{"id":"https://openalex.org/W4412131028","doi":"https://doi.org/10.1093/bioinformatics/btaf390","title":"ProtGO: universal protein function prediction utilizing multi-modal gene ontology knowledge","display_name":"ProtGO: universal protein function prediction utilizing multi-modal gene ontology knowledge","publication_year":2025,"publication_date":"2025-07-01","ids":{"openalex":"https://openalex.org/W4412131028","doi":"https://doi.org/10.1093/bioinformatics/btaf390","pmid":"https://pubmed.ncbi.nlm.nih.gov/40632605"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btaf390","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf390","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf390/63713029/btaf390.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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","license_id":"https://openalex.org/licenses/cc-by","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":"gold","oa_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf390/63713029/btaf390.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100736483","display_name":"Boyan Wang","orcid":"https://orcid.org/0000-0003-0088-2106"},"institutions":[{"id":"https://openalex.org/I308837","display_name":"Suzhou University of Science and Technology","ror":"https://ror.org/04en8wb91","country_code":"CN","type":"education","lineage":["https://openalex.org/I308837"]},{"id":"https://openalex.org/I36399199","display_name":"Nanjing University of Science and Technology","ror":"https://ror.org/00xp9wg62","country_code":"CN","type":"education","lineage":["https://openalex.org/I36399199"]},{"id":"https://openalex.org/I99065089","display_name":"Tsinghua University","ror":"https://ror.org/03cve4549","country_code":"CN","type":"education","lineage":["https://openalex.org/I99065089"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Boyan Wang","raw_affiliation_strings":["Computer Science and Technology, Tsinghua University , Beijing 100084,","School of Intelligence Science and Technology, Nanjing University , Suzhou, Jiangsu 215163,","Nanjing University School of Intelligence Science and Technology, , Suzhou,","Tsinghua University Computer Science and Technology, , Beijing,"],"raw_orcid":"https://orcid.org/0000-0003-0088-2106","affiliations":[{"raw_affiliation_string":"Computer Science and Technology, Tsinghua University , Beijing 100084,","institution_ids":["https://openalex.org/I99065089"]},{"raw_affiliation_string":"School of Intelligence Science and Technology, Nanjing University , Suzhou, Jiangsu 215163,","institution_ids":["https://openalex.org/I308837","https://openalex.org/I36399199"]},{"raw_affiliation_string":"Nanjing University School of Intelligence Science and Technology, , Suzhou,","institution_ids":["https://openalex.org/I308837","https://openalex.org/I36399199"]},{"raw_affiliation_string":"Tsinghua University Computer Science and Technology, , Beijing,","institution_ids":["https://openalex.org/I99065089"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102819696","display_name":"Yangli-ao Geng","orcid":"https://orcid.org/0000-0002-0084-5164"},"institutions":[{"id":"https://openalex.org/I21193070","display_name":"Beijing Jiaotong University","ror":"https://ror.org/01yj56c84","country_code":"CN","type":"education","lineage":["https://openalex.org/I21193070"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yangliao Geng","raw_affiliation_strings":["Key Laboratory of Big Data & Artificial Intelligence in Transportation (Ministry of Education), School of Computer Science and Technology, Beijing Jiaotong University , Beijing 100044,","Beijing Jiaotong University Key Laboratory of Big Data & Artificial Intelligence in Transportation (Ministry of Education), School of Computer Science and Technology, , Beijing,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Key Laboratory of Big Data & Artificial Intelligence in Transportation (Ministry of Education), School of Computer Science and Technology, Beijing Jiaotong University , Beijing 100044,","institution_ids":["https://openalex.org/I21193070"]},{"raw_affiliation_string":"Beijing Jiaotong University Key Laboratory of Big Data & Artificial Intelligence in Transportation (Ministry of Education), School of Computer Science and Technology, , Beijing,","institution_ids":["https://openalex.org/I21193070"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5034236827","display_name":"Xingyi Cheng","orcid":null},"institutions":[{"id":"https://openalex.org/I169724904","display_name":"Zimmer Biomet (Netherlands)","ror":"https://ror.org/034k8cv93","country_code":"NL","type":"company","lineage":["https://openalex.org/I169724904","https://openalex.org/I4210115238"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Xingyi Cheng","raw_affiliation_strings":["BioMap Research , Beijing 100190,","BioMap Research"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"BioMap Research , Beijing 100190,","institution_ids":["https://openalex.org/I169724904"]},{"raw_affiliation_string":"BioMap