TranSyT, an innovative framework for identifying transport systems

Detalhes bibliográficos
Autor(a) principal: Lagoa, Davide Rafael Santos
Data de Publicação: 2021
Outros Autores: Faria, José P., Liu, Filipe, Cunha, Emanuel Rodrigues, Henry, Christopher S., Dias, Oscar
Tipo de documento: Artigo
Idioma: eng
Título da fonte: Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
Texto Completo: http://hdl.handle.net/1822/77189
Resumo: The importance and rate of development of genome-scale metabolic models have been growing for the last years, increasing the demand for software solutions that automate several steps of this process. However, since TRIAGEs release, software development for automatic integration of transport reactions into models has stalled. Here we present the Transport Systems Tracker (TranSyT), the next iteration of TRIAGE. Unlike its predecessor, TranSyT does not rely on manual curation to expand its internal database, derived from highly-curated records retrieved from the Transporters Classification Database and complemented with information from other data sources. TranSyT compiles information regarding transporters families, transport proteins, and derives reactions into its internal database, making it available for rapid annotation of complete genomes. All transport reactions have GPR associations and can be exported with identifiers from four different metabolite databases. TranSyT is currently available as a plugin for merlin v4.0 and an app for KBase.
id RCAP_3ec0f7a230993d9312abf01d68855342
oai_identifier_str oai:repositorium.sdum.uminho.pt:1822/77189
network_acronym_str RCAP
network_name_str Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
repository_id_str 7160
spelling TranSyT, an innovative framework for identifying transport systemsThe importance and rate of development of genome-scale metabolic models have been growing for the last years, increasing the demand for software solutions that automate several steps of this process. However, since TRIAGEs release, software development for automatic integration of transport reactions into models has stalled. Here we present the Transport Systems Tracker (TranSyT), the next iteration of TRIAGE. Unlike its predecessor, TranSyT does not rely on manual curation to expand its internal database, derived from highly-curated records retrieved from the Transporters Classification Database and complemented with information from other data sources. TranSyT compiles information regarding transporters families, transport proteins, and derives reactions into its internal database, making it available for rapid annotation of complete genomes. All transport reactions have GPR associations and can be exported with identifiers from four different metabolite databases. TranSyT is currently available as a plugin for merlin v4.0 and an app for KBase.This study was supported by the Portuguese Foundation for Science and Technology(FCT) under the scope of the strategic funding of UIDB/04469/2020 unit. This work is supported by the Office of Biological and Environmental Research’s Genomic Science program within the US Department of Energy Office of Science, under award numbers DE-AC02-05CH11231, DE-AC02-06CH11357, DE AC05-00OR22725, and DE-AC02-98CH10886.info:eu-repo/semantics/publishedVersionCold Spring Harbor LaboratoryUniversidade do MinhoLagoa, Davide Rafael SantosFaria, José P.Liu, FilipeCunha, Emanuel RodriguesHenry, Christopher S.Dias, Oscar2021-04-302021-04-30T00:00:00Zinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleapplication/pdfhttp://hdl.handle.net/1822/77189engLagoa, D.; Faria, José P.; Liu, Filipe; Cunha, Emanuel; Henry, Christopher S.; Dias, Oscar, TranSyT, an innovative framework for identifying transport systems. bioRxiv - the Preprint Server for Biology, 202110.1101/2021.04.29.441738https://www.biorxiv.org/info:eu-repo/semantics/openAccessreponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãoinstacron:RCAAP2023-07-21T12:13:49Zoai:repositorium.sdum.uminho.pt:1822/77189Portal AgregadorONGhttps://www.rcaap.pt/oai/openaireopendoar:71602024-03-19T19:05:59.954648Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãofalse
dc.title.none.fl_str_mv TranSyT, an innovative framework for identifying transport systems
title TranSyT, an innovative framework for identifying transport systems
spellingShingle TranSyT, an innovative framework for identifying transport systems
Lagoa, Davide Rafael Santos
title_short TranSyT, an innovative framework for identifying transport systems
title_full TranSyT, an innovative framework for identifying transport systems
title_fullStr TranSyT, an innovative framework for identifying transport systems
title_full_unstemmed TranSyT, an innovative framework for identifying transport systems
title_sort TranSyT, an innovative framework for identifying transport systems
author Lagoa, Davide Rafael Santos
author_facet Lagoa, Davide Rafael Santos
Faria, José P.
Liu, Filipe
Cunha, Emanuel Rodrigues
Henry, Christopher S.
Dias, Oscar
author_role author
author2 Faria, José P.
Liu, Filipe
Cunha, Emanuel Rodrigues
Henry, Christopher S.
Dias, Oscar
author2_role author
author
author
author
author
dc.contributor.none.fl_str_mv Universidade do Minho
dc.contributor.author.fl_str_mv Lagoa, Davide Rafael Santos
Faria, José P.
Liu, Filipe
Cunha, Emanuel Rodrigues
Henry, Christopher S.
Dias, Oscar
description The importance and rate of development of genome-scale metabolic models have been growing for the last years, increasing the demand for software solutions that automate several steps of this process. However, since TRIAGEs release, software development for automatic integration of transport reactions into models has stalled. Here we present the Transport Systems Tracker (TranSyT), the next iteration of TRIAGE. Unlike its predecessor, TranSyT does not rely on manual curation to expand its internal database, derived from highly-curated records retrieved from the Transporters Classification Database and complemented with information from other data sources. TranSyT compiles information regarding transporters families, transport proteins, and derives reactions into its internal database, making it available for rapid annotation of complete genomes. All transport reactions have GPR associations and can be exported with identifiers from four different metabolite databases. TranSyT is currently available as a plugin for merlin v4.0 and an app for KBase.
publishDate 2021
dc.date.none.fl_str_mv 2021-04-30
2021-04-30T00:00:00Z
dc.type.status.fl_str_mv info:eu-repo/semantics/publishedVersion
dc.type.driver.fl_str_mv info:eu-repo/semantics/article
format article
status_str publishedVersion
dc.identifier.uri.fl_str_mv http://hdl.handle.net/1822/77189
url http://hdl.handle.net/1822/77189
dc.language.iso.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv Lagoa, D.; Faria, José P.; Liu, Filipe; Cunha, Emanuel; Henry, Christopher S.; Dias, Oscar, TranSyT, an innovative framework for identifying transport systems. bioRxiv - the Preprint Server for Biology, 2021
10.1101/2021.04.29.441738
https://www.biorxiv.org/
dc.rights.driver.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
dc.publisher.none.fl_str_mv Cold Spring Harbor Laboratory
publisher.none.fl_str_mv Cold Spring Harbor Laboratory
dc.source.none.fl_str_mv reponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação
instacron:RCAAP
instname_str Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação
instacron_str RCAAP
institution RCAAP
reponame_str Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
collection Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
repository.name.fl_str_mv Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação
repository.mail.fl_str_mv
_version_ 1799132472976343040

Registros relacionados