{"id":"https://openalex.org/W2018607179","doi":"https://doi.org/10.1145/2382936.2383015","title":"ngALL database","display_name":"ngALL database","publication_year":2012,"publication_date":"2012-10-07","ids":{"openalex":"https://openalex.org/W2018607179","doi":"https://doi.org/10.1145/2382936.2383015","mag":"2018607179"},"language":"en","primary_location":{"id":"doi:10.1145/2382936.2383015","is_oa":false,"landing_page_url":"https://doi.org/10.1145/2382936.2383015","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the ACM Conference on Bioinformatics, Computational Biology and Biomedicine","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5028383766","display_name":"Pascal St-Onge","orcid":"https://orcid.org/0000-0002-9322-1034"},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Pascal St-Onge","raw_affiliation_strings":["Sainte-Justine UHC Research Center, Montr\u00e9al (QC)"],"affiliations":[{"raw_affiliation_string":"Sainte-Justine UHC Research Center, Montr\u00e9al (QC)","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5088662102","display_name":"Robert Hamon","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Robert Hamon","raw_affiliation_strings":["Sainte-Justine UHC Research Center, Montr\u00e9al (QC)"],"affiliations":[{"raw_affiliation_string":"Sainte-Justine UHC Research Center, Montr\u00e9al (QC)","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5035718826","display_name":"Virginie Saillour","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Virginie Saillour","raw_affiliation_strings":["Sainte-Justine UHC Research Center, Montr\u00e9al (QC)"],"affiliations":[{"raw_affiliation_string":"Sainte-Justine UHC Research Center, Montr\u00e9al (QC)","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5112146709","display_name":"Jasmine Healy","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Jasmine Healy","raw_affiliation_strings":["Sainte-Justine UHC Research Center, Montr\u00e9al (QC)"],"affiliations":[{"raw_affiliation_string":"Sainte-Justine UHC Research Center, Montr\u00e9al (QC)","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5027608352","display_name":"Patrick Beaulieu","orcid":"https://orcid.org/0009-0001-1034-3627"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Patrick Beaulieu","raw_affiliation_strings":["Sainte-Justine UHC Research Center, Montr\u00e9al (QC)"],"affiliations":[{"raw_affiliation_string":"Sainte-Justine UHC Research Center, Montr\u00e9al (QC)","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5039922554","display_name":"Daniel Sinnett","orcid":"https://orcid.org/0000-0003-3625-6676"},"institutions":[{"id":"https://openalex.org/I70931966","display_name":"Universit\u00e9 de Montr\u00e9al","ror":"https://ror.org/0161xgx34","country_code":"CA","type":"education","lineage":["https://openalex.org/I70931966"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Daniel Sinnett","raw_affiliation_strings":["Sainte-Justine UHC Research Center, Montr\u00e9al (QC) and University of Montreal, Montr\u00e9al (QC)"],"affiliations":[{"raw_affiliation_string":"Sainte-Justine UHC Research Center, Montr\u00e9al (QC) and University of Montreal, Montr\u00e9al (QC)","institution_ids":["https://openalex.org/I70931966"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5028383766"],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.0894939,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"542","last_page":"544"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11642","display_name":"Genomics and Rare Diseases","score":0.9984999895095825,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/T11642","display_name":"Genomics and Rare Diseases","score":0.9984999895095825,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/T11287","display_name":"Cancer Genomics and Diagnostics","score":0.9962000250816345,"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/T11213","display_name":"Genomic variations and