{"id":"https://openalex.org/W2914779219","doi":"https://doi.org/10.1109/bibm.2018.8621171","title":"MetaFlow: an interactive user-friendly workflow for automated analysis of whole genome shotgun sequencing metagenomic data","display_name":"MetaFlow: an interactive user-friendly workflow for automated analysis of whole genome shotgun sequencing metagenomic data","publication_year":2018,"publication_date":"2018-12-01","ids":{"openalex":"https://openalex.org/W2914779219","doi":"https://doi.org/10.1109/bibm.2018.8621171","mag":"2914779219"},"language":"en","primary_location":{"id":"doi:10.1109/bibm.2018.8621171","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm.2018.8621171","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2018 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","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/A5053412561","display_name":"Usama Bakry","orcid":null},"institutions":[{"id":"https://openalex.org/I57629906","display_name":"Nile University","ror":"https://ror.org/03cg7cp61","country_code":"EG","type":"education","lineage":["https://openalex.org/I57629906"]}],"countries":["EG"],"is_corresponding":true,"raw_author_name":"Usama Bakry","raw_affiliation_strings":["Center for Informatics Science, Nile University, Giza, Egypt"],"affiliations":[{"raw_affiliation_string":"Center for Informatics Science, Nile University, Giza, Egypt","institution_ids":["https://openalex.org/I57629906"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5068690978","display_name":"Mohamed Fares","orcid":"https://orcid.org/0000-0003-3600-3716"},"institutions":[{"id":"https://openalex.org/I4210131959","display_name":"National Research Centre","ror":"https://ror.org/02n85j827","country_code":"EG","type":"facility","lineage":["https://openalex.org/I4210131959"]}],"countries":["EG"],"is_corresponding":false,"raw_author_name":"Mohamed Fares","raw_affiliation_strings":["Veterinary Research Division, National Research Centre, Giza, Egypt"],"affiliations":[{"raw_affiliation_string":"Veterinary Research Division, National Research Centre, Giza, Egypt","institution_ids":["https://openalex.org/I4210131959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5057750170","display_name":"Ali Kishk","orcid":"https://orcid.org/0000-0003-3710-5909"},"institutions":[{"id":"https://openalex.org/I57629906","display_name":"Nile University","ror":"https://ror.org/03cg7cp61","country_code":"EG","type":"education","lineage":["https://openalex.org/I57629906"]}],"countries":["EG"],"is_corresponding":false,"raw_author_name":"Ali Kishk","raw_affiliation_strings":["Center for Informatics Science, Nile University, Giza, Egypt"],"affiliations":[{"raw_affiliation_string":"Center for Informatics Science, Nile University, Giza, Egypt","institution_ids":["https://openalex.org/I57629906"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5069484090","display_name":"Mohamed El-Hadidi","orcid":"https://orcid.org/0000-0002-3593-8061"},"institutions":[{"id":"https://openalex.org/I57629906","display_name":"Nile University","ror":"https://ror.org/03cg7cp61","country_code":"EG","type":"education","lineage":["https://openalex.org/I57629906"]}],"countries":["EG"],"is_corresponding":false,"raw_author_name":"Mohamed El-Hadidi","raw_affiliation_strings":["Center for Informatics Science, Nile University, Giza, Egypt"],"affiliations":[{"raw_affiliation_string":"Center for Informatics Science, Nile University, Giza, Egypt","institution_ids":["https://openalex.org/I57629906"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5053412561"],"corresponding_institution_ids":["https://openalex.org/I57629906"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.1379955,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"2741","last_page":"2743"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9980000257492065,"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":0.9980000257492065,"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/T11791","display_name":"Microbial Community Ecology and Physiology","score":0.9901999831199646,"subfield":{"id":"https://openalex.org/subfields/2303","display_name":"Ecology"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.9900000095367432,"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/workflow","display_name":"Workflow","score":0.829461395740509},{"id":"https://openalex.org/keywords/metagenomics","display_name":"Metagenomics","score":0.7539066076278687},{"id":"https://openalex.org/keywords/shotgun-sequencing","display_name":"Shotgun sequencing","score":0.725180983543396},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6781648397445679},{"id":"https://openalex.org/keywords/shotgun","display_name":"Shotgun","score":0.6585536599159241},{"id":"https://openalex.org/keywords/user-friendly","display_name":"User Friendly","score":0.5761756896972656},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.3952403962612152},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3723284602165222},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.3460506200790405},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.22326111793518066},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1612955629825592},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.13130369782447815},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.08429384231567383},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.07937324047088623}],"concepts":[{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.829461395740509},{"id":"https://openalex.org/C15151743","wikidata":"https://www.wikidata.org/wiki/Q903778","display_name":"Metagenomics","level":3,"score":0.7539066076278687},{"id":"https://openalex.org/C101985253","wikidata":"https://www.wikidata.org/wiki/Q1073526","display_name":"Shotgun