{"id":"https://openalex.org/W2899955710","doi":"https://doi.org/10.1093/nar/gky1073","title":"Plasmid ATLAS: plasmid visual analytics and identification in high-throughput sequencing data","display_name":"Plasmid ATLAS: plasmid visual analytics and identification in high-throughput sequencing data","publication_year":2018,"publication_date":"2018-10-19","ids":{"openalex":"https://openalex.org/W2899955710","doi":"https://doi.org/10.1093/nar/gky1073","mag":"2899955710","pmid":"https://pubmed.ncbi.nlm.nih.gov/30395323"},"language":"en","primary_location":{"id":"doi:10.1093/nar/gky1073","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gky1073","pdf_url":"https://academic.oup.com/nar/article-pdf/47/D1/D188/27437338/gky1073.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/nar/article-pdf/47/D1/D188/27437338/gky1073.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5102991088","display_name":"Tiago F. Jesus","orcid":"https://orcid.org/0000-0001-8054-4136"},"institutions":[{"id":"https://openalex.org/I141596103","display_name":"University of Lisbon","ror":"https://ror.org/01c27hj86","country_code":"PT","type":"education","lineage":["https://openalex.org/I141596103"]}],"countries":["PT"],"is_corresponding":true,"raw_author_name":"Tiago F Jesus","raw_affiliation_strings":["Instituto de Microbiologia and Instituto de Medicina Molecular Jo\u00e3o Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Av. Professor Egaz Moniz, 1649-028 Lisboa, Portugal"],"affiliations":[{"raw_affiliation_string":"Instituto de Microbiologia and Instituto de Medicina Molecular Jo\u00e3o Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Av. Professor Egaz Moniz, 1649-028 Lisboa, Portugal","institution_ids":["https://openalex.org/I141596103"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5057669596","display_name":"Bruno Ribeiro-Gon\u00e7alves","orcid":"https://orcid.org/0000-0002-5775-6955"},"institutions":[{"id":"https://openalex.org/I141596103","display_name":"University of Lisbon","ror":"https://ror.org/01c27hj86","country_code":"PT","type":"education","lineage":["https://openalex.org/I141596103"]}],"countries":["PT"],"is_corresponding":false,"raw_author_name":"Bruno Ribeiro-Gon\u00e7alves","raw_affiliation_strings":["Instituto de Microbiologia and Instituto de Medicina Molecular Jo\u00e3o Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Av. Professor Egaz Moniz, 1649-028 Lisboa, Portugal"],"affiliations":[{"raw_affiliation_string":"Instituto de Microbiologia and Instituto de Medicina Molecular Jo\u00e3o Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Av. Professor Egaz Moniz, 1649-028 Lisboa, Portugal","institution_ids":["https://openalex.org/I141596103"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5047644722","display_name":"Diogo Nuno Silva","orcid":"https://orcid.org/0000-0002-6827-2673"},"institutions":[{"id":"https://openalex.org/I141596103","display_name":"University of Lisbon","ror":"https://ror.org/01c27hj86","country_code":"PT","type":"education","lineage":["https://openalex.org/I141596103"]}],"countries":["PT"],"is_corresponding":false,"raw_author_name":"Diogo N Silva","raw_affiliation_strings":["Instituto de Microbiologia and Instituto de Medicina Molecular Jo\u00e3o Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Av. Professor Egaz Moniz, 1649-028 Lisboa, Portugal"],"affiliations":[{"raw_affiliation_string":"Instituto de Microbiologia and Instituto de Medicina Molecular Jo\u00e3o Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Av. Professor Egaz Moniz, 1649-028 Lisboa, Portugal","institution_ids":["https://openalex.org/I141596103"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5007359437","display_name":"Valeria Bortolaia","orcid":"https://orcid.org/0000-0001-6559-7344"},"institutions":[{"id":"https://openalex.org/I96673099","display_name":"Technical University of Denmark","ror":"https://ror.org/04qtj9h94","country_code":"DK","type":"education","lineage":["https://openalex.org/I96673099"]}],"countries":["DK"],"is_corresponding":false,"raw_author_name":"Valeria Bortolaia","raw_affiliation_strings":["National Food Institute, Technical University of Denmark, Kemitorvet, Building 204, DK-2800 