chromosomal abnormalities","score":0.9943000078201294,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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":0.6899220943450928},{"id":"https://openalex.org/keywords/workflow","display_name":"Workflow","score":0.5451455116271973},{"id":"https://openalex.org/keywords/exome","display_name":"Exome","score":0.5264416933059692},{"id":"https://openalex.org/keywords/relational-database","display_name":"Relational database","score":0.5134104490280151},{"id":"https://openalex.org/keywords/epigenomics","display_name":"Epigenomics","score":0.4776686131954193},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.4336254298686981},{"id":"https://openalex.org/keywords/dbsnp","display_name":"dbSNP","score":0.4200475215911865},{"id":"https://openalex.org/keywords/exome-sequencing","display_name":"Exome sequencing","score":0.39379632472991943},{"id":"https://openalex.org/keywords/dna-methylation","display_name":"DNA methylation","score":0.18662995100021362},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1679489016532898}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6899220943450928},{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.5451455116271973},{"id":"https://openalex.org/C10590036","wikidata":"https://www.wikidata.org/wiki/Q417664","display_name":"Exome","level":5,"score":0.5264416933059692},{"id":"https://openalex.org/C5655090","wikidata":"https://www.wikidata.org/wiki/Q192588","display_name":"Relational database","level":2,"score":0.5134104490280151},{"id":"https://openalex.org/C121912465","wikidata":"https://www.wikidata.org/wiki/Q3589153","display_name":"Epigenomics","level":5,"score":0.4776686131954193},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.4336254298686981},{"id":"https://openalex.org/C35794970","wikidata":"https://www.wikidata.org/wiki/Q5243761","display_name":"dbSNP","level":5,"score":0.4200475215911865},{"id":"https://openalex.org/C16671776","wikidata":"https://www.wikidata.org/wiki/Q5420592","display_name":"Exome sequencing","level":4,"score":0.39379632472991943},{"id":"https://openalex.org/C190727270","wikidata":"https://www.wikidata.org/wiki/Q874745","display_name":"DNA methylation","level":4,"score":0.18662995100021362},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1679489016532898},{"id":"https://openalex.org/C501734568","wikidata":"https://www.wikidata.org/wiki/Q42918","display_name":"Mutation","level":3,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C135763542","wikidata":"https://www.wikidata.org/wiki/Q106016","display_name":"Genotype","level":3,"score":0.0},{"id":"https://openalex.org/C153209595","wikidata":"https://www.wikidata.org/wiki/Q501128","display_name":"Single-nucleotide polymorphism","level":4,"score":0.0},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1145/2382936.2383015","is_oa":false,"landing_page_url":"https://doi.org/10.1145/2382936.2383015","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the ACM Conference on Bioinformatics, Computational Biology and Biomedicine","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320321386","display_name":"Terry Fox Foundation","ror":"https://ror.org/05vd00053"},{"id":"https://openalex.org/F4320334506","display_name":"Canadian Institutes of Health Research","ror":"https://ror.org/01gavpb45"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":3,"referenced_works":["https://openalex.org/W2039785774","https://openalex.org/W2059145105","https://openalex.org/W2061680337"],"related_works":["https://openalex.org/W2093932542","https://openalex.org/W4402567428","https://openalex.org/W2043256480","https://openalex.org/W2172231381","https://openalex.org/W1983406990","https://openalex.org/W2106924416","https://openalex.org/W2772505697","https://openalex.org/W3083501552","https://openalex.org/W2400191746","https://openalex.org/W2018130645"],"abstract_inverted_index":{"The":[0,199],"massive":[1],"datasets