{"id":"https://openalex.org/W4294956060","doi":"https://doi.org/10.1093/bioinformatics/btac612","title":"Access to ground truth at unconstrained size makes simulated data as indispensable as experimental data for bioinformatics methods development and benchmarking","display_name":"Access to ground truth at unconstrained size makes simulated data as indispensable as experimental data for bioinformatics methods development and benchmarking","publication_year":2022,"publication_date":"2022-09-08","ids":{"openalex":"https://openalex.org/W4294956060","doi":"https://doi.org/10.1093/bioinformatics/btac612","pmid":"https://pubmed.ncbi.nlm.nih.gov/36073940"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btac612","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac612","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/38/21/4994/46697947/btac612.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"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":"letter","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/38/21/4994/46697947/btac612.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5054500587","display_name":"Geir Kjetil Sandve","orcid":"https://orcid.org/0000-0002-4959-1409"},"institutions":[{"id":"https://openalex.org/I184942183","display_name":"University of Oslo","ror":"https://ror.org/01xtthb56","country_code":"NO","type":"education","lineage":["https://openalex.org/I184942183"]}],"countries":["NO"],"is_corresponding":true,"raw_author_name":"Geir Kjetil Sandve","raw_affiliation_strings":["Centre of Bioinformatics, University of Oslo , 0316 Oslo, Norway","Department of Informatics, University of Oslo , 0316 Oslo, Norway","UiORealArt convergence environment, University of Oslo , 0316 Oslo, Norway"],"affiliations":[{"raw_affiliation_string":"Centre of Bioinformatics, University of Oslo , 0316 Oslo, Norway","institution_ids":["https://openalex.org/I184942183"]},{"raw_affiliation_string":"Department of Informatics, University of Oslo , 0316 Oslo, Norway","institution_ids":["https://openalex.org/I184942183"]},{"raw_affiliation_string":"UiORealArt convergence environment, University of Oslo , 0316 Oslo, Norway","institution_ids":["https://openalex.org/I184942183"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5089158926","display_name":"Victor Greiff","orcid":"https://orcid.org/0000-0003-2622-5032"},"institutions":[{"id":"https://openalex.org/I1281400175","display_name":"Oslo University Hospital","ror":"https://ror.org/00j9c2840","country_code":"NO","type":"healthcare","lineage":["https://openalex.org/I1281400175"]},{"id":"https://openalex.org/I184942183","display_name":"University of Oslo","ror":"https://ror.org/01xtthb56","country_code":"NO","type":"education","lineage":["https://openalex.org/I184942183"]}],"countries":["NO"],"is_corresponding":false,"raw_author_name":"Victor Greiff","raw_affiliation_strings":["Department of Immunology, University of Oslo and Oslo University Hospital , 0316 Oslo, Norway"],"affiliations":[{"raw_affiliation_string":"Department of Immunology, University of Oslo and Oslo University Hospital , 0316 Oslo, Norway","institution_ids":["https://openalex.org/I1281400175","https://openalex.org/I184942183"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5054500587"],"corresponding_institution_ids":["https://openalex.org/I184942183"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":13.4723,"has_fulltext":true,"cited_by_count":30,"citation_normalized_percentile":{"value":0.98214744,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":94,"max":100},"biblio":{"volume":"38","issue":"21","first_page":"4994","last_page":"4996"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11986","display_name":"Scientific Computing and Data Management","score":0.9970999956130981,"subfield":{"id":"https://openalex.org/subfields/1802","display_name":"Information Systems and Management"},"field":{"id":"https://openalex.org/fields/18","display_name":"Decision Sciences"},"domain":{"id":"https://openalex.org/domains/2","display_name":"Social Sciences"}},"topics":[{"id":"https://openalex.org/T11986","display_name":"Scientific Computing and Data Management","score":0.9970999956130981,"subfield":{"id":"https://openalex.org/subfields/1802","display_name":"Information Systems and Management"},"field":{"id":"https://openalex.org/fields/18","display_name":"Decision Sciences"},"domain":{"id":"https://openalex.org/domains/2","display_name":"Social Sciences"}},{"id":"https://openalex.org/T13937","display_name":"Genetics, Bioinformatics, and Biomedical