{"id":"https://openalex.org/W2115235175","doi":"https://doi.org/10.1093/bioinformatics/btp193","title":"From disease ontology to disease-ontology lite: statistical methods to adapt a general-purpose ontology for the test of gene-ontology associations","display_name":"From disease ontology to disease-ontology lite: statistical methods to adapt a general-purpose ontology for the test of gene-ontology associations","publication_year":2009,"publication_date":"2009-05-27","ids":{"openalex":"https://openalex.org/W2115235175","doi":"https://doi.org/10.1093/bioinformatics/btp193","mag":"2115235175","pmid":"https://pubmed.ncbi.nlm.nih.gov/19478018"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btp193","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btp193","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/25/12/i63/48991091/bioinformatics_25_12_i63.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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","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":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/25/12/i63/48991091/bioinformatics_25_12_i63.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5075682354","display_name":"Pan Du","orcid":"https://orcid.org/0000-0002-4561-6883"},"institutions":[{"id":"https://openalex.org/I40347166","display_name":"University of Chicago","ror":"https://ror.org/024mw5h28","country_code":"US","type":"education","lineage":["https://openalex.org/I40347166"]},{"id":"https://openalex.org/I111979921","display_name":"Northwestern University","ror":"https://ror.org/000e0be47","country_code":"US","type":"education","lineage":["https://openalex.org/I111979921"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Pan Du","raw_affiliation_strings":["1 The Biomedical Informatics Center, Northwestern University, Chicago, IL 60611, 2Department of Pathology, University of Chicago, IL 60637 and 3Department of Preventive Medicine, Northwestern University, Chicago, IL 60611, USA"],"affiliations":[{"raw_affiliation_string":"1 The Biomedical Informatics Center, Northwestern University, Chicago, IL 60611, 2Department of Pathology, University of Chicago, IL 60637 and 3Department of Preventive Medicine, Northwestern University, Chicago, IL 60611, USA","institution_ids":["https://openalex.org/I111979921","https://openalex.org/I40347166"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101514976","display_name":"Gang Feng","orcid":"https://orcid.org/0000-0001-9855-616X"},"institutions":[{"id":"https://openalex.org/I40347166","display_name":"University of Chicago","ror":"https://ror.org/024mw5h28","country_code":"US","type":"education","lineage":["https://openalex.org/I40347166"]},{"id":"https://openalex.org/I111979921","display_name":"Northwestern University","ror":"https://ror.org/000e0be47","country_code":"US","type":"education","lineage":["https://openalex.org/I111979921"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Gang Feng","raw_affiliation_strings":["1 The Biomedical Informatics Center, Northwestern University, Chicago, IL 60611, 2Department of Pathology, University of Chicago, IL 60637 and 3Department of Preventive Medicine, Northwestern University, Chicago, IL 60611, USA"],"affiliations":[{"raw_affiliation_string":"1 The Biomedical Informatics Center, Northwestern University, Chicago, IL 60611, 2Department of Pathology, University of Chicago, IL 60637 and 3Department of Preventive Medicine, Northwestern University, Chicago, IL 60611, USA","institution_ids":["https://openalex.org/I111979921","https://openalex.org/I40347166"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5091349266","display_name":"Jared Flatow","orcid":null},"institutions":[{"id":"https://openalex.org/I111979921","display_name":"Northwestern University","ror":"https://ror.org/000e0be47","country_code":"US","type":"education","lineage":["https://openalex.org/I111979921"]},{"id":"https://openalex.org/I40347166","display_name":"University of Chicago","ror":"https://ror.org/024mw5h28","country_code":"US","type":"education","lineage":["https://openalex.org/I40347166"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jared Flatow","raw_affiliation_strings":["1 The Biomedical Informatics Center, Northwestern University, Chicago, IL 60611, 2Department of Pathology, University of Chicago, IL 60637 and 3Department of Preventive Medicine, Northwestern University, Chicago, IL 60611, USA"],"affiliations":[{"raw_affiliation_string":"1 The Biomedical Informatics Center, Northwestern University, Chicago, IL 60611, 2Department of Pathology, University of Chicago, IL 60637 and 3Department of Preventive Medicine, Northwestern University, Chicago, IL 60611, USA","institution_ids":["https://openalex.org/I111979921","https://openalex.org/I40347166"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5002471015","display_name":"Jie Song","orcid":"https://orcid.org/0000-0002-5769-3886"},"institutions":[{"id":"https://openalex.org/I40347166","display_name":"University of Chicago","ror":"https://ror.org/024mw5h28","country_code":"US","type":"education","lineage":["https://openalex.org/I40347166"]},{"id":"https://openalex.org/I111979921","display_name":"Northwestern