{"id":"https://openalex.org/W2997582485","doi":"https://doi.org/10.1186/s13326-019-0217-1","title":"OHMI: the ontology of host-microbiome interactions","display_name":"OHMI: the ontology of host-microbiome interactions","publication_year":2019,"publication_date":"2019-12-01","ids":{"openalex":"https://openalex.org/W2997582485","doi":"https://doi.org/10.1186/s13326-019-0217-1","mag":"2997582485","pmid":"https://pubmed.ncbi.nlm.nih.gov/31888755"},"language":"en","primary_location":{"id":"doi:10.1186/s13326-019-0217-1","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13326-019-0217-1","pdf_url":"https://jbiomedsem.biomedcentral.com/track/pdf/10.1186/s13326-019-0217-1","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/track/pdf/10.1186/s13326-019-0217-1","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","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":true,"raw_author_name":"Yongqun He","raw_affiliation_strings":["University of Michigan Medical School, Ann Arbor, MI, 48109, USA. yongqunh@med.umich.edu","University of Michigan Medical School, Ann Arbor, MI, 48109, USA"],"raw_orcid":"https://orcid.org/0000-0001-9189-9661","affiliations":[{"raw_affiliation_string":"University of Michigan Medical School, Ann Arbor, MI, 48109, USA. yongqunh@med.umich.edu","institution_ids":["https://openalex.org/I27837315"]},{"raw_affiliation_string":"University of Michigan Medical School, Ann Arbor, MI, 48109, USA","institution_ids":["https://openalex.org/I27837315"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5050720879","display_name":"Haihe Wang","orcid":"https://orcid.org/0000-0002-9302-2334"},"institutions":[{"id":"https://openalex.org/I156144747","display_name":"Harbin Medical University","ror":"https://ror.org/05jscf583","country_code":"CN","type":"education","lineage":["https://openalex.org/I156144747"]},{"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"]},{"id":"https://openalex.org/I4210087423","display_name":"Daqing City People's Hospital","ror":"https://ror.org/010z8j306","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210087423"]}],"countries":["CN","US"],"is_corresponding":false,"raw_author_name":"Haihe Wang","raw_affiliation_strings":["Daqing Branch of Harbin Medical University, Daqing, 163319, Heilongjiang, China","University of Michigan Medical School, Ann Arbor, MI, 48109, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Daqing Branch of Harbin Medical University, Daqing, 163319, Heilongjiang, China","institution_ids":["https://openalex.org/I156144747","https://openalex.org/I4210087423"]},{"raw_affiliation_string":"University of Michigan Medical School, Ann Arbor, MI, 48109, 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, 19104, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA","institution_ids":["https://openalex.org/I79576946"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5090415813","display_name":"Daniel P. Beiting","orcid":"https://orcid.org/0000-0002-2865-4589"},"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":"Daniel P. Beiting","raw_affiliation_strings":["University of Pennsylvania School of Veterinary Medicine, Philadelphia, PA, 19104, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Pennsylvania School of Veterinary Medicine, Philadelphia, PA, 19104, USA","institution_ids":["https://openalex.org/I79576946"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5088261794","display_name":"Anna Maria Masci","orcid":"https://orcid.org/0000-0003-1940-6740"},"institutions":[{"id":"https://openalex.org/I170897317","display_name":"Duke University","ror":"https://ror.org/00py81415","country_code":"US","type":"education","lineage":["https://openalex.org/I170897317"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Anna Maria Masci","raw_affiliation_strings":["Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, NC, 27710, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, NC, 27710, USA","institution_ids":["https://openalex.org/I170897317"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100639636","display_name":"Hong Yu","orcid":null},"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"]},{"id":"https://openalex.org/I4210154454","display_name":"Guizhou Provincial People's Hospital","ror":"https://ror.org/046q1bp69","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210154454"]}],"countries":["CN","US"],"is_corresponding":false,"raw_author_name":"Hong Yu","raw_affiliation_strings":["People's Hospital of Guizhou Province, Guiyang, 550025, Guizhou, China","University of Michigan Medical School, Ann Arbor, MI, 48109, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"People's Hospital of Guizhou Province, Guiyang, 