{"id":"https://openalex.org/W3011893537","doi":"https://doi.org/10.1186/s12859-020-3429-6","title":"A big data approach to metagenomics for all-food-sequencing","display_name":"A big data approach to metagenomics for all-food-sequencing","publication_year":2020,"publication_date":"2020-03-12","ids":{"openalex":"https://openalex.org/W3011893537","doi":"https://doi.org/10.1186/s12859-020-3429-6","mag":"3011893537","pmid":"https://pubmed.ncbi.nlm.nih.gov/32164527"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-020-3429-6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-020-3429-6","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-020-3429-6","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-020-3429-6","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5043372390","display_name":"Robin Kobus","orcid":"https://orcid.org/0000-0003-2726-1908"},"institutions":[{"id":"https://openalex.org/I197323543","display_name":"Johannes Gutenberg University Mainz","ror":"https://ror.org/023b0x485","country_code":"DE","type":"education","lineage":["https://openalex.org/I197323543"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Robin Kobus","raw_affiliation_strings":["Department of Computer Science, Johannes Gutenberg University, Mainz, 55099, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Johannes Gutenberg University, Mainz, 55099, Germany","institution_ids":["https://openalex.org/I197323543"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5041366936","display_name":"Jos\u00e9 M. Abu\u00edn","orcid":"https://orcid.org/0000-0001-9771-818X"},"institutions":[{"id":"https://openalex.org/I185808892","display_name":"Polytechnic Institute of C\u00e1vado and Ave","ror":"https://ror.org/0448qsq10","country_code":"PT","type":"education","lineage":["https://openalex.org/I185808892"]},{"id":"https://openalex.org/I200284239","display_name":"Universidade de Santiago de Compostela","ror":"https://ror.org/030eybx10","country_code":"ES","type":"education","lineage":["https://openalex.org/I200284239"]}],"countries":["ES","PT"],"is_corresponding":false,"raw_author_name":"Jos\u00e9 M. Abu\u00edn","raw_affiliation_strings":["CiTIUS, Universidade de Santiago de Compostela, Santiago de Compostela, 15782, Spain","IPCA, Polytechnic Institute of C\u00e1vado and Ave, Barcelos, 4750-810, Portugal"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"CiTIUS, Universidade de Santiago de Compostela, Santiago de Compostela, 15782, Spain","institution_ids":["https://openalex.org/I200284239"]},{"raw_affiliation_string":"IPCA, Polytechnic Institute of C\u00e1vado and Ave, Barcelos, 4750-810, Portugal","institution_ids":["https://openalex.org/I185808892"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5107834032","display_name":"Andr\u00e9 C. M\u00fcller","orcid":"https://orcid.org/0000-0002-0608-8176"},"institutions":[{"id":"https://openalex.org/I197323543","display_name":"Johannes Gutenberg University Mainz","ror":"https://ror.org/023b0x485","country_code":"DE","type":"education","lineage":["https://openalex.org/I197323543"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Andr\u00e9 M\u00fcller","raw_affiliation_strings":["Department of Computer Science, Johannes Gutenberg University, Mainz, 55099, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Johannes Gutenberg University, Mainz, 55099, Germany","institution_ids":["https://openalex.org/I197323543"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5025437219","display_name":"S\u00f6ren Lukas Hellmann","orcid":"https://orcid.org/0000-0003-4958-1419"},"institutions":[{"id":"https://openalex.org/I197323543","display_name":"Johannes Gutenberg University Mainz","ror":"https://ror.org/023b0x485","country_code":"DE","type":"education","lineage":["https://openalex.org/I197323543"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"S\u00f6ren Lukas Hellmann","raw_affiliation_strings":["Molecular Genetics and Genome Analysis, Institute of Organismal and Molecular Evolution, Johannes Gutenberg University, Mainz, 55099, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Molecular Genetics and Genome Analysis, Institute of Organismal and Molecular Evolution, Johannes Gutenberg University, Mainz, 55099, Germany","institution_ids":["https://openalex.org/I197323543"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5007913294","display_name":"Juan C. Pichel","orcid":"https://orcid.org/0000-0001-9505-6493"},"institutions":[{"id":"https://openalex.org/I200284239","display_name":"Universidade de Santiago de Compostela","ror":"https://ror.org/030eybx10","country_code":"ES","type":"education","lineage":["https://openalex.org/I200284239"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Juan