{"doi":"10.1093/nar/gkae955","title":"ScRAPdb: an integrated pan-omics database for the <i>Saccharomyces cerevisiae</i> reference assembly panel","abstract":"<jats:title>Abstract</jats:title>\n               <jats:p>As a unicellular eukaryote, the budding yeast Saccharomyces cerevisiae strikes a unique balance between biological complexity and experimental tractability, serving as a long-standing classic model for both basic and applied studies. Recently, S. cerevisiae further emerged as a leading system for studying natural diversity of genome evolution and its associated functional implication at population scales. Having high-quality comparative and functional genomics data are critical for such efforts. Here, we exhaustively expanded the telomere-to-telomere (T2T) S. cerevisiae reference assembly panel (ScRAP) that we previously constructed for 142 strains to cover high-quality genome assemblies and annotations of 264 S. cerevisiae strains from diverse geographical and ecological niches and also 33 outgroup strains from all the other Saccharomyces species complex. We created a dedicated online database, ScRAPdb (https://www.evomicslab.org/db/ScRAPdb/), to host this expanded pangenome collection. Furthermore, ScRAPdb also integrates an array of population-scale pan-omics atlases (pantranscriptome, panproteome and panphenome) and extensive data exploration toolkits for intuitive genomics analyses. All curated data and downstream analysis results can be easily downloaded from ScRAPdb. We expect ScRAPdb to become a highly valuable platform for the yeast community and beyond, leading to a pan-omics understanding of the global genetic and phenotypic diversity.</jats:p>","journal":"Nucleic Acids Research","year":2025,"id":644688,"datarank":0.5011357417312927,"base_score":2.9444389791664403,"endowment":2.9444389791664403,"self_citation_contribution":0.44166584687496613,"citation_network_contribution":0.05946989485632662,"self_endowment_contribution":0.44166584687496613,"citer_contribution":0.05946989485632662,"corpus_percentile":62.1,"corpus_rank":5152,"citation_count":18,"citer_count":12,"citers_with_citation_signal":6,"citers_with_endowment":6,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":null,"is_data_producer":false,"deposit_databanks":null,"is_oa":false,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":null,"fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":1538005,"name":"Yifan Ren","orcid":"0000-0002-5141-8947","position":1,"is_corresponding":false},{"id":1678188,"name":"Andrea Tarabini","orcid":"0009-0001-5033-7045","position":2,"is_corresponding":false},{"id":1678189,"name":"Ludong Yang","orcid":"0009-0007-6684-5689","position":3,"is_corresponding":false},{"id":550614,"name":"Huihui Li","orcid":"0000-0002-4469-3705","position":4,"is_corresponding":false},{"id":841799,"name":"Chang Ye","orcid":"0000-0003-0236-5671","position":5,"is_corresponding":false},{"id":381270,"name":"Gianni Liti","orcid":"0000-0002-2318-0775","position":6,"is_corresponding":false},{"id":1564242,"name":"Gilles Fischer","orcid":"0000-0001-5732-2682","position":7,"is_corresponding":false},{"id":238231,"name":"Jing Li","orcid":"0000-0001-5697-9527","position":8,"is_corresponding":false},{"id":381266,"name":"Jia‐Xing Yue","orcid":"0000-0002-2122-9221","position":9,"is_corresponding":false},{"id":1550145,"name":"Zepu Miao","orcid":"0000-0002-9734-682X","position":0,"is_corresponding":false}],"reference_count":0,"raw_metadata":{"has_enrichment":true,"resolved":true,"title":"ScRAPdb: an integrated pan-omics database for the <i>Saccharomyces cerevisiae</i> reference assembly panel","abstract":"<jats:title>Abstract</jats:title>\n               <jats:p>As a unicellular eukaryote, the budding yeast Saccharomyces cerevisiae strikes a unique balance between biological complexity and experimental tractability, serving as a long-standing classic model for both basic and applied studies. Recently, S. cerevisiae further emerged as a leading system for studying natural diversity of genome evolution and its associated functional implication at population scales. Having high-quality comparative and functional genomics data are critical for such efforts. Here, we exhaustively expanded the telomere-to-telomere (T2T) S. cerevisiae reference