{"id":"https://openalex.org/W4206476086","doi":"https://doi.org/10.1093/bib/bbac005","title":"Ontology-aware neural network: a general framework for pattern mining from microbiome data","display_name":"Ontology-aware neural network: a general framework for pattern mining from microbiome data","publication_year":2022,"publication_date":"2022-01-11","ids":{"openalex":"https://openalex.org/W4206476086","doi":"https://doi.org/10.1093/bib/bbac005","pmid":"https://pubmed.ncbi.nlm.nih.gov/35091743"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbac005","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbac005","pdf_url":"https://academic.oup.com/bib/article-pdf/23/2/bbac005/42806483/bbac005.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bib/article-pdf/23/2/bbac005/42806483/bbac005.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5055014462","display_name":"Yuguo Zha","orcid":"https://orcid.org/0000-0003-3702-9416"},"institutions":[{"id":"https://openalex.org/I47720641","display_name":"Huazhong University of Science and Technology","ror":"https://ror.org/00p991c53","country_code":"CN","type":"education","lineage":["https://openalex.org/I47720641"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yuguo Zha","raw_affiliation_strings":["Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Department of Bioinformatics and Systems Biology, Center of AI Biology, College of Life Science and Technology, Huazhong University of Science and Technology, 1037 Luoyu Road Wuhan, Hubei, Wuhan 430074, China"],"raw_orcid":"https://orcid.org/0000-0003-3702-9416","affiliations":[{"raw_affiliation_string":"Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Department of Bioinformatics and Systems Biology, Center of AI Biology, College of Life Science and Technology, Huazhong University of Science and Technology, 1037 Luoyu Road Wuhan, Hubei, Wuhan 430074, China","institution_ids":["https://openalex.org/I47720641"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5076346443","display_name":"Kang Ning","orcid":"https://orcid.org/0000-0003-3325-5387"},"institutions":[{"id":"https://openalex.org/I47720641","display_name":"Huazhong University of Science and Technology","ror":"https://ror.org/00p991c53","country_code":"CN","type":"education","lineage":["https://openalex.org/I47720641"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Kang Ning","raw_affiliation_strings":["Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Department of Bioinformatics and Systems Biology, Center of AI Biology, College of Life Science and Technology, Huazhong University of Science and Technology, 1037 Luoyu Road Wuhan, Hubei, Wuhan 430074, China"],"raw_orcid":"https://orcid.org/0000-0003-3325-5387","affiliations":[{"raw_affiliation_string":"Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Department of Bioinformatics and Systems Biology, Center of AI Biology, College of Life Science and Technology, Huazhong University of Science and Technology, 1037 Luoyu Road Wuhan, Hubei, Wuhan 430074, China","institution_ids":["https://openalex.org/I47720641"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5076346443"],"corresponding_institution_ids":["https://openalex.org/I47720641"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":{"value":4011,"currency":"USD","value_usd":4011},"fwci":0.26,"has_fulltext":false,"cited_by_count":5,"citation_normalized_percentile":{"value":0.50132291,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":99},"biblio":{"volume":"23","issue":"2","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9975000023841858,"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":0.9975000023841858,"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":0.9970999956130981,"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":0.9871000051498413,"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/ontology","display_name":"Ontology","score":0.7745840549468994},{"id":"https://openalex.org/keywords/microbiome","display_name":"Microbiome","score":0.7633387446403503},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6445544362068176},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.5654292702674866},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4964964985847473},{"id":"https://openalex.org/keywords/knowledge-extraction","display_name":"Knowledge extraction","score":0.4748126268386841},{"id":"https://openalex.org/keywords/human-microbiome-project","display_name":"Human Microbiome