{"id":"https://openalex.org/W2042831991","doi":"https://doi.org/10.1186/s12859-015-0474-7","title":"Measuring semantic similarities by combining gene ontology annotations and gene co-function networks","display_name":"Measuring semantic similarities by combining gene ontology annotations and gene co-function networks","publication_year":2015,"publication_date":"2015-02-13","ids":{"openalex":"https://openalex.org/W2042831991","doi":"https://doi.org/10.1186/s12859-015-0474-7","mag":"2042831991","pmid":"https://pubmed.ncbi.nlm.nih.gov/25886899"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-015-0474-7","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-015-0474-7","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-015-0474-7","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-015-0474-7","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5084343474","display_name":"Jiajie Peng","orcid":"https://orcid.org/0000-0002-3857-7927"},"institutions":[{"id":"https://openalex.org/I204983213","display_name":"Harbin Institute of Technology","ror":"https://ror.org/01yqg2h08","country_code":"CN","type":"education","lineage":["https://openalex.org/I204983213"]},{"id":"https://openalex.org/I87216513","display_name":"Michigan State University","ror":"https://ror.org/05hs6h993","country_code":"US","type":"education","lineage":["https://openalex.org/I87216513"]}],"countries":["CN","US"],"is_corresponding":false,"raw_author_name":"Jiajie Peng","raw_affiliation_strings":["Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, MI, 48824, USA. jiajiepeng@hit.edu.cn","School of Computer Science and Technology, Harbin Institute of Technology, Harbin, China. jiajiepeng@hit.edu.cn","School of Computer Science and Technology, Harbin Institute of Technology, Harbin, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, MI, 48824, USA. jiajiepeng@hit.edu.cn","institution_ids":["https://openalex.org/I87216513"]},{"raw_affiliation_string":"School of Computer Science and Technology, Harbin Institute of Technology, Harbin, China. jiajiepeng@hit.edu.cn","institution_ids":["https://openalex.org/I204983213"]},{"raw_affiliation_string":"School of Computer Science and Technology, Harbin Institute of Technology, Harbin, China","institution_ids":["https://openalex.org/I204983213"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101775741","display_name":"Sahra Uygun","orcid":"https://orcid.org/0000-0003-0863-0384"},"institutions":[{"id":"https://openalex.org/I87216513","display_name":"Michigan State University","ror":"https://ror.org/05hs6h993","country_code":"US","type":"education","lineage":["https://openalex.org/I87216513"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Sahra Uygun","raw_affiliation_strings":["Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, MI, 48824, USA. uygunsah@msu.edu","Genetics Program, Michigan State University, East Lansing, MI, 48824, USA. uygunsah@msu.edu","Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, MI, 48824, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, MI, 48824, USA. uygunsah@msu.edu","institution_ids":["https://openalex.org/I87216513"]},{"raw_affiliation_string":"Genetics Program, Michigan State University, East Lansing, MI, 48824, USA. uygunsah@msu.edu","institution_ids":["https://openalex.org/I87216513"]},{"raw_affiliation_string":"Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, MI, 48824, USA","institution_ids":["https://openalex.org/I87216513"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5000439325","display_name":"Tae Hyong Kim","orcid":"https://orcid.org/0000-0003-2920-9038"},"institutions":[{"id":"https://openalex.org/I196817621","display_name":"Carnegie Institution for Science","ror":"https://ror.org/04jr01610","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I196817621"]},{"id":"https://openalex.org/I4210095419","display_name":"Carnegie Department of Plant Biology","ror":"https://ror.org/00tdyb139","country_code":"US","type":"facility","lineage":["https://openalex.org/I196817621","https://openalex.org/I4210095419"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Taehyong Kim","raw_affiliation_strings":["Department of Plant Biology, Carnegie Institution for Science, 260 Panama St, Stanford, CA, 94305, USA. thkim04@gmail.com","Department of Plant Biology, Carnegie Institution for Science, 260 Panama St, Stanford, CA, 94305, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Plant Biology, Carnegie Institution for Science, 260 Panama St, Stanford, CA, 94305, USA. thkim04@gmail.com","institution_ids":["https://openalex.org/I196817621"]},{"raw_affiliation_string":"Department of Plant