C. Pichel","raw_affiliation_strings":["CiTIUS, Universidade de Santiago de Compostela, Santiago de Compostela, 15782, Spain"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"CiTIUS, Universidade de Santiago de Compostela, Santiago de Compostela, 15782, Spain","institution_ids":["https://openalex.org/I200284239"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5084306280","display_name":"Tom\u00e1s F. Pena","orcid":"https://orcid.org/0000-0002-7622-4698"},"institutions":[{"id":"https://openalex.org/I200284239","display_name":"Universidade de Santiago de Compostela","ror":"https://ror.org/030eybx10","country_code":"ES","type":"education","lineage":["https://openalex.org/I200284239"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Tom\u00e1s F. Pena","raw_affiliation_strings":["CiTIUS, Universidade de Santiago de Compostela, Santiago de Compostela, 15782, Spain"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"CiTIUS, Universidade de Santiago de Compostela, Santiago de Compostela, 15782, Spain","institution_ids":["https://openalex.org/I200284239"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5015934308","display_name":"Andreas Hildebrandt","orcid":"https://orcid.org/0000-0003-2180-6516"},"institutions":[{"id":"https://openalex.org/I197323543","display_name":"Johannes Gutenberg University Mainz","ror":"https://ror.org/023b0x485","country_code":"DE","type":"education","lineage":["https://openalex.org/I197323543"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Andreas Hildebrandt","raw_affiliation_strings":["Department of Computer Science, Johannes Gutenberg University, Mainz, 55099, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Johannes Gutenberg University, Mainz, 55099, Germany","institution_ids":["https://openalex.org/I197323543"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5003394017","display_name":"Thomas Hankeln","orcid":"https://orcid.org/0000-0002-0677-8417"},"institutions":[{"id":"https://openalex.org/I197323543","display_name":"Johannes Gutenberg University Mainz","ror":"https://ror.org/023b0x485","country_code":"DE","type":"education","lineage":["https://openalex.org/I197323543"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Thomas Hankeln","raw_affiliation_strings":["Molecular Genetics and Genome Analysis, Institute of Organismal and Molecular Evolution, Johannes Gutenberg University, Mainz, 55099, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Molecular Genetics and Genome Analysis, Institute of Organismal and Molecular Evolution, Johannes Gutenberg University, Mainz, 55099, Germany","institution_ids":["https://openalex.org/I197323543"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5020388832","display_name":"Bertil Schmidt","orcid":"https://orcid.org/0000-0003-2597-8331"},"institutions":[{"id":"https://openalex.org/I197323543","display_name":"Johannes Gutenberg University Mainz","ror":"https://ror.org/023b0x485","country_code":"DE","type":"education","lineage":["https://openalex.org/I197323543"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Bertil Schmidt","raw_affiliation_strings":["Department of Computer Science, Johannes Gutenberg University, Mainz, 55099, Germany. bertil.schmidt@uni-mainz.de","Department of Computer Science, Johannes Gutenberg University, Mainz, 55099, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Johannes Gutenberg University, Mainz, 55099, Germany. bertil.schmidt@uni-mainz.de","institution_ids":["https://openalex.org/I197323543"]},{"raw_affiliation_string":"Department of Computer Science, Johannes Gutenberg University, Mainz, 55099, Germany","institution_ids":["https://openalex.org/I197323543"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5020388832"],"corresponding_institution_ids":["https://openalex.org/I197323543"],"apc_list":{"value":2790,"currency":"USD","value_usd":2790},"apc_paid":{"value":2790,"currency":"USD","value_usd":2790},"fwci":1.6402,"has_fulltext":true,"cited_by_count":29,"citation_normalized_percentile":{"value":0.83803784,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":99},"biblio":{"volume":"21","issue":"1","first_page":"102","last_page":"102"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.8012999892234802,"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":0.8012999892234802,"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":0.0203000009059906,"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/T12388","display_name":"Identification and Quantification in Food","score":0.018699999898672104,"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/metagenomics","display_name":"Metagenomics","score":0.7656371593475342},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6598432660102844},{"id":"https://openalex.org/keywords/shotgun-sequencing","display_name":"Shotgun