{"id":"https://openalex.org/W2098987784","doi":"https://doi.org/10.1186/2041-1480-4-33","title":"Network-based analysis of vaccine-related associations reveals consistent knowledge with the vaccine ontology","display_name":"Network-based analysis of vaccine-related associations reveals consistent knowledge with the vaccine ontology","publication_year":2013,"publication_date":"2013-01-01","ids":{"openalex":"https://openalex.org/W2098987784","doi":"https://doi.org/10.1186/2041-1480-4-33","mag":"2098987784","pmid":"https://pubmed.ncbi.nlm.nih.gov/24209834"},"language":"en","primary_location":{"id":"doi:10.1186/2041-1480-4-33","is_oa":true,"landing_page_url":"https://doi.org/10.1186/2041-1480-4-33","pdf_url":"https://jbiomedsem.biomedcentral.com/counter/pdf/10.1186/2041-1480-4-33","source":{"id":"https://openalex.org/S172276550","display_name":"Journal of Biomedical Semantics","issn_l":"2041-1480","issn":["2041-1480"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Biomedical Semantics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://jbiomedsem.biomedcentral.com/counter/pdf/10.1186/2041-1480-4-33","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5000223629","display_name":"Yuji Zhang","orcid":"https://orcid.org/0000-0002-5429-6762"},"institutions":[{"id":"https://openalex.org/I4210146710","display_name":"Mayo Clinic in Florida","ror":"https://ror.org/03zzw1w08","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1330342723","https://openalex.org/I4210146710"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Yuji Zhang","raw_affiliation_strings":["Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA. Zhang.Yuji@Mayo.edu","Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA. Zhang.Yuji@Mayo.edu","institution_ids":["https://openalex.org/I4210146710"]},{"raw_affiliation_string":"Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, USA","institution_ids":["https://openalex.org/I4210146710"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5076058129","display_name":"Cui Tao","orcid":"https://orcid.org/0000-0002-4267-1924"},"institutions":[{"id":"https://openalex.org/I919571938","display_name":"The University of Texas Health Science Center at Houston","ror":"https://ror.org/03gds6c39","country_code":"US","type":"education","lineage":["https://openalex.org/I919571938"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Cui Tao","raw_affiliation_strings":["School of Biomedical Informatics, University of Texas Health Science Center at Houston, Houston, TX, 77030, USA","[School of Biomedical Informatics, University of Texas Health Science Center at Houston, Houston, USA]"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Biomedical Informatics, University of Texas Health Science Center at Houston, Houston, TX, 77030, USA","institution_ids":["https://openalex.org/I919571938"]},{"raw_affiliation_string":"[School of Biomedical Informatics, University of Texas Health Science Center at Houston, Houston, USA]","institution_ids":["https://openalex.org/I919571938"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5024742201","display_name":"Yongqun He","orcid":"https://orcid.org/0000-0001-9189-9661"},"institutions":[{"id":"https://openalex.org/I27837315","display_name":"University of Michigan","ror":"https://ror.org/00jmfr291","country_code":"US","type":"education","lineage":["https://openalex.org/I27837315"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yongqun He","raw_affiliation_strings":["Unit of Laboratory of Animal Medicine, University of Michigan, Ann Arbor, MI, 48109, USA","Unit of Laboratory of Animal Medicine, University of Michigan, Ann Arbor, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Unit of Laboratory of Animal Medicine, University of Michigan, Ann Arbor, MI, 48109, USA","institution_ids":["https://openalex.org/I27837315"]},{"raw_affiliation_string":"Unit of Laboratory of Animal Medicine, University of Michigan, Ann Arbor, USA","institution_ids":["https://openalex.org/I27837315"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5067940335","display_name":"Pradip Kanjamala","orcid":null},"institutions":[{"id":"https://openalex.org/I4210146710","display_name":"Mayo Clinic in Florida","ror":"https://ror.org/03zzw1w08","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1330342723","https://openalex.org/I4210146710"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Pradip Kanjamala","raw_affiliation_strings":["Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, MN, 55905, USA","Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, MN, 55905, USA","institution_ids":["https://openalex.org/I4210146710"]},{"raw_affiliation_string":"Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, USA","institution_ids":["https://openalex.org/I4210146710"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5101585391","display_name":"Hongfang Liu","orcid":"https://orcid.org/0000-0003-2570-3741"},"institutions":[{"id":"https://openalex.org/I4210146710","display_name":"Mayo Clinic in Florida","ror":"https://ror.org/03zzw1w08","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1330342723","https://openalex.org/I4210146710"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Hongfang Liu","raw_affiliation_strings":["Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, MN, 