{"id":"https://openalex.org/W4311076549","doi":"https://doi.org/10.3389/fbinf.2022.1054578","title":"Molecular cartooning with knowledge graphs","display_name":"Molecular cartooning with knowledge graphs","publication_year":2022,"publication_date":"2022-12-08","ids":{"openalex":"https://openalex.org/W4311076549","doi":"https://doi.org/10.3389/fbinf.2022.1054578","pmid":"https://pubmed.ncbi.nlm.nih.gov/36568701"},"language":"en","primary_location":{"id":"doi:10.3389/fbinf.2022.1054578","is_oa":true,"landing_page_url":"https://doi.org/10.3389/fbinf.2022.1054578","pdf_url":"https://www.frontiersin.org/articles/10.3389/fbinf.2022.1054578/pdf","source":{"id":"https://openalex.org/S4210219554","display_name":"Frontiers in Bioinformatics","issn_l":"2673-7647","issn":["2673-7647"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320527","host_organization_name":"Frontiers Media","host_organization_lineage":["https://openalex.org/P4310320527"],"host_organization_lineage_names":["Frontiers Media"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Frontiers in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://www.frontiersin.org/articles/10.3389/fbinf.2022.1054578/pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5090030592","display_name":"Brook Santangelo","orcid":"https://orcid.org/0000-0002-9266-5813"},"institutions":[{"id":"https://openalex.org/I921990950","display_name":"University of Colorado Denver","ror":"https://ror.org/02hh7en24","country_code":"US","type":"education","lineage":["https://openalex.org/I921990950"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Brook E. Santangelo","raw_affiliation_strings":["Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, CO, United States","Department of Biomedical Informatics, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, CO, United States","institution_ids":["https://openalex.org/I921990950"]},{"raw_affiliation_string":"Department of Biomedical Informatics, United States","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5054972170","display_name":"Lucas A. Gillenwater","orcid":"https://orcid.org/0000-0002-6995-0130"},"institutions":[{"id":"https://openalex.org/I921990950","display_name":"University of Colorado Denver","ror":"https://ror.org/02hh7en24","country_code":"US","type":"education","lineage":["https://openalex.org/I921990950"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Lucas A. Gillenwater","raw_affiliation_strings":["Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, CO, United States","Department of Biomedical Informatics, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, CO, United States","institution_ids":["https://openalex.org/I921990950"]},{"raw_affiliation_string":"Department of Biomedical Informatics, United States","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5052904141","display_name":"Nourah M. Salem","orcid":"https://orcid.org/0000-0002-6617-4404"},"institutions":[{"id":"https://openalex.org/I921990950","display_name":"University of Colorado Denver","ror":"https://ror.org/02hh7en24","country_code":"US","type":"education","lineage":["https://openalex.org/I921990950"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Nourah M. Salem","raw_affiliation_strings":["Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, CO, United States","Department of Biomedical Informatics, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, CO, United States","institution_ids":["https://openalex.org/I921990950"]},{"raw_affiliation_string":"Department of Biomedical Informatics, United States","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5041860080","display_name":"Lawrence Hunter","orcid":"https://orcid.org/0000-0003-1455-3370"},"institutions":[{"id":"https://openalex.org/I921990950","display_name":"University of Colorado Denver","ror":"https://ror.org/02hh7en24","country_code":"US","type":"education","lineage":["https://openalex.org/I921990950"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Lawrence E. Hunter","raw_affiliation_strings":["Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, CO, United States","Department of Biomedical Informatics, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, CO, United States","institution_ids":["https://openalex.org/I921990950"]},{"raw_affiliation_string":"Department of Biomedical Informatics, United