{"id":"https://openalex.org/W2995850610","doi":"https://doi.org/10.1186/s12859-019-3194-6","title":"VIO: ontology classification and study of vaccine responses given various experimental and analytical conditions","display_name":"VIO: ontology classification and study of vaccine responses given various experimental and analytical conditions","publication_year":2019,"publication_date":"2019-12-01","ids":{"openalex":"https://openalex.org/W2995850610","doi":"https://doi.org/10.1186/s12859-019-3194-6","mag":"2995850610","pmid":"https://pubmed.ncbi.nlm.nih.gov/31865910"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-019-3194-6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-019-3194-6","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-019-3194-6","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"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":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-019-3194-6","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5007063951","display_name":"Edison Ong","orcid":"https://orcid.org/0000-0002-5159-414X"},"institutions":[{"id":"https://openalex.org/I27837315","display_name":"University of Michigan\u2013Ann Arbor","ror":"https://ror.org/00jmfr291","country_code":"US","type":"education","lineage":["https://openalex.org/I27837315"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Edison Ong","raw_affiliation_strings":["Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA","institution_ids":["https://openalex.org/I27837315"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5112619430","display_name":"Peter Sun","orcid":null},"institutions":[{"id":"https://openalex.org/I27837315","display_name":"University of Michigan\u2013Ann Arbor","ror":"https://ror.org/00jmfr291","country_code":"US","type":"education","lineage":["https://openalex.org/I27837315"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Peter Sun","raw_affiliation_strings":["College of Literature, Science, and the Arts, University of Michigan, Ann Arbor, MI, USA"],"affiliations":[{"raw_affiliation_string":"College of Literature, Science, and the Arts, University of Michigan, Ann Arbor, MI, USA","institution_ids":["https://openalex.org/I27837315"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5064008810","display_name":"Kimberly Berke","orcid":null},"institutions":[{"id":"https://openalex.org/I27837315","display_name":"University of Michigan\u2013Ann Arbor","ror":"https://ror.org/00jmfr291","country_code":"US","type":"education","lineage":["https://openalex.org/I27837315"]},{"id":"https://openalex.org/I1629065","display_name":"Central Michigan University","ror":"https://ror.org/02xawj266","country_code":"US","type":"education","lineage":["https://openalex.org/I1629065"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Kimberly Berke","raw_affiliation_strings":["Central Michigan University College of Medicine, Mount Pleasant, MI, USA","College of Literature, Science, and the Arts, University of Michigan, Ann Arbor, MI, USA"],"affiliations":[{"raw_affiliation_string":"Central Michigan University College of Medicine, Mount Pleasant, MI, USA","institution_ids":["https://openalex.org/I1629065"]},{"raw_affiliation_string":"College of Literature, Science, and the Arts, University of Michigan, Ann Arbor, MI, USA","institution_ids":["https://openalex.org/I27837315"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100652277","display_name":"Jie Zheng","orcid":"https://orcid.org/0000-0002-2999-0103"},"institutions":[{"id":"https://openalex.org/I79576946","display_name":"University of Pennsylvania","ror":"https://ror.org/00b30xv10","country_code":"US","type":"education","lineage":["https://openalex.org/I79576946"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jie Zheng","raw_affiliation_strings":["University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA"],"affiliations":[{"raw_affiliation_string":"University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA","institution_ids":["https://openalex.org/I79576946"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5006718188","display_name":"Guanming Wu","orcid":"https://orcid.org/0000-0001-8196-1177"},"institutions":[{"id":"https://openalex.org/I165690674","display_name":"Oregon Health & Science University","ror":"https://ror.org/009avj582","country_code":"US","type":"education","lineage":["https://openalex.org/I165690674"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Guanming Wu","raw_affiliation_strings":["Oregon Health & Science University, Portland, OR, USA"],"affiliations":[{"raw_affiliation_string":"Oregon Health & Science University, Portland, OR, USA","institution_ids":["https://openalex.org/I165690674"]}]},{"author_position":"last","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\u2013Ann Arbor","ror":"https://ror.org/00jmfr291","country_code":"US","type":"education","lineage":["https://openalex.org/I27837315"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Yongqun He","raw_affiliation_strings":["Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA. yongqunh@med.umich.edu","Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA. yongqunh@med.umich.edu","Unit of Laboratory Animal Medicine, University of Michigan, Ann Arbor, MI, USA. yongqunh@med.umich.edu","Unit of Laboratory Animal Medicine, University of Michigan, Ann Arbor, MI, USA"],"affiliations":[{"raw_affiliation_string":"Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA. yongqunh@med.umich.edu","institution_ids":[]},{"raw_affiliation_string":"Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA. yongqunh@med.umich.edu","institution_ids":[]},{"raw_affiliation_string":"Unit of Laboratory Animal Medicine, University of Michigan, Ann Arbor, MI, USA. yongqunh@med.umich.edu","institution_ids":[]},{"raw_affiliation_string":"Unit of Laboratory Animal Medicine, University of Michigan, Ann Arbor, MI, USA","institution_ids":["https://openalex.org/I27837315"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5024742201"],"corresponding_institution_ids":["https://openalex.org/I27837315"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":0.7707,"has_fulltext":true,"cited_by_count":13,"citation_normalized_percentile":{"value":0.71802467,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"20","issue":"S21","first_page":"704","last_page":"704"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12576","display_name":"vaccines and immunoinformatics approaches","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/T12576","display_name":"vaccines and immunoinformatics approaches","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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9952999949455261,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9866999983787537,"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/gene-ontology","display_name":"Gene ontology","score":0.5911152958869934},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5244158506393433},{"id":"https://openalex.org/keywords/ontology","display_name":"Ontology","score":0.5112953186035156},{"id":"https://openalex.org/keywords/normalization","display_name":"Normalization (sociology)","score":0.5053680539131165},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5049973130226135},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.4598598778247833},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.4293382465839386},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.41970765590667725},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.41223621368408203},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.3321071267127991},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3254167139530182},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.20977747440338135},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.1768580973148346}],"concepts":[{"id":"https://openalex.org/C2987395477","wikidata":"https://www.wikidata.org/wiki/Q135085","display_name":"Gene ontology","level":4,"score":0.5911152958869934},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5244158506393433},{"id":"https://openalex.org/C25810664","wikidata":"https://www.wikidata.org/wiki/Q44325","display_name":"Ontology","level":2,"score":0.5112953186035156},{"id":"https://openalex.org/C136886441","wikidata":"https://www.wikidata.org/wiki/Q926129","display_name":"Normalization (sociology)","level":2,"score":0.5053680539131165},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5049973130226135},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.4598598778247833},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.4293382465839386},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.41970765590667725},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.41223621368408203},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.3321071267127991},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3254167139530182},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.20977747440338135},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.1768580973148346},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C19165224","wikidata":"https://www.wikidata.org/wiki/Q23404","display_name":"Anthropology","level":1,"score":0.0},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.0},{"id":"https://openalex.org/C144024400","wikidata":"https://www.wikidata.org/wiki/Q21201","display_name":"Sociology","level":0,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014612","descriptor_name":"Vaccines","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014612","descriptor_name":"Vaccines","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014612","descriptor_name":"Vaccines","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D064229","descriptor_name":"Biological Ontologies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D064229","descriptor_name":"Biological Ontologies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D064229","descriptor_name":"Biological Ontologies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1186/s12859-019-3194-6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-019-3194-6","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-019-3194-6","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"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":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:31865910","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31865910","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:deepblue.lib.umich.edu:2027.42/173428","is_oa":false,"landing_page_url":"https://hdl.handle.net/2027.42/173428","pdf_url":null,"source":{"id":"https://openalex.org/S4306400393","display_name":"Deep Blue (University of Michigan)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I27837315","host_organization_name":"University of Michigan","host_organization_lineage":["https://openalex.org/I27837315"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Journal Article"},{"id":"pmh:oai:doaj.org/article:6c6aae1b56854e74a954a58b71075435","is_oa":true,"landing_page_url":"https://doaj.org/article/6c6aae1b56854e74a954a58b71075435","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 20, Iss S21, Pp 1-10 (2019)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:6927110","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6927110","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s12859-019-3194-6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-019-3194-6","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-019-3194-6","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"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":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Good health and well-being","id":"https://metadata.un.org/sdg/3","score":0.699999988079071}],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2995850610.pdf","grobid_xml":"https://content.openalex.org/works/W2995850610.grobid-xml"},"referenced_works_count":45,"referenced_works":["https://openalex.org/W1546952499","https://openalex.org/W1802346448","https://openalex.org/W1976424397","https://openalex.org/W1978711639","https://openalex.org/W1989277387","https://openalex.org/W2000061106","https://openalex.org/W2010637767","https://openalex.org/W2021074129","https://openalex.org/W2021560851","https://openalex.org/W2025738474","https://openalex.org/W2062022660","https://openalex.org/W2062558911","https://openalex.org/W2062715434","https://openalex.org/W2072096009","https://openalex.org/W2073217938","https://openalex.org/W2081098333","https://openalex.org/W2090033717","https://openalex.org/W2090970088","https://openalex.org/W2101803749","https://openalex.org/W2111547563","https://openalex.org/W2113142309","https://openalex.org/W2118258530","https://openalex.org/W2124538722","https://openalex.org/W2142635855","https://openalex.org/W2144902263","https://openalex.org/W2158217645","https://openalex.org/W2163401084","https://openalex.org/W2163827272","https://openalex.org/W2171178051","https://openalex.org/W2229895077","https://openalex.org/W2236822143","https://openalex.org/W2405832052","https://openalex.org/W2520193009","https://openalex.org/W2531883117","https://openalex.org/W2761516325","https://openalex.org/W2766123177","https://openalex.org/W2770091772","https://openalex.org/W2783839275","https://openalex.org/W2953253500","https://openalex.org/W3133895878","https://openalex.org/W4234509242","https://openalex.org/W4291941637","https://openalex.org/W6666086819","https://openalex.org/W6689293516","https://openalex.org/W6842138004"],"related_works":["https://openalex.org/W2953716828","https://openalex.org/W2904857019","https://openalex.org/W2944728705","https://openalex.org/W3011538607","https://openalex.org/W2904022177","https://openalex.org/W2591697403","https://openalex.org/W4321441197","https://openalex.org/W2359348847","https://openalex.org/W4294432981","https://openalex.org/W4321276295"],"abstract_inverted_index":{"The":[0],"ontology-based":[1],"analysis":[2,9],"framework":[3],"supports":[4],"standardized":[5],"representation,":[6],"integration,":[7],"and":[8],"of":[10,13],"heterogeneous":[11],"data":[12],"host":[14],"responses":[15],"to":[16],"vaccines.":[17],"Our":[18],"study":[19],"also":[20],"showed":[21],"that":[22],"differences":[23],"in":[24],"specific":[25],"variables":[26],"might":[27],"explain":[28],"different":[29],"results":[30],"drawn":[31],"from":[32],"similar":[33],"studies.":[34]},"counts_by_year":[{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":1},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":5},{"year":2019,"cited_by_count":1}],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2025-10-10T00:00:00"}
