{"id":"https://openalex.org/W2941682155","doi":"https://doi.org/10.7490/f1000research.1116625.1","title":"Yeast Complexome \u2013 The Complex Portal rising to the challenge","display_name":"Yeast Complexome \u2013 The Complex Portal rising to the challenge","publication_year":2019,"publication_date":"2019-04-16","ids":{"openalex":"https://openalex.org/W2941682155","doi":"https://doi.org/10.7490/f1000research.1116625.1","mag":"2941682155"},"language":"en","primary_location":{"id":"doi:10.7490/f1000research.1116625.1","doi":"https://doi.org/10.7490/f1000research.1116625.1","is_oa":true,"landing_page_url":"https://doi.org/10.7490/f1000research.1116625.1","pdf_url":null,"source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":null,"raw_type":"posted-content"},"volume":null,"type":"other","indexed_in":["crossref","datacite"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.7490/f1000research.1116625.1","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5060701006","display_name":"Birgit Meldal","orcid":"https://orcid.org/0000-0003-4062-6158","observed_orcids":["https://orcid.org/0000-0003-4062-6158"]},"institutions":[{"id":"https://openalex.org/I1303153112","display_name":"European Bioinformatics Institute","ror":"https://ror.org/02catss52","country_code":"GB","type":"facility","lineage":["https://openalex.org/I1303153112","https://openalex.org/I4210138560"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Birgit Meldal","raw_affiliation_strings":["EMBL European Bioinformatics Institute, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"EMBL European Bioinformatics Institute, UK","institution_ids":["https://openalex.org/I1303153112"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5050128493","display_name":"Livia Perfetto","orcid":"https://orcid.org/0000-0003-4392-8725","observed_orcids":["https://orcid.org/0000-0003-4392-8725"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Livia Perfetto","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5047406019","display_name":"Edith D. Wong","orcid":"https://orcid.org/0000-0001-9799-5523","observed_orcids":["https://orcid.org/0000-0001-9799-5523"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Edith Wong","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5026050023","display_name":"Sandra E. Orchard","orcid":"https://orcid.org/0000-0002-8878-3972","observed_orcids":["https://orcid.org/0000-0002-8878-3972"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Sandra Orchard","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5066783652","display_name":"Henning Hermjakob","orcid":"https://orcid.org/0000-0001-8479-0262","observed_orcids":["https://orcid.org/0000-0001-8479-0262"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Henning Hermjakob","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5051653715","display_name":"Pablo Porras","orcid":"https://orcid.org/0000-0002-8429-8793","observed_orcids":["https://orcid.org/0000-0002-8429-8793"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Pablo Porras","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5060701006"],"corresponding_institution_ids":["https://openalex.org/I1303153112"],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":"8","issue":null,"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":0.9390000104904175,"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":0.9390000104904175,"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":0.014700000174343586,"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/T10519","display_name":"Advanced Proteomics Techniques and Applications","score":0.010999999940395355,"subfield":{"id":"https://openalex.org/subfields/1607","display_name":"Spectroscopy"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/macromolecular-complexes","display_name":"macromolecular complexes","score":0.824999988079071},{"id":"https://openalex.org/keywords/saccharomyces-cerevisiae","display_name":"Saccharomyces cerevisiae","score":0.9900000095367432},{"id":"https://openalex.org/keywords/manual-curation","display_name":"manual curation","score":0.6740000247955322},{"id":"https://openalex.org/keywords/gene-ontology-annotation","display_name":"gene ontology annotation","score":0.7720000147819519},{"id":"https://openalex.org/keywords/protein-complexes","display_name":"protein complexes","score":0.4350000023841858},{"id":"https://openalex.org/keywords/subunit-composition","display_name":"subunit composition","score":0.671999990940094},{"id":"https://openalex.org/keywords/network-topology","display_name":"network topology","score":0.375},{"id":"https://openalex.org/keywords/protein-protein-interaction","display_name":"protein-protein interaction","score":0.4699999988079071}],"concepts":[{"id":"https://openalex.org/C2983643791","wikidata":"https://www.wikidata.org/wiki/Q1999993","display_name":"Open peer review","level":3,"score":0.8631490468978882},{"id":"https://openalex.org/C2992936677","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Plant biology","level":2,"score":0.7502005100250244},{"id":"https://openalex.org/C42407357","wikidata":"https://www.wikidata.org/wiki/Q521","display_name":"Physiology","level":1,"score":0.539901077747345},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4769788682460785},{"id":"https://openalex.org/C2779222958","wikidata":"https://www.wikidata.org/wiki/Q45422","display_name":"Yeast","level":2,"score":0.41458308696746826},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.389358788728714},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.37726661562919617},{"id":"https://openalex.org/C169760540","wikidata":"https://www.wikidata.org/wiki/Q207011","display_name":"Neuroscience","level":1,"score":0.36959147453308105},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.334460586309433},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.16552817821502686},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.10694622993469238}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.7490/f1000research.1116625.1","doi":"https://doi.org/10.7490/f1000research.1116625.1","is_oa":true,"landing_page_url":"https://doi.org/10.7490/f1000research.1116625.1","pdf_url":null,"source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":null,"raw_type":"posted-content"},{"id":"doi:10.7490/f1000research.1116625.1","doi":"https://doi.org/10.7490/f1000research.1116625.1","is_oa":true,"landing_page_url":"https://doi.org/10.7490/f1000research.1116625.1","pdf_url":null,"source":{"id":"https://openalex.org/S7407050752","display_name":"Faculty