{"id":"https://openalex.org/W4409107237","doi":"https://doi.org/10.1093/bioinformatics/btaf149","title":"uHAF: a unified hierarchical annotation framework for cell type standardization and harmonization","display_name":"uHAF: a unified hierarchical annotation framework for cell type standardization and harmonization","publication_year":2025,"publication_date":"2025-03-29","ids":{"openalex":"https://openalex.org/W4409107237","doi":"https://doi.org/10.1093/bioinformatics/btaf149","pmid":"https://pubmed.ncbi.nlm.nih.gov/40172934"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btaf149","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf149","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf149/62844076/btaf149.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/btaf149/62844076/btaf149.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5019235398","display_name":"Haiyang Bian","orcid":"https://orcid.org/0000-0002-6010-3314"},"institutions":[{"id":"https://openalex.org/I4210148498","display_name":"Bioinformatics Institute","ror":"https://ror.org/044w3nw43","country_code":"SG","type":"facility","lineage":["https://openalex.org/I115228651","https://openalex.org/I2801752549","https://openalex.org/I4210148498"]},{"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","SG"],"is_corresponding":false,"raw_author_name":"Haiyang Bian","raw_affiliation_strings":["MOE Key Laboratory of Bioinformatics and Bioinformatics Division of BNRIST, Department of Automation, Tsinghua University , Beijing 100084,","Tsinghua University , Department of Automation, , Beijing 100084,","MOE Key Laboratory of Bioinformatics and Bioinformatics Division of BNRIST , Department of Automation, , Beijing 100084,"],"raw_orcid":"https://orcid.org/0000-0002-6010-3314","affiliations":[{"raw_affiliation_string":"MOE Key Laboratory of Bioinformatics and Bioinformatics Division of BNRIST, Department of Automation, Tsinghua University , Beijing 100084,","institution_ids":["https://openalex.org/I99065089"]},{"raw_affiliation_string":"Tsinghua University , Department of Automation, , Beijing 100084,","institution_ids":["https://openalex.org/I99065089"]},{"raw_affiliation_string":"MOE Key Laboratory of Bioinformatics and Bioinformatics Division of BNRIST , Department of Automation, , Beijing 100084,","institution_ids":["https://openalex.org/I4210148498"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Yinxin Chen","orcid":null},"institutions":[{"id":"https://openalex.org/I4210148498","display_name":"Bioinformatics Institute","ror":"https://ror.org/044w3nw43","country_code":"SG","type":"facility","lineage":["https://openalex.org/I115228651","https://openalex.org/I2801752549","https://openalex.org/I4210148498"]},{"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","SG"],"is_corresponding":false,"raw_author_name":"Yinxin Chen","raw_affiliation_strings":["MOE Key Laboratory of Bioinformatics and Bioinformatics Division of BNRIST, Department of Automation, Tsinghua University , Beijing 100084,","Tsinghua University , Department of Automation, , Beijing 100084,","MOE Key Laboratory of Bioinformatics and Bioinformatics Division of BNRIST , Department of Automation, , Beijing 100084,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"MOE Key Laboratory of Bioinformatics and Bioinformatics Division of BNRIST, Department of Automation, Tsinghua University , Beijing 100084,","institution_ids":["https://openalex.org/I99065089"]},{"raw_affiliation_string":"Tsinghua University , Department of Automation, , Beijing 100084,","institution_ids":["https://openalex.org/I99065089"]},{"raw_affiliation_string":"MOE Key Laboratory of Bioinformatics and Bioinformatics Division of BNRIST , Department of Automation, , Beijing 100084,","institution_ids":["https://openalex.org/I4210148498"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100634707","display_name":"Lei Wei","orcid":"https://orcid.org/0000-0002-1546-6458"},"institutions":[{"id":"https://openalex.org/I4210148498","display_name":"Bioinformatics Institute","ror":"https://ror.org/044w3nw43","country_code":"SG","type":"facility","lineage":["https://openalex.org/I115228651","https://openalex.org/I2801752549","https://openalex.org/I4210148498"]},{"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","SG"],"is_corresponding":false,"raw_author_name":"Lei Wei","raw_affiliation_strings":["MOE Key Laboratory of Bioinformatics and Bioinformatics Division of BNRIST, Department of Automation, Tsinghua University , Beijing 100084,","Tsinghua University , Department