550025, Guizhou, China","institution_ids":["https://openalex.org/I4210154454"]},{"raw_affiliation_string":"University of Michigan Medical School, Ann Arbor, MI, 48109, USA","institution_ids":["https://openalex.org/I27837315"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5006959835","display_name":"Kaiyong Liu","orcid":"https://orcid.org/0000-0002-4492-9474"},"institutions":[{"id":"https://openalex.org/I197869895","display_name":"Anhui Medical University","ror":"https://ror.org/03xb04968","country_code":"CN","type":"education","lineage":["https://openalex.org/I197869895"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Kaiyong Liu","raw_affiliation_strings":["School of Public Health, Anhui Medical University, No 81 Meishan Road, Hefei, 230032, Anhui, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Public Health, Anhui Medical University, No 81 Meishan Road, Hefei, 230032, Anhui, China","institution_ids":["https://openalex.org/I197869895"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5068746343","display_name":"Jianmin Wu","orcid":"https://orcid.org/0000-0002-8876-128X"},"institutions":[{"id":"https://openalex.org/I20231570","display_name":"Peking University","ror":"https://ror.org/02v51f717","country_code":"CN","type":"education","lineage":["https://openalex.org/I20231570"]},{"id":"https://openalex.org/I4210093964","display_name":"Peking University Cancer Hospital","ror":"https://ror.org/00nyxxr91","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210093964"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jianmin Wu","raw_affiliation_strings":["Center for Cancer Bioinformatics, Peking University Cancer Hospital & Institute, Beijing, 100142, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Cancer Bioinformatics, Peking University Cancer Hospital & Institute, Beijing, 100142, China","institution_ids":["https://openalex.org/I20231570","https://openalex.org/I4210093964"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5052110481","display_name":"Jeffrey L. Curtis","orcid":"https://orcid.org/0000-0001-5191-4847"},"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"]},{"id":"https://openalex.org/I4210102099","display_name":"VA Ann Arbor Healthcare System","ror":"https://ror.org/018txrr13","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1322918889","https://openalex.org/I2799886695","https://openalex.org/I4210102099","https://openalex.org/I4210127612"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jeffrey L. Curtis","raw_affiliation_strings":["Pulmonary & Critical Care Medicine Section, Medical Service, VA Ann Arbor Healthcare System, Ann Arbor, MI, 48105, USA","University of Michigan Medical School, Ann Arbor, MI, 48109, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Pulmonary & Critical Care Medicine Section, Medical Service, VA Ann Arbor Healthcare System, Ann Arbor, MI, 48105, USA","institution_ids":["https://openalex.org/I4210102099"]},{"raw_affiliation_string":"University of Michigan Medical School, Ann Arbor, MI, 48109, USA","institution_ids":["https://openalex.org/I27837315"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5051216244","display_name":"Barry Smith","orcid":"https://orcid.org/0000-0003-1384-116X"},"institutions":[{"id":"https://openalex.org/I63190737","display_name":"University at Buffalo, State University of New York","ror":"https://ror.org/01y64my43","country_code":"US","type":"education","lineage":["https://openalex.org/I63190737"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Barry Smith","raw_affiliation_strings":["University at Buffalo, Buffalo, NY, 14260, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University at Buffalo, Buffalo, NY, 14260, USA","institution_ids":["https://openalex.org/I63190737"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5014960492","display_name":"Alexander V. Alekseyenko","orcid":"https://orcid.org/0000-0002-5748-2085"},"institutions":[{"id":"https://openalex.org/I153297377","display_name":"Medical University of South Carolina","ror":"https://ror.org/012jban78","country_code":"US","type":"education","lineage":["https://openalex.org/I153297377"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Alexander V. Alekseyenko","raw_affiliation_strings":["Department of Public Health Sciences, Medical University of South Carolina, Charleston, SC, 29425, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Public Health Sciences, Medical University of South Carolina, Charleston, SC, 29425, USA","institution_ids":["https://openalex.org/I153297377"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5026367973","display_name":"Jihad S. Obeid","orcid":"https://orcid.org/0000-0002-7193-7779"},"institutions":[{"id":"https://openalex.org/I153297377","display_name":"Medical