SMARTER-database: a tool to integrate SNP array datasets for sheep and goat breeds.
ABSTRACT.- Underutilized sheep and goat breeds can adapt to challenging environments due to their genetics. Integrating publicly available genomic datasets with new data will facilitate genetic diversity analyses; however, this process is complicated by data discrepancies, such as outdated assembly...
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| מחברים אחרים: | , , , , , , , , , , , , , , , , |
| פורמט: | article |
| שפה: | אנגלית |
| יצא לאור: |
2024
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| נושאים: | |
| גישה מקוונת: | https://ainfo.inia.uy/consulta/busca?b=pc&id=64970&biblioteca=vazio&busca=64970&qFacets=64970 |
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| _version_ | 1868890174024318976 |
|---|---|
| author | COZZI, P. |
| author2 | MANUNZA, A. RAMIREZ-DIAZ, J. TSARTSIANIDOU, V. GKAGKAVOUZIS, K. PERAZA, P. JOHANSSON, A. M. ARRANZ, J. J. FREIRE, F. KUSZA, S. BISCARINI, F. PETERS, L. TOSSER-KLOPP, G. CIAPPESONI, G. TRIANTAFYLLIDIS, A. RUPP, R. SERVIN, B. STELLA, A. |
| author2_role | author author author author author author author author author author author author author author author author author |
| author_browse | ARRANZ, J. J. BISCARINI, F. CIAPPESONI, G. COZZI, P. FREIRE, F. GKAGKAVOUZIS, K. JOHANSSON, A. M. KUSZA, S. MANUNZA, A. PERAZA, P. PETERS, L. RAMIREZ-DIAZ, J. RUPP, R. SERVIN, B. STELLA, A. TOSSER-KLOPP, G. TRIANTAFYLLIDIS, A. TSARTSIANIDOU, V. |
| author_facet | COZZI, P. MANUNZA, A. RAMIREZ-DIAZ, J. TSARTSIANIDOU, V. GKAGKAVOUZIS, K. PERAZA, P. JOHANSSON, A. M. ARRANZ, J. J. FREIRE, F. KUSZA, S. BISCARINI, F. PETERS, L. TOSSER-KLOPP, G. CIAPPESONI, G. TRIANTAFYLLIDIS, A. RUPP, R. SERVIN, B. STELLA, A. |
| author_role | author |
| collection | AINFO |
| dc.creator.none.fl_str_mv | COZZI, P. MANUNZA, A. RAMIREZ-DIAZ, J. TSARTSIANIDOU, V. GKAGKAVOUZIS, K. PERAZA, P. JOHANSSON, A. M. ARRANZ, J. J. FREIRE, F. KUSZA, S. BISCARINI, F. PETERS, L. TOSSER-KLOPP, G. CIAPPESONI, G. TRIANTAFYLLIDIS, A. RUPP, R. SERVIN, B. STELLA, A. |
| dc.date.none.fl_str_mv | 2024 2025-06-23T18:45:57Z 2025-06-23T18:45:57Z 2025-06-23T18:45:57Z |
| dc.identifier.none.fl_str_mv | https://ainfo.inia.uy/consulta/busca?b=pc&id=64970&biblioteca=vazio&busca=64970&qFacets=64970 |
| dc.language.none.fl_str_mv | en eng |
| dc.rights.none.fl_str_mv | info:eu-repo/semantics/openAccess Acceso abierto |
| dc.source.none.fl_str_mv | reponame:AINFO instname:Instituto Nacional de Investigación Agropecuaria instacron:Instituto Nacional de Investigación Agropecuaria |
| dc.subject.none.fl_str_mv | Animal and Plant Sciences Bioinformatics Animal Genetics SISTEMA GANADERO EXTENSIVO - INIA SMARTER-database |
| dc.title.none.fl_str_mv | SMARTER-database: a tool to integrate SNP array datasets for sheep and goat breeds. |
| dc.type.none.fl_str_mv | Article PublishedVersion info:eu-repo/semantics/article info:eu-repo/semantics/publishedVersion |
