{"id":"https://openalex.org/W2557833792","doi":"https://doi.org/10.1093/nar/gkw1068","title":"TransportDB 2.0: a database for exploring membrane transporters in sequenced genomes from all domains of life","display_name":"TransportDB 2.0: a database for exploring membrane transporters in sequenced genomes from all domains of life","publication_year":2016,"publication_date":"2016-10-25","ids":{"openalex":"https://openalex.org/W2557833792","doi":"https://doi.org/10.1093/nar/gkw1068","mag":"2557833792","pmid":"https://pubmed.ncbi.nlm.nih.gov/27899676"},"language":"en","primary_location":{"id":"doi:10.1093/nar/gkw1068","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkw1068","pdf_url":"https://academic.oup.com/nar/article-pdf/45/D1/D320/8846735/gkw1068.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":null,"license_id":null,"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/45/D1/D320/8846735/gkw1068.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5061444276","display_name":"Liam D. H. Elbourne","orcid":"https://orcid.org/0000-0002-9784-0959"},"institutions":[{"id":"https://openalex.org/I99043593","display_name":"Macquarie University","ror":"https://ror.org/01sf06y89","country_code":"AU","type":"education","lineage":["https://openalex.org/I99043593"]}],"countries":["AU"],"is_corresponding":true,"raw_author_name":"Liam\u00a0D.\u00a0H. Elbourne","raw_affiliation_strings":["Department of Chemistry and Biomolecular Sciences, Macquarie University, NSW 2109, Australia liam.elbourne@mq.edu.au","Department of Chemistry and Biomolecular Sciences, Macquarie University, NSW 2109, Australia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemistry and Biomolecular Sciences, Macquarie University, NSW 2109, Australia liam.elbourne@mq.edu.au","institution_ids":[]},{"raw_affiliation_string":"Department of Chemistry and Biomolecular Sciences, Macquarie University, NSW 2109, Australia","institution_ids":["https://openalex.org/I99043593"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5030211839","display_name":"Sasha G. Tetu","orcid":"https://orcid.org/0000-0002-8943-3499"},"institutions":[{"id":"https://openalex.org/I99043593","display_name":"Macquarie University","ror":"https://ror.org/01sf06y89","country_code":"AU","type":"education","lineage":["https://openalex.org/I99043593"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Sasha G. Tetu","raw_affiliation_strings":["Department of Chemistry and Biomolecular Sciences, Macquarie University, NSW 2109, Australia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemistry and Biomolecular Sciences, Macquarie University, NSW 2109, Australia","institution_ids":["https://openalex.org/I99043593"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5062811599","display_name":"Karl A. Hassan","orcid":"https://orcid.org/0000-0003-2031-9679"},"institutions":[{"id":"https://openalex.org/I99043593","display_name":"Macquarie University","ror":"https://ror.org/01sf06y89","country_code":"AU","type":"education","lineage":["https://openalex.org/I99043593"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Karl A. Hassan","raw_affiliation_strings":["Department of Chemistry and Biomolecular Sciences, Macquarie University, NSW 2109, Australia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemistry and Biomolecular Sciences, Macquarie University, NSW 2109, Australia","institution_ids":["https://openalex.org/I99043593"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5069669892","display_name":"Ian T. Paulsen","orcid":"https://orcid.org/0000-0001-9015-9418"},"institutions":[{"id":"https://openalex.org/I99043593","display_name":"Macquarie University","ror":"https://ror.org/01sf06y89","country_code":"AU","type":"education","lineage":["https://openalex.org/I99043593"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Ian T. Paulsen","raw_affiliation_strings":["Department of Chemistry and Biomolecular Sciences, Macquarie University, NSW 2109, Australia ian.paulsen@mq.edu.au","Department of Chemistry and Biomolecular Sciences, Macquarie University, NSW 2109, Australia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemistry and Biomolecular Sciences, Macquarie University, NSW 2109, Australia ian.paulsen@mq.edu.au","institution_ids":[]},{"raw_affiliation_string":"Department of Chemistry and Biomolecular Sciences, Macquarie University, NSW 