University of South Carolina","ror":"https://ror.org/012jban78","country_code":"US","type":"education","lineage":["https://openalex.org/I153297377"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jihad S. Obeid","raw_affiliation_strings":["Department of Public Health Sciences, Medical University of South Carolina, Charleston, SC, 29425, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Public Health Sciences, Medical University of South Carolina, Charleston, SC, 29425, USA","institution_ids":["https://openalex.org/I153297377"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":12,"corresponding_author_ids":["https://openalex.org/A5024742201"],"corresponding_institution_ids":["https://openalex.org/I27837315"],"apc_list":{"value":1190,"currency":"GBP","value_usd":1459},"apc_paid":{"value":1190,"currency":"GBP","value_usd":1459},"fwci":0.4274,"has_fulltext":true,"cited_by_count":10,"citation_normalized_percentile":{"value":0.63350362,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"10","issue":"1","first_page":"25","last_page":"25"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.5985999703407288,"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":0.5985999703407288,"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":0.13369999825954437,"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/T10200","display_name":"Rheumatoid Arthritis Research and Therapies","score":0.04780000075697899,"subfield":{"id":"https://openalex.org/subfields/2745","display_name":"Rheumatology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/microbiome","display_name":"Microbiome","score":0.7729113101959229},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7239705324172974},{"id":"https://openalex.org/keywords/ontology","display_name":"Ontology","score":0.719246506690979},{"id":"https://openalex.org/keywords/open-biomedical-ontologies","display_name":"Open Biomedical Ontologies","score":0.6034613251686096},{"id":"https://openalex.org/keywords/host","display_name":"Host (biology)","score":0.5030061602592468},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.4481295645236969},{"id":"https://openalex.org/keywords/data-integration","display_name":"Data integration","score":0.4382249414920807},{"id":"https://openalex.org/keywords/biological-data","display_name":"Biological data","score":0.43134018778800964},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3422898054122925},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.2944578528404236},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.24316248297691345},{"id":"https://openalex.org/keywords/semantic-web","display_name":"Semantic Web","score":0.21954989433288574},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.20150217413902283},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1577596664428711},{"id":"https://openalex.org/keywords/ontology-based-data-integration","display_name":"Ontology-based data integration","score":0.14335742592811584},{"id":"https://openalex.org/keywords/ecology","display_name":"Ecology","score":0.1230243444442749},{"id":"https://openalex.org/keywords/ontology-alignment","display_name":"Ontology alignment","score":0.10546305775642395}],"concepts":[{"id":"https://openalex.org/C143121216","wikidata":"https://www.wikidata.org/wiki/Q1330402","display_name":"Microbiome","level":2,"score":0.7729113101959229},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7239705324172974},{"id":"https://openalex.org/C25810664","wikidata":"https://www.wikidata.org/wiki/Q44325","display_name":"Ontology","level":2,"score":0.719246506690979},{"id":"https://openalex.org/C137982476","wikidata":"https://www.wikidata.org/wiki/Q7072326","display_name":"Open Biomedical Ontologies","level":5,"score":0.6034613251686096},{"id":"https://openalex.org/C126831891","wikidata":"https://www.wikidata.org/wiki/Q221673","display_name":"Host (biology)","level":2,"score":0.5030061602592468},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.4481295645236969},{"id":"https://openalex.org/C72634772","wikidata":"https://www.wikidata.org/wiki/Q386824","display_name":"Data integration","level":2,"score":0.4382249414920807},{"id":"https://openalex.org/C201797286","wikidata":"https://www.wikidata.org/wiki/Q4914986","display_name":"Biological data","level":2,"score":0.43134018778800964},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3422898054122925},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.2944578528404236},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.24316248297691345},{"id":"https://openalex.org/C2129575","wikidata":"https://www.wikidata.org/wiki/Q54837","display_name":"Semantic