University","ror":"https://ror.org/000e0be47","country_code":"US","type":"education","lineage":["https://openalex.org/I111979921"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jie Song","raw_affiliation_strings":["1 The Biomedical Informatics Center, Northwestern University, Chicago, IL 60611, 2Department of Pathology, University of Chicago, IL 60637 and 3Department of Preventive Medicine, Northwestern University, Chicago, IL 60611, USA"],"affiliations":[{"raw_affiliation_string":"1 The Biomedical Informatics Center, Northwestern University, Chicago, IL 60611, 2Department of Pathology, University of Chicago, IL 60637 and 3Department of Preventive Medicine, Northwestern University, Chicago, IL 60611, USA","institution_ids":["https://openalex.org/I111979921","https://openalex.org/I40347166"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5026954579","display_name":"Michelle Holko","orcid":null},"institutions":[{"id":"https://openalex.org/I40347166","display_name":"University of Chicago","ror":"https://ror.org/024mw5h28","country_code":"US","type":"education","lineage":["https://openalex.org/I40347166"]},{"id":"https://openalex.org/I111979921","display_name":"Northwestern University","ror":"https://ror.org/000e0be47","country_code":"US","type":"education","lineage":["https://openalex.org/I111979921"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Michelle Holko","raw_affiliation_strings":["1 The Biomedical Informatics Center, Northwestern University, Chicago, IL 60611, 2Department of Pathology, University of Chicago, IL 60637 and 3Department of Preventive Medicine, Northwestern University, Chicago, IL 60611, USA"],"affiliations":[{"raw_affiliation_string":"1 The Biomedical Informatics Center, Northwestern University, Chicago, IL 60611, 2Department of Pathology, University of Chicago, IL 60637 and 3Department of Preventive Medicine, Northwestern University, Chicago, IL 60611, USA","institution_ids":["https://openalex.org/I111979921","https://openalex.org/I40347166"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5038170232","display_name":"Warren A. Kibbe","orcid":"https://orcid.org/0000-0001-5622-7659"},"institutions":[{"id":"https://openalex.org/I40347166","display_name":"University of Chicago","ror":"https://ror.org/024mw5h28","country_code":"US","type":"education","lineage":["https://openalex.org/I40347166"]},{"id":"https://openalex.org/I111979921","display_name":"Northwestern University","ror":"https://ror.org/000e0be47","country_code":"US","type":"education","lineage":["https://openalex.org/I111979921"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Warren A. Kibbe","raw_affiliation_strings":["1 The Biomedical Informatics Center, Northwestern University, Chicago, IL 60611, 2Department of Pathology, University of Chicago, IL 60637 and 3Department of Preventive Medicine, Northwestern University, Chicago, IL 60611, USA"],"affiliations":[{"raw_affiliation_string":"1 The Biomedical Informatics Center, Northwestern University, Chicago, IL 60611, 2Department of Pathology, University of Chicago, IL 60637 and 3Department of Preventive Medicine, Northwestern University, Chicago, IL 60611, USA","institution_ids":["https://openalex.org/I111979921","https://openalex.org/I40347166"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5111991056","display_name":"Simon Lin","orcid":null},"institutions":[{"id":"https://openalex.org/I40347166","display_name":"University of Chicago","ror":"https://ror.org/024mw5h28","country_code":"US","type":"education","lineage":["https://openalex.org/I40347166"]},{"id":"https://openalex.org/I111979921","display_name":"Northwestern University","ror":"https://ror.org/000e0be47","country_code":"US","type":"education","lineage":["https://openalex.org/I111979921"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Simon M. Lin","raw_affiliation_strings":["1 The Biomedical Informatics Center, Northwestern University, Chicago, IL 60611, 2Department of Pathology, University of Chicago, IL 60637 and 3Department of Preventive Medicine, Northwestern University, Chicago, IL 60611, USA"],"affiliations":[{"raw_affiliation_string":"1 The Biomedical Informatics Center, Northwestern University, Chicago, IL 60611, 2Department of Pathology, University of Chicago, IL 60637 and 3Department of Preventive Medicine, Northwestern University, Chicago, IL 60611, USA","institution_ids":["https://openalex.org/I111979921","https://openalex.org/I40347166"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5075682354"],"corresponding_institution_ids":["https://openalex.org/I111979921","https://openalex.org/I40347166"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":4.3003,"has_fulltext":true,"cited_by_count":110,"citation_normalized_percentile":{"value":0.95105506,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":100},"biblio":{"volume":"25","issue":"12","first_page":"i63","last_page":"i68"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.996999979019165,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.996999979019165,"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":0.9958999752998352,"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/T10885","display_name":"Gene