{"id":"https://openalex.org/W2972776872","doi":"https://doi.org/10.1145/3307339.3342187","title":"Extracting Molecular Entities and Their Interactions from Pathway Figures Based on Deep Learning","display_name":"Extracting Molecular Entities and Their Interactions from Pathway Figures Based on Deep Learning","publication_year":2019,"publication_date":"2019-09-04","ids":{"openalex":"https://openalex.org/W2972776872","doi":"https://doi.org/10.1145/3307339.3342187","mag":"2972776872"},"language":"en","primary_location":{"id":"doi:10.1145/3307339.3342187","is_oa":false,"landing_page_url":"https://doi.org/10.1145/3307339.3342187","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 10th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics","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/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":true,"raw_author_name":"Fei He","raw_affiliation_strings":["University of Missouri, Columbia, MO, USA"],"affiliations":[{"raw_affiliation_string":"University of Missouri, Columbia, MO, USA","institution_ids":["https://openalex.org/I76835614"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5003943520","display_name":"Duolin Wang","orcid":"https://orcid.org/0000-0003-1649-460X"},"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":"Duolin Wang","raw_affiliation_strings":["University of Missouri, Columbia, MO, USA"],"affiliations":[{"raw_affiliation_string":"University of Missouri, Columbia, MO, USA","institution_ids":["https://openalex.org/I76835614"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5065455945","display_name":"Yulia Innokenteva","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 Innokenteva","raw_affiliation_strings":["University of Missouri, Columbia, MO, USA"],"affiliations":[{"raw_affiliation_string":"University of Missouri, Columbia, MO, 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":["University of Missouri, Columbia, MO, USA"],"affiliations":[{"raw_affiliation_string":"University of Missouri, Columbia, MO, 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":["University of Missouri, Columbia, MO, USA"],"affiliations":[{"raw_affiliation_string":"University of Missouri, Columbia, MO, USA","institution_ids":["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":["University of Missouri, Columbia, MO, USA"],"affiliations":[{"raw_affiliation_string":"University of Missouri, Columbia, MO, USA","institution_ids":["https://openalex.org/I76835614"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5087149818"],"corresponding_institution_ids":["https://openalex.org/I76835614"],"apc_list":null,"apc_paid":null,"fwci":0.3409,"has_fulltext":false,"cited_by_count":8,"citation_normalized_percentile":{"value":0.59242678,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":93,"max":98},"biblio":{"volume":null,"issue":null,"first_page":"397","last_page":"404"},"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/T13083","display_name":"Advanced Text Analysis Techniques","score":0.9927999973297119,"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":0.9922999739646912,"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/pipeline","display_name":"Pipeline (software)","score":0.8054507970809937},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7469872236251831},{"id":"https://openalex.org/keywords/pace","display_name":"Pace","score":0.5969357490539551},{"id":"https://openalex.org/keywords/data-curation","display_name":"Data curation","score":0.594316303730011},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.5120282769203186},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4976237118244171},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.47068458795547485},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.35844892263412476}],"concepts":[{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.8054507970809937},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7469872236251831},{"id":"https://openalex.org/C2777526511","wikidata":"https://www.wikidata.org/wiki/Q691543","display_name":"Pace","level":2,"score":0.5969357490539551},{"id":"https://openalex.org/C91632574","wikidata":"https://www.wikidata.org/wiki/Q15088675","display_name":"Data curation","level":2,"score":0.594316303730011},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.5120282769203186},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4976237118244171},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.47068458795547485},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.35844892263412476},{"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/C13280743","wikidata":"https://www.wikidata.org/wiki/Q131089","display_name":"Geodesy","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}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1145/3307339.3342187","is_oa":false,"landing_page_url":"https://doi.org/10.1145/3307339.3342187","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 10th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/4","score":0.6800000071525574,"display_name":"Quality Education"}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":19,"referenced_works":["https://openalex.org/W104184427","https://openalex.org/W845365781","https://openalex.org/W943972918","https://openalex.org/W1536680647","https://openalex.org/W1901129140","https://openalex.org/W1970933811","https://openalex.org/W2072332496","https://openalex.org/W2104167295","https://openalex.org/W2108598243","https://openalex.org/W2110764733","https://openalex.org/W2114363816","https://openalex.org/W2117516905","https://openalex.org/W2156651988","https://openalex.org/W2160591663","https://openalex.org/W2325767305","https://openalex.org/W2566288590","https://openalex.org/W2605982830","https://openalex.org/W2901929601","https://openalex.org/W2964121718"],"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/W4306317641","https://openalex.org/W1488337274","https://openalex.org/W4287611188","https://openalex.org/W2216178707","https://openalex.org/W3095602079"],"abstract_inverted_index":{"Many":[0],"new":[1],"molecular":[2,132],"mechanisms":[3,175],"of":[4,40,59,107],"genomics,":[5],"pharmacogenomics,":[6],"immunology,":[7],"and":[8,16,95,105,134,172],"other":[9],"fields":[10],"are":[11,32],"reflected":[12],"in":[13,25,34,50,71,110,153],"pathway":[14,48,68,80,108,138,174],"figures":[15,49,69,119,139],"need":[17],"to":[18,74,100,151,168],"be":[19],"curated":[20],"for":[21,66],"various":[22],"applications,":[23],"especially":[24],"precision":[26],"medicine.":[27],"Current":[28],"manual":[29],"curation":[30,81],"approaches":[31],"inadequate":[33],"keeping":[35],"up":[36],"with":[37,45,89,165],"the":[38,51,60,102,111,118],"pace":[39],"biomedical":[41,52],"literature":[42,53,155],"growth.":[43],"Compared":[44],"textual":[46],"representations,":[47],"often":[54],"contain":[55],"more":[56,176],"direct":[57],"representations":[58],"mechanisms.":[61],"However,":[62],"no":[63],"systematic":[64],"method":[65,94,164],"curating":[67],"exists":[70],"publications":[72],"due":[73],"date.":[75],"Here,":[76],"we":[77,160],"propose":[78],"a":[79,85,141,148],"pipeline,":[82],"which":[83],"integrates":[84],"deep":[86],"learning":[87],"model":[88,128],"an":[90,96],"optical":[91],"character":[92],"recognition":[93],"image":[97],"processing":[98],"strategy":[99],"capture":[101],"locations,":[103],"names,":[104],"interactions":[106,136],"entities":[109,133],"figure.":[112],"Our":[113],"pipeline":[114,146],"was":[115],"evaluated":[116],"on":[117],"from":[120,137],"PubMed":[121],"publications.":[122],"The":[123,144],"results":[124],"demonstrate":[125],"that":[126],"our":[127,163],"can":[129],"effectively":[130],"retrieve":[131],"their":[135],"at":[140],"large":[142],"scale.":[143],"proposed":[145],"provides":[147],"complementary":[149],"approach":[150],"text-mining":[152,166],"biological":[154],"mining.":[156],"In":[157],"future":[158],"work,":[159],"will":[161],"combine":[162],"tools":[167],"enrich":[169],"extracted":[170],"information":[171],"reconstruct":[173],"precisely.":[177]},"counts_by_year":[{"year":2024,"cited_by_count":4},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":2}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
