{"id":"https://openalex.org/W4386686585","doi":"https://doi.org/10.1186/s12859-023-05464-0","title":"An approach for proteins and their encoding genes synonyms integration based on protein ontology","display_name":"An approach for proteins and their encoding genes synonyms integration based on protein ontology","publication_year":2023,"publication_date":"2023-09-12","ids":{"openalex":"https://openalex.org/W4386686585","doi":"https://doi.org/10.1186/s12859-023-05464-0","pmid":"https://pubmed.ncbi.nlm.nih.gov/37700258"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-023-05464-0","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-023-05464-0","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-023-05464-0","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/s12859-023-05464-0","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100455436","display_name":"Xiaohong Wang","orcid":"https://orcid.org/0000-0001-8628-243X"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Xiaohong Wang","raw_affiliation_strings":["Teaching Affairs Department, Shandong Foreign Trade Vocational College, Qingdao, 266100, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Teaching Affairs Department, Shandong Foreign Trade Vocational College, Qingdao, 266100, China","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101560595","display_name":"Xiaoli Jing","orcid":"https://orcid.org/0009-0002-5918-1531"},"institutions":[{"id":"https://openalex.org/I4210161003","display_name":"Qingdao Center of Resource Chemistry and New Materials","ror":"https://ror.org/05x85k702","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210089297","https://openalex.org/I4210161003"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Xiaoli Jing","raw_affiliation_strings":["Network and Information Center, Qingdao Marine Science and Technology Center, Qingdao, 266237, China. xljing@qnlm.ac","Network and Information Center, Qingdao Marine Science and Technology Center, Qingdao, 266237, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Network and Information Center, Qingdao Marine Science and Technology Center, Qingdao, 266237, China. xljing@qnlm.ac","institution_ids":["https://openalex.org/I4210161003"]},{"raw_affiliation_string":"Network and Information Center, Qingdao Marine Science and Technology Center, Qingdao, 266237, China","institution_ids":["https://openalex.org/I4210161003"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5092857508","display_name":"Fangkun Dou","orcid":null},"institutions":[{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"government","lineage":["https://openalex.org/I19820366"]},{"id":"https://openalex.org/I4210101167","display_name":"Institute of Oceanology","ror":"https://ror.org/018yw5541","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210101167"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Fangkun Dou","raw_affiliation_strings":["Oceanographic Data Center, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Oceanographic Data Center, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China","institution_ids":["https://openalex.org/I19820366","https://openalex.org/I4210101167"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5101198700","display_name":"Haowei Cao","orcid":null},"institutions":[{"id":"https://openalex.org/I152269853","display_name":"Qilu University of Technology","ror":"https://ror.org/04hyzq608","country_code":"CN","type":"education","lineage":["https://openalex.org/I152269853"]},{"id":"https://openalex.org/I154099455","display_name":"Shandong University","ror":"https://ror.org/0207yh398","country_code":"CN","type":"education","lineage":["https://openalex.org/I154099455"]},{"id":"https://openalex.org/I4210142748","display_name":"Shandong Academy of Sciences","ror":"https://ror.org/04y8d6y55","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210142748"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Haowei Cao","raw_affiliation_strings":["Key Laboratory of Computing Power Network and Information Security, Ministry of Education, Shandong Computer Science Center, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250000, China","Shandong Provincial Key Laboratory of Computer Networks, Shandong Fundamental Research Center for Computer Science, Jinan, 250000, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Key Laboratory of Computing Power Network and Information Security, Ministry of Education, Shandong Computer Science Center, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250000, China","institution_ids":["https://openalex.org/I152269853","https://openalex.org/I4210142748"]},{"raw_affiliation_string":"Shandong Provincial Key Laboratory of Computer Networks, Shandong Fundamental Research Center for Computer Science, Jinan, 250000, China","institution_ids":["https://openalex.org/I154099455"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5101560595"],"corresponding_institution_ids":["https://openalex.org/I4210161003"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2790},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2790},"fwci":0.2812,"has_fulltext":true,"cited_by_count":3,"citation_normalized_percentile":{"value":0.50989473,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":96},"biblio":{"volume":"24","issue":"1","first_page":"339","last_page":"339"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9132999777793884,"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":0.9132999777793884,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.06539999693632126,"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":0.006200000178068876,"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":0.7188106775283813},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6279149055480957},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.6131964921951294},{"id":"https://openalex.org/keywords/dna-microarray","display_name":"DNA microarray","score":0.5987933874130249},{"id":"https://openalex.org/keywords/encoding","display_name":"Encoding (memory)","score":0.5556111335754395},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.49744895100593567},{"id":"https://openalex.org/keywords/ontology","display_name":"Ontology","score":0.48731836676597595},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3979151248931885},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.37028923630714417},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.36614564061164856},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.13937810063362122},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.08108294010162354}],"concepts":[{"id":"https://openalex.org/C2987395477","wikidata":"https://www.wikidata.org/wiki/Q135085","display_name":"Gene