Research","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101784459","display_name":"Bo Chen","orcid":"https://orcid.org/0000-0002-9629-5493"},"institutions":[{"id":"https://openalex.org/I99065089","display_name":"Tsinghua University","ror":"https://ror.org/03cve4549","country_code":"CN","type":"education","lineage":["https://openalex.org/I99065089"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Bo Chen","raw_affiliation_strings":["Computer Science and Technology, Tsinghua University , Beijing 100084,","Tsinghua University Computer Science and Technology, , Beijing,"],"raw_orcid":"https://orcid.org/0000-0002-9629-5493","affiliations":[{"raw_affiliation_string":"Computer Science and Technology, Tsinghua University , Beijing 100084,","institution_ids":["https://openalex.org/I99065089"]},{"raw_affiliation_string":"Tsinghua University Computer Science and Technology, , Beijing,","institution_ids":["https://openalex.org/I99065089"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5093688255","display_name":"Zhilei Bei","orcid":"https://orcid.org/0009-0008-7663-5551"},"institutions":[{"id":"https://openalex.org/I99065089","display_name":"Tsinghua University","ror":"https://ror.org/03cve4549","country_code":"CN","type":"education","lineage":["https://openalex.org/I99065089"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhilei Bei","raw_affiliation_strings":["Computer Science and Technology, Tsinghua University , Beijing 100084,","Tsinghua University Computer Science and Technology, , Beijing,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computer Science and Technology, Tsinghua University , Beijing 100084,","institution_ids":["https://openalex.org/I99065089"]},{"raw_affiliation_string":"Tsinghua University Computer Science and Technology, , Beijing,","institution_ids":["https://openalex.org/I99065089"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100757829","display_name":"Wei Wang","orcid":"https://orcid.org/0000-0002-8598-0831"},"institutions":[{"id":"https://openalex.org/I205237279","display_name":"Nankai University","ror":"https://ror.org/01y1kjr75","country_code":"CN","type":"education","lineage":["https://openalex.org/I205237279"]},{"id":"https://openalex.org/I99065089","display_name":"Tsinghua University","ror":"https://ror.org/03cve4549","country_code":"CN","type":"education","lineage":["https://openalex.org/I99065089"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Wei Wang","raw_affiliation_strings":["College of Computer Science, Nankai University , Tianjin 300350,","Computer Science and Technology, Tsinghua University , Beijing 100084,","Nankai University College of Computer Science, , Tianjin,","Tsinghua University Computer Science and Technology, , Beijing,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Computer Science, Nankai University , Tianjin 300350,","institution_ids":["https://openalex.org/I205237279"]},{"raw_affiliation_string":"Computer Science and Technology, Tsinghua University , Beijing 100084,","institution_ids":["https://openalex.org/I99065089"]},{"raw_affiliation_string":"Nankai University College of Computer Science, , Tianjin,","institution_ids":["https://openalex.org/I205237279"]},{"raw_affiliation_string":"Tsinghua University Computer Science and Technology, , Beijing,","institution_ids":["https://openalex.org/I99065089"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5044791875","display_name":"Jie Tang","orcid":"https://orcid.org/0000-0003-3487-4593"},"institutions":[{"id":"https://openalex.org/I99065089","display_name":"Tsinghua University","ror":"https://ror.org/03cve4549","country_code":"CN","type":"education","lineage":["https://openalex.org/I99065089"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jie Tang","raw_affiliation_strings":["Computer Science and Technology, Tsinghua University , Beijing 100084,","Tsinghua University Computer Science and Technology, , Beijing,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computer Science and Technology, Tsinghua University , Beijing 100084,","institution_ids":["https://openalex.org/I99065089"]},{"raw_affiliation_string":"Tsinghua University Computer Science and Technology, , Beijing,","institution_ids":["https://openalex.org/I99065089"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5030589527","display_name":"Le Song","orcid":"https://orcid.org/0000-0002-9655-2787"},"institutions":[{"id":"https://openalex.org/I4210113480","display_name":"Mohamed bin Zayed University of Artificial Intelligence","ror":"https://ror.org/0258gkt32","country_code":"AE","type":"education","lineage":["https://openalex.org/I4210113480"]}],"countries":["AE"],"is_corresponding":false,"raw_author_name":"Le Song","raw_affiliation_strings":["GenBio AI, MBZUAI , Abu Dhabi,","MBZUAI , Abu Dhabi,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"GenBio AI, MBZUAI , Abu Dhabi,","institution_ids":["https://openalex.org/I4210113480"]},{"raw_affiliation_string":"MBZUAI , Abu Dhabi,","institution_ids":["https://openalex.org/I4210113480"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5100736483"],"corresponding_institution_ids":["https://openalex.org/I308837","https://openalex.org/I36399199","https://openalex.org/I99065089"],"apc_list":{"value":3989,"currency":"USD","value_usd":3989},"apc_paid":{"value":3989,"currency":"USD","value_usd":3989},"fwci":3.8361,"has_fulltext":true,"cited_by_count":10,"citation_normalized_percentile":{"value":0.94115739,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":95,"max":100},"biblio":{"volume":"41","issue":"7","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.5533000230789185,"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":0.5533000230789185,"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":0.33660000562667847,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.04690000042319298,"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/computer-science","display_name":"Computer science","score":0.677664041519165},{"id":"https://openalex.org/keywords/modal","display_name":"Modal","score":0.665165901184082},{"id":"https://openalex.org/keywords/gene-ontology","display_name":"Gene ontology","score":0.5842600464820862},{"id":"https://openalex.org/keywords/function","display_name":"Function (biology)","score":0.5709453821182251},{"id":"https://openalex.org/keywords/ontology","display_name":"Ontology","score":0.546369194984436},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4235008656978607},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3743157386779785},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.31366097927093506},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1463317573070526},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.10363566875457764},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.09814471006393433}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.677664041519165},{"id":"https://openalex.org/C71139939","wikidata":"https://www.wikidata.org/wiki/Q910194","display_name":"Modal","level":2,"score":0.665165901184082},{"id":"https://openalex.org/C2987395477","wikidata":"https://www.wikidata.org/wiki/Q135085","display_name":"Gene ontology","level":4,"score":0.5842600464820862},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.5709453821182251},{"id":"https://openalex.org/C25810664","wikidata":"https://www.wikidata.org/wiki/Q44325","display_name":"Ontology","level":2,"score":0.546369194984436},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4235008656978607},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3743157386779785},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.31366097927093506},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1463317573070526},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.10363566875457764},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.09814471006393433},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C188027245","wikidata":"https://www.wikidata.org/wiki/Q750446","display_name":"Polymer chemistry","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/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.0}],"mesh":[{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","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":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","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":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","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":true},{"descriptor_ui":"D063990","descriptor_name":"Gene Ontology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btaf390","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf390","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf390/63713029/btaf390.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:40632605","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40632605","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":"Journal Article"},{"id":"pmh:oai:pubmedcentral.nih.gov:12296341","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12296341","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btaf390","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf390","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf390/63713029/btaf390.