Biology, Carnegie Institution for Science, 260 Panama St, Stanford, CA, 94305, USA","institution_ids":["https://openalex.org/I196817621","https://openalex.org/I4210095419"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100392447","display_name":"Yadong Wang","orcid":"https://orcid.org/0000-0001-6500-6217"},"institutions":[{"id":"https://openalex.org/I204983213","display_name":"Harbin Institute of Technology","ror":"https://ror.org/01yqg2h08","country_code":"CN","type":"education","lineage":["https://openalex.org/I204983213"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yadong Wang","raw_affiliation_strings":["School of Computer Science and Technology, Harbin Institute of Technology, Harbin, China. ydwang@hit.edu.cn","School of Computer Science and Technology, Harbin Institute of Technology, Harbin, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science and Technology, Harbin Institute of Technology, Harbin, China. ydwang@hit.edu.cn","institution_ids":["https://openalex.org/I204983213"]},{"raw_affiliation_string":"School of Computer Science and Technology, Harbin Institute of Technology, Harbin, China","institution_ids":["https://openalex.org/I204983213"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5076665375","display_name":"Seung Y. Rhee","orcid":"https://orcid.org/0000-0002-7572-4762"},"institutions":[{"id":"https://openalex.org/I196817621","display_name":"Carnegie Institution for Science","ror":"https://ror.org/04jr01610","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I196817621"]},{"id":"https://openalex.org/I4210095419","display_name":"Carnegie Department of Plant Biology","ror":"https://ror.org/00tdyb139","country_code":"US","type":"facility","lineage":["https://openalex.org/I196817621","https://openalex.org/I4210095419"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Seung Y Rhee","raw_affiliation_strings":["Department of Plant Biology, Carnegie Institution for Science, 260 Panama St, Stanford, CA, 94305, USA. srhee@carnegiescience.edu","Department of Plant Biology, Carnegie Institution for Science, 260 Panama St, Stanford, CA, 94305, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Plant Biology, Carnegie Institution for Science, 260 Panama St, Stanford, CA, 94305, USA. srhee@carnegiescience.edu","institution_ids":["https://openalex.org/I196817621"]},{"raw_affiliation_string":"Department of Plant Biology, Carnegie Institution for Science, 260 Panama St, Stanford, CA, 94305, USA","institution_ids":["https://openalex.org/I196817621","https://openalex.org/I4210095419"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100651872","display_name":"Jin Chen","orcid":"https://orcid.org/0000-0002-0123-5093"},"institutions":[{"id":"https://openalex.org/I87216513","display_name":"Michigan State University","ror":"https://ror.org/05hs6h993","country_code":"US","type":"education","lineage":["https://openalex.org/I87216513"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jin Chen","raw_affiliation_strings":["Department of Computer Science and Engineering, Michigan State University, East Lansing, MI, 48824, USA. jinchen@msu.edu","Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, MI, 48824, USA. jinchen@msu.edu","Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, MI, 48824, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, Michigan State University, East Lansing, MI, 48824, USA. jinchen@msu.edu","institution_ids":["https://openalex.org/I87216513"]},{"raw_affiliation_string":"Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, MI, 48824, USA. jinchen@msu.edu","institution_ids":["https://openalex.org/I87216513"]},{"raw_affiliation_string":"Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, MI, 48824, USA","institution_ids":["https://openalex.org/I87216513"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":6,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":4.3678,"has_fulltext":true,"cited_by_count":44,"citation_normalized_percentile":{"value":0.95035405,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"16","issue":"1","first_page":"44","last_page":"44"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9929999709129333,"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":0.9929999709129333,"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/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.0017000000225380063,"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":0.0007999999797903001,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/gene-ontology","display_name":"Gene ontology","score":0.7889500856399536},{"id":"https://openalex.org/keywords/dna-microarray","display_name":"DNA