{"id":"https://openalex.org/W2747366572","doi":"https://doi.org/10.1145/3107411.3108208","title":"Analysis of 16S Genomic Data using Graphical Databases","display_name":"Analysis of 16S Genomic Data using Graphical Databases","publication_year":2017,"publication_date":"2017-08-20","ids":{"openalex":"https://openalex.org/W2747366572","doi":"https://doi.org/10.1145/3107411.3108208","mag":"2747366572"},"language":"en","primary_location":{"id":"doi:10.1145/3107411.3108208","is_oa":false,"landing_page_url":"https://doi.org/10.1145/3107411.3108208","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 8th ACM International Conference on Bioinformatics, Computational Biology,and Health Informatics","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://digitalcommons.uri.edu/cs_facpubs/33","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5032446998","display_name":"Olivia M. Ahern","orcid":"https://orcid.org/0000-0003-4787-7582"},"institutions":[{"id":"https://openalex.org/I17626003","display_name":"University of Rhode Island","ror":"https://ror.org/013ckk937","country_code":"US","type":"education","lineage":["https://openalex.org/I17626003"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Olivia M. Ahern","raw_affiliation_strings":["University of Rhode Island, Narragansett, RI, USA"],"affiliations":[{"raw_affiliation_string":"University of Rhode Island, Narragansett, RI, USA","institution_ids":["https://openalex.org/I17626003"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5032522230","display_name":"Rebecca J. Stevick","orcid":"https://orcid.org/0000-0001-7918-6546"},"institutions":[{"id":"https://openalex.org/I17626003","display_name":"University of Rhode Island","ror":"https://ror.org/013ckk937","country_code":"US","type":"education","lineage":["https://openalex.org/I17626003"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Rebecca J. Stevick","raw_affiliation_strings":["University of Rhode Island, Narragansett, RI, USA"],"affiliations":[{"raw_affiliation_string":"University of Rhode Island, Narragansett, RI, USA","institution_ids":["https://openalex.org/I17626003"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5061860143","display_name":"Yuan Li","orcid":"https://orcid.org/0000-0003-4263-9569"},"institutions":[{"id":"https://openalex.org/I17626003","display_name":"University of Rhode Island","ror":"https://ror.org/013ckk937","country_code":"US","type":"education","lineage":["https://openalex.org/I17626003"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Li Yuan","raw_affiliation_strings":["University of Rhode Island, Kingston, RI, USA"],"affiliations":[{"raw_affiliation_string":"University of Rhode Island, Kingston, RI, USA","institution_ids":["https://openalex.org/I17626003"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5071391690","display_name":"Noah M. Daniels","orcid":"https://orcid.org/0000-0002-9538-825X"},"institutions":[{"id":"https://openalex.org/I17626003","display_name":"University of Rhode Island","ror":"https://ror.org/013ckk937","country_code":"US","type":"education","lineage":["https://openalex.org/I17626003"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Noah M. Daniels","raw_affiliation_strings":["University of Rhode Island, Kingston, RI, USA"],"affiliations":[{"raw_affiliation_string":"University of Rhode Island, Kingston, RI, USA","institution_ids":["https://openalex.org/I17626003"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5032446998"],"corresponding_institution_ids":["https://openalex.org/I17626003"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.0906587,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"599","last_page":"599"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9998000264167786,"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":0.9998000264167786,"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/T11269","display_name":"Algorithms and Data Compression","score":0.9957000017166138,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9886999726295471,"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":0.7810965776443481},{"id":"https://openalex.org/keywords/graph-database","display_name":"Graph