{"id":"https://openalex.org/W4385898770","doi":"https://doi.org/10.1093/bioinformatics/btad466","title":"<i>TranSyT</i>, an innovative framework for identifying transport systems","display_name":"<i>TranSyT</i>, an innovative framework for identifying transport systems","publication_year":2023,"publication_date":"2023-08-01","ids":{"openalex":"https://openalex.org/W4385898770","doi":"https://doi.org/10.1093/bioinformatics/btad466","pmid":"https://pubmed.ncbi.nlm.nih.gov/37589572"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btad466","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad466","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad466/51135241/btad466.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"Bioinformatics","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/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad466/51135241/btad466.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5058280742","display_name":"Emanuel Cunha","orcid":"https://orcid.org/0000-0003-0893-0563"},"institutions":[{"id":"https://openalex.org/I99682543","display_name":"University of Minho","ror":"https://ror.org/037wpkx04","country_code":"PT","type":"education","lineage":["https://openalex.org/I99682543"]}],"countries":["PT"],"is_corresponding":false,"raw_author_name":"Emanuel Cunha","raw_affiliation_strings":["Centre of Biological Engineering, University of Minho , Braga 4704-553, Portugal","Centre of Biological Engineering, University of Minho, Braga, 4704-553, Portugal"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Centre of Biological Engineering, University of Minho , Braga 4704-553, Portugal","institution_ids":["https://openalex.org/I99682543"]},{"raw_affiliation_string":"Centre of Biological Engineering, University of Minho, Braga, 4704-553, Portugal","institution_ids":["https://openalex.org/I99682543"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5080202278","display_name":"Davide Lagoa","orcid":null},"institutions":[{"id":"https://openalex.org/I1282105669","display_name":"Argonne National Laboratory","ror":"https://ror.org/05gvnxz63","country_code":"US","type":"facility","lineage":["https://openalex.org/I1282105669","https://openalex.org/I1330989302","https://openalex.org/I39565521","https://openalex.org/I40347166"]},{"id":"https://openalex.org/I99682543","display_name":"University of Minho","ror":"https://ror.org/037wpkx04","country_code":"PT","type":"education","lineage":["https://openalex.org/I99682543"]}],"countries":["PT","US"],"is_corresponding":false,"raw_author_name":"Davide Lagoa","raw_affiliation_strings":["Centre of Biological Engineering, University of Minho , Braga 4704-553, Portugal","Computing, Environment, and Life Sciences Division, Argonne National Laboratory , Lemont, IL 60439, United States","Centre of Biological Engineering, University of Minho, Braga, 4704-553, Portugal"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Centre of Biological Engineering, University of Minho , Braga 4704-553, Portugal","institution_ids":["https://openalex.org/I99682543"]},{"raw_affiliation_string":"Computing, Environment, and Life Sciences Division, Argonne National Laboratory , Lemont, IL 60439, United States","institution_ids":["https://openalex.org/I1282105669"]},{"raw_affiliation_string":"Centre of Biological Engineering, University of Minho, Braga, 4704-553, Portugal","institution_ids":["https://openalex.org/I99682543"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5057203488","display_name":"Jos\u00e9 P. Faria","orcid":"https://orcid.org/0000-0001-9302-7250"},"institutions":[{"id":"https://openalex.org/I1282105669","display_name":"Argonne National Laboratory","ror":"https://ror.org/05gvnxz63","country_code":"US","type":"facility","lineage":["https://openalex.org/I1282105669","https://openalex.org/I1330989302","https://openalex.org/I39565521","https://openalex.org/I40347166"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jos\u00e9 P Faria","raw_affiliation_strings":["Computing, Environment, and Life Sciences Division, Argonne National Laboratory , Lemont, IL 60439, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computing, Environment, and Life Sciences Division, Argonne National Laboratory , Lemont, IL 60439, United States","institution_ids":["https://openalex.org/I1282105669"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5044587877","display_name":"Filipe