Web","level":2,"score":0.21954989433288574},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.20150217413902283},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1577596664428711},{"id":"https://openalex.org/C22550185","wikidata":"https://www.wikidata.org/wiki/Q7095047","display_name":"Ontology-based data integration","level":3,"score":0.14335742592811584},{"id":"https://openalex.org/C18903297","wikidata":"https://www.wikidata.org/wiki/Q7150","display_name":"Ecology","level":1,"score":0.1230243444442749},{"id":"https://openalex.org/C98893333","wikidata":"https://www.wikidata.org/wiki/Q4339878","display_name":"Ontology alignment","level":4,"score":0.10546305775642395},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D054884","descriptor_name":"Host-Pathogen Interactions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D054884","descriptor_name":"Host-Pathogen Interactions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D054884","descriptor_name":"Host-Pathogen Interactions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D054884","descriptor_name":"Host-Pathogen Interactions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D054884","descriptor_name":"Host-Pathogen Interactions","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":true},{"descriptor_ui":"D064229","descriptor_name":"Biological Ontologies","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":true},{"descriptor_ui":"D064229","descriptor_name":"Biological Ontologies","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":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},{"descriptor_ui":"D064307","descriptor_name":"Microbiota","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":7,"locations":[{"id":"doi:10.1186/s13326-019-0217-1","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13326-019-0217-1","pdf_url":"https://jbiomedsem.biomedcentral.com/track/pdf/10.1186/s13326-019-0217-1","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:31888755","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31888755","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:pubmedcentral.nih.gov:6937947","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6937947","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":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"J Biomed Semantics","raw_type":"Text"},{"id":"pmh:oai:deepblue.lib.umich.edu:2027.42/173932","is_oa":false,"landing_page_url":"https://hdl.handle.net/2027.42/173932","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:f741cfba19274b27b9b0504b6bd064ff","is_oa":true,"landing_page_url":"https://doaj.org/article/f741cfba19274b27b9b0504b6bd064ff","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":"Journal of Biomedical Semantics, Vol 10, Iss 1, Pp 1-14 (2019)","raw_type":"article"},{"id":"pmh:oai:philarchive.org/rec/HEOTO-3","is_oa":false,"landing_page_url":"https://philarchive.org/rec/HEOTO-3","pdf_url":null,"source":{"id":"https://openalex.org/S4306402130","display_name":"PhilPapers (PhilPapers Foundation)","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:philpapers.org/rec/HEOTO-3","is_oa":false,"landing_page_url":"https://philpapers.org/rec/HEOTO-3","pdf_url":null,"source":{"id":"https://openalex.org/S4306402131","display_name":"PhilPapers (PhilPapers Foundation)","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":{"id":"doi:10.1186/s13326-019-0217-1","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13326-019-0217-1","pdf_url":"https://jbiomedsem.biomedcentral.com/track/pdf/10.1186/s13326-019-0217-1","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":[{"display_name":"Partnerships for the goals","id":"https://metadata.un.org/sdg/17","score":0.5099999904632568}],"awards":[{"id":"https://openalex.org/G1293109142","display_name":null,"funder_award_id":"R01 GM080646","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G1867918060","display_name":null,"funder_award_id":"U54 CA210963","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G2049072053","display_name":null,"funder_award_id":"UL1TR002240","funder_id":"https://openalex.org/F4320309652","funder_display_name":"University of Michigan"},{"id":"https://openalex.org/G2169531248","display_name":null,"funder_award_id":"UL1TR001450","funder_id":"https://openalex.org/F4320309383","funder_display_name":"Medical University of South Carolina"},{"id":"https://openalex.org/G2331765193","display_name":null,"funder_award_id":"I01 CX000911","funder_id":"https://openalex.org/F4320306127","funder_display_name":"U.S. Department of Veterans