Kgs. Lyngby, Denmark"],"affiliations":[{"raw_affiliation_string":"National Food Institute, Technical University of Denmark, Kemitorvet, Building 204, DK-2800 Kgs. Lyngby, Denmark","institution_ids":["https://openalex.org/I96673099"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5082344930","display_name":"M\u00e1rio Ramirez","orcid":"https://orcid.org/0000-0002-4084-6233"},"institutions":[{"id":"https://openalex.org/I141596103","display_name":"University of Lisbon","ror":"https://ror.org/01c27hj86","country_code":"PT","type":"education","lineage":["https://openalex.org/I141596103"]}],"countries":["PT"],"is_corresponding":false,"raw_author_name":"M\u00e1rio Ramirez","raw_affiliation_strings":["Instituto de Microbiologia and Instituto de Medicina Molecular Jo\u00e3o Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Av. Professor Egaz Moniz, 1649-028 Lisboa, Portugal"],"affiliations":[{"raw_affiliation_string":"Instituto de Microbiologia and Instituto de Medicina Molecular Jo\u00e3o Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Av. Professor Egaz Moniz, 1649-028 Lisboa, Portugal","institution_ids":["https://openalex.org/I141596103"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5057086640","display_name":"Jo\u00e3o Andr\u00e9 Carri\u00e7o","orcid":"https://orcid.org/0000-0002-5274-2722"},"institutions":[{"id":"https://openalex.org/I141596103","display_name":"University of Lisbon","ror":"https://ror.org/01c27hj86","country_code":"PT","type":"education","lineage":["https://openalex.org/I141596103"]}],"countries":["PT"],"is_corresponding":true,"raw_author_name":"Jo\u00e3o A Carri\u00e7o","raw_affiliation_strings":["Instituto de Microbiologia and Instituto de Medicina Molecular Jo\u00e3o Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Av. Professor Egaz Moniz, 1649-028 Lisboa, Portugal"],"affiliations":[{"raw_affiliation_string":"Instituto de Microbiologia and Instituto de Medicina Molecular Jo\u00e3o Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Av. Professor Egaz Moniz, 1649-028 Lisboa, Portugal","institution_ids":["https://openalex.org/I141596103"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5057086640","https://openalex.org/A5102991088"],"corresponding_institution_ids":["https://openalex.org/I141596103"],"apc_list":{"value":3630,"currency":"USD","value_usd":3630},"apc_paid":{"value":3630,"currency":"USD","value_usd":3630},"fwci":2.327,"has_fulltext":false,"cited_by_count":52,"citation_normalized_percentile":{"value":0.89504357,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":99},"biblio":{"volume":"47","issue":"D1","first_page":"D188","last_page":"D194"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9995999932289124,"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":0.9995999932289124,"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/T12167","display_name":"Bacterial Identification and Susceptibility Testing","score":0.9991999864578247,"subfield":{"id":"https://openalex.org/subfields/1308","display_name":"Clinical Biochemistry"},"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":0.9754999876022339,"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/plasmid","display_name":"Plasmid","score":0.8224981427192688},{"id":"https://openalex.org/keywords/refseq","display_name":"RefSeq","score":0.7787735462188721},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.6850583553314209},{"id":"https://openalex.org/keywords/analytics","display_name":"Analytics","score":0.5138821601867676},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.48742011189460754},{"id":"https://openalex.org/keywords/metadata","display_name":"Metadata","score":0.442254900932312},{"id":"https://openalex.org/keywords/json","display_name":"JSON","score":0.429962694644928},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.41307133436203003},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.3778233230113983},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.3666309714317322},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.32050490379333496},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.31024688482284546},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.258406400680542}],"concepts":[{"id":"https://openalex.org/C22744801","wikidata":"https://www.wikidata.org/wiki/Q172778","display_name":"Plasmid","level":3,"score":0.8224981427192688},{"id":"https://openalex.org/C151810110","wikidata":"https://www.wikidata.org/wiki/Q7307074","display_name":"RefSeq","level":4,"score":0.7787735462188721},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.6850583553314209},{"id":"https://openalex.org/C79158427","wikidata":"https://www.wikidata.org/wiki/Q485396","display_name":"Analytics","level":2,"score":0.5138821601867676},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.48742011189460754},{"id":"https://openalex.org/C93518851","wikidata":"https://www.wikidata.org/wiki/Q180160","display_name":"Metadata","level":2,"score":0.442254900932312},{"id":"https://openalex.org/C2780416260","wikidata":"https://www.wikidata.org/wiki/Q2063","display_name":"JSON","level":2,"score":0.429962694644928},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.41307133436203003},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.3778233230113983},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3666309714317322},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.32050490379333496},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.31024688482284546},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.258406400680542}],"mesh":[{"descriptor_ui":"D010957","descriptor_name":"Plasmids","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D010957","descriptor_name":"Plasmids","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D010957","descriptor_name":"Plasmids","qualifier_ui":"Q000235","qualifier_name":"genetics","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":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","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":true},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D064878","descriptor_name":"Web Browser","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D064878","descriptor_name":"Web Browser","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D064878","descriptor_name":"Web Browser","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1093/nar/gky1073","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gky1073","pdf_url":"https://academic.oup.com/nar/article-pdf/47/D1/D188/27437338/gky1073.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},{"id":"pmid:30395323","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/30395323","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":"Nucleic acids research","raw_type":null},{"id":"pmh:oai:europepmc.org:5301973","is_oa":true,"landing_page_url":"http://europepmc.org/pmc/articles/PMC6323984","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:6323984","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6323984","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Nucleic Acids Res","raw_type":"Text"},{"id":"pmh:oai:pure.atira.dk:publications/1db525de-ba6e-4fa8-b62a-dc0178874df4","is_oa":true,"landing_page_url":"https://orbit.dtu.dk/en/publications/1db525de-ba6e-4fa8-b62a-dc0178874df4","pdf_url":null,"source":{"id":"https://openalex.org/S4306400705","display_name":"Technical University of Denmark, DTU Orbit (Technical University of Denmark, DTU)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I96673099","host_organization_name":"Technical University of Denmark","host_organization_lineage":["https://openalex.org/I96673099"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Jesus , T F , Ribeiro-Gon\u00e7alves , B , Silva , D N , Bortolaia , V , Ramirez , M &amp; Carri\u00e7o , J A 2019 , ' Plasmid ATLAS: plasmid visual analytics and identification in high-throughput sequencing data ' , Nucleic Acids Research , vol. 47 , no. D1 , pp. 188-194 . https://doi.org/10.1093/nar/gky1073","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1093/nar/gky1073","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gky1073","pdf_url":"https://academic.oup.com/nar/article-pdf/47/D1/D188/27437338/gky1073.