assembly panel (ScRAP) that we previously constructed for 142 strains to cover high-quality genome assemblies and annotations of 264 S. cerevisiae strains from diverse geographical and ecological niches and also 33 outgroup strains from all the other Saccharomyces species complex. We created a dedicated online database, ScRAPdb (https://www.evomicslab.org/db/ScRAPdb/), to host this expanded pangenome collection. Furthermore, ScRAPdb also integrates an array of population-scale pan-omics atlases (pantranscriptome, panproteome and panphenome) and extensive data exploration toolkits for intuitive genomics analyses. All curated data and downstream analysis results can be easily downloaded from ScRAPdb. We expect ScRAPdb to become a highly valuable platform for the yeast community and beyond, leading to a pan-omics understanding of the global genetic and phenotypic diversity.</jats:p>","is_dataset_classified":null,"base_score":2.8903717578961645,"endowment":2.8903717578961645,"datacite_reuse_total":0,"file_count":0,"downloads":0,"views":0,"has_version_chain":false,"is_dataset":false,"is_oa":false,"pmid":"39470715","pmcid":"PMC11701598","openalex_id":"https://openalex.org/W4403852240","authors":[],"funders":[{"funder_name":"National Natural Science Foundation of China","grant_id":"32070592","title":null},{"funder_name":"National Natural Science Foundation of China","grant_id":"32000395","title":null},{"funder_name":"Guangdong Basic and Applied Basic Research Foundation","grant_id":"2022A1515010717","title":null},{"funder_name":"Guangdong Basic and Applied Basic Research Foundation","grant_id":"2022A1515011873","title":null},{"funder_name":"Guangdong Pearl River Talents Program","grant_id":"2019QN01Y183","title":null},{"funder_name":"Guangdong Pearl River Talents Program","grant_id":"2021QN02Y168","title":null},{"funder_name":"Sun Yat-sen University Cancer Center","grant_id":"YTP-SYSUCC-0042","title":null},{"funder_name":"Sun Yat-sen University Cancer Center","grant_id":"YTP-SYSUCC-0040","title":null},{"funder_name":"Fundamental Research Funds for the Central Universities","grant_id":"24qnpy293","title":null}],"total_grants":9,"fwci":2.7208,"citation_percentile":0.91285654,"influential_citations":0,"citation_trend":[{"year":2024,"count":1},{"year":2025,"count":6},{"year":2026,"count":10}],"oa_status":"gold","license":"cc-by-nc","oa_locations":[{"url":"https://academic.oup.com/nar/article-pdf/53/D1/D852/60197979/gkae955.pdf","host_type":"journal"},{"url":"https://academic.oup.com/nar/article-pdf/53/D1/D852/60197979/gkae955.pdf","host_type":"publisher"},{"url":"https://doi.org/10.1093/nar/gkae955","host_type":"journal"},{"url":"https://pubmed.ncbi.nlm.nih.gov/39470715","host_type":"repository"},{"url":"https://hal.science/hal-04797383","host_type":"repository"},{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11701598","host_type":"repository"},{"url":"https://doi.org/10.25504/fairsharing.ad40a6","host_type":"repository"},{"url":"https://hal.science/hal-04797383/document","host_type":"repository"},{"url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11701598/pdf/gkae955.pdf","host_type":"repository"},{"url":"https://europepmc.org/articles/PMC11701598","host_type":"Europe_PMC"},{"url":"https://europepmc.org/articles/PMC11701598?pdf=render","host_type":"Europe_PMC"}],"fields_of_study":["Fungal and yeast genetics research","Fermentation and Sensory Analysis","Bioinformatics and Genomic Networks","Saccharomyces cerevisiae","Genome, Fungal","Databases, Genetic","Genomics","Telomere","Molecular Sequence Annotation","Proteomics","Multiomics"],"mesh_terms":["Multiomics","Saccharomyces cerevisiae","Telomere","Genome, Fungal","Genomics","Databases, Genetic","Proteomics","Molecular Sequence Annotation"],"keywords":["Biology","Saccharomyces cerevisiae","Computational biology","Population genomics","Genome","Genomics","Population","Functional genomics","Phenomics","Budding yeast","Genetics","Yeast","Evolutionary biology","Gene"],"sdg_mappings":[{"sdg_number":0,"sdg_label":"Life in Land"}],"linked_datasets":[],"clinical_trials":[],"software_tools":[],"database_accessions":[],"source":"live","citation_network_status":"fetched"},"created_at":"2026-08-09T01:49:42.456398Z","pmid":null,"pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}