Liu","orcid":"https://orcid.org/0000-0001-8701-2984"},"institutions":[{"id":"https://openalex.org/I1282105669","display_name":"Argonne National Laboratory","ror":"https://ror.org/05gvnxz63","country_code":"US","type":"facility","lineage":["https://openalex.org/I1282105669","https://openalex.org/I1330989302","https://openalex.org/I39565521","https://openalex.org/I40347166"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Filipe Liu","raw_affiliation_strings":["Computing, Environment, and Life Sciences Division, Argonne National Laboratory , Lemont, IL 60439, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computing, Environment, and Life Sciences Division, Argonne National Laboratory , Lemont, IL 60439, United States","institution_ids":["https://openalex.org/I1282105669"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5017949757","display_name":"Christopher S. Henry","orcid":"https://orcid.org/0000-0001-8058-9123"},"institutions":[{"id":"https://openalex.org/I1282105669","display_name":"Argonne National Laboratory","ror":"https://ror.org/05gvnxz63","country_code":"US","type":"facility","lineage":["https://openalex.org/I1282105669","https://openalex.org/I1330989302","https://openalex.org/I39565521","https://openalex.org/I40347166"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Christopher S Henry","raw_affiliation_strings":["Computing, Environment, and Life Sciences Division, Argonne National Laboratory , Lemont, IL 60439, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computing, Environment, and Life Sciences Division, Argonne National Laboratory , Lemont, IL 60439, United States","institution_ids":["https://openalex.org/I1282105669"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5044535959","display_name":"\u00d3scar Dias","orcid":"https://orcid.org/0000-0002-1765-7178"},"institutions":[{"id":"https://openalex.org/I99682543","display_name":"University of Minho","ror":"https://ror.org/037wpkx04","country_code":"PT","type":"education","lineage":["https://openalex.org/I99682543"]}],"countries":["PT"],"is_corresponding":true,"raw_author_name":"Oscar Dias","raw_affiliation_strings":["Centre of Biological Engineering, University of Minho , Braga 4704-553, Portugal","LABBELS\u2014Associate Laboratory , Braga/Guimar\u00e3es, Portugal","Centre of Biological Engineering, University of Minho, Braga, 4704-553, Portugal"],"raw_orcid":"https://orcid.org/0000-0002-1765-7178","affiliations":[{"raw_affiliation_string":"Centre of Biological Engineering, University of Minho , Braga 4704-553, Portugal","institution_ids":["https://openalex.org/I99682543"]},{"raw_affiliation_string":"LABBELS\u2014Associate Laboratory , Braga/Guimar\u00e3es, Portugal","institution_ids":[]},{"raw_affiliation_string":"Centre of Biological Engineering, University of Minho, Braga, 4704-553, Portugal","institution_ids":["https://openalex.org/I99682543"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5044535959"],"corresponding_institution_ids":["https://openalex.org/I99682543"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":1.0276,"has_fulltext":true,"cited_by_count":12,"citation_normalized_percentile":{"value":0.74446312,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"39","issue":"8","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.8952999711036682,"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/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.8952999711036682,"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/T10836","display_name":"Metabolomics and Mass Spectrometry Studies","score":0.017999999225139618,"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/T10631","display_name":"Cancer, Hypoxia, and Metabolism","score":0.011599999852478504,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"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/computer-science","display_name":"Computer science","score":0.7912554740905762},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.6133740544319153},{"id":"https://openalex.org/keywords/process","display_name":"Process (computing)","score":0.44258052110671997},{"id":"https://openalex.org/keywords/traffic-simulation","display_name":"Traffic simulation","score":0.4238385260105133},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.36404556035995483},{"id":"https://openalex.org/keywords/transport-engineering","display_name":"Transport