Project","score":0.44148677587509155},{"id":"https://openalex.org/keywords/metagenomics","display_name":"Metagenomics","score":0.4137105345726013},{"id":"https://openalex.org/keywords/human-microbiome","display_name":"Human microbiome","score":0.40803763270378113},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.21085390448570251},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.11736559867858887},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.07501843571662903}],"concepts":[{"id":"https://openalex.org/C25810664","wikidata":"https://www.wikidata.org/wiki/Q44325","display_name":"Ontology","level":2,"score":0.7745840549468994},{"id":"https://openalex.org/C143121216","wikidata":"https://www.wikidata.org/wiki/Q1330402","display_name":"Microbiome","level":2,"score":0.7633387446403503},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6445544362068176},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.5654292702674866},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4964964985847473},{"id":"https://openalex.org/C120567893","wikidata":"https://www.wikidata.org/wiki/Q1582085","display_name":"Knowledge extraction","level":2,"score":0.4748126268386841},{"id":"https://openalex.org/C190944805","wikidata":"https://www.wikidata.org/wiki/Q3922751","display_name":"Human Microbiome Project","level":4,"score":0.44148677587509155},{"id":"https://openalex.org/C15151743","wikidata":"https://www.wikidata.org/wiki/Q903778","display_name":"Metagenomics","level":3,"score":0.4137105345726013},{"id":"https://openalex.org/C91478284","wikidata":"https://www.wikidata.org/wiki/Q6623796","display_name":"Human microbiome","level":3,"score":0.40803763270378113},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.21085390448570251},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.11736559867858887},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.07501843571662903},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D064307","descriptor_name":"Microbiota","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D064307","descriptor_name":"Microbiota","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D064307","descriptor_name":"Microbiota","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D064307","descriptor_name":"Microbiota","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bib/bbac005","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbac005","pdf_url":"https://academic.oup.com/bib/article-pdf/23/2/bbac005/42806483/bbac005.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:35091743","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/35091743","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":"Briefings in bioinformatics","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:8921649","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8921649","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":"Brief Bioinform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bib/bbac005","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbac005","pdf_url":"https://academic.oup.com/bib/article-pdf/23/2/bbac005/42806483/bbac005.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1370989627","display_name":null,"funder_award_id":"2018YFC0910502","funder_id":"https://openalex.org/F4320335777","funder_display_name":"National Key Research and Development Program of China"},{"id":"https://openalex.org/G4052770625","display_name":null,"funder_award_id":"32071465","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G4196378014","display_name":null,"funder_award_id":"31671374","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G6392341960","display_name":null,"funder_award_id":"31871334","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320335777","display_name":"National Key Research and Development Program of China","ror":null}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4206476086.pdf","grobid_xml":"https://content.openalex.org/works/W4206476086.grobid-xml"},"referenced_works_count":67,"referenced_works":["https://openalex.org/W1433995531","https://openalex.org/W1505191356","https://openalex.org/W1968105193","https://openalex.org/W2009257824","https://openalex.org/W2011375141","https://openalex.org/W2018459257","https://openalex.org/W2032230795","https://openalex.org/W2045204781","https://openalex.org/W2054407804","https://openalex.org/W2088170171","https://openalex.org/W2097124003","https://openalex.org/W2127175247","https://openalex.org/W2137195441","https://openalex.org/W2143196592","https://openalex.org/W2166562121","https://openalex.org/W2190487303","https