of Automation, , Beijing 100084,","MOE Key Laboratory of Bioinformatics and Bioinformatics Division of BNRIST , Department of Automation, , Beijing 100084,"],"raw_orcid":"https://orcid.org/0000-0002-1546-6458","affiliations":[{"raw_affiliation_string":"MOE Key Laboratory of Bioinformatics and Bioinformatics Division of BNRIST, Department of Automation, Tsinghua University , Beijing 100084,","institution_ids":["https://openalex.org/I99065089"]},{"raw_affiliation_string":"Tsinghua University , Department of Automation, , Beijing 100084,","institution_ids":["https://openalex.org/I99065089"]},{"raw_affiliation_string":"MOE Key Laboratory of Bioinformatics and Bioinformatics Division of BNRIST , Department of Automation, , Beijing 100084,","institution_ids":["https://openalex.org/I4210148498"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5081242795","display_name":"Xuegong Zhang","orcid":"https://orcid.org/0000-0002-9684-5643"},"institutions":[{"id":"https://openalex.org/I4210148498","display_name":"Bioinformatics Institute","ror":"https://ror.org/044w3nw43","country_code":"SG","type":"facility","lineage":["https://openalex.org/I115228651","https://openalex.org/I2801752549","https://openalex.org/I4210148498"]},{"id":"https://openalex.org/I4210160507","display_name":"Center for Life Sciences","ror":"https://ror.org/05kje8j93","country_code":"CN","type":"education","lineage":["https://openalex.org/I20231570","https://openalex.org/I4210160507","https://openalex.org/I99065089"]},{"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","SG"],"is_corresponding":false,"raw_author_name":"Xuegong Zhang","raw_affiliation_strings":["Center for Synthetic and Systems Biology, School of Life Sciences and School of Medicine, Tsinghua University , Beijing 100084,","MOE Key Laboratory of Bioinformatics and Bioinformatics Division of BNRIST, Department of Automation, Tsinghua University , Beijing 100084,","MOE Key Laboratory of Bioinformatics and Bioinformatics Division of BNRIST , Department of Automation, , Beijing 100084,","Tsinghua University Center for Synthetic and Systems Biology, School of Life Sciences and School of Medicine, , Beijing 100084,","Tsinghua University , Department of Automation, , Beijing 100084,"],"raw_orcid":"https://orcid.org/0000-0002-9684-5643","affiliations":[{"raw_affiliation_string":"Center for Synthetic and Systems Biology, School of Life Sciences and School of Medicine, Tsinghua University , Beijing 100084,","institution_ids":["https://openalex.org/I99065089","https://openalex.org/I4210160507"]},{"raw_affiliation_string":"MOE Key Laboratory of Bioinformatics and Bioinformatics Division of BNRIST, Department of Automation, Tsinghua University , Beijing 100084,","institution_ids":["https://openalex.org/I99065089"]},{"raw_affiliation_string":"MOE Key Laboratory of Bioinformatics and Bioinformatics Division of BNRIST , Department of Automation, , Beijing 100084,","institution_ids":["https://openalex.org/I4210148498"]},{"raw_affiliation_string":"Tsinghua University Center for Synthetic and Systems Biology, School of Life Sciences and School of Medicine, , Beijing 100084,","institution_ids":["https://openalex.org/I99065089"]},{"raw_affiliation_string":"Tsinghua University , Department of Automation, , Beijing 100084,","institution_ids":["https://openalex.org/I99065089"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":2.9207,"has_fulltext":true,"cited_by_count":6,"citation_normalized_percentile":{"value":0.90519663,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":97,"max":98},"biblio":{"volume":"41","issue":"4","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9937999844551086,"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/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9937999844551086,"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/T12859","display_name":"Cell Image Analysis Techniques","score":0.0019000000320374966,"subfield":{"id":"https://openalex.org/subfields/1304","display_name":"Biophysics"},"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/T13410","display_name":"Immune responses and vaccinations","score":0.00019999999494757503,"subfield":{"id":"https://openalex.org/subfields/2403","display_name":"Immunology"},"field":{"id":"https://openalex.org/fields/24","display_name":"Immunology and