":[2],"generated":[3,308],"by":[4],"next-generation":[5],"sequencing":[6,148,186],"(NGS)":[7],"studies":[8],"present":[9],"major":[10],"challenges":[11],"for":[12,192,210,317],"data":[13,206,307],"management":[14],"and":[15,44,70,145,188,195,203,208,215,223,232,242,263,301],"analysis.":[16],"In":[17,99,125],"our":[18,251],"ongoing":[19],"pediatric":[20,42],"oncogenomics":[21],"study,":[22],"we":[23,112,127],"have":[24,113,128],"sequenced":[25],"over":[26],"120":[27],"childhood":[28,79,133,267,324],"acute":[29],"lymphoblastic":[30],"(ALL)":[31],"quartets":[32],"(matched":[33],"normal-tumor,":[34],"father,":[35],"mother).":[36],"ALL":[37],"is":[38,253,272,285],"the":[39,102,157,161,164,168,172,182,197,230,238,247,256,269,283,303,318],"most":[40],"common":[41],"cancer":[43],"leading":[45],"cause":[46],"of":[47,67,105,110,217,237,250,259,306,320],"cancer-related":[48],"deaths":[49],"among":[50],"children,":[51],"however":[52],"its":[53],"underlying":[54],"causes":[55],"remain":[56],"largely":[57],"unknown.":[58],"We":[59],"set":[60],"out":[61],"to":[62,101,119,141,159,171,228,254,274,299],"build":[63],"a":[64,115,130,211,275,296,313],"comprehensive":[65],"catalogue":[66],"genomic":[68,241],"(sequence":[69],"structural)":[71],"as":[72,74,85,87,93,95,246],"well":[73,86,94],"epigenomic":[75,243],"variations":[76],"involved":[77,265],"in":[78,266,282,323],"ALL,":[80,268],"through":[81,163],"deep":[82],"exome":[83],"resequencing,":[84],"transcriptome":[88],"analysis":[89],"(RNA-seq),":[90],"genome-wide":[91],"genotyping,":[92],"array-based":[96],"methylation":[97],"profiling.":[98],"response":[100],"important":[103],"challenge":[104],"integrating":[106],"these":[107,122],"various":[108],"sources":[109],"information,":[111],"created":[114],"flexible":[116,297],"database":[117,151,200,231,278,293],"system":[118],"effectively":[120],"manage":[121],"ambitious":[123],"datasets.":[124],"particular,":[126],"implemented":[129],"custom":[131,218],"Next-Generation":[132],"Acute":[134],"Lymphoblastic":[135],"Leukemia":[136],"relational":[137],"Database":[138],"(ngALL":[139],"DB)":[140],"report":[142],"workflow":[143],"analyses":[144],"integrate":[146],"whole-exome":[147],"data.":[149,198,244],"This":[150,291],"also":[152],"provides":[153,179],"progress":[154],"reports,":[155],"allowing":[156],"user":[158],"track":[160],"samples":[162],"project":[165,252],"pipeline":[166],"from":[167,309],"biospecimen":[169],"repository":[170],"annotated":[173],"SNP":[174],"list":[175],"output.":[176],"Moreover,":[177],"it":[178],"information":[180],"about":[181],"different":[183],"bioinformatics":[184],"tools,":[185],"runs":[187],"computing":[189],"platforms":[190],"used":[191],"mapping,":[193],"cleaning":[194],"analyzing":[196],"design's":[201],"flexibility":[202],"reusability":[204],"facilitates":[205],"integration":[207],"allows":[209],"customizable":[212],"analytical":[213],"approach":[214],"execution":[216],"structured":[219],"queries.":[220],"Complex":[221],"queries":[222],"procedures":[224],"can":[225],"be":[226],"written":[227],"interrogate":[229],"analyse":[233],"virtually":[234],"any":[235],"aspect":[236],"integrated":[239,292],"NGS,":[240],"Furthermore,":[245],"main":[248],"goal":[249],"identify":[255],"full":[257],"complement":[258],"genetic":[260],"variants":[261,322],"(inherited":[262],"somatic)":[264],"ngALL":[270],"DB":[271],"linked":[273],"high-resolution":[276],"annotation":[277],"where":[279],"each":[280],"position":[281],"genome":[284],"represented":[286],"with":[287],"detailed":[288],"functional":[289],"annotation.":[290],"structure":[294],"offers":[295],"framework":[298],"compile":[300],"characterize":[302],"large":[304],"amounts":[305],"NGS":[310],"studies,":[311],"providing":[312],"powerful":[314],"research":[315],"tool":[316],"identification":[319],"causal":[321],"ALL.":[325]},"counts_by_year":[],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2016-06-24T00:00:00"}
