{"id":"https://openalex.org/W4386895866","doi":"https://doi.org/10.3389/fbinf.2023.1248732","title":"VariBench, new variation benchmark categories and data sets","display_name":"VariBench, new variation benchmark categories and data sets","publication_year":2023,"publication_date":"2023-09-19","ids":{"openalex":"https://openalex.org/W4386895866","doi":"https://doi.org/10.3389/fbinf.2023.1248732","pmid":"https://pubmed.ncbi.nlm.nih.gov/37795169"},"language":"en","primary_location":{"id":"doi:10.3389/fbinf.2023.1248732","is_oa":true,"landing_page_url":"https://doi.org/10.3389/fbinf.2023.1248732","pdf_url":"https://www.frontiersin.org/articles/10.3389/fbinf.2023.1248732/pdf?isPublishedV2=False","source":{"id":"https://openalex.org/S4210219554","display_name":"Frontiers in Bioinformatics","issn_l":"2673-7647","issn":["2673-7647"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320527","host_organization_name":"Frontiers Media","host_organization_lineage":["https://openalex.org/P4310320527"],"host_organization_lineage_names":["Frontiers Media"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Frontiers in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://www.frontiersin.org/articles/10.3389/fbinf.2023.1248732/pdf?isPublishedV2=False","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5019967877","display_name":"Niloofar Shirvanizadeh","orcid":"https://orcid.org/0000-0002-4527-9522"},"institutions":[{"id":"https://openalex.org/I187531555","display_name":"Lund University","ror":"https://ror.org/012a77v79","country_code":"SE","type":"education","lineage":["https://openalex.org/I187531555"]}],"countries":["SE"],"is_corresponding":false,"raw_author_name":"Niloofar Shirvanizadeh","raw_affiliation_strings":["Department of Experimental Medical Science, Lund University, Lund, Sweden"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Experimental Medical Science, Lund University, Lund, Sweden","institution_ids":["https://openalex.org/I187531555"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5020878971","display_name":"Mauno Vihinen","orcid":"https://orcid.org/0000-0002-9614-7976"},"institutions":[{"id":"https://openalex.org/I187531555","display_name":"Lund University","ror":"https://ror.org/012a77v79","country_code":"SE","type":"education","lineage":["https://openalex.org/I187531555"]}],"countries":["SE"],"is_corresponding":false,"raw_author_name":"Mauno Vihinen","raw_affiliation_strings":["Department of Experimental Medical Science, Lund University, Lund, Sweden"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Experimental Medical Science, Lund University, Lund, Sweden","institution_ids":["https://openalex.org/I187531555"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":1900,"currency":"USD","value_usd":1900},"apc_paid":{"value":424,"currency":"EUR","value_usd":457},"fwci":0.5706,"has_fulltext":true,"cited_by_count":4,"citation_normalized_percentile":{"value":0.69710596,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":97},"biblio":{"volume":"3","issue":null,"first_page":"1248732","last_page":"1248732"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9993000030517578,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9993000030517578,"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/T10515","display_name":"Cancer-related molecular mechanisms research","score":0.9993000030517578,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"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/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.998199999332428,"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/benchmark","display_name":"Benchmark (surveying)","score":0.7326504588127136},{"id":"https://openalex.org/keywords/variation","display_name":"Variation (astronomy)","score":0.6270354986190796},{"id":"https://openalex.org/keywords/volume","display_name":"Volume (thermodynamics)","score":0.5165871381759644},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.3774113655090332},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.3634253740310669},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.34543728828430176},{"id":"https://openalex.org/keywords/operations-research","display_name":"Operations research","score":0.32774481177330017},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.2186993956565857},{"id":"https://openalex.org/keywords/geography","display_name":"Geography","score":0.19598418474197388},{"id":"https://openalex.org/keywords/cartography","display_name":"Cartography","score":0.13452491164207458},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.06319209933280945}],"concepts":[{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.7326504588127136},{"id":"https://openalex.org/C2778334786","wikidata":"https://www.wikidata.org/wiki/Q1586270","display_name":"Variation (astronomy)","level":2,"score":0.6270354986190796},{"id":"https://openalex.org/C20556612","wikidata":"https://www.wikidata.org/wiki/Q4469374","display_name":"Volume (thermodynamics)","level":2,"score":0.5165871381759644},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.3774113655090332},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3634253740310669},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.34543728828430176},{"id":"https://openalex.org/C42475967","wikidata":"https://www.wikidata.org/wiki/Q194292","display_name":"Operations