Research","score":0.9969000220298767,"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":0.995199978351593,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/benchmarking","display_name":"Benchmarking","score":0.7698889970779419},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7642451524734497},{"id":"https://openalex.org/keywords/ground-truth","display_name":"Ground truth","score":0.7297506332397461},{"id":"https://openalex.org/keywords/experimental-data","display_name":"Experimental data","score":0.6741384863853455},{"id":"https://openalex.org/keywords/generality","display_name":"Generality","score":0.6387540698051453},{"id":"https://openalex.org/keywords/fidelity","display_name":"Fidelity","score":0.6338536739349365},{"id":"https://openalex.org/keywords/transparency","display_name":"Transparency (behavior)","score":0.580555260181427},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.5775625705718994},{"id":"https://openalex.org/keywords/scale","display_name":"Scale (ratio)","score":0.5169833898544312},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.25577491521835327},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.09410545229911804},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.08251503109931946}],"concepts":[{"id":"https://openalex.org/C86251818","wikidata":"https://www.wikidata.org/wiki/Q816754","display_name":"Benchmarking","level":2,"score":0.7698889970779419},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7642451524734497},{"id":"https://openalex.org/C146849305","wikidata":"https://www.wikidata.org/wiki/Q370766","display_name":"Ground truth","level":2,"score":0.7297506332397461},{"id":"https://openalex.org/C55037315","wikidata":"https://www.wikidata.org/wiki/Q5421151","display_name":"Experimental data","level":2,"score":0.6741384863853455},{"id":"https://openalex.org/C2780767217","wikidata":"https://www.wikidata.org/wiki/Q5532421","display_name":"Generality","level":2,"score":0.6387540698051453},{"id":"https://openalex.org/C2776459999","wikidata":"https://www.wikidata.org/wiki/Q2119376","display_name":"Fidelity","level":2,"score":0.6338536739349365},{"id":"https://openalex.org/C2780233690","wikidata":"https://www.wikidata.org/wiki/Q535347","display_name":"Transparency (behavior)","level":2,"score":0.580555260181427},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.5775625705718994},{"id":"https://openalex.org/C2778755073","wikidata":"https://www.wikidata.org/wiki/Q10858537","display_name":"Scale (ratio)","level":2,"score":0.5169833898544312},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.25577491521835327},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.09410545229911804},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.08251503109931946},{"id":"https://openalex.org/C38652104","wikidata":"https://www.wikidata.org/wiki/Q3510521","display_name":"Computer security","level":1,"score":0.0},{"id":"https://openalex.org/C162853370","wikidata":"https://www.wikidata.org/wiki/Q39809","display_name":"Marketing","level":1,"score":0.0},{"id":"https://openalex.org/C144133560","wikidata":"https://www.wikidata.org/wiki/Q4830453","display_name":"Business","level":0,"score":0.0},{"id":"https://openalex.org/C542102704","wikidata":"https://www.wikidata.org/wiki/Q183257","display_name":"Psychotherapist","level":1,"score":0.0},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0},{"id":"https://openalex.org/C15744967","wikidata":"https://www.wikidata.org/wiki/Q9418","display_name":"Psychology","level":0,"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/C76155785","wikidata":"https://www.wikidata.org/wiki/Q418","display_name":"Telecommunications","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019985","descriptor_name":"Benchmarking","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019985","descriptor_name":"Benchmarking","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btac612","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac612","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/38/21/4994/46697947/btac612.