Affairs"},{"id":"https://openalex.org/G2502558408","display_name":null,"funder_award_id":"GM080646","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G2807480105","display_name":null,"funder_award_id":"R21TR002513","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G3382472323","display_name":null,"funder_award_id":"R21 TR002513","funder_id":"https://openalex.org/F4320337472","funder_display_name":"National Center for Advancing Translational Sciences"},{"id":"https://openalex.org/G4230598807","display_name":null,"funder_award_id":"UL1TR001450","funder_id":"https://openalex.org/F4320337472","funder_display_name":"National Center for Advancing Translational Sciences"},{"id":"https://openalex.org/G5133862005","display_name":null,"funder_award_id":"R01 LM012517","funder_id":"https://openalex.org/F4320337372","funder_display_name":"U.S. National Library of Medicine"},{"id":"https://openalex.org/G5382207646","display_name":null,"funder_award_id":"UL1 TR001412","funder_id":"https://openalex.org/F4320337472","funder_display_name":"National Center for Advancing Translational Sciences"},{"id":"https://openalex.org/G572550317","display_name":null,"funder_award_id":"UL1TR002240","funder_id":"https://openalex.org/F4320337472","funder_display_name":"National Center for Advancing Translational Sciences"},{"id":"https://openalex.org/G6147947074","display_name":null,"funder_award_id":"UL1TR001412","funder_id":"https://openalex.org/F4320337472","funder_display_name":"National Center for Advancing Translational Sciences"},{"id":"https://openalex.org/G6387646245","display_name":null,"funder_award_id":"UL1TR002240","funder_id":"https://openalex.org/F4320332658","funder_display_name":"Michigan Institute for Clinical and Health Research"},{"id":"https://openalex.org/G7916689590","display_name":null,"funder_award_id":"I01 CX000911","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G8247752239","display_name":null,"funder_award_id":"UL1 TR002240","funder_id":"https://openalex.org/F4320337472","funder_display_name":"National Center for Advancing Translational Sciences"},{"id":"https://openalex.org/G8446955773","display_name":null,"funder_award_id":"R01LM012517","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G947173365","display_name":null,"funder_award_id":"U54 CA210962","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"}],"funders":[{"id":"https://openalex.org/F4320306127","display_name":"U.S. Department of Veterans Affairs","ror":"https://ror.org/05rsv9s98"},{"id":"https://openalex.org/F4320309383","display_name":"Medical University of South Carolina","ror":"https://ror.org/012jban78"},{"id":"https://openalex.org/F4320309652","display_name":"University of Michigan","ror":"https://ror.org/00jmfr291"},{"id":"https://openalex.org/F4320310846","display_name":"University of South Carolina","ror":"https://ror.org/02b6qw903"},{"id":"https://openalex.org/F4320324787","display_name":"Peking University","ror":"https://ror.org/02v51f717"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320332658","display_name":"Michigan Institute for Clinical and Health Research","ror":"https://ror.org/00jmfr291"},{"id":"https://openalex.org/F4320337351","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"},{"id":"https://openalex.org/F4320337372","display_name":"U.S. National Library of Medicine","ror":"https://ror.org/0060t0j89"},{"id":"https://openalex.org/F4320337472","display_name":"National Center for Advancing Translational Sciences","ror":"https://ror.org/04pw6fb54"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2997582485.pdf","grobid_xml":"https://content.openalex.org/works/W2997582485.grobid-xml"},"referenced_works_count":54,"referenced_works":["https://openalex.org/W36111702","https://openalex.org/W1513304325","https://openalex.org/W1537617436","https://openalex.org/W1570492102","https://openalex.org/W1802346448","https://openalex.org/W1917207513","https://openalex.org/W1978709058","https://openalex.org/W1991056282","https://openalex.org/W2009170813","https://openalex.org/W2017247892","https://openalex.org/W2021074129","https://openalex.org/W2025142263","https://openalex.org/W2062558911","https://openalex.org/W2075479850","https://openalex.org/W2097877306","https://openalex.org/W2100181262","https://openalex.org/W2103017472","https://openalex.org/W2103260426","https://openalex.org/W2106830745","https://openalex.org/W2113142309","https://openalex.org/W2113552312","https://openalex.org/W2116034137","https://openalex.org/W2127175247","https://openalex.org/W2129687578","https://openalex.org/W2130420078","https://openalex.org/W2133465414","https://openalex.org/W2133653338","https://openalex.org/W2138007859","https://openalex.org/W2140611297","https://openalex.org/W2151277589","https://openalex.org/W2171475272","https://openalex.org/W2171571559","https://openalex.org/W2302501749","https