microarray","score":0.629460334777832},{"id":"https://openalex.org/keywords/function","display_name":"Function (biology)","score":0.5850023031234741},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5669466853141785},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.5294871926307678},{"id":"https://openalex.org/keywords/gene-annotation","display_name":"Gene Annotation","score":0.49563300609588623},{"id":"https://openalex.org/keywords/gene-regulatory-network","display_name":"Gene regulatory network","score":0.49085909128189087},{"id":"https://openalex.org/keywords/ontology","display_name":"Ontology","score":0.4888414740562439},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4422861933708191},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.37019848823547363},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.30318814516067505},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.26538190245628357},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.177748441696167}],"concepts":[{"id":"https://openalex.org/C2987395477","wikidata":"https://www.wikidata.org/wiki/Q135085","display_name":"Gene ontology","level":4,"score":0.7889500856399536},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.629460334777832},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.5850023031234741},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5669466853141785},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.5294871926307678},{"id":"https://openalex.org/C2908923196","wikidata":"https://www.wikidata.org/wiki/Q5205742","display_name":"Gene Annotation","level":4,"score":0.49563300609588623},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.49085909128189087},{"id":"https://openalex.org/C25810664","wikidata":"https://www.wikidata.org/wiki/Q44325","display_name":"Ontology","level":2,"score":0.4888414740562439},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4422861933708191},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.37019848823547363},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.30318814516067505},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.26538190245628357},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.177748441696167},{"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":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003577","descriptor_name":"Cytochrome P-450 Enzyme System","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D003577","descriptor_name":"Cytochrome P-450 Enzyme System","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D003577","descriptor_name":"Cytochrome P-450 Enzyme System","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D005810","descriptor_name":"Multigene Family","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005810","descriptor_name":"Multigene Family","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005810","descriptor_name":"Multigene Family","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012660","descriptor_name":"Semantics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012660","descriptor_name":"Semantics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012660","descriptor_name":"Semantics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","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":false},{"descriptor_ui":"D018875","descriptor_name":"Vocabulary, Controlled","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":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":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D029681","descriptor_name":"Arabidopsis Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D029681","descriptor_name":"Arabidopsis Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D029681","descriptor_name":"Arabidopsis Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D029701","descriptor_name":"Saccharomyces cerevisiae Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D029701","descriptor_name":"Saccharomyces cerevisiae Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D029701","descriptor_name":"Saccharomyces cerevisiae Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053858","descriptor_name":"Metabolic Networks and Pathways","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053858","descriptor_name":"Metabolic Networks and Pathways","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053858","descriptor_name":"Metabolic Networks and Pathways","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D063990","descriptor_name":"Gene Ontology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D063990","descriptor_name":"Gene Ontology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D063990","descriptor_name":"Gene