{"id":"https://openalex.org/W4205730624","doi":"https://doi.org/10.1109/bibm52615.2021.9669391","title":"Identifying Genes and Their Interactions from Pathway Figures and Text in Biomedical Articles","display_name":"Identifying Genes and Their Interactions from Pathway Figures and Text in Biomedical Articles","publication_year":2021,"publication_date":"2021-12-09","ids":{"openalex":"https://openalex.org/W4205730624","doi":"https://doi.org/10.1109/bibm52615.2021.9669391"},"language":"en","primary_location":{"id":"doi:10.1109/bibm52615.2021.9669391","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm52615.2021.9669391","pdf_url":null,"source":{"id":"https://openalex.org/S4363607735","display_name":"2021 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":"2021 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"},"type":"article","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/A5087149818","display_name":"Fei He","orcid":"https://orcid.org/0000-0002-3284-9506"},"institutions":[{"id":"https://openalex.org/I184983240","display_name":"Northeast Normal University","ror":"https://ror.org/02rkvz144","country_code":"CN","type":"education","lineage":["https://openalex.org/I184983240"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Fei He","raw_affiliation_strings":["School of Information Science and Technology, Northeast Normal University, Changchun, China"],"affiliations":[{"raw_affiliation_string":"School of Information Science and Technology, Northeast Normal University, Changchun, China","institution_ids":["https://openalex.org/I184983240"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102744009","display_name":"Joshua Thompson","orcid":"https://orcid.org/0000-0001-9430-1282"},"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":"Joshua Thompson","raw_affiliation_strings":["Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, Missouri, USA"],"affiliations":[{"raw_affiliation_string":"Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, Missouri, USA","institution_ids":["https://openalex.org/I76835614"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5079677902","display_name":"Ziting Mao","orcid":null},"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":"Ziting Mao","raw_affiliation_strings":["Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, Missouri, USA"],"affiliations":[{"raw_affiliation_string":"Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, Missouri, USA","institution_ids":["https://openalex.org/I76835614"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5016791068","display_name":"Yijie Ren","orcid":"https://orcid.org/0000-0002-4867-2338"},"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":"Yijie Ren","raw_affiliation_strings":["Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, Missouri, USA"],"affiliations":[{"raw_affiliation_string":"Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, Missouri, USA","institution_ids":["https://openalex.org/I76835614"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5069872712","display_name":"Yulia I. Nussbaum","orcid":null},"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":"Yulia Nussbaum","raw_affiliation_strings":["Institute for Data Science and Informatics University of Missouri, Columbia, Missouri, USA"],"affiliations":[{"raw_affiliation_string":"Institute for Data Science and Informatics University of Missouri, Columbia, Missouri, USA","institution_ids":["https://openalex.org/I76835614"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5052141799","display_name":"Olha Kholod","orcid":"https://orcid.org/0000-0001-6257-4948"},"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":"Olha Kholod","raw_affiliation_strings":["Institute for Data Science and Informatics University of Missouri, Columbia, Missouri, USA"],"affiliations":[{"raw_affiliation_string":"Institute for Data Science and Informatics University of Missouri, Columbia, Missouri, USA","institution_ids":["https://openalex.org/I76835614"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5034457600","display_name":"Dmitriy Shin","orcid":"https://orcid.org/0000-0002-5571-9384"},"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":"Dmitriy Shin","raw_affiliation_strings":["Department of Pathology and Anatomical Sciences, University of Missouri, Columbia, Missouri, USA"],"affiliations":[{"raw_affiliation_string":"Department of Pathology and Anatomical Sciences, University of Missouri, Columbia, Missouri, USA","institution_ids":["https://openalex.org/I76835614"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5009891360","display_name":"Mark Hannink","orcid":"https://orcid.org/0000-0002-7319-6572"},"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":"Mark