expression and cancer classification","score":0.9786999821662903,"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":0.7348154783248901},{"id":"https://openalex.org/keywords/cluster-analysis","display_name":"Cluster analysis","score":0.6553080081939697},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6187981963157654},{"id":"https://openalex.org/keywords/open-biomedical-ontologies","display_name":"Open Biomedical Ontologies","score":0.5965150594711304},{"id":"https://openalex.org/keywords/ontology-based-data-integration","display_name":"Ontology-based data integration","score":0.5684694051742554},{"id":"https://openalex.org/keywords/semantic-similarity","display_name":"Semantic similarity","score":0.563819169998169},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.49376997351646423},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.42514997720718384},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.41902679204940796},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.398703396320343},{"id":"https://openalex.org/keywords/suggested-upper-merged-ontology","display_name":"Suggested Upper Merged Ontology","score":0.345309853553772},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.27449721097946167},{"id":"https://openalex.org/keywords/semantic-web","display_name":"Semantic Web","score":0.206170916557312},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.14797213673591614}],"concepts":[{"id":"https://openalex.org/C25810664","wikidata":"https://www.wikidata.org/wiki/Q44325","display_name":"Ontology","level":2,"score":0.7348154783248901},{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.6553080081939697},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6187981963157654},{"id":"https://openalex.org/C137982476","wikidata":"https://www.wikidata.org/wiki/Q7072326","display_name":"Open Biomedical Ontologies","level":5,"score":0.5965150594711304},{"id":"https://openalex.org/C22550185","wikidata":"https://www.wikidata.org/wiki/Q7095047","display_name":"Ontology-based data integration","level":3,"score":0.5684694051742554},{"id":"https://openalex.org/C130318100","wikidata":"https://www.wikidata.org/wiki/Q2268914","display_name":"Semantic similarity","level":2,"score":0.563819169998169},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.49376997351646423},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.42514997720718384},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.41902679204940796},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.398703396320343},{"id":"https://openalex.org/C50971890","wikidata":"https://www.wikidata.org/wiki/Q7635093","display_name":"Suggested Upper Merged Ontology","level":4,"score":0.345309853553772},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.27449721097946167},{"id":"https://openalex.org/C2129575","wikidata":"https://www.wikidata.org/wiki/Q54837","display_name":"Semantic Web","level":2,"score":0.206170916557312},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.14797213673591614},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","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/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D003627","descriptor_name":"Data Interpretation, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003627","descriptor_name":"Data Interpretation, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003627","descriptor_name":"Data Interpretation, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003628","descriptor_name":"Database Management Systems","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003628","descriptor_name":"Database Management Systems","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003628","descriptor_name":"Database Management Systems","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004194","descriptor_name":"Disease","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004194","descriptor_name":"Disease","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004194","descriptor_name":"Disease","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D009626","descriptor_name":"Terminology as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009626","descriptor_name":"Terminology as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009626","descriptor_name":"Terminology as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018875","descriptor_name":"Vocabulary, Controlled","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D018875","descriptor_name":"Vocabulary, Controlled","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D018875","descriptor_name":"Vocabulary, Controlled","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btp193","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btp193","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/25/12/i63/48991091/bioinformatics_25_12_i63.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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:19478018","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/19478018","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:europepmc.org:1855979","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2687947","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btp193","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btp193","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/25/12/i63/48991091/bioinformatics_25_12_i63.