sequencing","score":0.6451399922370911},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.5676644444465637},{"id":"https://openalex.org/keywords/spark","display_name":"SPARK (programming language)","score":0.528481125831604},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.47810834646224976},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.44952598214149475},{"id":"https://openalex.org/keywords/reference-genome","display_name":"Reference genome","score":0.44808804988861084},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.42089617252349854},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.28519734740257263},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.13566458225250244},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.09967166185379028}],"concepts":[{"id":"https://openalex.org/C15151743","wikidata":"https://www.wikidata.org/wiki/Q903778","display_name":"Metagenomics","level":3,"score":0.7656371593475342},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6598432660102844},{"id":"https://openalex.org/C101985253","wikidata":"https://www.wikidata.org/wiki/Q1073526","display_name":"Shotgun sequencing","level":4,"score":0.6451399922370911},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.5676644444465637},{"id":"https://openalex.org/C2781215313","wikidata":"https://www.wikidata.org/wiki/Q3493345","display_name":"SPARK (programming language)","level":2,"score":0.528481125831604},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.47810834646224976},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.44952598214149475},{"id":"https://openalex.org/C192953774","wikidata":"https://www.wikidata.org/wiki/Q7307127","display_name":"Reference genome","level":4,"score":0.44808804988861084},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.42089617252349854},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.28519734740257263},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.13566458225250244},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.09967166185379028},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000073336","descriptor_name":"Whole Genome Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D000073336","descriptor_name":"Whole Genome Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D000073336","descriptor_name":"Whole Genome Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D000073336","descriptor_name":"Whole Genome Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D000077558","descriptor_name":"Big Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077558","descriptor_name":"Big Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077558","descriptor_name":"Big Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077558","descriptor_name":"Big Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005504","descriptor_name":"Food Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D005504","descriptor_name":"Food Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D005504","descriptor_name":"Food Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D005504","descriptor_name":"Food Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016680","descriptor_name":"Genome, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016680","descriptor_name":"Genome, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016680","descriptor_name":"Genome, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016680","descriptor_name":"Genome, Bacterial","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":false},{"descriptor_ui":"D054892","descriptor_name":"Metagenome","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":false},{"descriptor_ui":"D054892","descriptor_name":"Metagenome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055877","descriptor_name":"Biosurveillance","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055877","descriptor_name":"Biosurveillance","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055877","descriptor_name":"Biosurveillance","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055877","descriptor_name":"Biosurveillance","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056186","descriptor_name":"Metagenomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D056186","descriptor_name":"Metagenomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D056186","descriptor_name":"Metagenomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D056186","descriptor_name":"Metagenomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D064307","descriptor_name":"Microbiota","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D064307","descriptor_name":"Microbiota","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D064307","descriptor_name":"Microbiota","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D064307","descriptor_name":"Microbiota","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1186/s12859-020-3429-6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-020-3429-6","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-020-3429-6","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:32164527","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/32164527","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:dnet:minerva_____::5b7cc10ae42633fcc6022fc389379db3","is_oa":true,"landing_page_url":"http://hdl.handle.net/10347/21839","pdf_url":null,"source":{"id":"https://openalex.org/S4306402641","display_name":"LA Referencia (Red Federada de Repositorios Institucionales de Publicaciones Cient\u00edficas)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4383465926","host_organization_name":"LA Referencia","host_organization_lineage":["https://openalex.org/I4383465926"],"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":"","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:doaj.org/article:52b8dda9f3684cd6a38d2bbc7c876b0f","is_oa":true,"landing_page_url":"https://doaj.org/article/52b8dda9f3684cd6a38d2bbc7c876b0f","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":"BMC Bioinformatics, Vol 21, Iss 1, Pp 1-15 (2020)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:7069206","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7069206","pdf_url":null,"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":"BMC Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s12859-020-3429-6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-020-3429-6","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-020-3429-6","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Zero hunger","id":"https://metadata.un.org/sdg/2","score":0.4099999964237213}],"awards":[{"id":"https://openalex.org/G1299093556","display_name":null,"funder_award_id":"RTI2018-093336-B-C21","funder_id":"https://openalex.org/F4320321837","funder_display_name":"Ministerio de Econom\u00eda y Competitividad"},{"id":"https://openalex.org/G1496055848","display_name":null,"funder_award_id":"ED431C","funder_id":"https://openalex.org/F4320326655","funder_display_name":"Xunta de Galicia"},{"id":"https://openalex.org/G257270287","display_name":null,"funder_award_id":"ED431C 2018/19","funder_id":"https://openalex.org/F4320335322","funder_display_name":"European Regional Development Fund"},{"id":"https://openalex.org/G3013207569","display_name":null,"funder_award_id":"ED431C 2018","funder_id":"https://openalex.org/F4320326655","funder_display_name":"Xunta de Galicia"},{"id":"https://openalex.org/G3694284866","display_name":null,"funder_award_id":"ED431C","funder_id":"https://openalex.org/F4320335322","funder_display_name":"European Regional Development Fund"},{"id":"https://openalex.org/G4072056071","display_name":null,"funder_award_id":"ED481B","funder_id":"https://openalex.org/F4320326655","funder_display_name":"Xunta de Galicia"},{"id":"https://openalex.org/G4772835309","display_name":null,"funder_award_id":"ED481B 2018/013 and ED431C 2018/19","funder_id":"https://openalex.org/F4320326655","funder_display_name":"Xunta de Galicia"},{"id":"https://openalex.org/G5776204854","display_name":null,"funder_award_id":"ED481B 2018/013","funder_id":"https://openalex.org/F4320326655","funder_display_name":"Xunta de Galicia"},{"id":"https://openalex.org/G6298273575","display_name":null,"funder_award_id":"RTI2018","funder_id":"https://openalex.org/F4320335322","funder_display_name":"European Regional Development Fund"},{"id":"https://openalex.org/G6485345562","display_name":null,"funder_award_id":"ED431C 2018/19","funder_id":"https://openalex.org/F4320326655","funder_display_name":"Xunta de Galicia"}],"funders":[{"id":"https://openalex.org/F4320320879","display_name":"Deutsche Forschungsgemeinschaft","ror":"https://ror.org/018mejw64"},{"id":"https://openalex.org/F4320321837","display_name":"Ministerio de Econom\u00eda y Competitividad","ror":"https://ror.org/034900433"},{"id":"https://openalex.org/F4320326464","display_name":"Bundesamt f\u00fcr Landwirtschaft","ror":null},{"id":"https://openalex.org/F4320326655","display_name":"Xunta de Galicia","ror":"https://ror.org/0181xnw06"},{"id":"https://openalex.org/F4320335322","display_name":"European Regional Development