2109, Australia","institution_ids":["https://openalex.org/I99043593"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5061444276"],"corresponding_institution_ids":["https://openalex.org/I99043593"],"apc_list":{"value":3630,"currency":"USD","value_usd":3630},"apc_paid":{"value":3630,"currency":"USD","value_usd":3630},"fwci":14.6225,"has_fulltext":true,"cited_by_count":337,"citation_normalized_percentile":{"value":0.99236171,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":99,"max":100},"biblio":{"volume":"45","issue":"D1","first_page":"D320","last_page":"D324"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9994000196456909,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9994000196456909,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9988999962806702,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9977999925613403,"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/pipeline","display_name":"Pipeline (software)","score":0.7806745767593384},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.7127678394317627},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.683023989200592},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.635162353515625},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5032808184623718},{"id":"https://openalex.org/keywords/javascript","display_name":"JavaScript","score":0.42541688680648804},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.39097145199775696},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.38655516505241394},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.3042118549346924},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.2835833430290222},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.22913861274719238},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.18586206436157227},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.07162263989448547}],"concepts":[{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.7806745767593384},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.7127678394317627},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.683023989200592},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.635162353515625},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5032808184623718},{"id":"https://openalex.org/C544833334","wikidata":"https://www.wikidata.org/wiki/Q2005","display_name":"JavaScript","level":2,"score":0.42541688680648804},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.39097145199775696},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.38655516505241394},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.3042118549346924},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.2835833430290222},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.22913861274719238},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.18586206436157227},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.07162263989448547}],"mesh":[{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D026901","descriptor_name":"Membrane Transport Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D026901","descriptor_name":"Membrane Transport Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D026901","descriptor_name":"Membrane Transport Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D026901","descriptor_name":"Membrane Transport Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D026901","descriptor_name":"Membrane Transport Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D026901","descriptor_name":"Membrane Transport Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D026901","descriptor_name":"Membrane Transport Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D026901","descriptor_name":"Membrane Transport Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D026901","descriptor_name":"Membrane Transport Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","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":4,"locations":[{"id":"doi:10.1093/nar/gkw1068","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkw1068","pdf_url":"https://academic.oup.com/nar/article-pdf/45/D1/D320/8846735/gkw1068.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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},{"id":"pmid:27899676","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/27899676","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:pubmedcentral.nih.gov:5210551","is_oa":true,"landing_page_url":"http://doi.org/10.1093/nar/gkw1068","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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"","raw_type":"Text"},{"id":"pmh:oai:open-archive.highwire.org:nar:45/D1/D320","is_oa":false,"landing_page_url":"http://nar.oxfordjournals.org/cgi/content/short/45/D1/D320","pdf_url":null,"source":{"id":"https://openalex.org/S4406923041","display_name":"HighWire Press Open Archive","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"TEXT"}],"best_oa_location":{"id":"doi:10.1093/nar/gkw1068","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkw1068","pdf_url":"https://academic.oup.com/nar/article-pdf/45/D1/D320/8846735/gkw1068.