of 1000 Research Ltd","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Other"},{"id":"mag:2941682155","doi":null,"is_oa":true,"landing_page_url":"https://f1000research.com/posters/8-496","pdf_url":null,"source":{"id":"https://openalex.org/S4210239046","display_name":"F1000Research","issn_l":"2046-1402","issn":["2046-1402"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["anvur-scientific","cwts-core","doaj","jufo-1","ki-jl-1","medline","norway-1","oarl","poland-70","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310320357","host_organization_name":"Faculty of 1000","host_organization_lineage":["https://openalex.org/P4310320357","https://openalex.org/P4310320547"],"host_organization_lineage_names":["Faculty of 1000","Taylor & Francis"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":false,"raw_source_name":"F1000Research","raw_type":null}],"best_oa_location":{"id":"doi:10.7490/f1000research.1116625.1","doi":"https://doi.org/10.7490/f1000research.1116625.1","is_oa":true,"landing_page_url":"https://doi.org/10.7490/f1000research.1116625.1","pdf_url":null,"source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":null,"raw_type":"posted-content"},"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W3133954608","https://openalex.org/W2911953899","https://openalex.org/W7097862572","https://openalex.org/W2107067224","https://openalex.org/W2898458979","https://openalex.org/W3210712771","https://openalex.org/W7203738211","https://openalex.org/W2727362955","https://openalex.org/W7100433605","https://openalex.org/W2791777656"],"abstract_inverted_index":{"The":[0],"Complex":[1,158],"Portal":[2,159],"(":[3],"www.ebi.ac.uk/complexportal":[4],")":[5],"is":[6,17,192,206,243,249],"an":[7,152],"encyclopedia":[8],"of":[9,31,59,86,93,131,155,213,236,240,263,274,291],"macromolecular":[10],"complexes":[11,64,73,82,109,143,161,168,202,219,230,258],"from":[12,169,266],"20":[13],"model":[14],"organisms":[15],"that":[16,190,204,231,290],"manually":[18,135,166],"curated":[19,160,167],"based":[20],"on":[21,110],"literature":[22],"evidence.":[23],"In":[24,89],"2018":[25],"we":[26,45,104,116],"completed":[27,297],"the":[28,39,43,94,129,156,164,170,180,197,210,214,246],"first":[29],"draft":[30],"all":[32,60],"Saccharomyces":[33],"cerevisiae":[34],"complexes,":[35],"also":[36],"known":[37,61],"as":[38,84,144],"\u2018yeast":[40],"complexome\u2019.":[41],"Throughout":[42],"project":[44],"worked":[46],"in":[47,65,99,125,222,282,298],"close":[48],"collaboration":[49],"with":[50,163,289],"SGD":[51],"and":[52,62,78,225,269,277,287],"UniProt":[53],"curators":[54],"to":[55,142,228,256,295],"build":[56],"a":[57,111,193,253],"list":[58],"predicted":[63,259],"yeast.":[66,185],"It":[67],"contains":[68],"nearly":[69],"600":[70],"well":[71],"defined":[72],"including":[74,284],"super-structures":[75],"like":[76],"polymerases":[77],"ribosomal":[79],"processomes":[80],"where":[81],"act":[83],"participants":[85],"larger":[87,215],"complexes.":[88,102,216],"total,":[90],"approx":[91],"30%":[92],"yeast":[95],"proteome":[96],"are":[97,220,281],"represented":[98],"these":[100],"stable":[101],"Additionally,":[103],"have":[105,146,150],"roughly":[106],"30":[107],"potential":[108],"\u2018watch":[112],"list\u2019":[113],"for":[114,122,184,200,270],"which":[115],"could":[117],"not":[118],"find":[119],"enough":[120],"evidence":[121],"their":[123],"existence":[124],"vivo":[126],".":[127],"During":[128],"course":[130],"this":[132,226,241],"project,1382":[133],"new,":[134],"assigned,":[136],"Gene":[137],"Ontology":[138],"(GO)":[139],"annotations":[140],"specific":[141],"entities":[145],"been":[147],"produced.":[148],"We":[149],"performed":[151],"initial":[153,187],"comparison":[154,188],"589":[157],"(CPX)":[162],"408":[165],"Pu":[171],"et":[172],"al.":[173],"(2009)":[174],"CYC2008":[175],"dataset":[176,242],"(CYC),":[177],"previously":[178],"considered":[179],"biggest":[181],"reference":[182],"complexome":[183],"An":[186],"showed":[189],"there":[191,205],"good":[194],"agreement":[195],"between":[196],"2":[198],"datasets":[199],"smaller":[201],"but":[203],"growing":[207],"disparity":[208],"over":[209],"subunit":[211],"composition":[212],"Overall,":[217],"281":[218],"identical":[221],"both":[223],"datasets,":[224],"increases":[227],"500":[229],"share":[232],"at":[233],"least":[234],"50%":[235],"subunits.":[237],"Further":[238],"analysis":[239,273],"ongoing.":[244],"Further,":[245],"Yeast":[247],"Complexome":[248],"now":[250],"being":[251],"used":[252],"gold":[254],"standard":[255],"validate":[257],"by":[260],"topological":[261],"analyses":[262],"networks":[264],"derived":[265],"large-scale":[267],"experiments":[268],"GO":[271],"enrichment":[272],"participant":[275],"proteins":[276],"genes.":[278],"Additional":[279],"complexomes":[280],"preparation,":[283],"human,":[285],"mouse":[286],"C.elegans,":[288],"Escherichia":[292],"coli":[293],"scheduled":[294],"be":[296],"2019.":[299]},"counts_by_year":[],"updated_date":"2026-10-28T10:33:24.094632","created_date":"2019-05-03T00:00:00"}