research","level":1,"score":0.32774481177330017},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.2186993956565857},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.19598418474197388},{"id":"https://openalex.org/C58640448","wikidata":"https://www.wikidata.org/wiki/Q42515","display_name":"Cartography","level":1,"score":0.13452491164207458},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.06319209933280945},{"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/C44870925","wikidata":"https://www.wikidata.org/wiki/Q37547","display_name":"Astrophysics","level":1,"score":0.0}],"mesh":[],"locations_count":5,"locations":[{"id":"doi:10.3389/fbinf.2023.1248732","is_oa":true,"landing_page_url":"https://doi.org/10.3389/fbinf.2023.1248732","pdf_url":"https://www.frontiersin.org/articles/10.3389/fbinf.2023.1248732/pdf?isPublishedV2=False","source":{"id":"https://openalex.org/S4210219554","display_name":"Frontiers in Bioinformatics","issn_l":"2673-7647","issn":["2673-7647"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320527","host_organization_name":"Frontiers Media","host_organization_lineage":["https://openalex.org/P4310320527"],"host_organization_lineage_names":["Frontiers Media"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Frontiers in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:37795169","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37795169","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":"Frontiers in bioinformatics","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:10546188","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10546188","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10546188/pdf/fbinf-03-1248732.pdf","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":"Front Bioinform","raw_type":"Text"},{"id":"pmh:oai:doaj.org/article:3e2c7ccf1a3948feb864db9f6b5c66b8","is_oa":true,"landing_page_url":"https://doaj.org/article/3e2c7ccf1a3948feb864db9f6b5c66b8","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Frontiers in Bioinformatics, Vol 3 (2023)","raw_type":"article"},{"id":"pmh:oai:lup.lub.lu.se:52a18d56-f68d-48e8-a9ca-b3a1b76ea82d","is_oa":false,"landing_page_url":"https://lup.lub.lu.se/record/52a18d56-f68d-48e8-a9ca-b3a1b76ea82d","pdf_url":null,"source":{"id":"https://openalex.org/S4306400536","display_name":"Lund University Publications (Lund University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I187531555","host_organization_name":"Lund University","host_organization_lineage":["https://openalex.org/I187531555"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"ISSN: 2673-7647","raw_type":"text"}],"best_oa_location":{"id":"doi:10.3389/fbinf.2023.1248732","is_oa":true,"landing_page_url":"https://doi.org/10.3389/fbinf.2023.1248732","pdf_url":"https://www.frontiersin.org/articles/10.3389/fbinf.2023.1248732/pdf?isPublishedV2=False","source":{"id":"https://openalex.org/S4210219554","display_name":"Frontiers in Bioinformatics","issn_l":"2673-7647","issn":["2673-7647"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320527","host_organization_name":"Frontiers Media","host_organization_lineage":["https://openalex.org/P4310320527"],"host_organization_lineage_names":["Frontiers Media"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Frontiers in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/2","display_name":"Zero hunger","score":0.5400000214576721}],"awards":[{"id":"https://openalex.org/G2191163065","display_name":null,"funder_award_id":"CAN 20 1350","funder_id":"https://openalex.org/F4320321491","funder_display_name":"Cancerfonden"},{"id":"https://openalex.org/G4302323072","display_name":null,"funder_award_id":"2019-01403","funder_id":"https://openalex.org/F4320322581","funder_display_name":"Vetenskapsr\u00e5det"},{"id":"https://openalex.org/G5988104266","display_name":null,"funder_award_id":"20 1350","funder_id":"https://openalex.org/F4320321491","funder_display_name":"Cancerfonden"},{"id":"https://openalex.org/G6265702644","display_name":null,"funder_award_id":"2019-","funder_id":"https://openalex.org/F4320321491","funder_display_name":"Cancerfonden"}],"funders":[{"id":"https://openalex.org/F4320321491","display_name":"Cancerfonden","ror":"https://ror.org/0527jb766"},{"id":"https://openalex.org/F4320322581","display_name":"Vetenskapsr\u00e5det","ror":"https://ror.org/03zttf063"}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4386895866.pdf"},"referenced_works_count":125,"referenced_works":["https://openalex.org/W1935098740","https://openalex.org/W1963697504","https://openalex.org/W1967209541","https://openalex.org/W1968422606","https://openalex.org/W1978287590","https://openalex.org/W1981553631","https://openalex.org/W2051978340","https://openalex.org/W2054804513","https://openalex.org/W2063714349","https://openalex.org/W2084638727","https://openalex.org/W2099672241","https://openalex.org/W2103145565","https://openalex.org/W2104549677","https://openalex.org/W2105993518","https://openalex.org/W2114394955","https://openalex.org/W2117856964","https://openalex.org/W2120819598","https://openalex.org/W2122732537","https://openalex.org/W2132312350","https://openalex.org/W2146841526","https://openalex.org/W2149756336","https://openalex.org/W2151529283","https://openalex.org/W2172215746","https://openalex.org/W2212528563","https://openalex.org/W2310980987","https://openalex.org/W2340330302","https://openalex.org/W2345331