sequencing","level":4,"score":0.725180983543396},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6781648397445679},{"id":"https://openalex.org/C2781434637","wikidata":"https://www.wikidata.org/wiki/Q486396","display_name":"Shotgun","level":3,"score":0.6585536599159241},{"id":"https://openalex.org/C61437842","wikidata":"https://www.wikidata.org/wiki/Q281291","display_name":"User Friendly","level":2,"score":0.5761756896972656},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.3952403962612152},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3723284602165222},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.3460506200790405},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.22326111793518066},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1612955629825592},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.13130369782447815},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.08429384231567383},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.07937324047088623}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/bibm.2018.8621171","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm.2018.8621171","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2018 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":12,"referenced_works":["https://openalex.org/W2045204781","https://openalex.org/W2129991502","https://openalex.org/W2131271579","https://openalex.org/W2153109441","https://openalex.org/W2432815617","https://openalex.org/W2465681871","https://openalex.org/W2790372567","https://openalex.org/W2897204056","https://openalex.org/W2917207851","https://openalex.org/W2950464960","https://openalex.org/W4233004170","https://openalex.org/W6661742627"],"related_works":["https://openalex.org/W4210312276","https://openalex.org/W3036436206","https://openalex.org/W4394334725","https://openalex.org/W4394325869","https://openalex.org/W3043668926","https://openalex.org/W4394383033","https://openalex.org/W4394278351","https://openalex.org/W4394378620","https://openalex.org/W4394291587","https://openalex.org/W4321764688"],"abstract_inverted_index":{"Metagenomics":[0],"is":[1,7],"a":[2,47,55,183,189,212],"rapidly":[3,217],"emerging":[4],"field":[5],"that":[6],"concerned":[8],"with":[9,84,188],"the":[10,36,52,60,72,81,110,205],"study":[11],"of":[12,19,54,80,105,109,154,198,207],"microbial":[13,56,64],"communities":[14],"\u201cmicrobiomes\u201d":[15],"on":[16,211],"both":[17],"levels":[18],"taxonomic":[20],"classification":[21],"and":[22,29,66,89,112,142,161,173,222,227],"functional":[23,95],"annotation.":[24],"Targeted":[25],"amplicon":[26,44],"(16S":[27],"rRNA)":[28],"whole":[30],"genome":[31],"shotgun":[32,199],"(WGS)":[33],"sequencing":[34,39,45,76,106],"are":[35,101,124,158],"two":[37],"main":[38],"strategies":[40],"in":[41,103,170,218],"metagenomics.":[42],"As":[43],"provides":[46],"cheap":[48],"way":[49,224],"to":[50,62,131,136],"classify":[51],"composition":[53],"community,":[57],"it":[58],"lacks":[59],"ability":[61],"identify":[63],"genes":[65],"annotate":[67],"its":[68,129,137],"corresponding":[69],"functions.":[70],"On":[71],"other":[73],"hand,":[74],"WGS":[75,120,208],"allows":[77],"further":[78],"investigation":[79],"complete":[82],"genomes":[83],"all":[85],"associated":[86],"genetic":[87],"information,":[88],"hence,":[90],"gives":[91],"another":[92],"dimension":[93],"for":[94,119,151,164,195,225],"analysis,":[96,111],"however,":[97],"these":[98],"mentioned":[99],"advantages":[100],"not":[102,162],"favor":[104],"cost,":[107],"duration":[108],"required":[113,150],"computational":[114],"resources.":[115],"Currently,":[116],"most":[117],"tools":[118,149],"microbiome":[121,155],"data":[122,156,210],"analysis":[123,157,197,206],"command-line":[125],"based,":[126],"which":[127],"limits":[128],"use":[130],"only":[132],"experienced":[133],"bioinformaticians,":[134],"due":[135],"complexity":[138],"during":[139],"installation,":[140],"usage":[141],"fine":[143],"tuning":[144],"numerous":[145],"parameters.":[146],"Moreover,":[147],"current":[148],"different":[152],"steps":[153],"platform":[159],"specific":[160],"user-friendly":[163],"biologists":[165,226],"without":[166],"previous":[167],"deep":[168],"knowledge":[169],"command":[171],"line":[172],"installation/configuration":[174],"troubleshooting":[175],"abilities.":[176],"In":[177],"this":[178],"paper,":[179],"we":[180],"present":[181],"MetaFlow;":[182],"comprehensive":[184,221],"automatic":[185],"platform-independent":[186],"workflow":[187],"friendly":[190],"graphical":[191],"user":[192],"interface":[193],"(GUI),":[194],"interactive":[196,223],"metagenomic":[200,209],"data.":[201],"MetaFlow":[202],"will":[203],"facilitate":[204],"personal":[213],"laptop,":[214],"more":[215],"smoothly,":[216],"an":[219],"automatic,":[220],"microbiologists.":[228]},"counts_by_year":[],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
