{"id":"https://openalex.org/W2920792755","doi":"https://doi.org/10.1093/database/baz023","title":"YESdb: integrative analysis of environmental stress in yeast","display_name":"YESdb: integrative analysis of environmental stress in yeast","publication_year":2019,"publication_date":"2019-01-01","ids":{"openalex":"https://openalex.org/W2920792755","doi":"https://doi.org/10.1093/database/baz023","mag":"2920792755","pmid":"https://pubmed.ncbi.nlm.nih.gov/30821814"},"language":"en","primary_location":{"id":"doi:10.1093/database/baz023","is_oa":true,"landing_page_url":"https://doi.org/10.1093/database/baz023","pdf_url":null,"source":{"id":"https://openalex.org/S4210201630","display_name":"Database","issn_l":"1758-0463","issn":["1758-0463"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311647","host_organization_name":"University of Oxford","host_organization_lineage":["https://openalex.org/P4310311647"],"host_organization_lineage_names":["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":"Database","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1093/database/baz023","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5061972807","display_name":"Evi Berchtold","orcid":"https://orcid.org/0000-0002-0393-8120"},"institutions":[{"id":"https://openalex.org/I8204097","display_name":"Ludwig-Maximilians-Universit\u00e4t M\u00fcnchen","ror":"https://ror.org/05591te55","country_code":"DE","type":"education","lineage":["https://openalex.org/I8204097"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Evi Berchtold","raw_affiliation_strings":["Institute of Bioinformatics, Department of Informatics, Ludwig-Maximilians-Universit\u00e4t M\u00fcnchen, Amalienstra\u00dfe, M\u00fcnchen, Germany"],"affiliations":[{"raw_affiliation_string":"Institute of Bioinformatics, Department of Informatics, Ludwig-Maximilians-Universit\u00e4t M\u00fcnchen, Amalienstra\u00dfe, M\u00fcnchen, Germany","institution_ids":["https://openalex.org/I8204097"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5061017439","display_name":"Gergely Csaba","orcid":"https://orcid.org/0000-0002-4320-3989"},"institutions":[{"id":"https://openalex.org/I8204097","display_name":"Ludwig-Maximilians-Universit\u00e4t M\u00fcnchen","ror":"https://ror.org/05591te55","country_code":"DE","type":"education","lineage":["https://openalex.org/I8204097"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Gergely Csaba","raw_affiliation_strings":["Institute of Bioinformatics, Department of Informatics, Ludwig-Maximilians-Universit\u00e4t M\u00fcnchen, Amalienstra\u00dfe, M\u00fcnchen, Germany"],"affiliations":[{"raw_affiliation_string":"Institute of Bioinformatics, Department of Informatics, Ludwig-Maximilians-Universit\u00e4t M\u00fcnchen, Amalienstra\u00dfe, M\u00fcnchen, Germany","institution_ids":["https://openalex.org/I8204097"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5068859428","display_name":"Ralf Zimmer","orcid":"https://orcid.org/0000-0003-1439-2327"},"institutions":[{"id":"https://openalex.org/I8204097","display_name":"Ludwig-Maximilians-Universit\u00e4t M\u00fcnchen","ror":"https://ror.org/05591te55","country_code":"DE","type":"education","lineage":["https://openalex.org/I8204097"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Ralf Zimmer","raw_affiliation_strings":["Institute of Bioinformatics, Department of Informatics, Ludwig-Maximilians-Universit\u00e4t M\u00fcnchen, Amalienstra\u00dfe, M\u00fcnchen, Germany"],"affiliations":[{"raw_affiliation_string":"Institute of Bioinformatics, Department of Informatics, Ludwig-Maximilians-Universit\u00e4t M\u00fcnchen, Amalienstra\u00dfe, M\u00fcnchen, Germany","institution_ids":["https://openalex.org/I8204097"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5061972807","https://openalex.org/A5068859428"],"corresponding_institution_ids":["https://openalex.org/I8204097"],"apc_list":{"value":1415,"currency":"GBP","value_usd":1735},"apc_paid":{"value":1415,"currency":"GBP","value_usd":1735},"fwci":0.0856,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.45580363,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"2019","issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10497","display_name":"Fungal and yeast genetics research","score":0.9994999766349792,"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/T10497","display_name":"Fungal and yeast genetics research","score":0.9994999766349792,"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":0.9994000196456909,"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":0.9940000176429749,"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":0.6934271454811096},{"id":"https://openalex.org/keywords/construct","display_name":"Construct (python library)","score":0.6578542590141296},{"id":"https://openalex.org/keywords/stress","display_name":"Stress (linguistics)","score":0.586675226688385},{"id":"https://openalex.org/keywords/ontology","display_name":"Ontology","score":0.5003492832183838},{"id":"https://openalex.org/keywords/workflow","display_name":"Workflow","score":0.4659361243247986},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.45486894249916077},{"id":"https://openalex.org/keywords/petri-net","display_name":"Petri net","score":0.45348283648490906},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.37939366698265076},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.3772590160369873},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.2375456988811493},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.08585873246192932}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6934271454811096},{"id":"https://openalex.org/C2780801425","wikidata":"https://www.wikidata.org/wiki/Q5164392","display_name":"Construct (python library)","level":2,"score":0.6578542590141296},{"id":"https://openalex.org/C21036866","wikidata":"https://www.wikidata.org/wiki/Q181767","display_name":"Stress (linguistics)","level":2,"score":0.586675226688385},{"id":"https://openalex.org/C25810664","wikidata":"https://www.wikidata.org/wiki/Q44325","display_name":"Ontology","level":2,"score":0.5003492832183838},{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.4659361243247986},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.45486894249916077},{"id":"https://openalex.org/C38677869","wikidata":"https://www.wikidata.org/wiki/Q724168","display_name":"Petri net","level":2,"score":0.45348283648490906},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.37939366698265076},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.3772590160369873},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.2375456988811493},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.08585873246192932},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","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/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D004777","descriptor_name":"Environment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D004777","descriptor_name":"Environment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D004777","descriptor_name":"Environment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D013312","descriptor_name":"Stress, Physiological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D013312","descriptor_name":"Stress, Physiological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D013312","descriptor_name":"Stress, Physiological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","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":true},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D066289","descriptor_name":"Data Curation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D066289","descriptor_name":"Data Curation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D066289","descriptor_name":"Data Curation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/database/baz023","is_oa":true,"landing_page_url":"https://doi.org/10.1093/database/baz023","pdf_url":null,"source":{"id":"https://openalex.org/S4210201630","display_name":"Database","issn_l":"1758-0463","issn":["1758-0463"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311647","host_organization_name":"University of Oxford","host_organization_lineage":["https://openalex.org/P4310311647"],"host_organization_lineage_names":["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":"Database","raw_type":"journal-article"},{"id":"pmid:30821814","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/30821814","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":"Database : the journal of biological databases and curation","raw_type":null},{"id":"pmh:oai:europepmc.org:5390840","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6396637","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"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":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/database/baz023","is_oa":true,"landing_page_url":"https://doi.org/10.1093/database/baz023","pdf_url":null,"source":{"id":"https://openalex.org/S4210201630","display_name":"Database","issn_l":"1758-0463","issn":["1758-0463"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311647","host_organization_name":"University of Oxford","host_organization_lineage":["https://openalex.org/P4310311647"],"host_organization_lineage_names":["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":"Database","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/15","score":0.4300000071525574,"display_name":"Life in Land"}],"awards":[{"id":"https://openalex.org/G1901460537","display_name":null,"funder_award_id":"SFB1123","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"}],"funders":[{"id":"https://openalex.org/F4320320879","display_name":"Deutsche