engineering","score":0.2661502957344055},{"id":"https://openalex.org/keywords/intersection","display_name":"Intersection (aeronautics)","score":0.17741763591766357},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.09420806169509888}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7912554740905762},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.6133740544319153},{"id":"https://openalex.org/C98045186","wikidata":"https://www.wikidata.org/wiki/Q205663","display_name":"Process (computing)","level":2,"score":0.44258052110671997},{"id":"https://openalex.org/C2778391309","wikidata":"https://www.wikidata.org/wiki/Q7832527","display_name":"Traffic simulation","level":3,"score":0.4238385260105133},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.36404556035995483},{"id":"https://openalex.org/C22212356","wikidata":"https://www.wikidata.org/wiki/Q775325","display_name":"Transport engineering","level":1,"score":0.2661502957344055},{"id":"https://openalex.org/C64543145","wikidata":"https://www.wikidata.org/wiki/Q162942","display_name":"Intersection (aeronautics)","level":2,"score":0.17741763591766357},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.09420806169509888},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1093/bioinformatics/btad466","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad466","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad466/51135241/btad466.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:37589572","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37589572","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:osti.gov:2404991","is_oa":true,"landing_page_url":"https://www.osti.gov/biblio/2404991","pdf_url":"https://www.osti.gov/servlets/purl/2404991","source":{"id":"https://openalex.org/S4306402487","display_name":"OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I139351228","host_organization_name":"Office of Scientific and Technical Information","host_organization_lineage":["https://openalex.org/I139351228"],"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":null},{"id":"pmh:oai:pubmedcentral.nih.gov:10444967","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10444967","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10444967/pdf/btad466.pdf","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":"public-domain","license_id":"https://openalex.org/licenses/public-domain","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:repositorium.sdum.uminho.pt:1822/86626","is_oa":false,"landing_page_url":"https://hdl.handle.net/1822/86626","pdf_url":null,"source":{"id":"https://openalex.org/S4306400354","display_name":"Reposit\u00f3riUM (Universidade do Minho)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I99682543","host_organization_name":"University of Minho","host_organization_lineage":["https://openalex.org/I99682543"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":null}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btad466","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad466","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad466/51135241/btad466.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Industry, innovation and infrastructure","score":0.5699999928474426,"id":"https://metadata.un.org/sdg/9"}],"awards":[{"id":"https://openalex.org/G1055550527","display_name":null,"funder_award_id":"DE-AC02-06CH11357","funder_id":"https://openalex.org/F4320309626","funder_display_name":"University of Chicago"},{"id":"https://openalex.org/G1142505772","display_name":null,"funder_award_id":"DFA/BD/8076/2020","funder_id":"https://openalex.org/F4320334779","funder_display_name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia"},{"id":"https://openalex.org/G1203399442","display_name":"Centre of Biological Engineering of the University of Minho","funder_award_id":"UIDB/04469/2020","funder_id":"https://openalex.org/F4320334779","funder_display_name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia"},{"id":"https://openalex.org/G1286236842","display_name":null,"funder_award_id":"-AC02-05CH11231","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G1313983767","display_name":null,"funder_award_id":"DE-AC02","funder_id":"https://openalex.org/F4320338284","funder_display_name":"Argonne National Laboratory"},{"id":"https://openalex.org/G1337544421","display_name":null,"funder_award_id":"05CH11231","funder_id":"https://openalex.org/F4320337509","funder_display_name":"Biological