55905, USA","Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, MN, 55905, USA","institution_ids":["https://openalex.org/I4210146710"]},{"raw_affiliation_string":"Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, USA","institution_ids":["https://openalex.org/I4210146710"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5000223629","https://openalex.org/A5076058129"],"corresponding_institution_ids":["https://openalex.org/I4210146710","https://openalex.org/I919571938"],"apc_list":{"value":1340,"currency":"USD","value_usd":1340},"apc_paid":{"value":1340,"currency":"USD","value_usd":1340},"fwci":1.1002,"has_fulltext":true,"cited_by_count":25,"citation_normalized_percentile":{"value":0.76891882,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"4","issue":"1","first_page":"33","last_page":"33"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.4537999927997589,"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":0.4537999927997589,"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/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.2632000148296356,"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/T12576","display_name":"vaccines and immunoinformatics approaches","score":0.15860000252723694,"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":0.6016913652420044},{"id":"https://openalex.org/keywords/ontology","display_name":"Ontology","score":0.5848279595375061},{"id":"https://openalex.org/keywords/gene-ontology","display_name":"Gene ontology","score":0.580759584903717},{"id":"https://openalex.org/keywords/construct","display_name":"Construct (python library)","score":0.4339154064655304},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.41651850938796997},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.38168513774871826},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.26595252752304077},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.17466887831687927},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.1103728711605072},{"id":"https://openalex.org/keywords/computer-network","display_name":"Computer network","score":0.08089375495910645}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6016913652420044},{"id":"https://openalex.org/C25810664","wikidata":"https://www.wikidata.org/wiki/Q44325","display_name":"Ontology","level":2,"score":0.5848279595375061},{"id":"https://openalex.org/C2987395477","wikidata":"https://www.wikidata.org/wiki/Q135085","display_name":"Gene ontology","level":4,"score":0.580759584903717},{"id":"https://openalex.org/C2780801425","wikidata":"https://www.wikidata.org/wiki/Q5164392","display_name":"Construct (python library)","level":2,"score":0.4339154064655304},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.41651850938796997},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.38168513774871826},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.26595252752304077},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.17466887831687927},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.1103728711605072},{"id":"https://openalex.org/C31258907","wikidata":"https://www.wikidata.org/wiki/Q1301371","display_name":"Computer network","level":1,"score":0.08089375495910645},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","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},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.0}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1186/2041-1480-4-33","is_oa":true,"landing_page_url":"https://doi.org/10.1186/2041-1480-4-33","pdf_url":"https://jbiomedsem.biomedcentral.com/counter/pdf/10.1186/2041-1480-4-33","source":{"id":"https://openalex.org/S172276550","display_name":"Journal of Biomedical Semantics","issn_l":"2041-1480","issn":["2041-1480"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Biomedical Semantics","raw_type":"journal-article"},{"id":"pmid:24209834","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/24209834","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":"Journal of biomedical semantics","raw_type":null},{"id":"pmh:oai:europepmc.org:3145995","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4177205","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/2041-1480-4-33","is_oa":true,"landing_page_url":"https://doi.org/10.1186/2041-1480-4-33","pdf_url":"https://jbiomedsem.biomedcentral.com/counter/pdf/10.1186/2041-1480-4-33","source":{"id":"https://openalex.org/S172276550","display_name":"Journal of Biomedical Semantics","issn_l":"2041-1480","issn":["2041-1480"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Biomedical Semantics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G6928638874","display_name":"Ontology-based Information Network to Support Vaccine