gene":[33],"collected":[35],"from":[36,42,51,123,145,168],"the":[37,56,78,127,146,164,174,189],"KEGG":[38],"Pathway":[39],"database":[40],"and":[41,90,101,110,187],"217":[43],"non-small":[44],"cell":[45],"lung":[46],"cancer":[47],"(NSCLC)":[48],"articles":[49],"retrieved":[50],"PubMed.":[52],"We":[53],"found":[54],"that":[55,142,151],"representation":[58,175],"of":[59,126,154,163,171,191],"disease":[60,155],"was":[62],"able":[63],"display":[65],"relations":[67],"between":[68],"two":[69],"genes":[70],"even":[71],"though":[72],"they":[73,133],"were":[74],"not":[75,177],"mentioned":[76],"same":[79],"article.":[80],"Besides,":[81],"contradictory":[82,119],"pathway":[83,165],"relations,":[84,128],"for":[85],"example":[86],"\u201cEGFR":[87,91,107],"activates":[88,99,108,112],"RAS\u201d":[89,109],"inhibits":[92],"RAS\u201d,":[93],"self-activation":[94],"self-inhibition":[96],"like":[97,106],"\u201cAKT":[98],"AKT\u201d,":[100],"with":[103],"different":[104,124,129],"direction":[105],"\u201cRAS":[111],"EGFR\u201d":[113],"may":[114,121,176],"also":[115],"be":[116,134],"investigated.":[117],"This":[118],"information":[120,144],"come":[122],"conditions":[125],"scientific":[130],"opinions":[131],"mistakes":[135],"made":[136],"by":[137],"our":[138],"deep":[139],"learning":[140],"pipeline":[141],"extracts":[143],"literature.":[147],"Overall,":[148],"concluded":[150],"representations":[153],"can":[157],"give":[158],"us":[159],"panoramic":[161],"view":[162],"knowledge":[166],"obtained":[167],"various":[169],"kinds":[170],"sources.":[172],"Although":[173],"manifest":[178],"real":[179],"underlying":[180],"mechanisms,":[181],"it":[182],"helps":[183],"provide":[184],"research":[185],"focus":[186],"propel":[188],"development":[190]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":1}],"updated_date":"2026-07-14T23:27:15.235271","created_date":"2025-10-10T00:00:00"}