Microbiology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.8135059475898743},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.778118908405304},{"id":"https://openalex.org/keywords/harmonization","display_name":"Harmonization","score":0.660253643989563},{"id":"https://openalex.org/keywords/standardization","display_name":"Standardization","score":0.6326208710670471},{"id":"https://openalex.org/keywords/unification","display_name":"Unification","score":0.6034346222877502},{"id":"https://openalex.org/keywords/metadata","display_name":"Metadata","score":0.49262887239456177},{"id":"https://openalex.org/keywords/resource","display_name":"Resource (disambiguation)","score":0.4917176067829132},{"id":"https://openalex.org/keywords/granularity","display_name":"Granularity","score":0.46064263582229614},{"id":"https://openalex.org/keywords/data-type","display_name":"Data type","score":0.43123751878738403},{"id":"https://openalex.org/keywords/data-integration","display_name":"Data integration","score":0.43074777722358704},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.3588167726993561},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.27319419384002686},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.2330627143383026},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.22849708795547485},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.2146211564540863}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8135059475898743},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.778118908405304},{"id":"https://openalex.org/C2779962950","wikidata":"https://www.wikidata.org/wiki/Q5659376","display_name":"Harmonization","level":2,"score":0.660253643989563},{"id":"https://openalex.org/C188087704","wikidata":"https://www.wikidata.org/wiki/Q369577","display_name":"Standardization","level":2,"score":0.6326208710670471},{"id":"https://openalex.org/C96146094","wikidata":"https://www.wikidata.org/wiki/Q609057","display_name":"Unification","level":2,"score":0.6034346222877502},{"id":"https://openalex.org/C93518851","wikidata":"https://www.wikidata.org/wiki/Q180160","display_name":"Metadata","level":2,"score":0.49262887239456177},{"id":"https://openalex.org/C206345919","wikidata":"https://www.wikidata.org/wiki/Q20380951","display_name":"Resource (disambiguation)","level":2,"score":0.4917176067829132},{"id":"https://openalex.org/C177774035","wikidata":"https://www.wikidata.org/wiki/Q1246948","display_name":"Granularity","level":2,"score":0.46064263582229614},{"id":"https://openalex.org/C138958017","wikidata":"https://www.wikidata.org/wiki/Q190087","display_name":"Data type","level":2,"score":0.43123751878738403},{"id":"https://openalex.org/C72634772","wikidata":"https://www.wikidata.org/wiki/Q386824","display_name":"Data integration","level":2,"score":0.43074777722358704},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.3588167726993561},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.27319419384002686},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.2330627143383026},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.22849708795547485},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.2146211564540863},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0},{"id":"https://openalex.org/C24890656","wikidata":"https://www.wikidata.org/wiki/Q82811","display_name":"Acoustics","level":1,"score":0.0},{"id":"https://openalex.org/C31258907","wikidata":"https://www.wikidata.org/wiki/Q1301371","display_name":"Computer network","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","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":"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":"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":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":"Q000592","qualifier_name":"standards","is_major_topic":true},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":"Q000592","qualifier_name":"standards","is_major_topic":true},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":"Q000592","qualifier_name":"standards","is_major_topic":true},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000592","qualifier_name":"standards","is_major_topic":true},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000592","qualifier_name":"standards","is_major_topic":true},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000592","qualifier_name":"standards","is_major_topic":true},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btaf149","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf149","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf149/62844076/btaf149.