290","https://openalex.org/W2400041270","https://openalex.org/W2414128301","https://openalex.org/W2467466454","https://openalex.org/W2470845910","https://openalex.org/W2554576124","https://openalex.org/W2582396271","https://openalex.org/W2596744302","https://openalex.org/W2605361745","https://openalex.org/W2611549356","https://openalex.org/W2742600815","https://openalex.org/W2766808155","https://openalex.org/W2770026599","https://openalex.org/W2790103870","https://openalex.org/W2794541436","https://openalex.org/W2799503158","https://openalex.org/W2883814060","https://openalex.org/W2890223884","https://openalex.org/W2891924624","https://openalex.org/W2902224630","https://openalex.org/W2903344416","https://openalex.org/W2904602199","https://openalex.org/W2905130244","https://openalex.org/W2911615806","https://openalex.org/W2936956377","https://openalex.org/W2945403072","https://openalex.org/W2949787032","https://openalex.org/W2950104856","https://openalex.org/W2951373902","https://openalex.org/W2953301805","https://openalex.org/W2956094221","https://openalex.org/W2961258159","https://openalex.org/W2970783812","https://openalex.org/W2972605721","https://openalex.org/W2979256289","https://openalex.org/W2980372463","https://openalex.org/W2982561640","https://openalex.org/W2986272622","https://openalex.org/W2990387654","https://openalex.org/W2995387264","https://openalex.org/W2997930593","https://openalex.org/W3004798288","https://openalex.org/W3005822506","https://openalex.org/W3007500173","https://openalex.org/W3010364596","https://openalex.org/W3010879523","https://openalex.org/W3025754288","https://openalex.org/W3026933860","https://openalex.org/W3028862763","https://openalex.org/W3036197410","https://openalex.org/W3038248848","https://openalex.org/W3038927768","https://openalex.org/W3047331506","https://openalex.org/W3048479836","https://openalex.org/W3081409951","https://openalex.org/W3087319558","https://openalex.org/W3092634594","https://openalex.org/W3094083226","https://openalex.org/W3094314446","https://openalex.org/W3098344054","https://openalex.org/W3104081477","https://openalex.org/W3104285666","https://openalex.org/W3104783716","https://openalex.org/W3107086932","https://openalex.org/W3109312535","https://openalex.org/W3118865711","https://openalex.org/W3120180752","https://openalex.org/W3129351841","https://openalex.org/W3132165787","https://openalex.org/W3136963718","https://openalex.org/W3144619518","https://openalex.org/W3154495123","https://openalex.org/W3156417804","https://openalex.org/W3163900535","https://openalex.org/W3165327420","https://openalex.org/W3168211704","https://openalex.org/W3183009512","https://openalex.org/W3183890486","https://openalex.org/W3184970622","https://openalex.org/W3185823040","https://openalex.org/W3188212317","https://openalex.org/W3191108515","https://openalex.org/W3199639770","https://openalex.org/W3205974488","https://openalex.org/W3209370467","https://openalex.org/W3216625938","https://openalex.org/W4205748098","https://openalex.org/W4206007286","https://openalex.org/W4210397295","https://openalex.org/W4214674964","https://openalex.org/W4220697516","https://openalex.org/W4220999759","https://openalex.org/W4226250469","https://openalex.org/W4282968518","https://openalex.org/W4292962348","https://openalex.org/W4315797462","https://openalex.org/W4366283705","https://openalex.org/W6796328082","https://openalex.org/W6842120097"],"related_works":["https://openalex.org/W2386430105","https://openalex.org/W2356521405","https://openalex.org/W2378211422","https://openalex.org/W2745001401","https://openalex.org/W4321353415","https://openalex.org/W2130974462","https://openalex.org/W2384358604","https://openalex.org/W972276598","https://openalex.org/W4246352526","https://openalex.org/W2028665553"],"abstract_inverted_index":{"IntroductionGenetic":[0],"variation":[1,112],"data":[2],"is":[3,22,54],"nowadays":[4],"easy":[5],"to":[6,20,37,64,87],"generate.Variation":[7],"interpretation":[8],"means":[9],"the":[10,13,73,89,102,108],"description":[11],"of":[12,15,40,51,81,104,111],"significance":[14],"variations,":[16,90],"often":[17],"in":[18,42,101],"relation":[19],"disease.This":[21],"substantially":[23],"more":[24],"difficult":[25],"a":[26],"problem":[27],"than":[28],"sequence":[29],"generation.Experimental":[30],"methods":[31,83,105],"provide":[32],"verified":[33],"interpretations;":[34],"however,":[35],"due":[36],"huge":[38],"amounts":[39],"variations":[41],"every":[43],"individual,":[44],"computational":[45],"approaches":[46],"are":[47,84],"widely":[48,85],"used.The":[49],"length":[50],"human":[52],"genome":[53,75],"over":[55],"3":[56],"billion":[57],"base":[58],"pairs":[59],"(Nurk":[60],"et":[61,77],"al.,":[62,78],"2022).Due":[63],"individual":[65],"genetic":[66],"heterogeneity,":[67],"4.1-5.0":[68],"million":[69],"sites":[70],"differ":[71],"from":[72],"reference":[74],"(Auton":[76],"2015).Various":[79],"types":[80],"prediction":[82,113],"used":[86],"interpret":[88],"see":[91,115],"(Niroula":[92],"and":[93],"Vihinen,":[94],"2016).Benchmark":[95],"studies":[96],"have":[97],"indicated":[98],"large":[99],"differences":[100],"performance":[103],"developed":[106],"for":[107],"same":[109],"type":[110],"tasks,":[114],"e.g.,":[116]},"counts_by_year":[{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":1}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}