ontology","level":4,"score":0.7188106775283813},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6279149055480957},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.6131964921951294},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.5987933874130249},{"id":"https://openalex.org/C125411270","wikidata":"https://www.wikidata.org/wiki/Q18653","display_name":"Encoding (memory)","level":2,"score":0.5556111335754395},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.49744895100593567},{"id":"https://openalex.org/C25810664","wikidata":"https://www.wikidata.org/wiki/Q44325","display_name":"Ontology","level":2,"score":0.48731836676597595},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3979151248931885},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.37028923630714417},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.36614564061164856},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.13937810063362122},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.08108294010162354},{"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":"D005075","descriptor_name":"Biological Evolution","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005075","descriptor_name":"Biological Evolution","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005075","descriptor_name":"Biological Evolution","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":false},{"descriptor_ui":"D012660","descriptor_name":"Semantics","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":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019359","descriptor_name":"Knowledge","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019359","descriptor_name":"Knowledge","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019359","descriptor_name":"Knowledge","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1186/s12859-023-05464-0","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-023-05464-0","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-023-05464-0","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:37700258","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37700258","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:pubmedcentral.nih.gov:10496362","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10496362","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10496362/pdf/12859_2023_Article_5464.pdf","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"},{"id":"pmh:oai:doaj.org/article:019b6906f00b4cdc8977e601c00ecee6","is_oa":true,"landing_page_url":"https://doaj.org/article/019b6906f00b4cdc8977e601c00ecee6","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 24, Iss 1, Pp 1-13 (2023)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1186/s12859-023-05464-0","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-023-05464-0","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-023-05464-0","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/G7932224713","display_name":null,"funder_award_id":"ZR2020MF145","funder_id":"https://openalex.org/F4320324174","funder_display_name":"Natural Science Foundation of Shandong Province"}],"funders":[{"id":"https://openalex.org/F4320324174","display_name":"Natural Science Foundation of Shandong Province","ror":null}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4386686585.pdf"},"referenced_works_count":8,"referenced_works":["https://openalex.org/W1974896839","https://openalex.org/W2042037135","https://openalex.org/W2165270659","https://openalex.org/W2900255713","https://openalex.org/W2917858269","https://openalex.org/W3047366767","https://openalex.org/W4200139355","https://openalex.org/W6755825154"],"related_works":["https://openalex.org/W2003333417","https://openalex.org/W2378862226","https://openalex.org/W118236634","https://openalex.org/W2355326633","https://openalex.org/W2804669904","https://openalex.org/W2149777447","https://openalex.org/W2347456287","https://openalex.org/W2121651557","https://openalex.org/W2782969047","https://openalex.org/W2393581236"],"abstract_inverted_index":{"BACKGROUND:":[0],"Biological":[1],"research":[2],"is":[3,53,91,124,241],"generating":[4],"high":[5],"volumes":[6],"of":[7,16,49,68,74,88,118,126,144,185],"data":[8,27,129,174,179],"distributed":[9],"across":[10],"various":[11],"sources.":[12],"The":[13,72,116,191],"inconsistent":[14],"naming":[15],"proteins":[17,29,52,145],"and":[18,30,39,51,55,70,106,120,132,137,146,158,188,209],"their":[19,31,147],"encoding":[20,108],"genes":[21,33,50,69,149],"brings":[22],"great":[23],"challenges":[24],"to":[25,44,59,171,176,224],"protein":[26,105,114,119,186],"integration:":[28],"coding":[32,148],"usually":[34],"have":[35,65],"multiple":[36],"related":[37],"names":[38],"notations,":[40],"which":[41],"are":[42],"difficult":[43],"match":[45],"absolutely;":[46],"the":[47,75,140,162,165,183,226,232,237,242],"nomenclature":[48,67,187],"complex":[54],"varies":[56,78],"from":[57],"species":[58,64,220,230],"species;":[60],"some":[61],"less":[62],"studied":[63],"no":[66],"proteins;":[71],"annotation":[73],"same":[76],"protein/gene":[77,89],"greatly":[79],"in":[80],"different":[81],"databases.":[82],"In":[83,97],"summary,":[84],"a":[85,173],"comprehensive":[86,166,238],"set":[87,143,168,193,240],"synonyms":[90,216,239],"necessary":[92],"for":[93,104,202,245],"relevant":[94],"studies.":[95],"RESULTS:":[96],"this":[98],"study,":[99],"we":[100],"propose":[101],"an":[102,199],"approach":[103],"its":[107],"gene":[109,121],"synonym":[110,122,142,167,192],"integration":[111,123,136],"based":[112],"on":[113,249],"ontology.":[115],"workflow":[117],"composed":[125],"three":[127],"modules:":[128],"acquisition,":[130],"entity":[131,205],"attribute":[133,135],"alignment,":[134],"deduplication.":[138],"Finally,":[139],"integrated":[141],"contains":[150],"over":[151],"128.59":[152],"million":[153],"terminologies":[154],"covering":[155],"560,275":[156],"proteins/genes":[157],"13,781":[159],"species.":[160,189],"As":[161],"semantic":[163,243],"basis,":[164],"was":[169],"used":[170],"develop":[172],"platform":[175],"provide":[177],"one-stop":[178],"retrieval":[180,211],"without":[181,212],"considering":[182],"diversity":[184],"CONCLUSION:":[190],"constructed":[194],"here":[195],"can":[196,222],"serve":[197],"as":[198],"important":[200],"resource":[201],"biological":[203],"named":[204],"identification,":[206],"text":[207],"mining":[208],"information":[210],"name":[213],"ambiguity,":[214],"especially":[215],"associated":[217],"with":[218],"well-defined":[219],"categories":[221],"help":[223],"study":[225],"evolutionary":[227],"relationships":[228],"between":[229],"at":[231],"molecular":[233],"level.":[234],"More":[235],"importantly,":[236],"basis":[244],"our":[246],"subsequent":[247],"studies":[248],"Protein-protein":[250],"Interaction":[251],"(PPI)":[252],"knowledge":[253],"graph.":[254]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":1}],"updated_date":"2026-07-22T07:51:19.307946","created_date":"2025-10-10T00:00:00"}