States","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I921990950"],"apc_list":{"value":2125,"currency":"USD","value_usd":2125},"apc_paid":{"value":2125,"currency":"USD","value_usd":2125},"fwci":0.0783,"has_fulltext":true,"cited_by_count":1,"citation_normalized_percentile":{"value":0.39371812,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":94},"biblio":{"volume":"2","issue":null,"first_page":"1054578","last_page":"1054578"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9955000281333923,"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":0.9955000281333923,"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/T12478","display_name":"Wikis in Education and Collaboration","score":0.978600025177002,"subfield":{"id":"https://openalex.org/subfields/3315","display_name":"Communication"},"field":{"id":"https://openalex.org/fields/33","display_name":"Social Sciences"},"domain":{"id":"https://openalex.org/domains/2","display_name":"Social Sciences"}},{"id":"https://openalex.org/T10181","display_name":"Natural Language Processing Techniques","score":0.9648000001907349,"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/computer-science","display_name":"Computer science","score":0.33427804708480835}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.33427804708480835}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.3389/fbinf.2022.1054578","is_oa":true,"landing_page_url":"https://doi.org/10.3389/fbinf.2022.1054578","pdf_url":"https://www.frontiersin.org/articles/10.3389/fbinf.2022.1054578/pdf","source":{"id":"https://openalex.org/S4210219554","display_name":"Frontiers in Bioinformatics","issn_l":"2673-7647","issn":["2673-7647"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320527","host_organization_name":"Frontiers Media","host_organization_lineage":["https://openalex.org/P4310320527"],"host_organization_lineage_names":["Frontiers Media"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Frontiers in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:36568701","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/36568701","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":"Frontiers in bioinformatics","raw_type":null},{"id":"pmh:oai:doaj.org/article:d0f80cf8030242a6bd579af7800b152a","is_oa":true,"landing_page_url":"https://doaj.org/article/d0f80cf8030242a6bd579af7800b152a","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","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":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Frontiers in Bioinformatics, Vol 2 (2022)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:9772836","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9772836","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Front Bioinform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.3389/fbinf.2022.1054578","is_oa":true,"landing_page_url":"https://doi.org/10.3389/fbinf.2022.1054578","pdf_url":"https://www.frontiersin.org/articles/10.3389/fbinf.2022.1054578/pdf","source":{"id":"https://openalex.org/S4210219554","display_name":"Frontiers in Bioinformatics","issn_l":"2673-7647","issn":["2673-7647"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320527","host_organization_name":"Frontiers Media","host_organization_lineage":["https://openalex.org/P4310320527"],"host_organization_lineage_names":["Frontiers Media"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Frontiers in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Quality Education","id":"https://metadata.un.org/sdg/4","score":0.6299999952316284}],"awards":[{"id":"https://openalex.org/G166213354","display_name":null,"funder_award_id":"T15 LM009451","funder_id":"https://openalex.org/F4320337372","funder_display_name":"U.S. National Library of Medicine"},{"id":"https://openalex.org/G262569504","display_name":null,"funder_award_id":"OT2TR003422","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337372","display_name":"U.S. National Library of Medicine","ror":"https://ror.org/0060t0j89"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4311076549.pdf","grobid_xml":"https://content.openalex.org/works/W4311076549.grobid-xml"},"referenced_works_count":26,"referenced_works":["https://openalex.org/W1989277387","https://openalex.org/W2103017472","https://openalex.org/W2116759194","https://openalex.org/W2155613928","https://openalex.org/W2159675211","https://openalex.org/W2164298117","https://openalex.org/W2187413858","https://openalex.org/W2558643140","https://openalex.org/W2618235845","https://openalex.org/W2771692618","https://openalex.org/W2916475656","https://openalex.org/W2961798429","https://openalex.org/W2962756421","https://openalex.org/W2963387403","https://openalex.org/W3022051079","https://openalex.org/W3033604458","https://openalex.org/W3092672783","https