{"id":"https://openalex.org/W2127299687","doi":"https://doi.org/10.1093/bioinformatics/btu008","title":"Ontodog: a web-based ontology community view generation tool","display_name":"Ontodog: a web-based ontology community view generation tool","publication_year":2014,"publication_date":"2014-01-09","ids":{"openalex":"https://openalex.org/W2127299687","doi":"https://doi.org/10.1093/bioinformatics/btu008","mag":"2127299687","pmid":"https://pubmed.ncbi.nlm.nih.gov/24413522"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btu008","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btu008","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/30/9/1340/48922123/bioinformatics_30_9_1340.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/30/9/1340/48922123/bioinformatics_30_9_1340.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100652277","display_name":"Jie Zheng","orcid":"https://orcid.org/0000-0002-2999-0103"},"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/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":true,"raw_author_name":"Jie Zheng","raw_affiliation_strings":["1 Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 and 2Unit for Laboratory Animal Medicine, Department of Microbiology and Immunology, Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA"],"affiliations":[{"raw_affiliation_string":"1 Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 and 2Unit for Laboratory Animal Medicine, Department of Microbiology and Immunology, Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA","institution_ids":["https://openalex.org/I79576946","https://openalex.org/I27837315"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5112481250","display_name":"Zuoshuang Xiang","orcid":null},"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"]},{"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":"Zuoshuang Xiang","raw_affiliation_strings":["1 Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 and 2Unit for Laboratory Animal Medicine, Department of Microbiology and Immunology, Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA"],"affiliations":[{"raw_affiliation_string":"1 Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 and 2Unit for Laboratory Animal Medicine, Department of Microbiology and Immunology, Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA","institution_ids":["https://openalex.org/I79576946","https://openalex.org/I27837315"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5069334659","display_name":"Christian J. Stoeckert","orcid":"https://orcid.org/0000-0002-5714-991X"},"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/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":"Christian J. Stoeckert","raw_affiliation_strings":["1 Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 and 2Unit for Laboratory Animal Medicine, Department of Microbiology and Immunology, Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA"],"affiliations":[{"raw_affiliation_string":"1 Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 and 2Unit for Laboratory Animal Medicine, Department of Microbiology and Immunology, Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA","institution_ids":["https://openalex.org/I79576946","https://openalex.org/I27837315"]}]},{"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"]},{"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":"Yongqun He","raw_affiliation_strings":["1 Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 and 2Unit for Laboratory Animal Medicine, Department of Microbiology and Immunology, Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA"],"affiliations":[{"raw_affiliation_string":"1 Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 and 2Unit for Laboratory Animal Medicine, Department of Microbiology and Immunology, Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA","institution_ids":["https://openalex.org/I79576946","https://openalex.org/I27837315"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5100652277"],"corresponding_institution_ids":["https://openalex.org/I27837315","https://openalex.org/I79576946"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":1.1386,"has_fulltext":false,"cited_by_count":16,"citation_normalized_percentile":{"value":0.77862269,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"30","issue":"9","first_page":"1340","last_page":"1342"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9998000264167786,"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":0.9998000264167786,"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/T10215","display_name":"Semantic Web and Ontologies","score":0.9976999759674072,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9879000186920166,"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":0.8995269536972046},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.8328705430030823},{"id":"https://openalex.org/keywords/process-ontology","display_name":"Process ontology","score":0.8060256838798523},{"id":"https://openalex.org/keywords/open-biomedical-ontologies","display_name":"Open Biomedical Ontologies","score":0.7687299251556396},{"id":"https://openalex.org/keywords/ontology-based-data-integration","display_name":"Ontology-based data integration","score":0.7260871529579163},{"id":"https://openalex.org/keywords/suggested-upper-merged-ontology","display_name":"Suggested Upper Merged Ontology","score":0.7072027325630188},{"id":"https://openalex.org/keywords/upper-ontology","display_name":"Upper ontology","score":0.7042020559310913},{"id":"https://openalex.org/keywords/owl-s","display_name":"OWL-S","score":0.5868079662322998},{"id":"https://openalex.org/keywords/ontology-components","display_name":"Ontology components","score":0.5480176210403442},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.5217429399490356},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.4783198833465576},{"id":"https://openalex.org/keywords/ontology-inference-layer","display_name":"Ontology Inference Layer","score":0.46912479400634766},{"id":"https://openalex.org/keywords/semantic-web","display_name":"Semantic