Publicação
A model integration pipeline for the improvement of human genome-scale metabolic reconstructions
| Resumo: | Metabolism has been a major field of study in the last years, mainly due to its importance in understanding cell physiology and certain disease phenotypes due to its deregulation. Genome-scale metabolic models (GSMMs) have been established as important tools to help achieve a better understanding of human metabolism. Towards this aim, advances in systems biology and bioinformatics have allowed the reconstruction of several human GSMMs, although some limitations and challenges remain, such as the lack of external identifiers for both metabolites and reactions. A pipeline was developed to integrate multiple GSMMs, starting by retrieving information from the main human GSMMs and evaluating the presence of external database identifiers and annotations for both metabolites and reactions. Information from metabolites was included into a graph database with omics data repositories, allowing clustering of metabolites through their similarity regarding database cross-referencing. Metabolite annotation of several older GSMMs was enriched, allowing the identification and integration of common entities. Using this information, as well as other metrics, we successfully integrated reactions from these models. These methods can be leveraged towards the creation of a unified consensus model of human metabolism. |
|---|---|
| Autores principais: | Vieira, Vítor |
| Outros Autores: | Ferreira, Jorge; Rodrigues, Rúben André Costa; Liu, Filipe Alexandre Wang; Rocha, Miguel |
| Assunto: | Genome-scale metabolic models human metabolism omics databases database integration |
| Ano: | 2019 |
| País: | Portugal |
| Tipo de documento: | artigo |
| Tipo de acesso: | acesso aberto |
| Instituição associada: | Universidade do Minho |
| Idioma: | inglês |
| Origem: | RepositóriUM - Universidade do Minho |
| _version_ | 1866878256195567616 |
|---|---|
| author | Vieira, Vítor |
| author2 | Ferreira, Jorge Rodrigues, Rúben André Costa Liu, Filipe Alexandre Wang Rocha, Miguel |
| author2_role | author author author author |
| author_facet | Vieira, Vítor Ferreira, Jorge Rodrigues, Rúben André Costa Liu, Filipe Alexandre Wang Rocha, Miguel |
| author_role | author |
| contributor_name_str_mv | Universidade do Minho |
| country_str | PT |
| creators_json_txt | [{\"Person.name\":\"Vieira, Vítor\"},{\"Person.name\":\"Ferreira, Jorge\"},{\"Person.name\":\"Rodrigues, Rúben André Costa\"},{\"Person.name\":\"Liu, Filipe Alexandre Wang\"},{\"Person.name\":\"Rocha, Miguel\"}] |
| datacite.contributors.contributor.contributorName.fl_str_mv | Universidade do Minho |
| datacite.creators.creator.creatorName.fl_str_mv | Vieira, Vítor Ferreira, Jorge Rodrigues, Rúben André Costa Liu, Filipe Alexandre Wang Rocha, Miguel |
| datacite.date.Accepted.fl_str_mv | 2019-01-01T00:00:00Z |
| datacite.date.available.fl_str_mv | 2019-03-06T10:03:40Z |
| datacite.date.embargoed.fl_str_mv | 2019-03-06T10:03:40Z |
| datacite.rights.fl_str_mv | http://purl.org/coar/access_right/c_abf2 |
| datacite.subjects.subject.fl_str_mv | Genome-scale metabolic models human metabolism omics databases database integration |
| datacite.titles.title.fl_str_mv | A model integration pipeline for the improvement of human genome-scale metabolic reconstructions |
| dc.contributor.none.fl_str_mv | Universidade do Minho |
| dc.creator.none.fl_str_mv | Vieira, Vítor Ferreira, Jorge Rodrigues, Rúben André Costa Liu, Filipe Alexandre Wang Rocha, Miguel |
| dc.date.Accepted.fl_str_mv | 2019-01-01T00:00:00Z |
| dc.date.available.fl_str_mv | 2019-03-06T10:03:40Z |
| dc.date.embargoed.fl_str_mv | 2019-03-06T10:03:40Z |
| dc.format.none.fl_str_mv | application/pdf |
| dc.identifier.none.fl_str_mv | https://hdl.handle.net/1822/59342 |
| dc.language.none.fl_str_mv | eng |
| dc.publisher.none.fl_str_mv | De Gruyter Open |
| dc.rights.none.fl_str_mv | http://purl.org/coar/access_right/c_abf2 |
| dc.subject.none.fl_str_mv | Genome-scale metabolic models human metabolism omics databases database integration |
| dc.title.fl_str_mv | A model integration pipeline for the improvement of human genome-scale metabolic reconstructions |
| dc.type.none.fl_str_mv | http://purl.org/coar/resource_type/c_6501 |
| description | Metabolism has been a major field of study in the last years, mainly due to its importance in understanding cell physiology and certain disease phenotypes due to its deregulation. Genome-scale metabolic models (GSMMs) have been established as important tools to help achieve a better understanding of human metabolism. Towards this aim, advances in systems biology and bioinformatics have allowed the reconstruction of several human GSMMs, although some limitations and challenges remain, such as the lack of external identifiers for both metabolites and reactions. A pipeline was developed to integrate multiple GSMMs, starting by retrieving information from the main human GSMMs and evaluating the presence of external database identifiers and annotations for both metabolites and reactions. Information from metabolites was included into a graph database with omics data repositories, allowing clustering of metabolites through their similarity regarding database cross-referencing. Metabolite annotation of several older GSMMs was enriched, allowing the identification and integration of common entities. Using this information, as well as other metrics, we successfully integrated reactions from these models. These methods can be leveraged towards the creation of a unified consensus model of human metabolism. |