Ontology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1186/s12859-015-0474-7","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-015-0474-7","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-015-0474-7","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:25886899","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/25886899","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:osti.gov:1194164","is_oa":true,"landing_page_url":"https://www.osti.gov/biblio/1194164","pdf_url":"https://www.osti.gov/servlets/purl/1194164","source":{"id":"https://openalex.org/S4306402487","display_name":"OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I139351228","host_organization_name":"Office of Scientific and Technical Information","host_organization_lineage":["https://openalex.org/I139351228"],"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":null},{"id":"pmh:oai:europepmc.org:3304145","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4339680","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s12859-015-0474-7","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-015-0474-7","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-015-0474-7","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1962778516","display_name":"INTERDISCIPLINARY RESEARCH   PROGRAM IN THE FUNDAMENTAL    PLANT SCIENCES","funder_award_id":"FG02-91ER20021","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G2302937132","display_name":null,"funder_award_id":"DE-FG02-91ER20021","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G2324326578","display_name":"The Membrane-based Protein Interactome","funder_award_id":"1052348","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G2805687156","display_name":null,"funder_award_id":"MCB-1052348","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G2897611530","display_name":null,"funder_award_id":"IOS-1026003","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G4021177670","display_name":null,"funder_award_id":"DE-FG02-91ER20021","funder_id":"https://openalex.org/F4320337480","funder_display_name":"Basic Energy Sciences"},{"id":"https://openalex.org/G4596099206","display_name":null,"funder_award_id":"IOS-1026003","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G486817060","display_name":null,"funder_award_id":"DE-FG02-91ER20021","funder_id":"https://openalex.org/F4320332359","funder_display_name":"Office of Science"},{"id":"https://openalex.org/G5648016710","display_name":null,"funder_award_id":"DE-FG02","funder_id":"https://openalex.org/F4320337480","funder_display_name":"Basic Energy Sciences"},{"id":"https://openalex.org/G6819749481","display_name":"Building a Network of Plant Metabolic Pathway Databases and Communities","funder_award_id":"0640769","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G7186324567","display_name":null,"funder_award_id":"DE-FG02-","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G779462592","display_name":null,"funder_award_id":"DBI-0640769","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G7994157108","display_name":null,"funder_award_id":"DE-FG02-91ER20021","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G8304190164","display_name":"Building a Highly Automated Metabolic Pathway Reconstruction Infrastructure for Plants","funder_award_id":"1026003","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G8684078510","display_name":null,"funder_award_id":"DE-FG02","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G8850349022","display_name":null,"funder_award_id":"FG02-91ER20021","funder_id":"https://openalex.org/F4320337480","funder_display_name":"Basic Energy Sciences"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320306084","display_name":"U.S. Department of Energy","ror":"https://ror.org/01bj3aw27"},{"id":"https://openalex.org/F4320322725","display_name":"China Scholarship Council","ror":"https://ror.org/04atp4p48"},{"id":"https://openalex.org/F4320332359","display_name":"Office of Science","ror":"https://ror.org/00mmn6b08"},{"id":"https://openalex.org/F4320337480","display_name":"Basic Energy