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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G4802095428","display_name":null,"funder_award_id":"9201401563","funder_id":"https://openalex.org/F4320320591","funder_display_name":"Macquarie University"}],"funders":[{"id":"https://openalex.org/F4320320591","display_name":"Macquarie University","ror":"https://ror.org/01sf06y89"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2557833792.pdf","grobid_xml":"https://content.openalex.org/works/W2557833792.grobid-xml"},"referenced_works_count":25,"referenced_works":["https://openalex.org/W41278926","https://openalex.org/W1966876001","https://openalex.org/W1976325156","https://openalex.org/W1988004276","https://openalex.org/W2006632467","https://openalex.org/W2018345907","https://openalex.org/W2068204754","https://openalex.org/W2087928503","https://openalex.org/W2109318635","https://openalex.org/W2114347076","https://openalex.org/W2130956021","https://openalex.org/W2132247062","https://openalex.org/W2135415614","https://openalex.org/W2138122982","https://openalex.org/W2142678478","https://openalex.org/W2152770371","https://openalex.org/W2155606054","https://openalex.org/W2159299078","https://openalex.org/W2162219545","https://openalex.org/W2173732482","https://openalex.org/W2224056471","https://openalex.org/W2316715119","https://openalex.org/W3024531541","https://openalex.org/W4231897523","https://openalex.org/W6601720253"],"related_works":["https://openalex.org/W2361861616","https://openalex.org/W2263699433","https://openalex.org/W2377979023","https://openalex.org/W2218034408","https://openalex.org/W2461078469","https://openalex.org/W2392921965","https://openalex.org/W123790205","https://openalex.org/W2358755282","https://openalex.org/W2085515337","https://openalex.org/W3102852402"],"abstract_inverted_index":{"All":[0],"cellular":[1],"life":[2],"contains":[3],"an":[4],"extensive":[5],"array":[6],"of":[7,14,34,56,69,78,123,138,143],"membrane":[8],"transport":[9],"proteins.":[10],"The":[11,87],"vast":[12],"majority":[13],"these":[15],"transporters":[16,35],"have":[17,23],"not":[18],"been":[19,93],"experimentally":[20],"characterized.":[21],"We":[22],"developed":[24],"a":[25,65,101,121],"bioinformatic":[26],"pipeline":[27,41],"to":[28,48,74,95,105,116,134],"identify":[29],"and":[30,109,149],"annotate":[31],"complete":[32,152],"sets":[33],"in":[36,146],"any":[37],"sequenced":[38],"genome.":[39],"This":[40,59],"is":[42],"now":[43],"fully":[44],"automated":[45,83],"enabling":[46],"it":[47],"better":[49],"keep":[50],"pace":[51],"with":[52],"the":[53,75,106,118,141,147],"accelerating":[54],"rate":[55],"genome":[57],"sequencing.":[58],"manuscript":[60],"describes":[61],"TransportDB":[62,88,127],"2.0":[63,89,128],"(http://www.membranetransport.org/transportDB2/),":[64],"completely":[66],"updated":[67],"version":[68],"TransportDB,":[70],"which":[71],"provides":[72],"access":[73],"large":[76],"volumes":[77],"data":[79],"generated":[80],"by":[81],"our":[82],"transporter":[84,153],"annotation":[85,107],"pipeline.":[86],"web":[90],"portal":[91],"has":[92],"rebuilt":[94],"utilize":[96],"contemporary":[97],"JavaScript":[98],"libraries,":[99],"providing":[100],"highly":[102],"interactive":[103],"interface":[104],"information,":[108],"incorporates":[110],"analysis":[111],"tools":[112,130],"that":[113,131],"enable":[114],"users":[115,133],"query":[117],"database":[119,148],"on":[120],"number":[122],"levels.":[124],"For":[125],"example,":[126],"includes":[129],"allow":[132],"select":[135],"annotated":[136],"genomes":[137],"interest":[139],"from":[140],"thousands":[142],"species":[144],"held":[145],"compare":[150],"their":[151],"complements.":[154]},"counts_by_year":[{"year":2026,"cited_by_count":13},{"year":2025,"cited_by_count":25},{"year":2024,"cited_by_count":41},{"year":2023,"cited_by_count":46},{"year":2022,"cited_by_count":47},{"year":2021,"cited_by_count":50},{"year":2020,"cited_by_count":31},{"year":2019,"cited_by_count":40},{"year":2018,"cited_by_count":33},{"year":2017,"cited_by_count":11}],"updated_date":"2026-05-05T08:41:31.759640","created_date":"2025-10-10T00:00:00"}
