{"id":"https://openalex.org/W2132801908","doi":"https://doi.org/10.1093/bib/bbs033","title":"Functional assignment of metagenomic data: challenges and applications","display_name":"Functional assignment of metagenomic data: challenges and applications","publication_year":2012,"publication_date":"2012-07-06","ids":{"openalex":"https://openalex.org/W2132801908","doi":"https://doi.org/10.1093/bib/bbs033","mag":"2132801908","pmid":"https://pubmed.ncbi.nlm.nih.gov/22772835"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbs033","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbs033","pdf_url":"https://academic.oup.com/bib/article-pdf/13/6/711/480041/bbs033.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":"public-domain","license_id":"https://openalex.org/licenses/public-domain","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"review","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bib/article-pdf/13/6/711/480041/bbs033.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5029884541","display_name":"Tulika Prakash","orcid":"https://orcid.org/0000-0001-9270-8775"},"institutions":[{"id":"https://openalex.org/I4210088777","display_name":"MetaSystem (Italy)","ror":"https://ror.org/008yv5115","country_code":"IT","type":"company","lineage":["https://openalex.org/I4210088777"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"T. Prakash","raw_affiliation_strings":["Laboratory for MetaSystems Research at RIKEN, Japan"],"affiliations":[{"raw_affiliation_string":"Laboratory for MetaSystems Research at RIKEN, Japan","institution_ids":["https://openalex.org/I4210088777"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5053294157","display_name":"Todd D. Taylor","orcid":"https://orcid.org/0000-0003-4247-6253"},"institutions":[{"id":"https://openalex.org/I4210088777","display_name":"MetaSystem (Italy)","ror":"https://ror.org/008yv5115","country_code":"IT","type":"company","lineage":["https://openalex.org/I4210088777"]},{"id":"https://openalex.org/I4210150921","display_name":"RIKEN Center for Integrative Medical Sciences","ror":"https://ror.org/04mb6s476","country_code":"JP","type":"facility","lineage":["https://openalex.org/I4210110652","https://openalex.org/I4210150921"]}],"countries":["IT","JP"],"is_corresponding":true,"raw_author_name":"T. D. Taylor","raw_affiliation_strings":["Laboratory for MetaSystems Research at RIKEN, Japan","Laboratory for MetaSystems Research, Quantitative Biology Center, Riken, Yokohama, Kanagawa 230-0045, Japan","MetaSystems Research at RIKEN, Japan"],"affiliations":[{"raw_affiliation_string":"Laboratory for MetaSystems Research at RIKEN, Japan","institution_ids":["https://openalex.org/I4210088777"]},{"raw_affiliation_string":"Laboratory for MetaSystems Research, Quantitative Biology Center, Riken, Yokohama, Kanagawa 230-0045, Japan","institution_ids":["https://openalex.org/I4210150921"]},{"raw_affiliation_string":"MetaSystems Research at RIKEN, Japan","institution_ids":["https://openalex.org/I4210088777"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5053294157"],"corresponding_institution_ids":["https://openalex.org/I4210088777","https://openalex.org/I4210150921"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":{"value":4011,"currency":"USD","value_usd":4011},"fwci":6.3195,"has_fulltext":true,"cited_by_count":167,"citation_normalized_percentile":{"value":0.9751346,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":94,"max":100},"biblio":{"volume":"13","issue":"6","first_page":"711","last_page":"727"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9997000098228455,"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":0.9997000098228455,"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/T10066","display_name":"Gut microbiota and health","score":0.9975000023841858,"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":0.9970999956130981,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/metagenomics","display_name":"Metagenomics","score":0.9766222238540649},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5681198239326477},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5667038559913635},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.42547398805618286},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.38813483715057373},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.35354262590408325},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.14142560958862305},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.13496285676956177}],"concepts":[{"id":"https://openalex.org/C15151743","wikidata":"https://www.wikidata.org/wiki/Q903778","display_name":"Metagenomics","level":3,"score":0.9766222238540649},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5681198239326477},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5667038559913635},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.42547398805618286},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.38813483715057373},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.35354262590408325},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.14142560958862305},