and Environmental Research"},{"id":"https://openalex.org/G1489425746","display_name":null,"funder_award_id":"DE-AC05-00OR22725","funder_id":"https://openalex.org/F4320332359","funder_display_name":"Office of Science"},{"id":"https://openalex.org/G1637692498","display_name":null,"funder_award_id":"DE-AC05-00OR22725","funder_id":"https://openalex.org/F4320337509","funder_display_name":"Biological and Environmental Research"},{"id":"https://openalex.org/G1645119126","display_name":null,"funder_award_id":"AC05-00OR22725","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G1751644051","display_name":null,"funder_award_id":"DE-AC02-06CH11357","funder_id":"https://openalex.org/F4320332359","funder_display_name":"Office of Science"},{"id":"https://openalex.org/G2101401529","display_name":null,"funder_award_id":"Contract No. DE-AC02-06CH11357","funder_id":"https://openalex.org/F4320332359","funder_display_name":"Office of Science"},{"id":"https://openalex.org/G2638771445","display_name":null,"funder_award_id":"DE-AC02-05CH11231","funder_id":"https://openalex.org/F4320338284","funder_display_name":"Argonne National Laboratory"},{"id":"https://openalex.org/G2777053550","display_name":null,"funder_award_id":"AC02-06CH11357","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G2887060908","display_name":null,"funder_award_id":"No. DE-AC02-06CH11357","funder_id":"https://openalex.org/F4320338284","funder_display_name":"Argonne National Laboratory"},{"id":"https://openalex.org/G3075337988","display_name":null,"funder_award_id":"06CH11357","funder_id":"https://openalex.org/F4320338284","funder_display_name":"Argonne National Laboratory"},{"id":"https://openalex.org/G3083819904","display_name":null,"funder_award_id":"05CH11231","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G3121793570","display_name":null,"funder_award_id":"00OR22725","funder_id":"https://openalex.org/F4320337509","funder_display_name":"Biological and Environmental Research"},{"id":"https://openalex.org/G323769159","display_name":null,"funder_award_id":"PORTUGAL 2020","funder_id":"https://openalex.org/F4320334779","funder_display_name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia"},{"id":"https://openalex.org/G3243759740","display_name":null,"funder_award_id":"DE-AC02-98CH10886","funder_id":"https://openalex.org/F4320337509","funder_display_name":"Biological and Environmental Research"},{"id":"https://openalex.org/G3311144436","display_name":null,"funder_award_id":"DE-AC02-06CH11357","funder_id":"https://openalex.org/F4320337509","funder_display_name":"Biological and Environmental Research"},{"id":"https://openalex.org/G3562095311","display_name":null,"funder_award_id":"DE-AC02-05CH11231","funder_id":"https://openalex.org/F4320335322","funder_display_name":"European Regional Development Fund"},{"id":"https://openalex.org/G3817554387","display_name":null,"funder_award_id":"DE-AC02-98CH10886","funder_id":"https://openalex.org/F4320332359","funder_display_name":"Office of Science"},{"id":"https://openalex.org/G3944918260","display_name":null,"funder_award_id":"DE-AC02-05CH11231","funder_id":"https://openalex.org/F4320332359","funder_display_name":"Office of Science"},{"id":"https://openalex.org/G4403996651","display_name":null,"funder_award_id":"UIDB/04469/2020 unit","funder_id":"https://openalex.org/F4320334779","funder_display_name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia"},{"id":"https://openalex.org/G4501827968","display_name":null,"funder_award_id":"AC02-05CH11231","funder_id":"https://openalex.org/F4320332359","funder_display_name":"Office of Science"},{"id":"https://openalex.org/G4565140552","display_name":null,"funder_award_id":"-AC02-05CH11231","funder_id":"https://openalex.org/F4320332359","funder_display_name":"Office of Science"},{"id":"https://openalex.org/G4679938283","display_name":null,"funder_award_id":"Contract No. DE-AC02-06CH11357","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G4850785371","display_name":null,"funder_award_id":"UIDB/04469/2020","funder_id":"https://openalex.org/F4320335322","funder_display_name":"European Regional Development Fund"},{"id":"https://openalex.org/G498139845","display_name":null,"funder_award_id":"DE-AC02","funder_id":"https://openalex.org/F4320332359","funder_display_name":"Office of