Research","funder_award_id":"5r01ai081062-04","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"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2098987784.pdf","grobid_xml":"https://content.openalex.org/works/W2098987784.grobid-xml"},"referenced_works_count":37,"referenced_works":["https://openalex.org/W18016800","https://openalex.org/W22857079","https://openalex.org/W28906051","https://openalex.org/W44453898","https://openalex.org/W282983956","https://openalex.org/W1782336123","https://openalex.org/W1941728430","https://openalex.org/W1966129714","https://openalex.org/W1987868264","https://openalex.org/W2006667691","https://openalex.org/W2026897086","https://openalex.org/W2040878839","https://openalex.org/W2042651385","https://openalex.org/W2056235999","https://openalex.org/W2062533676","https://openalex.org/W2062558911","https://openalex.org/W2062941476","https://openalex.org/W2075406793","https://openalex.org/W2081228674","https://openalex.org/W2093313266","https://openalex.org/W2098044734","https://openalex.org/W2100025044","https://openalex.org/W2120652044","https://openalex.org/W2124757426","https://openalex.org/W2140541004","https://openalex.org/W2142635855","https://openalex.org/W2143448637","https://openalex.org/W2155142785","https://openalex.org/W2160603580","https://openalex.org/W2161604082","https://openalex.org/W2162054277","https://openalex.org/W2316160054","https://openalex.org/W2334055831","https://openalex.org/W2411349414","https://openalex.org/W2422524233","https://openalex.org/W2595613062","https://openalex.org/W4251986374"],"related_works":["https://openalex.org/W2366107444","https://openalex.org/W4388145910","https://openalex.org/W1976205134","https://openalex.org/W2381570729","https://openalex.org/W4248336175","https://openalex.org/W3009369890","https://openalex.org/W2031260042","https://openalex.org/W2391445434","https://openalex.org/W4312490297","https://openalex.org/W2062212388"],"abstract_inverted_index":{"BACKGROUND:":[0],"Ontologies":[1],"are":[2],"useful":[3],"in":[4,12,38,55,88,175,226],"many":[5],"branches":[6],"of":[7,46,71,154,168,307,318],"biomedical":[8,263],"research.":[9],"For":[10],"instance,":[11],"the":[13,16,39,84,89,105,108,125,130,145,159,165,176,227,278,304],"vaccine":[14,27,47,51,90,106,146,160,169],"domain,":[15],"community-based":[17],"Vaccine":[18],"Ontology":[19],"(VO)":[20],"has":[21,41],"been":[22,42],"widely":[23],"used":[24],"to":[25,43,98,124,143,256,262,269,287,297,315],"promote":[26],"data":[28],"standardization,":[29],"integration,":[30],"and":[31,53,86,95,107,138,171,203,222,234,252,265,268,310],"computer-assisted":[32],"reasoning.":[33],"However,":[34],"a":[35,112,119,182,243,247],"major":[36],"challenge":[37],"VO":[40,177],"construct":[44,144],"ontologies":[45],"functions,":[48],"given":[49],"incomplete":[50],"knowledge":[52,58,221,260],"inconsistencies":[54],"how":[56],"this":[57,64,189,238,289],"is":[59,254],"manually":[60],"curated.":[61],"RESULTS:":[62],"In":[63,134,188,237],"study,":[65,239],"we":[66,240,285],"show":[67],"that":[68,81,242],"network-based":[69],"analysis":[70,245],"vaccine-related":[72],"networks":[73],"can":[74],"identify":[75],"underlying":[76],"structural":[77],"information":[78],"consistent":[79],"with":[80,198,211,219],"captured":[82],"by":[83,117,291],"VO,":[85],"commonalities":[87],"adverse":[91],"events":[92],"for":[93,96,273],"vaccines":[94,137,155,205],"diseases":[97],"produce":[99],"new":[100,224],"hypotheses":[101,225,272],"about":[102],"pathomechanisms":[103],"involving":[104,231],"disease":[109],"status.":[110],"First,":[111],"vaccine-vaccine":[113],"network":[114,121,127,184],"was":[115,178,185],"inferred":[116],"applying":[118],"bipartite":[120],"projection":[122],"strategy":[123],"vaccine-disease":[126],"extracted":[128],"from":[129,280,322],"Semantic":[131,281,299],"MEDLINE":[132,282,300],"database.":[133],"total,":[135],"76":[136],"573":[139],"relationships":[140],"were":[141,156,193,206],"identified":[142,194,207],"network.":[147,161],"The":[148,162],"shortest":[149,166],"paths":[150,167],"between":[151,164],"all":[152],"pairs":[153,170],"calculated":[157],"within":[158],"correlation":[163],"their":[172],"semantic":[173,250],"similarities":[174],"then":[179],"investigated.":[180],"Second,":[181],"vaccine-gene":[183],"also":[186],"constructed.":[187],"network,":[190],"4":[191,204],"genes":[192,306],"as":[195,208],"hubs":[196,209],"interacting":[197],"at":[199,212],"least":[200,213],"3":[201,214],"vaccines,":[202,232],"associated":[210],"genes.":[215,235],"These":[216],"findings":[217],"correlate":[218],"existing":[220],"provide":[223],"fundamental":[228],"interaction":[229],"mechanisms":[230],"diseases,":[233],"CONCLUSIONS:":[236],"demonstrated":[241],"combinatorial":[244],"using":[246],"literature":[248],"knowledgebase,":[249],"technology,":[251],"ontology":[253],"able":[255],"reveal":[257],"important":[258],"unidentified":[259],"critical":[261],"research":[264],"public":[266],"health":[267],"generate":[270],"testable":[271],"future":[274],"experimental":[275],"verification.":[276],"As":[277],"associations":[279,319,321],"remain":[283],"incomplete,":[284],"expect":[286],"extend":[288],"work":[290],"(1)":[292],"integrating":[293],"additional":[294],"association":[295],"databases":[296],"complement":[298],"knowledge,":[301],"(2)":[302],"extending":[303],"neighbor":[305],"vaccine-associated":[308],"genes,":[309],"(3)":[311],"assigning":[312],"confidence":[313],"weights":[314],"different":[316,323],"types":[317],"or":[320],"sources.":[324]},"counts_by_year":[{"year":2024,"cited_by_count":4},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":3},{"year":2018,"cited_by_count":4},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":3},{"year":2014,"cited_by_count":4}],"updated_date":"2026-08-06T08:24:18.245995","created_date":"2025-10-10T00:00:00"}