Forschungsgemeinschaft","ror":"https://ror.org/018mejw64"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":24,"referenced_works":["https://openalex.org/W1527927437","https://openalex.org/W1964904043","https://openalex.org/W1973091058","https://openalex.org/W1976544696","https://openalex.org/W1988100928","https://openalex.org/W1993679825","https://openalex.org/W1999084705","https://openalex.org/W2030397967","https://openalex.org/W2071531591","https://openalex.org/W2080752012","https://openalex.org/W2085707114","https://openalex.org/W2102247469","https://openalex.org/W2109972881","https://openalex.org/W2112464428","https://openalex.org/W2118258530","https://openalex.org/W2135581618","https://openalex.org/W2159504331","https://openalex.org/W2163265140","https://openalex.org/W2165446840","https://openalex.org/W2179438025","https://openalex.org/W2229382718","https://openalex.org/W2310259903","https://openalex.org/W2915536738","https://openalex.org/W6697974936"],"related_works":["https://openalex.org/W2361861616","https://openalex.org/W1551257573","https://openalex.org/W2366107444","https://openalex.org/W4230983483","https://openalex.org/W2132799268","https://openalex.org/W1980200158","https://openalex.org/W2263699433","https://openalex.org/W2154794415","https://openalex.org/W791317142","https://openalex.org/W2377979023"],"abstract_inverted_index":{"The":[0,80,121,142,288],"stress":[1,38,53,77,107,115,243,341],"response":[2,33],"in":[3,21,78,126,171,296,356],"the":[4,42,49,61,83,88,100,105,140,182,186,192,195,204,249,256,258,267,328],"model":[5],"organisms":[6],"Saccharomyces":[7],"cerevisiae":[8],"is":[9,85,280],"a":[10,30,67],"well-studied":[11],"system":[12],"for":[13,219,346],"which":[14,154,284],"many":[15],"data":[16,97,143,183,217,251,337,350],"sets":[17,144,184,218,252,338,351,353],"are":[18,39,54,145,155,169,253,262,270,285],"available.":[19],"Already":[20],"2000,":[22],"it":[23],"was":[24],"discovered":[25],"that":[26],"yeast":[27,340],"cells":[28],"trigger":[29],"similar":[31],"transcriptional":[32],"when":[34,162],"different":[35,50,109],"types":[36,51,118,241],"of":[37,52,76,82,95,102,104,119,191,242,278,283,290,301,305,349,354],"applied.":[40],"However,":[41],"exact":[43],"regulatory":[44],"mechanisms":[45],"and":[46,129,138,189,198,226,234,264,266,344,352,360,363],"differences":[47,112],"between":[48,113],"still":[55],"not":[56],"understood.":[57],"Here,":[58],"we":[59],"present":[60],"Yeast":[62],"Environmental":[63],"Stress":[64],"database":[65,68,84],"(YESdb),":[66],"containing":[69],"all":[70,215,291,335],"high-throughput":[71],"experiments":[72],"measuring":[73],"various":[74,127],"kinds":[75],"yeast.":[79],"goal":[81],"to":[86,90,136,157,180,213,224,231,238,312,327,358],"allow":[87],"user":[89],"execute":[91,227],"complex,":[92],"integrative":[93],"analyses":[94,122,292],"selected":[96,254],"sets,":[98],"e.g.":[99],"comparison":[101],"measurements":[103,164],"same":[106],"using":[108],"platforms":[110],"or":[111,117,159,167,315],"strains,":[114],"strengths":[116],"stress.":[120],"can":[123,130,209,293,308,323],"be":[124,131,211,294,309,325],"visualized":[125],"ways":[128],"compiled":[132],"into":[133],"interactive":[134,298],"reports":[135],"summarize":[137],"communicate":[139],"results.":[141],"available":[146,281,343],"as":[147,201,203,318,320],"differential":[148],"conditions":[149],"(typically":[150],"stressed":[151],"vs":[152,246],"control),":[153],"grouped":[156],"time":[158,166],"concentration":[160],"series":[161],"multiple":[163],"over":[165],"concentrations":[168],"done":[170],"one":[172],"experiment.":[173],"An":[174],"annotation":[175],"ontology":[176],"has":[177],"been":[178],"constructed":[179],"annotate":[181],"with":[185],"type,":[187],"duration":[188],"strength":[190],"applied":[193],"stress,":[194],"used":[196],"strain":[197],"experimental":[199],"platform":[200],"well":[202,319],"publication":[205],"date.":[206],"These":[207],"annotations":[208],"easily":[210],"combined":[212,265],"select":[214],"relevant":[216],"an":[220,297],"analysis.":[221,274],"YESdb":[222,306,331],"allows":[223],"construct":[225],"Petri":[228],"net-based":[229],"workflows":[230,307],"perform":[232],"predefined":[233],"custom":[235],"analyses.":[236],"E.g.":[237],"compare":[239],"two":[240],"(e.g.":[244],"salt":[245],"oxidative":[247],"stress),":[248],"corresponding":[250],"from":[255],"database,":[257],"consistently":[259],"changed":[260],"genes":[261,269,355],"defined":[263],"shared":[268],"characterized":[271],"by":[272],"enrichment":[273],"A":[275],"broad":[276],"collection":[277],"visualizations":[279,317],"most":[282],"also":[286],"interactive.":[287],"results":[289],"summarized":[295],"report.":[299,329],"Visualizations":[300],"individual":[302],"steps":[303],"(transitions)":[304],"automatically":[310],"added":[311,326],"this":[313],"report":[314],"customized":[316],"interpretive":[321],"text":[322],"manually":[324],"Overall,":[330],"aims":[332],"at":[333],"making":[334],"published":[336],"on":[339],"immediately":[342],"comparable":[345],"integrated":[347],"analysis":[348],"order":[357],"identify":[359],"assess":[361],"hypotheses":[362],"mechanisms.":[364]},"counts_by_year":[{"year":2022,"cited_by_count":1}],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2025-10-10T00:00:00"}