Science"},{"id":"https://openalex.org/G5085543421","display_name":null,"funder_award_id":"AC02-06CH11357","funder_id":"https://openalex.org/F4320338284","funder_display_name":"Argonne National Laboratory"},{"id":"https://openalex.org/G5378045775","display_name":null,"funder_award_id":"AC02-98CH10886","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G5817817810","display_name":null,"funder_award_id":"No. DE-AC02-06CH11357","funder_id":"https://openalex.org/F4320332359","funder_display_name":"Office of Science"},{"id":"https://openalex.org/G6348972864","display_name":null,"funder_award_id":"AC02-05CH11231","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G6558272803","display_name":null,"funder_award_id":"DE-AC02","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G6565430356","display_name":null,"funder_award_id":"UIDB/04469","funder_id":"https://openalex.org/F4320334779","funder_display_name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia"},{"id":"https://openalex.org/G6848031779","display_name":null,"funder_award_id":"06CH11357","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G6918803902","display_name":null,"funder_award_id":"06CH11357","funder_id":"https://openalex.org/F4320332359","funder_display_name":"Office of Science"},{"id":"https://openalex.org/G7368700025","display_name":null,"funder_award_id":"No. DE-AC02-06CH11357","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G7629237052","display_name":null,"funder_award_id":"DE-AC02-05CH11231","funder_id":"https://openalex.org/F4320337509","funder_display_name":"Biological and Environmental Research"},{"id":"https://openalex.org/G7787287669","display_name":null,"funder_award_id":"AC02-05CH11231","funder_id":"https://openalex.org/F4320337509","funder_display_name":"Biological and Environmental Research"},{"id":"https://openalex.org/G7965203573","display_name":null,"funder_award_id":"01/SAICT/2016","funder_id":"https://openalex.org/F4320335322","funder_display_name":"European Regional Development Fund"},{"id":"https://openalex.org/G7991599336","display_name":null,"funder_award_id":"01/SAICT/2016","funder_id":"https://openalex.org/F4320334779","funder_display_name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia"},{"id":"https://openalex.org/G7995982022","display_name":null,"funder_award_id":"DE-AC05","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G8023005153","display_name":null,"funder_award_id":"DE-AC02-06CH11357, DE-AC05-00OR22725","funder_id":"https://openalex.org/F4320332359","funder_display_name":"Office of Science"},{"id":"https://openalex.org/G8103039852","display_name":null,"funder_award_id":"DE-AC02-05CH11231","funder_id":"https://openalex.org/F4320334779","funder_display_name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia"},{"id":"https://openalex.org/G8143874970","display_name":null,"funder_award_id":"AC02-06CH11357","funder_id":"https://openalex.org/F4320332359","funder_display_name":"Office of Science"},{"id":"https://openalex.org/G8269158468","display_name":null,"funder_award_id":"AC05-00OR22725","funder_id":"https://openalex.org/F4320332359","funder_display_name":"Office of Science"},{"id":"https://openalex.org/G8394328975","display_name":null,"funder_award_id":"Contract No. DE-AC02-06CH11357","funder_id":"https://openalex.org/F4320338284","funder_display_name":"Argonne National Laboratory"},{"id":"https://openalex.org/G8692966195","display_name":null,"funder_award_id":"22231/01/SAICT/2016","funder_id":"https://openalex.org/F4320335322","funder_display_name":"European Regional Development Fund"},{"id":"https://openalex.org/G8906985441","display_name":null,"funder_award_id":"00OR22725","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G969889393","display_name":null,"funder_award_id":"DE-AC02-","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"}],"funders":[{"id":"https://openalex.org/F4320306084","display_name":"U.S. Department of Energy","ror":"https://ror.org/01bj3aw27"},{"id":"https://openalex.org/F4320309626","display_name":"University of Chicago","ror":"https://ror.org/024mw5h28"},{"id":"https://openalex.org/F4320332359","display_name":"Office of Science","ror":"https://ror.org/00mmn6b08"},{"id":"https://openalex.org/F4320334779","display_name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia","ror":"https://ror.org/00snfqn58"},{"id":"https://openalex.org/F4320335322","display_name":"European Regional Development