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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/17","display_name":"Partnerships for the goals","score":0.4000000059604645}],"awards":[{"id":"https://openalex.org/G1618314471","display_name":null,"funder_award_id":"RR025741","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G4485584972","display_name":null,"funder_award_id":"UL1RR025741","funder_id":"https://openalex.org/F4320337375","funder_display_name":"National Center for Research Resources"},{"id":"https://openalex.org/G473738646","display_name":null,"funder_award_id":"UL1RR02574","funder_id":"https://openalex.org/F4320337375","funder_display_name":"National Center for Research Resources"},{"id":"https://openalex.org/G7229151005","display_name":null,"funder_award_id":"UL1RR025741","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337375","display_name":"National Center for Research Resources","ror":"https://ror.org/04pw6fb54"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2115235175.pdf","grobid_xml":"https://content.openalex.org/works/W2115235175.grobid-xml"},"referenced_works_count":19,"referenced_works":["https://openalex.org/W1527927437","https://openalex.org/W1659833910","https://openalex.org/W1985035274","https://openalex.org/W2102037268","https://openalex.org/W2106410227","https://openalex.org/W2122084873","https://openalex.org/W2122683221","https://openalex.org/W2128049108","https://openalex.org/W2138255346","https://openalex.org/W2141652419","https://openalex.org/W2141703917","https://openalex.org/W2149911752","https://openalex.org/W2150392051","https://openalex.org/W2151337118","https://openalex.org/W2159706884","https://openalex.org/W2159941448","https://openalex.org/W2953332543","https://openalex.org/W6675339850","https://openalex.org/W6683460732"],"related_works":["https://openalex.org/W26549824","https://openalex.org/W1506177826","https://openalex.org/W2732632690","https://openalex.org/W72173000","https://openalex.org/W2396086199","https://openalex.org/W2781967547","https://openalex.org/W2608149786","https://openalex.org/W28299180","https://openalex.org/W2127299687","https://openalex.org/W4255991504"],"abstract_inverted_index":{"Subjective":[0],"methods":[1,37],"have":[2],"been":[3,196],"reported":[4],"to":[5,24,38,105,123,141],"adapt":[6,39],"a":[7,11,26,57,165],"general-purpose":[8],"ontology":[9],"for":[10,48,188],"specific":[12],"application.":[13],"For":[14],"example,":[15],"Gene":[16],"Ontology":[17,46,174,202],"(GO)":[18],"Slim":[19],"was":[20],"created":[21],"from":[22,64,169],"GO":[23],"generate":[25],"highly":[27],"aggregated":[28,151],"report":[29],"of":[30,51,60,70,93,99],"the":[31,40,49,68,71,74,86,91,107,132,147,153,170,199],"human-genome":[32],"annotation.":[33],"We":[34,177],"propose":[35],"statistical":[36],"general":[41],"purpose,":[42],"OBO":[43],"Foundry":[44],"Disease":[45,173,201],"(DO)":[47],"identification":[50],"gene-disease":[52,189],"associations.":[53],"Thus,":[54],"we":[55,84,163],"need":[56],"simplified":[58,166],"definition":[59],"disease":[61],"categories":[62],"derived":[63],"implicated":[65],"genes.":[66],"On":[67],"basis":[69],"assumption":[72],"that":[73,179],"DO":[75,87,113,126,136,148,155,171,187],"terms":[76,88,137,149,156],"having":[77],"similar":[78,125],"associated":[79],"genes":[80],"are":[81,103,138,150,157],"closely":[82],"related,":[83],"group":[85,124],"based":[89],"on":[90],"similarity":[92,111],"gene-to-DO":[94],"mapping":[95],"profiles.":[96],"Two":[97],"types":[98],"binary":[100],"distance":[101],"metrics":[102],"defined":[104],"measure":[106],"overall":[108],"and":[109,152],"subset":[110],"between":[112,135],"terms.":[114,127],"A":[115],"compactness-scalable":[116],"fuzzy":[117],"clustering":[118,143],"method":[119],"is":[120],"then":[121],"applied":[122],"To":[128],"reduce":[129],"false":[130],"clustering,":[131],"semantic":[133],"similarities":[134],"also":[139],"used":[140,197],"constrain":[142],"results.":[144],"As":[145],"such,":[146],"redundant":[154],"largely":[158],"removed.":[159],"Using":[160],"these":[161],"methods,":[162],"constructed":[164],"vocabulary":[167],"list":[168],"called":[172],"Lite":[175],"(DOLite).":[176],"demonstrated":[178],"DOLite":[180,194],"results":[181,185],"in":[182,198],"more":[183],"interpretable":[184],"than":[186],"association":[190],"tests.":[191],"The":[192],"resultant":[193],"has":[195],"Functional":[200],"(FunDO)":[203],"Web":[204],"application":[205],"at":[206],"http://www.projects.bioinformatics.northwestern.edu/fundo.":[207]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":4},{"year":2018,"cited_by_count":4},{"year":2017,"cited_by_count":10},{"year":2016,"cited_by_count":9},{"year":2015,"cited_by_count":17},{"year":2014,"cited_by_count":12},{"year":2013,"cited_by_count":13},{"year":2012,"cited_by_count":12}],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2025-10-10T00:00:00"}