| dirty | 0 |
| eu_rights_str_mv | openAccess |
| format | article |
| fulltext.url.fl_str_mv | https://prod-dspace.uminho.pt/bitstreams/c578ed3f-3a7d-4cf5-86aa-5808ae32483e/download |
| id | rum_e463c0ee8eee8bdff28170e7016d17c2 |
| identifier.url.fl_str_mv | https://hdl.handle.net/1822/59342 |
| instacron_str | repositorium |
| institution | Universidade do Minho |
| instname_str | Universidade do Minho |
| language | eng |
| network_acronym_str | rum |
| network_name_str | RepositóriUM - Universidade do Minho |
| oai_identifier_str | oai:repositorium.uminho.pt:1822/59342 |
| organization_str_mv | urn:organizationAcronym:repositorium |
| person_str_mv | Vieira, Vítor Ferreira, Jorge Rodrigues, Rúben André Costa Liu, Filipe Alexandre Wang Rocha, Miguel |
| publishDate | 2019 |
| publisher.none.fl_str_mv | De Gruyter Open |
| reponame_str | RepositóriUM - Universidade do Minho |
| repository_id_str | urn:repositoryAcronym:rum |
| service_str_mv | urn:repositoryAcronym:rum |
| spelling | engDe Gruyter OpenporMetabolism has been a major field of study in the last years, mainly due to its importance in understanding cell physiology and certain disease phenotypes due to its deregulation. Genome-scale metabolic models (GSMMs) have been established as important tools to help achieve a better understanding of human metabolism. Towards this aim, advances in systems biology and bioinformatics have allowed the reconstruction of several human GSMMs, although some limitations and challenges remain, such as the lack of external identifiers for both metabolites and reactions. A pipeline was developed to integrate multiple GSMMs, starting by retrieving information from the main human GSMMs and evaluating the presence of external database identifiers and annotations for both metabolites and reactions. Information from metabolites was included into a graph database with omics data repositories, allowing clustering of metabolites through their similarity regarding database cross-referencing. Metabolite annotation of several older GSMMs was enriched, allowing the identification and integration of common entities. Using this information, as well as other metrics, we successfully integrated reactions from these models. These methods can be leveraged towards the creation of a unified consensus model of human metabolism.application/pdfporA model integration pipeline for the improvement of human genome-scale metabolic reconstructionsVieira, VítorFerreira, JorgeRodrigues, Rúben André CostaLiu, Filipe Alexandre WangRocha, MiguelHostingInstitutionOrganizationalUniversidade do Minhoe-mailmailto:repositorium@usdb.uminho.ptrepositorium@usdb.uminho.ptISSNIsPartOf1613-4516DOIIsPartOf10.1515/jib-2018-00682019-03-06T10:03:40Z20192019-03-02T18:43:50Z2019-01-01T00:00:00ZHandlehttps://hdl.handle.net/1822/59342http://purl.org/coar/access_right/c_abf2open accessGenome-scale metabolic modelshuman metabolismomics databasesdatabase integration3411306 bytesliteraturehttp://purl.org/coar/resource_type/c_6501journal articlehttp://purl.org/coar/access_right/c_abf2application/pdffulltexthttps://prod-dspace.uminho.pt/bitstreams/c578ed3f-3a7d-4cf5-86aa-5808ae32483e/download |
| spellingShingle | A model integration pipeline for the improvement of human genome-scale metabolic reconstructions Vieira, Vítor Genome-scale metabolic models human metabolism omics databases database integration |
| status | SINGLETON |
| subject.fl_str_mv | Genome-scale metabolic models human metabolism omics databases database integration |
| title | A model integration pipeline for the improvement of human genome-scale metabolic reconstructions |
| title_full | A model integration pipeline for the improvement of human genome-scale metabolic reconstructions |
| title_fullStr | A model integration pipeline for the improvement of human genome-scale metabolic reconstructions |
| title_full_unstemmed | A model integration pipeline for the improvement of human genome-scale metabolic reconstructions |
| title_short | A model integration pipeline for the improvement of human genome-scale metabolic reconstructions |
| title_sort | A model integration pipeline for the improvement of human genome-scale metabolic reconstructions |
| topic | Genome-scale metabolic models human metabolism omics databases database integration |
| topic_facet | Genome-scale metabolic models human metabolism omics databases database integration |
| url | https://hdl.handle.net/1822/59342 |
| visible | 1 |