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"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:36073940","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/36073940","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:9620827","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9620827","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"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"},{"id":"pmh:oai:www.duo.uio.no:10852/100514","is_oa":true,"landing_page_url":"http://hdl.handle.net/10852/100514","pdf_url":null,"source":{"id":"https://openalex.org/S4306401717","display_name":"Duo Research Archive (University of Oslo)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I184942183","host_organization_name":"University of Oslo","host_organization_lineage":["https://openalex.org/I184942183"],"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":"1367-4803","raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btac612","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac612","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/38/21/4994/46697947/btac612.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"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/G3748656914","display_name":null,"funder_award_id":"Norway","funder_id":"https://openalex.org/F4320323299","funder_display_name":"Norges Forskningsr\u00e5d"},{"id":"https://openalex.org/G4944382912","display_name":null,"funder_award_id":"#311341","funder_id":"https://openalex.org/F4320323299","funder_display_name":"Norges Forskningsr\u00e5d"},{"id":"https://openalex.org/G512131340","display_name":null,"funder_award_id":"311341","funder_id":"https://openalex.org/F4320323299","funder_display_name":"Norges Forskningsr\u00e5d"}],"funders":[{"id":"https://openalex.org/F4320323299","display_name":"Norges Forskningsr\u00e5d","ror":"https://ror.org/00epmv149"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4294956060.pdf","grobid_xml":"https://content.openalex.org/works/W4294956060.grobid-xml"},"referenced_works_count":18,"referenced_works":["https://openalex.org/W1952757896","https://openalex.org/W2007339694","https://openalex.org/W2064675550","https://openalex.org/W2096192437","https://openalex.org/W2103441770","https://openalex.org/W2108420460","https://openalex.org/W2112865076","https://openalex.org/W2757536903","https://openalex.org/W2775363893","https://openalex.org/W2794716113","https://openalex.org/W2971575097","https://openalex.org/W3011885318","https://openalex.org/W3098865414","https://openalex.org/W3102596196","https://openalex.org/W3130398990","https://openalex.org/W3186118520","https://openalex.org/W3211434666","https://openalex.org/W3217269327"],"related_works":["https://openalex.org/W4238897586","https://openalex.org/W435179959","https://openalex.org/W2619091065","https://openalex.org/W2059640416","https://openalex.org/W1490753184","https://openalex.org/W2284465472","https://openalex.org/W2291782699","https://openalex.org/W1993948687","https://openalex.org/W2045049461","https://openalex.org/W2011676020"],"abstract_inverted_index":{"The":[0],"author":[1],"instructions":[2],"of":[3,71,120],"this":[4],"journal":[5],"require":[6],"that":[7,63,97,137,148],"new":[8,138],"methodology":[9,93],"includes":[10],"assessment":[11,34],"on":[12,144],"\"actual":[13],"biological":[14],"data\"":[15],"as":[16],"opposed":[17],"to":[18,55,58,89,109,125],"simulated":[19,64,158],"data.":[20],"When":[21],"available":[22,46],"in":[23,74],"high":[24],"quantity,":[25],"fidelity,":[26],"and":[27,65,91,151],"generality,":[28],"experimental":[29,42,66,84,112,156],"(biological)":[30],"data":[31,43,67,85,113,131,147],"may":[32,99],"ensure":[33],"validity.":[35],"For":[36],"many":[37],"bioinformatics":[38,75,139],"application":[39],"areas,":[40],"however,":[41],"are":[44],"not":[45],"at":[47],"a":[48,101,121,129],"sufficient":[49,53],"scale":[50],"or":[51,157],"with":[52],"access":[54],"ground":[56,145],"truth":[57,146],"allow":[59,149],"conclusive":[60],"assessment.We":[61],"argue":[62,136],"should":[68,141],"be":[69,142,154],"considered":[70],"equal":[72],"importance":[73],"methods":[76,98,140],"assessment,":[77,153],"filling":[78],"complementary":[79],"roles.":[80],"Simulations":[81],"calibrated":[82],"by":[83,104,127],"offer":[86],"the":[87,105,107,118],"opportunity":[88],"assess":[90],"improve":[92],"early":[94],"on,":[95],"so":[96],"reach":[100],"mature":[102],"level":[103],"time":[106],"capacity":[108],"generate":[110],"large-scale":[111],"has":[114],"been":[115],"established.":[116],"Furthermore,":[117],"specification":[119],"simulation":[122],"algorithm":[123],"contributes":[124],"transparency":[126],"revealing":[128],"method's":[130],"assumptions.":[132],"In":[133],"summary,":[134],"we":[135],"validated":[143],"valid":[150],"reliable":[152],"it":[155],"(and":[159],"ideally":[160],"both).":[161]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":16},{"year":2023,"cited_by_count":7},{"year":2022,"cited_by_count":2}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}