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.13496285676956177}],"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":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D054892","descriptor_name":"Metagenome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D054892","descriptor_name":"Metagenome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D054892","descriptor_name":"Metagenome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D054892","descriptor_name":"Metagenome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056186","descriptor_name":"Metagenomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056186","descriptor_name":"Metagenomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056186","descriptor_name":"Metagenomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056186","descriptor_name":"Metagenomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bib/bbs033","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbs033","pdf_url":"https://academic.oup.com/bib/article-pdf/13/6/711/480041/bbs033.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":"public-domain","license_id":"https://openalex.org/licenses/public-domain","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:22772835","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/22772835","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":"Briefings in bioinformatics","raw_type":null},{"id":"pmh:oai:europepmc.org:2501831","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3504928","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bib/bbs033","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbs033","pdf_url":"https://academic.oup.com/bib/article-pdf/13/6/711/480041/bbs033.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":"public-domain","license_id":"https://openalex.org/licenses/public-domain","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320335125","display_name":"RIKEN","ror":"https://ror.org/01sjwvz98"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2132801908.pdf","grobid_xml":"https://content.openalex.org/works/W2132801908.grobid-xml"},"referenced_works_count":127,"referenced_works":["https://openalex.org/W1533936090","https://openalex.org/W1562379206","https://openalex.org/W1635391495","https://openalex.org/W1936995073","https://openalex.org/W1964508112","https://openalex.org/W1966952999","https://openalex.org/W1970472465","https://openalex.org/W1970717748","https://openalex.org/W1975140329","https://openalex.org/W1983169073","https://openalex.org/W1985151726","https://openalex.org/W1990364202","https://openalex.org/W1990453950","https://openalex.org/W1992579032","https://openalex.org/W1994441981","https://openalex.org/W1995117714","https://openalex.org/W1995511427","https://openalex.org/W1995734240","https://openalex.org/W1998077837","https://openalex.org/W1998767819","https://openalex.org/W2001620437","https://openalex.org/W2006465310","https://openalex.org/W2007153665","https://openalex.org/W2014982185","https://openalex.org/W2016760914","https://openalex.org/W2018686814","https://openalex.org/W2026716989","https://openalex.org/W2027496182","https://openalex.org/W2029437806","https://openalex.org/W2037532428","https://openalex.org/W2042056700","https://openalex.org/W2042924304","https://openalex.org/W2045119680","https://openalex.org/W2047341547","https://openalex.org/W2048673910","https://openalex.org/W2048818637","https://openalex.org/W2048947602","https://openalex.org/W2052002049","https://openalex.org/W2052921979","https://openalex.org/W2053611563","https://openalex.org/W2054539653","https://openalex.org/W2055043387","https://openalex.org/W2055503200","https://openalex.org/W2057885377","https://openalex.org/W2060915038","https://openalex.org/W2061581770","https://openalex.org/W2066718232","https://openalex.org/W2068687524","https://openalex.org/W2069689025","https://openalex.org/W2081226160","https://openalex.org/W2082019050","https://openalex.org/W2082464084","https://openalex.org/W2085631282","https://openalex.org/W2088347903","https://openalex.org/W2089691332","https://openalex.org/W2095200684","https://openalex.org/W2095648296","https://openalex.org/W2096525273","https://openalex.org/W2096576371","https://openalex.org/W2097485877","https://openalex.org/W2098023550","https://openalex.org/W2101098894","https://openalex.org/W2102118387","https://openalex.org/W2103017472","https://openalex.org/W2103306615","https://openalex.org/W2103461849","https://openalex.org/W2106073189","https://openalex.org/W2107369528","https://openalex.org/W2107424557","https://openalex.org/W2107644675","https://openalex.org/W2109715166","https://openalex.org/W2113129488","https://openalex.org/W2113601822","https://openalex.org/W2114034054","https://openalex.org/W2114200698","https://openalex.org/W2116398954","https://openalex.org/W2116704271","https://openalex.org/W2116895571","https://openalex.org/W2119030995","https://openalex.org/W2120365168","https://openalex.org/W2124410686","https://openalex.org/W2124637227","https://openalex.org/W2125826054","https://openalex.org/W2126809954","https://openalex.org/