{"id":"https://openalex.org/W4206054014","doi":"https://doi.org/10.1186/s12859-022-04557-6","title":"A novel gene functional similarity calculation model by utilizing the specificity of terms and relationships in gene ontology","display_name":"A novel gene functional similarity calculation model by utilizing the specificity of terms and relationships in gene ontology","publication_year":2022,"publication_date":"2022-01-20","ids":{"openalex":"https://openalex.org/W4206054014","doi":"https://doi.org/10.1186/s12859-022-04557-6","pmid":"https://pubmed.ncbi.nlm.nih.gov/35057740"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-022-04557-6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-022-04557-6","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-022-04557-6","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/track/pdf/10.1186/s12859-022-04557-6","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5037131488","display_name":"Zhen Tian","orcid":"https://orcid.org/0000-0003-0945-8168"},"institutions":[{"id":"https://openalex.org/I38877650","display_name":"Zhengzhou University","ror":"https://ror.org/04ypx8c21","country_code":"CN","type":"education","lineage":["https://openalex.org/I38877650"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhen Tian","raw_affiliation_strings":["School of Information Engineering, Zhengzhou University, Zhengzhou, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Information Engineering, Zhengzhou University, Zhengzhou, China","institution_ids":["https://openalex.org/I38877650"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5004359972","display_name":"Haichuan Fang","orcid":"https://orcid.org/0000-0002-1340-6937"},"institutions":[{"id":"https://openalex.org/I38877650","display_name":"Zhengzhou University","ror":"https://ror.org/04ypx8c21","country_code":"CN","type":"education","lineage":["https://openalex.org/I38877650"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Haichuan Fang","raw_affiliation_strings":["School of Information Engineering, Zhengzhou University, Zhengzhou, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Information Engineering, Zhengzhou University, Zhengzhou, China","institution_ids":["https://openalex.org/I38877650"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5045940041","display_name":"Yangdong Ye","orcid":"https://orcid.org/0000-0001-7027-8313"},"institutions":[{"id":"https://openalex.org/I38877650","display_name":"Zhengzhou University","ror":"https://ror.org/04ypx8c21","country_code":"CN","type":"education","lineage":["https://openalex.org/I38877650"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yangdong Ye","raw_affiliation_strings":["School of Information Engineering, Zhengzhou University, Zhengzhou, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Information Engineering, Zhengzhou University, Zhengzhou, China","institution_ids":["https://openalex.org/I38877650"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5044542014","display_name":"Zhenfeng Zhu","orcid":"https://orcid.org/0000-0003-3336-1614"},"institutions":[{"id":"https://openalex.org/I169689159","display_name":"PLA Information Engineering University","ror":"https://ror.org/00mm1qk40","country_code":"CN","type":"education","lineage":["https://openalex.org/I169689159"]},{"id":"https://openalex.org/I38877650","display_name":"Zhengzhou University","ror":"https://ror.org/04ypx8c21","country_code":"CN","type":"education","lineage":["https://openalex.org/I38877650"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Zhenfeng Zhu","raw_affiliation_strings":["School of Information Engineering, Zhengzhou University, Zhengzhou, China. iezfzhu@zzu.edu.cn","School of Information Engineering, Zhengzhou University, Zhengzhou, China"],"raw_orcid":"https://orcid.org/0000-0003-3336-1614","affiliations":[{"raw_affiliation_string":"School of Information Engineering, Zhengzhou University, Zhengzhou, China. iezfzhu@zzu.edu.cn","institution_ids":["https://openalex.org/I169689159","https://openalex.org/I38877650"]},{"raw_affiliation_string":"School of Information Engineering, Zhengzhou University, Zhengzhou, China","institution_ids":["https://openalex.org/I38877650"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5044542014"],"corresponding_institution_ids":["https://openalex.org/I169689159","https://openalex.org/I38877650"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2790},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2790},"fwci":0.0783,"has_fulltext":true,"cited_by_count":1,"citation_normalized_percentile":{"value":0.35124906,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"23","issue":"S1","first_page":"47","last_page":"47"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.984000027179718,"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":0.984000027179718,"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":0.009100000374019146,"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":0.001500000013038516,"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":0.6620553731918335},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.624904215335846},{"id":"https://openalex.org/keywords/similarity","display_name":"Similarity (geometry)","score":0.6214565634727478},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.5489448308944702},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.5310409665107727},{"id":"https://openalex.org/keywords/semantic-similarity","display_name":"Semantic similarity","score":0.5084208846092224},{"id":"https://openalex.org/keywords/exploit","display_name":"Exploit","score":0.49597224593162537},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.454928994178772},{"id":"https://openalex.org/keywords/dna-microarray","display_name":"DNA microarray","score":0.4541168212890625},{"id":"https://openalex.org/keywords/ontology","display_name":"Ontology","score":0.4355596601963043},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.43427619338035583},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.4237537384033203},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.36101511120796204},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.2532593607902527},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.21982121467590332},{"id":"https://openalex.org/keywords/image","display_name":"Image (mathematics)","score":0.15240943431854248},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.15043997764587402},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.1232718825340271}],"concepts":[{"id":"https://openalex.org/C2987395477","wikidata":"https://www.wikidata.org/wiki/Q135085","display_name":"Gene ontology","level":4,"score":0.6620553731918335},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.624904215335846},{"id":"https://openalex.org/C103278499","wikidata":"https://www.wikidata.org/wiki/Q254465","display_name":"Similarity (geometry)","level":3,"score":0.6214565634727478},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.5489448308944702},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.5310409665107727},{"id":"https://openalex.org/C130318100","wikidata":"https://www.wikidata.org/wiki/Q2268914","display_name":"Semantic similarity","level":2,"score":0.5084208846092224},{"id":"https://openalex.org/C165696696","wikidata":"https://www.wikidata.org/wiki/Q11287","display_name":"Exploit","level":2,"score":0.49597224593162537},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.454928994178772},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.4541168212890625},{"id":"https://openalex.org/C25810664","wikidata":"https://www.wikidata.org/wiki/Q44325","display_name":"Ontology","level":2,"score":0.4355596601963043},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.43427619338035583},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.4237537384033203},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.36101511120796204},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.2532593607902527},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.21982121467590332},{"id":"https://openalex.org/C115961682","wikidata":"https://www.wikidata.org/wiki/Q860623","display_name":"Image (mathematics)","level":2,"score":0.15240943431854248},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.15043997764587402},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.1232718825340271},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","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},{"id":"https://openalex.org/C38652104","wikidata":"https://www.wikidata.org/wiki/Q3510521","display_name":"Computer security","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}],"mesh":[{"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":"D063990","descriptor_name":"Gene Ontology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D063990","descriptor_name":"Gene Ontology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D063990","descriptor_name":"Gene Ontology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1186/s12859-022-04557-6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-022-04557-6","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-022-04557-6","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:35057740","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/35057740","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:doaj.org/article:5ddb81c0da66422292ad2ed4b06561a5","is_oa":true,"landing_page_url":"https://doaj.org/article/5ddb81c0da66422292ad2ed4b06561a5","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":"BMC Bioinformatics, Vol 23, Iss S1, Pp 1-14 (2022)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:8772239","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8772239","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s12859-022-04557-6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-022-04557-6","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-022-04557-6","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/G1130850028","display_name":"\u4f20\u64adIB\u65b9\u6cd5\u7684\u7814\u7a76","funder_award_id":"61772475","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G3530871281","display_name":null,"funder_award_id":"61801432","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4206054014.pdf","grobid_xml":"https://content.openalex.org/works/W4206054014.grobid-xml"},"referenced_works_count":27,"referenced_works":["https://openalex.org/W1527927437","https://openalex.org/W1566952502","https://openalex.org/W1659833910","https://openalex.org/W1964808688","https://openalex.org/W1980948656","https://openalex.org/W2042301222","https://openalex.org/W2045929671","https://openalex.org/W2100935296","https://openalex.org/W2107952955","https://openalex.org/W2108491719","https://openalex.org/W2108984616","https://openalex.org/W2128049108","https://openalex.org/W2138255346","https://openalex.org/W2161358836","https://openalex.org/W2163118979","https://openalex.org/W2230597785","https://openalex.org/W2323179903","https://openalex.org/W2602328737","https://openalex.org/W2737420028","https://openalex.org/W2770191688","https://openalex.org/W2792504918","https://openalex.org/W2805949464","https://openalex.org/W2912485311","https://openalex.org/W2950595506","https://openalex.org/W3014623641","https://openalex.org/W3126516421","https://openalex.org/W3194482250"],"related_works":["https://openalex.org/W2107952955","https://openalex.org/W2163095708","https://openalex.org/W2265558044","https://openalex.org/W1999493785","https://openalex.org/W2792440843","https://openalex.org/W175524671","https://openalex.org/W2042301222","https://openalex.org/W2565684071","https://openalex.org/W75900285","https://openalex.org/W2231731582"],"abstract_inverted_index":{"BACKGROUND:":[0],"Recently,":[1],"with":[2],"the":[3,34,37,44,68,108,132,139,143,151,160,164,168,173,179,184,194,203,209,214,239],"foundation":[4],"and":[5,23,74,112,231],"development":[6],"of":[7,21,26,36,41,47,57,70,86,110,134,147,153,183,196,211,242],"gene":[8,100,174,222,228],"ontology":[9],"(GO)":[10],"resources,":[11],"numerous":[12],"works":[13],"have":[14,62],"been":[15],"proposed":[16,97,116,190,244],"to":[17,130,141,178],"compute":[18,131],"functional":[19,55,84,101,175,223],"similarity":[20,56,85,102,176],"genes":[22,87,187],"achieved":[24],"series":[25],"successes":[27],"in":[28,167,213,225],"some":[29,63],"research":[30],"fields.":[31],"Focusing":[32],"on":[33,221],"calculation":[35,103],"information":[38,146],"content":[39],"(IC)":[40],"terms":[42,73,111,165,200],"is":[43,51,89,127],"main":[45],"idea":[46],"these":[48],"methods,":[49],"which":[50,105],"essential":[52],"for":[53],"measuring":[54,67,83],"genes.":[58],"However,":[59],"most":[60],"approaches":[61],"deficiencies,":[64],"especially":[65,106],"when":[66],"IC":[69,133,152,180,195],"both":[71],"GO":[72,148,199,215],"their":[75],"corresponding":[76,185],"annotated":[77,186,204],"term":[78,154,205],"sets.":[79,188],"To":[80],"this":[81,94],"end,":[82],"accurately":[88,192],"still":[90],"challenging.":[91],"RESULTS:":[92],"In":[93],"article,":[95],"we":[96,171],"a":[98,123],"novel":[99,124],"method,":[104],"encapsulates":[107],"specificity":[109,210],"edges":[113,212],"(STE).":[114],"The":[115,189],"method":[117,191],"mainly":[118],"contains":[119],"three":[120],"steps.":[121],"Firstly,":[122],"computing":[125],"model":[126,137],"put":[128],"forward":[129],"terms.":[135,149],"This":[136],"has":[138],"ability":[140],"exploit":[142],"specific":[144],"structural":[145],"Secondly,":[150],"sets":[155,206],"are":[156],"computed":[157],"by":[158,207],"capturing":[159],"genetic":[161],"structure":[162],"between":[163],"contained":[166],"set.":[169],"Lastly,":[170],"measure":[172],"according":[177],"overlap":[181],"ratio":[182],"measures":[193],"not":[197],"only":[198],"but":[201],"also":[202],"leveraging":[208],"graph.":[216],"CONCLUSIONS:":[217],"We":[218],"conduct":[219],"experiments":[220],"classification":[224],"biological":[226],"pathways,":[227],"expression":[229],"datasets,":[230],"protein-protein":[232],"interaction":[233],"datasets.":[234],"Extensive":[235],"experimental":[236],"results":[237],"show":[238],"better":[240],"performances":[241],"our":[243],"STE":[245],"against":[246],"several":[247],"baseline":[248],"methods.":[249]},"counts_by_year":[{"year":2022,"cited_by_count":1}],"updated_date":"2026-07-22T07:51:19.307946","created_date":"2025-10-10T00:00:00"}