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G3352331163","display_name":null,"funder_award_id":"62406111","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G366719221","display_name":null,"funder_award_id":"62306028","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G6794409734","display_name":null,"funder_award_id":"BG2024031","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G758127907","display_name":null,"funder_award_id":"62406163","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"},{"id":"https://openalex.org/F4320321605","display_name":"Government of Jiangsu Province","ror":"https://ror.org/004svx814"},{"id":"https://openalex.org/F4320324852","display_name":"Nanjing University","ror":"https://ror.org/01rxvg760"},{"id":"https://openalex.org/F4320329860","display_name":"National Science and Technology Major Project","ror":null}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4412131028.pdf","grobid_xml":"https://content.openalex.org/works/W4412131028.grobid-xml"},"referenced_works_count":38,"referenced_works":["https://openalex.org/W2018661561","https://openalex.org/W2098432760","https://openalex.org/W2103017472","https://openalex.org/W2105668062","https://openalex.org/W2114315281","https://openalex.org/W2169887773","https://openalex.org/W2781236732","https://openalex.org/W2989608901","https://openalex.org/W3046375318","https://openalex.org/W3136918052","https://openalex.org/W3158777740","https://openalex.org/W3164046276","https://openalex.org/W3177828909","https://openalex.org/W3179436811","https://openalex.org/W3186179742","https://openalex.org/W3202962917","https://openalex.org/W3217103056","https://openalex.org/W4213112325","https://openalex.org/W4225096104","https://openalex.org/W4282928794","https://openalex.org/W4308834893","https://openalex.org/W4321851522","https://openalex.org/W4323036511","https://openalex.org/W4327550249","https://openalex.org/W4361302966","https://openalex.org/W4382198799","https://openalex.org/W4384561707","https://openalex.org/W4388694364","https://openalex.org/W4391316987","https://openalex.org/W4391432211","https://openalex.org/W4391821988","https://openalex.org/W4393403728","https://openalex.org/W4396721167","https://openalex.org/W4401660139","https://openalex.org/W4404092049","https://openalex.org/W4409152738","https://openalex.org/W6739901393","https://openalex.org/W6858636142"],"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/W2794019507"],"abstract_inverted_index":{"MOTIVATION:":[0],"As":[1],"one":[2],"of":[3,19,31,105,162,168,190,231],"the":[4,29,35,42,54,66,80,111,149,160,166,188,203,244],"recalcitrant":[5],"challenges":[6],"in":[7,28,52,176,202,222],"life":[8],"sciences":[9],"and":[10,60,87,132,146,171,233,242],"biomedicine,":[11],"protein":[12,76,98,108,195,223],"function":[13,224],"prediction":[14,38,179,225],"suffers":[15],"from":[16],"a":[17,46,71,117,125,133,228],"deluge":[18],"AI-designed":[20],"proteins,":[21],"particularly":[22],"having":[23],"to":[24,40,193,199,209,218],"face":[25],"multi-modal":[26,48,113],"information":[27],"era":[30],"big":[32],"data.":[33],"Importing":[34],"high-throughput":[36],"neural-network-based":[37],"framework":[39,73],"replace":[41],"low-throughput":[43],"biological":[44,139,172],"experiments,":[45],"universal":[47],"method":[49],"is":[50,144],"straightforward":[51],"addressing":[53],"growing":[55],"gap":[56],"between":[57],"known":[58],"sequences":[59],"predicting":[61,75],"functions.":[62],"RESULTS:":[63],"To":[64],"bridge":[65],"gap,":[67],"we":[68,93,115],"propose":[69],"ProtGO,":[70],"three-step":[72],"for":[74,102,121,129,138,148],"function,":[77],"which":[78],"leverages":[79],"credible":[81],"Gene":[82],"Ontology":[83],"(GO)":[84],"knowledge":[85,156],"base":[86,210],"integrates":[88],"four":[89,155],"common":[90],"modalities.":[91,151],"Specifically,":[92],"first":[94],"introduce":[95],"frontier":[96],"pre-trained":[97],"language":[99,173],"models":[100,174],"(PLMs)":[101],"representation":[103],"learning":[104],"mainstay":[106],"functional":[107,232],"sequences.":[109],"For":[110],"remaining":[112],"data,":[114],"design":[116],"text":[118,123],"alignment":[119],"module":[120,128,137,143],"explainable":[122],"descriptions,":[124],"taxonomy":[126],"encoding":[127],"species-specific":[130],"taxonomy,":[131],"GO":[134,140,163,178],"graph":[135],"embedding":[136],"relations.":[141],"Each":[142],"independent":[145],"adaptive":[147],"referenced":[150],"By":[152],"harnessing":[153],"these":[154],"representations,":[157],"ProtGO":[158,185],"maximizes":[159],"potential":[161],"resources,":[164],"enhancing":[165],"performance":[167,221],"vanilla":[169],"PLMs":[170,192],"(LMs)":[175],"downstream":[177],"tasks.":[180],"Extensive":[181],"experiments":[182],"demonstrate":[183],"that":[184],"significantly":[186],"advances":[187],"abilities":[189],"state-of-the-art":[191],"predict":[194],"functions:":[196],"approximately":[197],"8%":[198],"27%":[200],"increase":[201],"maximum":[204],"F1":[205],"measure":[206],"(Fmax)":[207],"compared":[208],"models.":[211],"These":[212],"comprehensive":[213],"studies":[214],"confirm":[215],"ProtGO's":[216],"capability":[217],"deliver":[219],"outstanding":[220],"by":[226],"utilizing":[227],"rich":[229],"blend":[230],"evolutionary":[234],"knowledge.":[235],"AVAILABILITY":[236],"AND":[237],"IMPLEMENTATION:":[238],"Our":[239],"source":[240],"code":[241],"all":[243],"data":[245],"are":[246],"available":[247],"at":[248],"https://github.com/sunyatawang/ProtGO.":[249]},"counts_by_year":[{"year":2026,"cited_by_count":8},{"year":2025,"cited_by_count":2}],"updated_date":"2026-08-21T09:56:20.448147","created_date":"2025-10-10T00:00:00"}