Fund","ror":"https://ror.org/00k4n6c32"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3011893537.pdf","grobid_xml":"https://content.openalex.org/works/W3011893537.grobid-xml"},"referenced_works_count":36,"referenced_works":["https://openalex.org/W1579534339","https://openalex.org/W1703384511","https://openalex.org/W2001405665","https://openalex.org/W2003347102","https://openalex.org/W2042417858","https://openalex.org/W2072970694","https://openalex.org/W2080347240","https://openalex.org/W2085926377","https://openalex.org/W2095680943","https://openalex.org/W2103441770","https://openalex.org/W2104846587","https://openalex.org/W2107824361","https://openalex.org/W2121522962","https://openalex.org/W2124927293","https://openalex.org/W2148885851","https://openalex.org/W2159954944","https://openalex.org/W2163347114","https://openalex.org/W2164133314","https://openalex.org/W2170551349","https://openalex.org/W2337747100","https://openalex.org/W2345658906","https://openalex.org/W2525954034","https://openalex.org/W2542459869","https://openalex.org/W2568812888","https://openalex.org/W2585711475","https://openalex.org/W2615471603","https://openalex.org/W2745994342","https://openalex.org/W2888277738","https://openalex.org/W2907193672","https://openalex.org/W2910724177","https://openalex.org/W2950150251","https://openalex.org/W2951176108","https://openalex.org/W2987650093","https://openalex.org/W3101818138","https://openalex.org/W4247053599","https://openalex.org/W4301775964"],"related_works":["https://openalex.org/W3043668926","https://openalex.org/W3036436206","https://openalex.org/W4389452281","https://openalex.org/W4238948313","https://openalex.org/W3111832393","https://openalex.org/W3000916974","https://openalex.org/W3183189600","https://openalex.org/W3134948850","https://openalex.org/W4394325869","https://openalex.org/W4394082811"],"abstract_inverted_index":{"BACKGROUND:":[0],"All-Food-Sequencing":[1],"(AFS)":[2],"is":[3,88,108],"an":[4,68,122],"untargeted":[5],"metagenomic":[6,201],"sequencing":[7],"method":[8,72,160],"that":[9],"allows":[10,127],"for":[11,60,73,128,161,199,211,218],"the":[12,30,38,58,100,119,129],"detection":[13,74],"and":[14,22,75,82,105,115,189,194,214],"quantification":[15,76,116],"of":[16,29,32,40,46,53,77,112,121,131,134,186],"food":[17,81,170],"ingredients":[18],"including":[19],"animals,":[20],"plants,":[21],"microbiota.":[23],"While":[24],"this":[25],"approach":[26,178],"avoids":[27],"some":[28],"shortcomings":[31],"targeted":[33],"PCR-based":[34],"methods,":[35],"it":[36,107,179],"requires":[37],"comparison":[39,98],"sequence":[41],"reads":[42],"to":[43,99],"large":[44],"collections":[45,133,185],"reference":[47,55,135,191],"genomes.":[48,192],"The":[49],"steadily":[50],"increasing":[51],"amount":[52],"available":[54,206],"genomes":[56,136],"establishes":[57],"need":[59],"efficient":[61,123],"big":[62,176,219],"data":[63,177,220],"approaches.":[64],"RESULTS:":[65],"We":[66,153],"introduce":[67],"alignment-free":[69],"k-mer":[70],"based":[71],"species":[78],"composition":[79],"in":[80,110],"other":[83],"complex":[84,187],"biological":[85],"matters.":[86],"It":[87],"orders-of-magnitude":[89],"faster":[90],"than":[91],"our":[92],"previous":[93],"alignment-based":[94],"AFS":[95],"pipeline.":[96],"In":[97],"established":[101],"tools":[102,198],"CLARK,":[103],"Kraken2,":[104],"Kraken2+Bracken":[106],"superior":[109],"terms":[111],"false-positive":[113],"rate":[114],"accuracy.":[117],"Furthermore,":[118],"usage":[120],"database":[124],"partitioning":[125],"scheme":[126],"processing":[130],"massive":[132],"with":[137],"reduced":[138],"memory":[139],"requirements":[140],"on":[141,146,174],"a":[142,147,155,175,212],"workstation":[143],"(AFS-MetaCache)":[144],"or":[145],"Spark-based":[148],"compute":[149],"cluster":[150],"(MetaCacheSpark).":[151],"CONCLUSIONS:":[152],"present":[154],"fast":[156],"yet":[157],"accurate":[158],"screening":[159,202],"whole":[162],"genome":[163],"shotgun":[164],"sequencing-based":[165],"biosurveillance":[166],"applications":[167],"such":[168],"as":[169],"testing.":[171],"By":[172],"relying":[173],"can":[180],"scale":[181],"efficiently":[182],"towards":[183],"large-scale":[184],"eukaryotic":[188],"bacterial":[190],"AFS-MetaCache":[193],"MetaCacheSpark":[195],"are":[196,205],"suitable":[197],"broad-scale":[200],"applications.":[203],"They":[204],"at":[207],"https://muellan.github.io/metacache/afs.html":[208],"(C++":[209],"version":[210,217],"workstation)":[213],"https://github.com/jmabuin/MetaCacheSpark":[215],"(Spark":[216],"clusters).":[221]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":6},{"year":2022,"cited_by_count":8},{"year":2021,"cited_by_count":6},{"year":2020,"cited_by_count":2}],"updated_date":"2026-07-23T08:03:31.855105","created_date":"2025-10-10T00:00:00"}