Web","score":0.2697610557079315},{"id":"https://openalex.org/keywords/semantic-web-stack","display_name":"Semantic Web Stack","score":0.0763072669506073}],"concepts":[{"id":"https://openalex.org/C25810664","wikidata":"https://www.wikidata.org/wiki/Q44325","display_name":"Ontology","level":2,"score":0.8995269536972046},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8328705430030823},{"id":"https://openalex.org/C137003198","wikidata":"https://www.wikidata.org/wiki/Q7247296","display_name":"Process ontology","level":3,"score":0.8060256838798523},{"id":"https://openalex.org/C137982476","wikidata":"https://www.wikidata.org/wiki/Q7072326","display_name":"Open Biomedical Ontologies","level":5,"score":0.7687299251556396},{"id":"https://openalex.org/C22550185","wikidata":"https://www.wikidata.org/wiki/Q7095047","display_name":"Ontology-based data integration","level":3,"score":0.7260871529579163},{"id":"https://openalex.org/C50971890","wikidata":"https://www.wikidata.org/wiki/Q7635093","display_name":"Suggested Upper Merged Ontology","level":4,"score":0.7072027325630188},{"id":"https://openalex.org/C78726541","wikidata":"https://www.wikidata.org/wiki/Q3882785","display_name":"Upper ontology","level":3,"score":0.7042020559310913},{"id":"https://openalex.org/C50382505","wikidata":"https://www.wikidata.org/wiki/Q2553356","display_name":"OWL-S","level":4,"score":0.5868079662322998},{"id":"https://openalex.org/C154210476","wikidata":"https://www.wikidata.org/wiki/Q7095057","display_name":"Ontology components","level":5,"score":0.5480176210403442},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.5217429399490356},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.4783198833465576},{"id":"https://openalex.org/C115408247","wikidata":"https://www.wikidata.org/wiki/Q3882789","display_name":"Ontology Inference Layer","level":5,"score":0.46912479400634766},{"id":"https://openalex.org/C2129575","wikidata":"https://www.wikidata.org/wiki/Q54837","display_name":"Semantic Web","level":2,"score":0.2697610557079315},{"id":"https://openalex.org/C167379230","wikidata":"https://www.wikidata.org/wiki/Q1026884","display_name":"Semantic Web Stack","level":3,"score":0.0763072669506073},{"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":"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":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","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":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}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btu008","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btu008","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/30/9/1340/48922123/bioinformatics_30_9_1340.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:24413522","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/24413522","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:3998133","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3998133","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btu008","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btu008","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/30/9/1340/48922123/bioinformatics_30_9_1340.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Quality Education","score":0.7300000190734863,"id":"https://metadata.un.org/sdg/4"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320309652","display_name":"University of Michigan","ror":"https://ror.org/00jmfr291"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2127299687.pdf","grobid_xml":"https://content.openalex.org/works/W2127299687.grobid-xml"},"referenced_works_count":10,"referenced_works":["https://openalex.org/W2062558911","https://openalex.org/W2103017472","https://openalex.org/W2144303444","https://openalex.org/W2149378423","https://openalex.org/W2396910800","https://openalex.org/W2405173947","https://openalex.org/W4285719527","https://openalex.org/W6626641764","https://openalex.org/W6712655274","https://openalex.org/W6713662731"],"related_works":["https://openalex.org/W2130691104","https://openalex.org/W2401469280","https://openalex.org/W2072752921","https://openalex.org/W2394747331","https://openalex.org/W2369088979","https://openalex.org/W2732632690","https://openalex.org/W4298842574","https://openalex.org/W2185688944","https://openalex.org/W2395396051","https://openalex.org/W2084805105"],"abstract_inverted_index":{"Biomedical":[0,137],"ontologies":[1,105,110],"are":[2,111],"often":[3],"very":[4],"large":[5],"and":[6,57,96],"complex.":[7],"Only":[8],"a":[9,18,44,72],"subset":[10,52,73],"of":[11,60,74,125,130],"the":[12,36,69,75,115,123,128,134,140],"ontology":[13,24,40,51,62,77,94],"may":[14],"be":[15],"needed":[16],"for":[17,127,136],"specified":[19],"application":[20,124],"or":[21,71,100],"community.":[22],"For":[23],"end":[25],"users,":[26],"it":[27],"is":[28,43,66],"desirable":[29],"to":[30,87,113],"have":[31],"community-based":[32],"labels":[33,37],"rather":[34],"than":[35],"generated":[38],"by":[39],"developers.":[41],"Ontodog":[42,84,126],"web-based":[45],"system":[46],"that":[47],"can":[48],"generate":[49,89,114],"an":[50,61],"based":[53,117],"on":[54,118],"Excel":[55],"input,":[56],"support":[58],"generation":[59,129],"community":[63,90,131],"view,":[64],"which":[65],"defined":[67],"as":[68,139],"whole":[70],"source":[76,141],"with":[78,92],"user-specified":[79],"annotations":[80],"including":[81,106],"user-preferred":[82],"labels.":[83],"allows":[85],"users":[86],"easily":[88],"views":[91,116,132],"minimal":[93],"knowledge":[95],"no":[97],"programming":[98],"skills":[99],"installation":[101],"required.":[102],"Currently":[103],">100":[104],"all":[107],"OBO":[108],"Foundry":[109],"available":[112],"user":[119],"needs.":[120],"We":[121],"demonstrate":[122],"using":[133],"Ontology":[135],"Investigations":[138],"ontology.":[142]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":4},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":2}],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2025-10-10T00:00:00"}