://openalex.org/W2315521535","https://openalex.org/W2465534016","https://openalex.org/W2562468253","https://openalex.org/W2567465856","https://openalex.org/W2586360538","https://openalex.org/W2590194234","https://openalex.org/W2615066396","https://openalex.org/W2736839127","https://openalex.org/W2749822530","https://openalex.org/W2765950793","https://openalex.org/W2766358903","https://openalex.org/W2888825623","https://openalex.org/W2895335732","https://openalex.org/W2900750626","https://openalex.org/W2901218091","https://openalex.org/W2915583118","https://openalex.org/W2917599954","https://openalex.org/W2920009718","https://openalex.org/W2922701384","https://openalex.org/W2924333283","https://openalex.org/W2936073877","https://openalex.org/W2940897462","https://openalex.org/W2944239259","https://openalex.org/W2951002538","https://openalex.org/W2951274106","https://openalex.org/W2951702646","https://openalex.org/W2967688728","https://openalex.org/W2981463149","https://openalex.org/W2982531601","https://openalex.org/W2984894304","https://openalex.org/W2990249310","https://openalex.org/W2991615383","https://openalex.org/W2998718302","https://openalex.org/W3013056488","https://openalex.org/W3025757981","https://openalex.org/W3048398081","https://openalex.org/W3087332590","https://openalex.org/W3096117901","https://openalex.org/W3096352079","https://openalex.org/W3112600195","https://openalex.org/W3128120098","https://openalex.org/W3161596995","https://openalex.org/W3175203932","https://openalex.org/W3175516073","https://openalex.org/W4211248483","https://openalex.org/W4224442792","https://openalex.org/W4231218848","https://openalex.org/W6769556952","https://openalex.org/W6769989246","https://openalex.org/W6784717622","https://openalex.org/W6784799039"],"related_works":["https://openalex.org/W1968369492","https://openalex.org/W2043102924","https://openalex.org/W2995607319","https://openalex.org/W2391004329","https://openalex.org/W2315403509","https://openalex.org/W1222064643","https://openalex.org/W2624135745","https://openalex.org/W2291217197","https://openalex.org/W2591857450","https://openalex.org/W3139084279"],"abstract_inverted_index":{"With":[0],"the":[1,8,89,105,129,158],"rapid":[2],"accumulation":[3],"of":[4,42,107,128,133,160],"microbiome":[5,23,26,99,146,166,180,200],"data":[6,27,100,147,167,201],"around":[7],"world,":[9],"numerous":[10],"computational":[11],"bioinformatics":[12],"methods":[13,71,164],"have":[14,46,73,87,103,124,152],"been":[15],"developed":[16],"for":[17,98,176],"pattern":[18,69,121,177],"mining":[19,28,70,81,116,148,178],"from":[20,179,182],"such":[21,30],"paramount":[22],"data.":[24],"Current":[25],"methods,":[29,44],"as":[31,94],"gene":[32,113],"and":[33,58,68,83,117,189],"species":[34,115],"mining,":[35,114],"rely":[36],"heavily":[37],"on":[38],"sequence":[39],"comparison.":[40],"Most":[41],"these":[43],"however,":[45],"a":[47,95,142,173],"clear":[48],"trade-off,":[49],"particularly,":[50],"when":[51],"it":[52],"comes":[53],"to":[54,156,187],"big-data":[55],"analytical":[56],"efficiency":[57,82],"accuracy.":[59,84],"Microbiome":[60],"entities":[61],"are":[62],"usually":[63],"organized":[64],"in":[65,80,109,165,199],"ontology":[66,75],"structures,":[67],"that":[72],"considered":[74],"structures":[76],"could":[77],"offer":[78],"advantages":[79],"Here,":[85],"we":[86,151],"summarized":[88],"ontology-aware":[90,188],"neural":[91],"network":[92],"(ONN)":[93],"novel":[96,136],"framework":[97],"mining.":[101,122,168,202],"We":[102,123],"discussed":[104],"applications":[106,155],"ONN":[108,141,161,171],"multiple":[110],"contexts,":[111],"including":[112],"microbial":[118],"community":[119],"dynamic":[120],"then":[125],"highlighted":[126],"one":[127],"most":[130],"important":[131],"characteristics":[132],"ONN,":[134],"namely,":[135],"knowledge":[137],"discovery,":[138],"which":[139,192],"makes":[140],"standout":[143],"among":[144],"all":[145],"methods.":[149],"Finally,":[150],"provided":[153],"several":[154],"showcase":[157],"advantage":[159],"over":[162],"other":[163],"In":[169],"summary,":[170],"represents":[172],"paradigm":[174],"shift":[175],"data:":[181],"traditional":[183],"machine":[184],"learning":[185],"approach":[186],"model-based":[190],"approach,":[191],"has":[193],"found":[194],"its":[195],"broad":[196],"application":[197],"scenarios":[198]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":1},{"year":2023,"cited_by_count":2}],"updated_date":"2026-05-11T08:15:01.531666","created_date":"2025-10-10T00:00:00"}