Hannink","raw_affiliation_strings":["Department of Biochemistry, University of Missouri, Columbia, Missouri, USA"],"affiliations":[{"raw_affiliation_string":"Department of Biochemistry, University of Missouri, Columbia, Missouri, USA","institution_ids":["https://openalex.org/I76835614"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5060329217","display_name":"Mihail Popescu","orcid":"https://orcid.org/0000-0002-6145-8096"},"institutions":[{"id":"https://openalex.org/I2800649613","display_name":"University of Missouri Health System","ror":"https://ror.org/03yp8z857","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I2800649613"]},{"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":["Department of Health Management and Informatics, University of Missouri, Columbia, Missouri, USA"],"affiliations":[{"raw_affiliation_string":"Department of Health Management and Informatics, University of Missouri, Columbia, Missouri, USA","institution_ids":["https://openalex.org/I2800649613","https://openalex.org/I76835614"]}]},{"author_position":"last","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":["Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, Missouri, USA"],"affiliations":[{"raw_affiliation_string":"Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, Missouri, USA","institution_ids":["https://openalex.org/I76835614"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":10,"corresponding_author_ids":["https://openalex.org/A5087149818"],"corresponding_institution_ids":["https://openalex.org/I184983240"],"apc_list":null,"apc_paid":null,"fwci":4.6691,"has_fulltext":false,"cited_by_count":10,"citation_normalized_percentile":{"value":0.96747212,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":91,"max":98},"biblio":{"volume":null,"issue":null,"first_page":"398","last_page":"405"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9997000098228455,"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":0.9997000098228455,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9815999865531921,"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/T13937","display_name":"Genetics, Bioinformatics, and Biomedical Research","score":0.9811000227928162,"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/pipeline","display_name":"Pipeline (software)","score":0.6948873400688171},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6910334825515747},{"id":"https://openalex.org/keywords/upload","display_name":"Upload","score":0.6341068744659424},{"id":"https://openalex.org/keywords/data-curation","display_name":"Data curation","score":0.586253821849823},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.564445972442627},{"id":"https://openalex.org/keywords/pace","display_name":"Pace","score":0.5484713315963745},{"id":"https://openalex.org/keywords/biological-pathway","display_name":"Biological pathway","score":0.43662720918655396},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.3935149908065796},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.3850458264350891},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3781827688217163},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.33793288469314575},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3296574354171753},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.3080509901046753},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.17013686895370483},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.09414541721343994}],"concepts":[{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.6948873400688171},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6910334825515747},{"id":"https://openalex.org/C71901391","wikidata":"https://www.wikidata.org/wiki/Q7126699","display_name":"Upload","level":2,"score":0.6341068744659424},{"id":"https://openalex.org/C91632574","wikidata":"https://www.wikidata.org/wiki/Q15088675","display_name":"Data curation","level":2,"score":0.586253821849823},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.564445972442627},{"id":"https://openalex.org/C2777526511","wikidata":"https://www.wikidata.org/wiki/Q691543","display_name":"Pace","level":2,"score":0.5484713315963745},{"id":"https://openalex.org/C9927688","wikidata":"https://www.wikidata.org/wiki/Q4915012","display_name":"Biological