W2127415562","https://openalex.org/W2128124531","https://openalex.org/W2129873761","https://openalex.org/W2130669817","https://openalex.org/W2133253129","https://openalex.org/W2135621733","https://openalex.org/W2136145671","https://openalex.org/W2136651963","https://openalex.org/W2138874847","https://openalex.org/W2141885858","https://openalex.org/W2141920662","https://openalex.org/W2143842034","https://openalex.org/W2144662851","https://openalex.org/W2145336165","https://openalex.org/W2146312020","https://openalex.org/W2146918217","https://openalex.org/W2147847105","https://openalex.org/W2149429041","https://openalex.org/W2149573313","https://openalex.org/W2150337627","https://openalex.org/W2155606054","https://openalex.org/W2155744824","https://openalex.org/W2156701707","https://openalex.org/W2157389697","https://openalex.org/W2158253061","https://openalex.org/W2159788862","https://openalex.org/W2160969485","https://openalex.org/W2161546116","https://openalex.org/W2161794223","https://openalex.org/W2163105490","https://openalex.org/W2167062509","https://openalex.org/W2169230701","https://openalex.org/W2170089054","https://openalex.org/W2171571559","https://openalex.org/W2171585790","https://openalex.org/W2175093233","https://openalex.org/W2914081640","https://openalex.org/W4211049762","https://openalex.org/W4231170962","https://openalex.org/W4233334497","https://openalex.org/W4236236547","https://openalex.org/W4252706339","https://openalex.org/W4320301318"],"related_works":["https://openalex.org/W2210738511","https://openalex.org/W2474302342","https://openalex.org/W1910109602","https://openalex.org/W2080583581","https://openalex.org/W4297131566","https://openalex.org/W2017364432","https://openalex.org/W3156493549","https://openalex.org/W3195915274","https://openalex.org/W3158976456","https://openalex.org/W4285082713"],"abstract_inverted_index":{"Metagenomic":[0],"sequencing":[1,122,138],"provides":[2],"a":[3,30,46],"unique":[4],"opportunity":[5],"to":[6,36],"explore":[7,37],"earth's":[8],"limitless":[9],"environments":[10],"harboring":[11],"scores":[12],"of":[13,25,80,89,98,128,151,185,189,192,204,215,228],"yet":[14],"unknown":[15],"and":[16,20,57,104,124,144,199,208],"mostly":[17],"unculturable":[18],"microbes":[19,51],"other":[21,112],"organisms.":[22],"Functional":[23,78],"analysis":[24,79,191],"the":[26,38,50,86,116,129,134,146,161,186,229],"metagenomic":[27,68,81,130,167,193,219],"data":[28,82,90,99],"plays":[29],"central":[31],"role":[32],"in":[33,42,92,202,226],"projects":[34,69],"aiming":[35],"most":[39,162],"essential":[40],"questions":[41],"microbiology,":[43],"namely":[44],"'In":[45],"given":[47],"environment,":[48],"among":[49],"present,":[52],"what":[53],"are":[54,59,75,109,169],"they":[55,60],"doing,":[56],"how":[58],"doing":[61],"it?'":[62],"Toward":[63],"this":[64],"goal,":[65],"several":[66],"large-scale":[67],"have":[70,222],"recently":[71],"been":[72,223],"conducted":[73,225],"or":[74],"currently":[76,205],"underway.":[77],"mainly":[83],"suffers":[84],"from":[85,217],"vast":[87],"amount":[88,97],"generated":[91,136],"these":[93],"projects.":[94],"The":[95,149],"shear":[96],"requires":[100],"much":[101],"computational":[102],"time":[103],"storage":[105],"space.":[106],"These":[107],"problems":[108],"compounded":[110],"by":[111],"factors":[113],"potentially":[114],"affecting":[115],"functional":[117,147,154,164,190],"analysis,":[118],"including,":[119],"sample":[120],"preparation,":[121],"method":[123],"average":[125],"genome":[126],"size":[127],"samples.":[131],"In":[132],"addition,":[133],"read-lengths":[135],"during":[137],"influence":[139],"sequence":[140,178,194],"assembly,":[141],"gene":[142],"prediction":[143],"subsequently":[145],"analysis.":[148],"level":[150],"confidence":[152],"for":[153,166],"predictions":[155],"increases":[156],"with":[157],"increasing":[158],"read-length.":[159],"Usually,":[160],"reliable":[163],"annotations":[165],"sequences":[168],"achieved":[170],"using":[171],"homology-based":[172],"approaches":[173],"against":[174],"publicly":[175],"available":[176,206],"reference":[177],"databases.":[179],"Here,":[180],"we":[181,211],"present":[182],"an":[183],"overview":[184],"current":[187],"state":[188],"data,":[195],"bottlenecks":[196],"frequently":[197],"encountered":[198],"possible":[200],"solutions":[201],"light":[203],"resources":[207],"tools.":[209],"Finally,":[210],"provide":[212],"some":[213],"examples":[214],"applications":[216],"recent":[218],"studies":[220],"which":[221],"successfully":[224],"spite":[227],"known":[230],"difficulties.":[231]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":6},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":8},{"year":2022,"cited_by_count":13},{"year":2021,"cited_by_count":14},{"year":2020,"cited_by_count":11},{"year":2019,"cited_by_count":21},{"year":2018,"cited_by_count":16},{"year":2017,"cited_by_count":15},{"year":2016,"cited_by_count":12},{"year":2015,"cited_by_count":20},{"year":2014,"cited_by_count":17},{"year":2013,"cited_by_count":10}],"updated_date":"2026-04-05T17:49:38.594831","created_date":"2025-10-10T00:00:00"}