Sciences","ror":"https://ror.org/05mg91w61"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2042831991.pdf","grobid_xml":"https://content.openalex.org/works/W2042831991.grobid-xml"},"referenced_works_count":50,"referenced_works":["https://openalex.org/W105330602","https://openalex.org/W142944101","https://openalex.org/W1623768750","https://openalex.org/W1659833910","https://openalex.org/W1956694423","https://openalex.org/W1985307298","https://openalex.org/W1986566140","https://openalex.org/W2021129827","https://openalex.org/W2044314513","https://openalex.org/W2045729458","https://openalex.org/W2055043387","https://openalex.org/W2058290061","https://openalex.org/W2059102372","https://openalex.org/W2065996794","https://openalex.org/W2068055268","https://openalex.org/W2074755764","https://openalex.org/W2084168100","https://openalex.org/W2097542211","https://openalex.org/W2102221598","https://openalex.org/W2103017472","https://openalex.org/W2105924489","https://openalex.org/W2113524447","https://openalex.org/W2116351978","https://openalex.org/W2121343862","https://openalex.org/W2123717266","https://openalex.org/W2125118217","https://openalex.org/W2125776280","https://openalex.org/W2127968944","https://openalex.org/W2128049108","https://openalex.org/W2128601422","https://openalex.org/W2130139983","https://openalex.org/W2133014144","https://openalex.org/W2133298156","https://openalex.org/W2133809942","https://openalex.org/W2134394193","https://openalex.org/W2135230723","https://openalex.org/W2138203479","https://openalex.org/W2138255346","https://openalex.org/W2150227699","https://openalex.org/W2150646520","https://openalex.org/W2163118979","https://openalex.org/W2166023446","https://openalex.org/W2166043581","https://openalex.org/W2168316093","https://openalex.org/W2172136887","https://openalex.org/W2995395573","https://openalex.org/W4230770774","https://openalex.org/W4233287056","https://openalex.org/W4235169531","https://openalex.org/W4285719527"],"related_works":["https://openalex.org/W2164883151","https://openalex.org/W2112871141","https://openalex.org/W2967275775","https://openalex.org/W2136890152","https://openalex.org/W2107952955","https://openalex.org/W2122634659","https://openalex.org/W2095370181","https://openalex.org/W2062777149","https://openalex.org/W2245843636","https://openalex.org/W2047391928"],"abstract_inverted_index":{"BACKGROUND:":[0],"Gene":[1],"Ontology":[2],"(GO)":[3],"has":[4],"been":[5],"used":[6],"widely":[7],"to":[8,44,69,125],"study":[9],"functional":[10,137,186],"relationships":[11],"between":[12],"genes.":[13],"The":[14],"current":[15],"semantic":[16,157],"similarity":[17,33,58,158],"measures":[18],"rely":[19],"only":[20],"on":[21,115],"GO":[22,25,45,72,94,171,189,197,208],"annotations":[23,172,209],"and":[24,74,83,130,173,214],"structure.":[26],"This":[27],"limits":[28],"the":[29,36,71,91,127,153,183],"power":[30],"of":[31,35,39,80,93,139,155,188],"GO-based":[32],"because":[34],"limited":[37],"proportion":[38],"genes":[40,140],"that":[41,60,87,100,132,152,191],"are":[42,192,199,210,216],"annotated":[43],"in":[46,67,141,182,196,201],"most":[47],"organisms.":[48],"RESULTS:":[49],"We":[50,97,112],"introduce":[51],"a":[52,156,179,202],"novel":[53],"approach":[54],"called":[55],"NETSIM":[56,88,101,114,146,168],"(network-based":[57],"measure)":[59],"incorporates":[61,169],"information":[62,213],"from":[63],"gene":[64,109,118,174],"co-function":[65,175],"networks":[66],"addition":[68],"using":[70],"structure":[73],"annotations.":[75],"Using":[76,145],"metabolic":[77],"reaction":[78],"maps":[79],"yeast,":[81],"Arabidopsis,":[82],"human,":[84],"we":[85,150],"demonstrate":[86,99],"can":[89],"improve":[90],"accuracy":[92],"term":[95],"similarities.":[96],"also":[98],"works":[102],"well":[103],"even":[104],"for":[105],"genomes":[106],"with":[107],"sparser":[108],"annotation":[110],"data.":[111],"applied":[113],"large":[116],"Arabidopsis":[117],"families":[119],"such":[120],"as":[121,147,178],"cytochrome":[122],"P450":[123],"monooxygenases":[124],"group":[126],"members":[128],"functionally":[129],"show":[131],"this":[133],"grouping":[134],"could":[135,160],"facilitate":[136],"characterization":[138],"these":[142],"families.":[143],"CONCLUSIONS:":[144],"an":[148],"example,":[149],"demonstrated":[151],"performance":[154],"measure":[159],"be":[161],"significantly":[162],"improved":[163],"after":[164],"incorporating":[165],"genome-specific":[166],"information.":[167],"both":[170],"network":[176],"data":[177],"priori":[180],"knowledge":[181],"model.":[184],"Therefore,":[185],"similarities":[187],"terms":[190],"not":[193],"explicitly":[194],"encoded":[195],"but":[198],"relevant":[200],"taxon-specific":[203],"manner":[204],"become":[205],"measurable":[206],"when":[207],"limited.":[211],"Supplementary":[212],"software":[215],"available":[217],"at":[218],"http://www.msu.edu/~jinchen/NETSIM":[219],".":[220]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":5},{"year":2019,"cited_by_count":3},{"year":2018,"cited_by_count":4},{"year":2017,"cited_by_count":11},{"year":2016,"cited_by_count":10},{"year":2015,"cited_by_count":4}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}