://openalex.org/W3095380161","https://openalex.org/W3096634408","https://openalex.org/W3101791085","https://openalex.org/W3102147110","https://openalex.org/W3102245839","https://openalex.org/W3198411044","https://openalex.org/W4212919921","https://openalex.org/W4231254854","https://openalex.org/W4247393540"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W2358668433","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W2382290278","https://openalex.org/W2478288626","https://openalex.org/W2350741829","https://openalex.org/W2530322880","https://openalex.org/W1596801655"],"abstract_inverted_index":{"Molecular":[0],"\"cartoons,\"":[1],"such":[2,114],"as":[3],"pathway":[4,33,37,277],"diagrams,":[5],"provide":[6,106],"a":[7,54,87,135,161,185,207,245,249,252],"visual":[8,334],"summary":[9],"of":[10,32,47,57,134,155,173,180,187,219,248,258,296,313,332,336],"biomedical":[11,76,93,281,321],"research":[12],"results":[13,308],"and":[14,42,83,108,138,193,232,286,315,328],"hypotheses.":[15],"Their":[16],"ubiquitous":[17],"appearance":[18],"within":[19],"the":[20,103,131,153,170,178,195,215,220,256,293,297,300,311,325,330],"literature":[21],"indicates":[22],"their":[23],"universal":[24],"application":[25],"in":[26,53,86,98,112,206,241,251,279],"mechanistic":[27],"communication.":[28,338],"A":[29],"recent":[30],"survey":[31],"diagrams":[34,64,278,322],"identified":[35],"64,643":[36],"figures":[38],"published":[39],"between":[40,198],"1995":[41],"2019":[43],"with":[44],"1,112,551":[45],"mentions":[46],"13,464":[48],"unique":[49],"human":[50],"genes":[51],"participating":[52],"wide":[55],"variety":[56],"biological":[58,242],"processes.":[59],"Researchers":[60],"generally":[61,119],"create":[62],"these":[63],"using":[65],"generic":[66],"diagram":[67,211],"editing":[68],"software":[69],"that":[70,97,168,191,213,310],"does":[71],"not":[72,299],"itself":[73],"embody":[74],"any":[75],"knowledge.":[77],"Biomedical":[78],"knowledge":[79,85,94,174],"graphs":[80,175],"(KGs)":[81],"integrate":[82],"represent":[84],"semantically":[88],"consistent":[89],"way,":[90],"systematically":[91],"capturing":[92],"similar":[95],"to":[96,105,130,151,176,209,273,319],"molecular":[99,156,181],"cartoons.":[100],"KGs":[101,117,148,237,268,314],"have":[102,270],"potential":[104],"context":[107],"precise":[109],"details":[110],"useful":[111],"drawing":[113],"figures.":[115,124],"However,":[116],"cannot":[118],"be":[120,149],"translated":[121],"directly":[122],"into":[123],"They":[125],"include":[126],"substantial":[127],"material":[128],"irrelevant":[129],"scientific":[132,216,337],"point":[133],"given":[136],"figure":[137],"are":[139],"often":[140],"more":[141],"detailed":[142],"than":[143],"is":[144,290],"appropriate.":[145],"How":[146],"could":[147,269],"used":[150,272],"facilitate":[152],"creation":[154,167],"diagrams?":[157],"Here":[158],"we":[159,261],"present":[160],"new":[162],"approach":[163],"towards":[164],"cartoon":[165],"image":[166],"utilizes":[169],"semantic":[171,223,264,294,316],"structure":[172],"aid":[177],"production":[179],"diagrams.":[182],"We":[183],"introduce":[184],"set":[186],"\"semantic":[188],"graphical":[189,265,317],"actions\"":[190],"select":[192],"transform":[194],"relational":[196],"information":[197],"heterogeneous":[199],"entities":[200],"(e.g.,":[201],"genes,":[202],"proteins,":[203],"pathways,":[204],"diseases)":[205],"KG":[208],"produce":[210,274,320],"schematics":[212],"meet":[214],"communication":[217],"needs":[218],"user.":[221],"These":[222],"actions":[224,266,318],"search,":[225],"select,":[226],"filter,":[227],"transform,":[228],"group,":[229],"arrange,":[230],"connect":[231],"extract":[233],"relevant":[234],"subgraphs":[235],"from":[236],"based":[238],"on":[239,267,291],"meaning":[240],"terms,":[243],"e.g.,":[244],"protein":[246],"upstream":[247],"target":[250],"pathway.":[253],"To":[254],"demonstrate":[255],"utility":[257],"this":[259,333],"approach,":[260],"show":[262],"how":[263],"been":[271],"three":[275],"existing":[276],"diverse":[280],"domains:":[282],"Down":[283],"Syndrome,":[284],"COVID-19,":[285],"neuroinflammation.":[287],"Our":[288,307],"focus":[289],"recapitulating":[292],"content":[295],"figures,":[298],"layout,":[301],"glyphs,":[302],"or":[303],"other":[304],"aesthetic":[305],"aspects.":[306],"suggest":[309],"use":[312],"will":[323],"reduce":[324],"effort":[326],"required":[327],"improve":[329],"quality":[331],"form":[335]},"counts_by_year":[{"year":2024,"cited_by_count":1}],"updated_date":"2026-07-23T08:03:31.855105","created_date":"2025-10-10T00:00:00"}