Fund","ror":"https://ror.org/00k4n6c32"},{"id":"https://openalex.org/F4320337509","display_name":"Biological and Environmental Research","ror":"https://ror.org/0114b2m14"},{"id":"https://openalex.org/F4320338284","display_name":"Argonne National Laboratory","ror":"https://ror.org/05gvnxz63"}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4385898770.pdf"},"referenced_works_count":41,"referenced_works":["https://openalex.org/W1910839236","https://openalex.org/W1948859177","https://openalex.org/W1975729005","https://openalex.org/W1985451258","https://openalex.org/W1996034592","https://openalex.org/W2004548026","https://openalex.org/W2034890899","https://openalex.org/W2041786550","https://openalex.org/W2051014867","https://openalex.org/W2057741472","https://openalex.org/W2072167135","https://openalex.org/W2079244604","https://openalex.org/W2085966233","https://openalex.org/W2085993965","https://openalex.org/W2090075451","https://openalex.org/W2100084634","https://openalex.org/W2113024448","https://openalex.org/W2113948304","https://openalex.org/W2133452284","https://openalex.org/W2135834023","https://openalex.org/W2136563879","https://openalex.org/W2142237411","https://openalex.org/W2144944670","https://openalex.org/W2147472054","https://openalex.org/W2202347610","https://openalex.org/W2295215653","https://openalex.org/W2343726422","https://openalex.org/W2557833792","https://openalex.org/W2618327118","https://openalex.org/W2764202526","https://openalex.org/W2859249641","https://openalex.org/W2966778855","https://openalex.org/W2977870980","https://openalex.org/W3000015309","https://openalex.org/W3105895642","https://openalex.org/W3109735703","https://openalex.org/W3112376646","https://openalex.org/W4233659707","https://openalex.org/W4282838866","https://openalex.org/W4317234059","https://openalex.org/W6680068457"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W2358668433","https://openalex.org/W4396701345","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W4396696052","https://openalex.org/W2382290278","https://openalex.org/W4395014643"],"abstract_inverted_index":{"MOTIVATION:":[0],"The":[1],"importance":[2],"and":[3,89,103,105,127,148,168],"rate":[4],"of":[5,7,29,42,118],"development":[6,37],"genome-scale":[8],"metabolic":[9],"models":[10,46],"have":[11,124],"been":[12],"growing":[13],"for":[14,22,38,115,145,151,161],"the":[15,20,39,53,85,162],"last":[16],"few":[17],"years,":[18],"increasing":[19],"demand":[21],"software":[23,36],"solutions":[24],"that":[25],"automate":[26],"several":[27],"steps":[28],"this":[30],"process.":[31],"However,":[32],"since":[33],"TRIAGE's":[34],"release,":[35],"automatic":[40],"integration":[41],"transport":[43,60,122],"reactions":[44,107,123],"into":[45,108],"has":[47],"stalled.":[48],"RESULTS:":[49],"Here,":[50],"we":[51],"present":[52],"Transport":[54],"Systems":[55],"Tracker":[56],"(TranSyT).":[57],"Unlike":[58],"other":[59,94],"systems":[61],"annotation":[62,117],"software,":[63],"TranSyT":[64,97,138,156],"does":[65],"not":[66],"rely":[67],"on":[68],"manual":[69],"curation":[70],"to":[71,170],"expand":[72],"its":[73,109],"internal":[74,110],"database,":[75,111],"which":[76],"is":[77,139],"derived":[78],"from":[79,84,93,133],"highly":[80],"curated":[81],"records":[82],"retrieved":[83],"Transporters":[86],"Classification":[87],"Database":[88],"complemented":[90],"with":[91,131,166],"information":[92,99],"data":[95],"sources.":[96],"compiles":[98],"regarding":[100],"transporter":[101],"families":[102],"proteins,":[104],"derives":[106],"making":[112],"it":[113],"available":[114,141],"rapid":[116],"complete":[119],"genomes.":[120],"All":[121],"GPR":[125],"associations":[126],"can":[128],"be":[129],"exported":[130],"identifiers":[132],"four":[134],"different":[135],"metabolite":[136],"databases.":[137],"currently":[140],"as":[142],"a":[143],"plugin":[144],"merlin":[146],"v4.0":[147],"an":[149],"app":[150],"KBase.":[152],"AVAILABILITY":[153],"AND":[154],"IMPLEMENTATION:":[155],"web":[157],"service:":[158],"https://transyt.bio.di.uminho.pt/;":[159],"GitHub":[160,165],"tool:":[163],"https://github.com/BioSystemsUM/transyt;":[164],"examples":[167],"instructions":[169],"run":[171],"TranSyT:":[172],"https://github.com/ecunha1996/transyt_paper.":[173]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":5},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":1}],"updated_date":"2026-07-25T09:21:30.201066","created_date":"2023-08-18T00:00:00"}