database","score":0.6790292263031006},{"id":"https://openalex.org/keywords/search-engine-indexing","display_name":"Search engine indexing","score":0.5677552223205566},{"id":"https://openalex.org/keywords/relational-database","display_name":"Relational database","score":0.5497966408729553},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.5121991038322449},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.49109554290771484},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4804915189743042},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.4502156376838684},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.4293321669101715},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.3089260160923004}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7810965776443481},{"id":"https://openalex.org/C176225458","wikidata":"https://www.wikidata.org/wiki/Q595971","display_name":"Graph database","level":3,"score":0.6790292263031006},{"id":"https://openalex.org/C75165309","wikidata":"https://www.wikidata.org/wiki/Q2258979","display_name":"Search engine indexing","level":2,"score":0.5677552223205566},{"id":"https://openalex.org/C5655090","wikidata":"https://www.wikidata.org/wiki/Q192588","display_name":"Relational database","level":2,"score":0.5497966408729553},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.5121991038322449},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.49109554290771484},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4804915189743042},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.4502156376838684},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.4293321669101715},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.3089260160923004},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.0},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1145/3107411.3108208","is_oa":false,"landing_page_url":"https://doi.org/10.1145/3107411.3108208","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 8th ACM International Conference on Bioinformatics, Computational Biology,and Health Informatics","raw_type":"proceedings-article"},{"id":"pmh:oai:digitalcommons.uri.edu:cs_facpubs-1032","is_oa":true,"landing_page_url":"https://digitalcommons.uri.edu/cs_facpubs/33","pdf_url":null,"source":{"id":"https://openalex.org/S2764761010","display_name":"Journal of Media Literacy Education","issn_l":"2167-8715","issn":["2167-8715"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310316378","host_organization_name":"National Association for Media Literacy Education","host_organization_lineage":["https://openalex.org/P4310316378"],"host_organization_lineage_names":["National Association for Media Literacy Education"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Computer Science and Statistics Faculty Publications","raw_type":"text"}],"best_oa_location":{"id":"pmh:oai:digitalcommons.uri.edu:cs_facpubs-1032","is_oa":true,"landing_page_url":"https://digitalcommons.uri.edu/cs_facpubs/33","pdf_url":null,"source":{"id":"https://openalex.org/S2764761010","display_name":"Journal of Media Literacy Education","issn_l":"2167-8715","issn":["2167-8715"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310316378","host_organization_name":"National Association for Media Literacy Education","host_organization_lineage":["https://openalex.org/P4310316378"],"host_organization_lineage_names":["National Association for Media Literacy Education"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Computer Science and Statistics Faculty Publications","raw_type":"text"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G5490106789","display_name":null,"funder_award_id":"1244657","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":5,"referenced_works":["https://openalex.org/W2076510208","https://openalex.org/W2128162768","https://openalex.org/W2161048357","https://openalex.org/W2337508844","https://openalex.org/W4233928114"],"related_works":["https://openalex.org/W3024364549","https://openalex.org/W4206019083","https://openalex.org/W2048865712","https://openalex.org/W1976265003","https://openalex.org/W2370378377","https://openalex.org/W4281562483","https://openalex.org/W2800353001","https://openalex.org/W4391060474","https://openalex.org/W3115442681","https://openalex.org/W2391000461"],"abstract_inverted_index":{"Since":[0],"the":[1,75,80,86,97,130,142,208,222,238,249,261,274,279],"Human":[2],"Genome":[3],"Project":[4],"was":[5],"completed":[6],"in":[7,15,33,58,129,207,221,278,348,355,365,392],"2003,":[8],"many":[9,120],"data":[10,29,56,138,367],"scientists":[11],"have":[12,92],"developed":[13],"algorithms":[14,35],"order":[16],"to":[17,52,73,113,123,153,171,215,243,256,259,267,311,320,378],"store":[18,53,124],"and":[19,78,107,122,186,194,252,331,334,374],"query":[20,83,250,346],"high":[21,317],"volumes":[22],"of":[23,82,88,201,233,269,303,307,316,323,338,341,362,381],"genomic":[24,366],"data.":[25],"The":[26],"most":[27],"common":[28,118,152,162,170,184,192,245,312,330],"storage":[30,282],"techniques":[31,45],"employed":[32],"these":[34,125],"are":[36,117,189,203],"flat":[37,356],"files":[38,357],"or":[39,358],"relational":[40,359],"databases.":[41,360],"While":[42],"sophisticated":[43],"indexing":[44],"can":[46,240],"accelerate":[47],"queries,":[48,287],"an":[49],"alternative":[50],"is":[51,112,134,151,158,167,177,265,276,351,390],"biological":[54],"sequence":[55,144,286,342],"directly":[57],"a":[59,68,148,161,165,180,321,335],"way":[60],"that":[61,71,116,247,268,273,345],"supports":[62,293],"efficient":[63,382],"queries.":[64],"Here":[65],"we":[66],"introduce":[67],"new":[69],"algorithm":[70],"aims":[72],"compress":[74],"redundant":[76],"information":[77,104],"improve":[79],"performance":[81],"speed":[84],"with":[85],"help":[87],"graphical":[89,101,131,209,225,280,289,349,363],"databases,":[90],"which":[91,296,389],"been":[93],"commercial":[94],"available":[95],"since":[96],"mid-late":[98],"2000s.":[99],"A":[100],"database":[102,226,239,281,290],"stores":[103],"using":[105],"nodes":[106,185,188,202,246,258],"relationships":[108],"(edges).":[109],"Our":[110],"approach":[111,264],"identify":[114],"subsequences":[115],"among":[119],"sequences,":[121,155],"as":[126,139,160,179,385],"\"common":[127],"nodes\"":[128],"database.":[132],"This":[133,224,263],"accomplished":[135],"for":[136,229,371],"sequencing":[137],"follows:":[140],"split":[141],"whole":[143],"into":[145],"k-mers:":[146],"if":[147,164],"given":[149],"k-mer":[150,166],"enough":[154],"then":[156,175],"it":[157,176],"labeled":[159,178],"segment;":[163],"unique":[168],"(or":[169],"too":[172],"few":[173],"sequences),":[174],"single":[181,187,195,257,326,332],"segment.":[182],"Thus,":[183],"formed":[190],"from":[191],"segments":[193],"segments,":[196],"respectively.":[197],"These":[198],"two":[199],"kinds":[200],"connected":[204],"by":[205,218],"edges":[206,220,255],"database,":[210],"allowing":[211],"each":[212],"original":[213],"sequences":[214],"be":[216],"reconstructed":[217],"following":[219],"graph.":[223],"model":[227],"allows":[228],"fast":[230],"taxonomic":[231],"queries":[232],"16S":[234,304],"rDNA.":[235],"When":[236],"queried,":[237],"first":[241],"attempt":[242],"find":[244],"match":[248],"sequence,":[251],"subsequently":[253],"follow":[254],"refine":[260],"search.":[262],"analogous":[266],"\"compressive":[270],"genomics\",":[271],"except":[272],"compression":[275],"implicit":[277],"model.":[283],"Beyond":[284],"simple":[285],"this":[288],"representation":[291],"also":[292],"variability":[294,309,318],"analysis,":[295,383,388],"identifies":[297],"highly":[298],"variable":[299],"vs.":[300],"conserved":[301],"regions":[302,315],"sequence.":[305],"Regions":[306],"low":[308],"correspond":[310,319],"nodes,":[313,333],"while":[314],"variety":[322],"paths":[324],"through":[325],"nodes.":[327],"Figure":[328],"illustrates":[329],"corresponding":[336],"plot":[337],"variability.":[339],"Benchmarking":[340],"search":[343],"indicates":[344],"time":[347],"databases":[350,364],"significantly":[352],"faster":[353],"than":[354],"Implementation":[361],"analysis":[368],"will":[369],"allow":[370],"accelerated":[372],"search,":[373],"may":[375],"lend":[376],"itself":[377],"other":[379],"forms":[380],"such":[384],"tetramer":[386],"frequency":[387],"useful":[391],"metagenomic":[393],"binning.":[394]},"counts_by_year":[],"updated_date":"2026-03-10T16:38:18.471706","created_date":"2025-10-10T00:00:00"}