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.4099999964237213,"id":"https://metadata.un.org/sdg/9","display_name":"Industry, innovation and infrastructure"}],"awards":[{"id":"https://openalex.org/G3379308094","display_name":null,"funder_award_id":"LISBOA-01\u20130145-FEDER-016417","funder_id":"https://openalex.org/F4320307395","funder_display_name":"Oneida Nation Foundation"}],"funders":[{"id":"https://openalex.org/F4320307395","display_name":"Oneida Nation Foundation","ror":"https://ror.org/009xj7f03"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2899955710.pdf","grobid_xml":"https://content.openalex.org/works/W2899955710.grobid-xml"},"referenced_works_count":25,"referenced_works":["https://openalex.org/W1989342781","https://openalex.org/W1996650392","https://openalex.org/W2027831845","https://openalex.org/W2096525273","https://openalex.org/W2119497560","https://openalex.org/W2119902463","https://openalex.org/W2121438595","https://openalex.org/W2134852597","https://openalex.org/W2142678478","https://openalex.org/W2143325926","https://openalex.org/W2173732482","https://openalex.org/W2544493586","https://openalex.org/W2587678577","https://openalex.org/W2766738717","https://openalex.org/W2773835172","https://openalex.org/W2883838322","https://openalex.org/W2950150251","https://openalex.org/W2950530458","https://openalex.org/W2951325968","https://openalex.org/W2951563276","https://openalex.org/W4211193130","https://openalex.org/W4250297812","https://openalex.org/W6746421083","https://openalex.org/W6753451743","https://openalex.org/W6764184669"],"related_works":["https://openalex.org/W2753132265","https://openalex.org/W4234766820","https://openalex.org/W4321232174","https://openalex.org/W3117520771","https://openalex.org/W2482048793","https://openalex.org/W4388027365","https://openalex.org/W2938860153","https://openalex.org/W4312551432","https://openalex.org/W2365783963","https://openalex.org/W3113257914"],"abstract_inverted_index":{"Plasmid":[0],"ATLAS":[1],"(pATLAS,":[2],"http://www.patlas.site)":[3],"provides":[4],"an":[5,33],"easy-to-use":[6],"web":[7],"accessible":[8,177],"database":[9,171],"with":[10],"visual":[11],"analytics":[12],"tools":[13],"to":[14,31,36,49,90,155],"explore":[15],"the":[16,51,59,93,114,118,125,136,146,169],"relationships":[17,52,121],"of":[18,53,61,120,127,135,139],"plasmids":[19,39,54],"available":[20],"in":[21,41,55,92],"NCBI's":[22],"RefSeq":[23,43],"database.":[24],"pATLAS":[25,64,86,170],"has":[26],"two":[27],"main":[28],"goals:":[29],"(i)":[30],"provide":[32],"easy":[34],"way":[35],"search":[37],"for":[38,159],"deposited":[40],"NCBI":[42],"and":[44,75,80,84,131,161,172],"their":[45],"associated":[46],"metadata;":[47],"(ii)":[48],"visualize":[50],"a":[56,156,167],"graph,":[57],"allowing":[58,124],"exploration":[60],"plasmid":[62,68,78,94,96],"evolution.":[63],"allows":[65],"searching":[66],"by":[67,81,99,132,165,178],"name,":[69],"bacterial":[70],"host":[71],"taxa,":[72],"antibiotic":[73],"resistance":[74],"virulence":[76],"genes,":[77],"families,":[79],"sequence":[82],"length":[83],"similarity.":[85],"is":[87],"also":[88],"able":[89],"represent":[91],"network,":[95],"sets":[97],"identified":[98,115],"external":[100],"pipelines":[101],"using":[102],"mapping,":[103],"mash":[104],"screen":[105],"or":[106,181],"assembly":[107],"from":[108],"high-throughput":[109],"sequencing":[110],"data.":[111],"By":[112],"representing":[113],"hits":[116],"within":[117],"network":[119,173],"between":[122],"plasmids,":[123],"possibility":[126],"removing":[128],"redundant":[129],"results,":[130],"taking":[133],"advantage":[134],"browsing":[137],"capabilities":[138],"pATLAS,":[140],"users":[141],"can":[142,152],"more":[143],"easily":[144,176],"interpret":[145],"pipelines'":[147],"results.":[148],"All":[149],"these":[150],"analyses":[151],"be":[153],"saved":[154],"JSON":[157],"file":[158],"sharing":[160],"future":[162],"re-evaluation.":[163],"Furthermore,":[164],"offering":[166],"REST-API,":[168],"display":[174],"are":[175],"other":[179],"interfaces":[180],"pipelines.":[182]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":7},{"year":2024,"cited_by_count":9},{"year":2023,"cited_by_count":6},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":10},{"year":2020,"cited_by_count":10},{"year":2019,"cited_by_count":3},{"year":2018,"cited_by_count":2}],"updated_date":"2026-04-05T17:49:38.594831","created_date":"2025-10-10T00:00:00"}