pathway","level":4,"score":0.43662720918655396},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.3935149908065796},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.3850458264350891},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3781827688217163},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.33793288469314575},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3296574354171753},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.3080509901046753},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.17013686895370483},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.09414541721343994},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0},{"id":"https://openalex.org/C13280743","wikidata":"https://www.wikidata.org/wiki/Q131089","display_name":"Geodesy","level":1,"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/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.0},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/bibm52615.2021.9669391","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm52615.2021.9669391","pdf_url":null,"source":{"id":"https://openalex.org/S4363607735","display_name":"2021 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":"2021 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[{"display_name":"Quality Education","id":"https://metadata.un.org/sdg/4","score":0.47999998927116394}],"awards":[],"funders":[{"id":"https://openalex.org/F4320338440","display_name":"HORIZON EUROPE Health","ror":null}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":28,"referenced_works":["https://openalex.org/W104184427","https://openalex.org/W943972918","https://openalex.org/W1536680647","https://openalex.org/W1647671624","https://openalex.org/W1970933811","https://openalex.org/W2072332496","https://openalex.org/W2102605133","https://openalex.org/W2105440823","https://openalex.org/W2110764733","https://openalex.org/W2114363816","https://openalex.org/W2156651988","https://openalex.org/W2160591663","https://openalex.org/W2295176399","https://openalex.org/W2346452181","https://openalex.org/W2509752429","https://openalex.org/W2566288590","https://openalex.org/W2884972436","https://openalex.org/W2946690328","https://openalex.org/W2963351448","https://openalex.org/W2972776872","https://openalex.org/W3006308011","https://openalex.org/W4244393794","https://openalex.org/W6604254268","https://openalex.org/W6636915900","https://openalex.org/W6675026286","https://openalex.org/W6679388247","https://openalex.org/W6753222870","https://openalex.org/W6887904542"],"related_works":["https://openalex.org/W2386723501","https://openalex.org/W2387879414","https://openalex.org/W2390304029","https://openalex.org/W2354923724","https://openalex.org/W2146830340","https://openalex.org/W2377101853","https://openalex.org/W2362180844","https://openalex.org/W2105573916","https://openalex.org/W2378405797","https://openalex.org/W4288601434"],"abstract_inverted_index":{"Many":[0],"high-quality":[1],"biological":[2,20],"pathways":[3,27],"are":[4,14,44,59],"presented":[5],"in":[6,10,46,144],"figures":[7,70,88,124,176],"and":[8,22,34,71,83,89,112,141,177],"text":[9,90],"biomedical":[11,92,157],"literature.":[12],"They":[13],"great":[15],"resources":[16],"for":[17,80],"studies":[18],"of":[19,52,65,91,154],"mechanisms":[21],"precision":[23],"medicine":[24],"practices.":[25],"These":[26],"need":[28],"to":[29,61,109,167],"be":[30],"carefully":[31],"curated,":[32],"reconciled,":[33],"transformed":[35],"into":[36],"a":[37,76,103,162],"computable":[38],"form.":[39],"Current":[40],"manual":[41,129],"curation":[42,78,172],"approaches":[43,58],"inadequate":[45],"keeping":[47],"up":[48],"with":[49,102,128],"the":[50,53,63,123,155,169],"pace":[51],"literature":[54],"growth.":[55],"New":[56],"bio-curation":[57],"needed":[60],"streamline":[62],"identification":[64],"gene":[66,170],"interactions":[67,85,114,143],"from":[68,115,125],"pathway":[69,77,116,145,175],"text.":[72],"This":[73],"paper":[74],"proposes":[75],"approach":[79],"identifying":[81],"genes":[82,111,140],"their":[84,113,142],"using":[86],"both":[87],"articles.":[93,179],"Our":[94,118],"method":[95],"integrates":[96],"deep":[97],"learning-based":[98],"object":[99],"detection":[100],"models":[101],"Google":[104],"optical":[105],"character":[106],"recognition":[107],"service":[108],"extract":[110],"figures.":[117,146],"pipeline":[119,149],"was":[120],"evaluated":[121],"on":[122,173],"PubMed":[126],"publications":[127],"annotations.":[130],"The":[131,147],"results":[132],"demonstrated":[133],"that":[134],"our":[135],"model":[136],"could":[137],"effectively":[138],"retrieve":[139],"proposed":[148],"may":[150],"accelerate":[151],"various":[152],"applications":[153],"latest":[156],"discoveries.":[158],"We":[159],"also":[160],"developed":[161],"web":[163],"server":[164],"at":[165],"http://pathwaydeep.top":[166],"provide":[168],"interaction":[171],"uploaded":[174],"corresponding":[178]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":4},{"year":2023,"cited_by_count":3},{"year":2022,"cited_by_count":2}],"updated_date":"2026-02-07T06:11:34.122080","created_date":"2025-10-10T00:00:00"}