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:40172934","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40172934","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:12002906","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12002906","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":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btaf149","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf149","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf149/62844076/btaf149.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/G2460525815","display_name":null,"funder_award_id":"62433001","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G5797066792","display_name":null,"funder_award_id":"2021YFF1200900","funder_id":"https://openalex.org/F4320335777","funder_display_name":"National Key Research and Development Program of China"},{"id":"https://openalex.org/G5881847713","display_name":null,"funder_award_id":"92470105","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G6722913013","display_name":null,"funder_award_id":"62373210","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G97774448","display_name":null,"funder_award_id":"62250005","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/F4320335777","display_name":"National Key Research and Development Program of China","ror":null},{"id":"https://openalex.org/F4320337107","display_name":"Tsinghua-Fuzhou Institute for Data Technology","ror":null}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4409107237.pdf","grobid_xml":"https://content.openalex.org/works/W4409107237.grobid-xml"},"referenced_works_count":17,"referenced_works":["https://openalex.org/W1757909678","https://openalex.org/W2462007197","https://openalex.org/W2950891712","https://openalex.org/W3013151148","https://openalex.org/W3045953207","https://openalex.org/W3173802674","https://openalex.org/W3212552860","https://openalex.org/W3213918788","https://openalex.org/W4206902726","https://openalex.org/W4220708949","https://openalex.org/W4280596398","https://openalex.org/W4280598116","https://openalex.org/W4282937885","https://openalex.org/W4320717228","https://openalex.org/W4327575912","https://openalex.org/W4362737480","https://openalex.org/W4379879135"],"related_works":["https://openalex.org/W2367630557","https://openalex.org/W2931688134","https://openalex.org/W101666983","https://openalex.org/W2183792531","https://openalex.org/W2377919138","https://openalex.org/W2595286499","https://openalex.org/W2794344379","https://openalex.org/W2378857091","https://openalex.org/W3179516695","https://openalex.org/W4285502407"],"abstract_inverted_index":{"SUMMARY:":[0],"In":[1],"single-cell":[2,132],"transcriptomics,":[3],"inconsistent":[4],"cell":[5,41,84,123],"type":[6,42,85,124],"annotations":[7,125],"due":[8],"to":[9,78],"varied":[10],"naming":[11],"conventions":[12],"and":[13,22,45,68,82,106,126,144],"hierarchical":[14,40,58],"granularity":[15],"impede":[16],"data":[17,100],"integration,":[18,101],"machine":[19,103],"learning":[20,104],"applications,":[21,105],"meaningful":[23,109],"evaluations.":[24],"To":[25],"address":[26],"this":[27],"challenge,":[28],"we":[29],"developed":[30],"the":[31,91,131],"unified":[32],"Hierarchical":[33],"Annotation":[34],"Framework":[35],"(uHAF),":[36],"which":[37],"includes":[38],"organ-specific":[39],"trees":[43],"(uHAF-T)":[44],"a":[46],"mapping":[47],"tool":[48],"(uHAF-Agent)":[49],"based":[50],"on":[51],"large":[52],"language":[53],"models.":[54],"uHAF-T":[55,88],"provides":[56],"standardized":[57],"references":[59],"for":[60,64,121],"38":[61],"organs,":[62],"allowing":[63],"consistent":[65],"label":[66,96],"unification":[67],"analysis":[69],"at":[70],"different":[71],"levels":[72],"of":[73,111],"granularity.":[74],"uHAF-Agent":[75],"leverages":[76],"GPT-4":[77],"accurately":[79],"map":[80],"diverse":[81],"informal":[83],"labels":[86],"onto":[87],"nodes,":[89],"streamlining":[90],"harmonization":[92],"process.":[93],"By":[94],"simplifying":[95],"unification,":[97],"uHAF":[98,138],"enhances":[99],"supports":[102],"enables":[107],"biologically":[108],"evaluations":[110],"annotation":[112],"methods.":[113],"Our":[114],"framework":[115],"serves":[116],"as":[117],"an":[118],"essential":[119],"resource":[120],"standardizing":[122],"fostering":[127],"collaborative":[128],"refinement":[129],"in":[130],"research":[133],"community.":[134],"AVAILABILITY":[135],"AND":[136],"IMPLEMENTATION:":[137],"is":[139],"publicly":[140],"available":[141],"at:":[142],"https://uhaf.unifiedcellatlas.org":[143],"https://github.com/SuperBianC/uhaf.":[145]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":4}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