://openalex.org/W2341651398","https://openalex.org/W2413269306","https://openalex.org/W2417290868","https://openalex.org/W2428300182","https://openalex.org/W2476273855","https://openalex.org/W2519009893","https://openalex.org/W2531883117","https://openalex.org/W2559003643","https://openalex.org/W2559999430","https://openalex.org/W2589364187","https://openalex.org/W2597000813","https://openalex.org/W2607879065","https://openalex.org/W2765266909","https://openalex.org/W2766843384","https://openalex.org/W2771045365","https://openalex.org/W2773787581","https://openalex.org/W2783839275","https://openalex.org/W2860502903","https://openalex.org/W2949435898","https://openalex.org/W2972021296","https://openalex.org/W4253308075"],"related_works":["https://openalex.org/W2127299687","https://openalex.org/W1506177826","https://openalex.org/W2532736362","https://openalex.org/W2726617685","https://openalex.org/W2307569040","https://openalex.org/W2131941936","https://openalex.org/W2366067673","https://openalex.org/W1562796463","https://openalex.org/W3135477004","https://openalex.org/W1530162452"],"abstract_inverted_index":{"BACKGROUND:":[0],"Host-microbiome":[1],"interactions":[2],"(HMIs)":[3],"are":[4,13,198],"critical":[5],"for":[6,277],"the":[7,30,34,41,79,131,190,253],"modulation":[8],"of":[9,25,33,44,52,56,72,100,122,255,274,279],"biological":[10],"processes":[11,48],"and":[12,40,47,54,58,110,115,120,125,187,195,223,250,263,266,268],"associated":[14,117,199],"with":[15,130,150,200],"several":[16],"diseases.":[17],"Extensive":[18],"HMI":[19,61],"studies":[20],"have":[21],"generated":[22,161],"large":[23,240],"amounts":[24],"data.":[26],"We":[27,225],"propose":[28],"that":[29,197],"logical":[31],"representation":[32,43],"knowledge":[35,62,260],"derived":[36],"from":[37,143,177,189,238],"these":[38],"data":[39,53,123,176,244,262,280],"standardized":[42],"experimental":[45,126],"variables":[46],"can":[49,269],"foster":[50],"integration":[51],"reproducibility":[55],"experiments":[57],"thereby":[59],"further":[60],"discovery.":[63],"METHODS:":[64],"Through":[65],"a":[66,69,239],"multi-institutional":[67],"collaboration,":[68],"community-based":[70],"Ontology":[71],"Host-Microbiome":[73],"Interactions":[74],"(OHMI)":[75],"was":[76,160],"developed":[77],"following":[78],"Open":[80],"Biological/Biomedical":[81],"Ontologies":[82],"(OBO)":[83],"Foundry":[84],"principles.":[85],"As":[86,168],"an":[87],"OBO":[88],"library":[89],"ontology,":[90],"OHMI":[91,135,157,171,231,247],"leverages":[92],"established":[93],"ontologies":[94,148],"to":[95,162,229,232],"create":[96],"logically":[97],"structured":[98],"representations":[99],"(1)":[101],"microbiomes,":[102],"microbial":[103],"taxonomy,":[104],"host":[105,107],"species,":[106],"anatomical":[108],"entities,":[109],"HMIs":[111],"under":[112],"different":[113],"conditions":[114],"(2)":[116],"study":[118,209],"protocols":[119],"types":[121],"analysis":[124],"results.":[127],"RESULTS:":[128],"Aligned":[129],"Basic":[132],"Formal":[133],"Ontology,":[134],"comprises":[136],"over":[137,178,184],"1000":[138],"terms,":[139],"including":[140,204],"terms":[141],"imported":[142],"more":[144],"than":[145],"10":[146],"existing":[147,241],"together":[149],"some":[151],"500":[152],"OHMI-specific":[153],"terms.":[154],"A":[155],"specific":[156],"design":[158],"pattern":[159],"represent":[163,233],"typical":[164],"host-microbiome":[165],"interaction":[166],"studies.":[167],"one":[169],"major":[170],"use":[172,230],"case,":[173],"drawing":[174],"on":[175],"50":[179],"peer-reviewed":[180],"publications,":[181],"we":[182],"identified":[183,210,237],"100":[185],"bacteria":[186],"fungi":[188],"gut,":[191],"oral":[192],"cavity,":[193],"skin,":[194],"airway":[196],"six":[201],"rheumatic":[202],"diseases":[203],"rheumatoid":[205],"arthritis.":[206],"Our":[207],"ontological":[208],"new":[211],"high-level":[212],"microbiota":[213],"taxonomical":[214],"structures.":[215],"Two":[216],"microbiome-related":[217],"competency":[218],"questions":[219],"were":[220,226],"also":[221,227],"designed":[222],"addressed.":[224],"able":[228],"statistically":[234],"significant":[235],"results":[236],"microbiome":[242],"database":[243],"analysis.":[245,281],"CONCLUSION:":[246],"represents":[248],"entities":[249],"relations":[251],"in":[252,272],"domain":[254],"HMIs.":[256],"It":[257],"supports":[258],"shared":[259],"representation,":[261],"metadata":[264],"standardization":[265],"integration,":[267],"be":[270],"used":[271],"formulation":[273],"advanced":[275],"queries":[276],"purposes":[278]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":2}],"updated_date":"2026-06-29T08:53:18.405633","created_date":"2025-10-10T00:00:00"}