| description | ABSTRACT.- Underutilized sheep and goat breeds can adapt to challenging environments due to their genetics. Integrating publicly available genomic datasets with new data will facilitate genetic diversity analyses; however, this process is complicated by data discrepancies, such as outdated assembly versions or different data formats. Here, we present the SMARTER-database, a collection of tools and scripts to standardize genomic data and metadata, mainly from SNP chip arrays on global small ruminant populations, with a focus on reproducibility. SMARTER-database harmonizes genotypes for about 12,000 sheep and 6,000 goats to a uniform coding and assembly version. Users can access the genotype data via File Transfer Protocol and interact with the metadata through a web interface or using their custom scripts, enabling efficient filtering and selection of samples. These tools will empower researchers to focus on the crucial aspects of adaptation and contribute to livestock sustainability, leveraging the rich dataset provided by the SMARTER-database. © 2024 GigaScience Press. All rights reserved. .-.-.-.-.-.-.-.-.-. Availability and implementation:The code is available as open-source software under the MIT license at https://github.com/cnr-ibba/SMARTER-database. |
| eu_rights_str_mv | openAccess |
| format | article |
| id | anni_b772477a167108ee9b4f5c7eb5e0f2bc |
| instacron_str | Instituto Nacional de Investigación Agropecuaria |
| institution | Instituto Nacional de Investigación Agropecuaria |
| instname_str | Instituto Nacional de Investigación Agropecuaria |
| language | eng |
| language_invalid_str_mv | en |
| network_acronym_str | anni |
| network_name_str | oai-lr-anni |
| oai_identifier_str | oai:redi.anii.org.uy:20.500.12381/4950 |
| publishDate | 2024 |
| publishDateSort | 2024 |
| reponame_str | AINFO |
| repository.mail.fl_str_mv | |
| repository.name.fl_str_mv | |
| repository_id_str | |
| rights_invalid_str_mv | Acceso abierto |
| spelling | SMARTER-database: a tool to integrate SNP array datasets for sheep and goat breeds.COZZI, P.MANUNZA, A.RAMIREZ-DIAZ, J.TSARTSIANIDOU, V.GKAGKAVOUZIS, K.PERAZA, P.JOHANSSON, A. M.ARRANZ, J. J.FREIRE, F.KUSZA, S.BISCARINI, F.PETERS, L.TOSSER-KLOPP, G.CIAPPESONI, G.TRIANTAFYLLIDIS, A.RUPP, R.SERVIN, B.STELLA, A.Animal and Plant SciencesBioinformaticsAnimal GeneticsSISTEMA GANADERO EXTENSIVO - INIASMARTER-databaseABSTRACT.- Underutilized sheep and goat breeds can adapt to challenging environments due to their genetics. Integrating publicly available genomic datasets with new data will facilitate genetic diversity analyses; however, this process is complicated by data discrepancies, such as outdated assembly versions or different data formats. Here, we present the SMARTER-database, a collection of tools and scripts to standardize genomic data and metadata, mainly from SNP chip arrays on global small ruminant populations, with a focus on reproducibility. SMARTER-database harmonizes genotypes for about 12,000 sheep and 6,000 goats to a uniform coding and assembly version. Users can access the genotype data via File Transfer Protocol and interact with the metadata through a web interface or using their custom scripts, enabling efficient filtering and selection of samples. These tools will empower researchers to focus on the crucial aspects of adaptation and contribute to livestock sustainability, leveraging the rich dataset provided by the SMARTER-database. © 2024 GigaScience Press. All rights reserved. .-.-.-.-.-.-.-.-.-. Availability and implementation:The code is available as open-source software under the MIT license at https://github.com/cnr-ibba/SMARTER-database.2025-06-23T18:45:57Z2025-06-23T18:45:57Z20242025-06-23T18:45:57ZArticlePublishedVersioninfo:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttps://ainfo.inia.uy/consulta/busca?b=pc&id=64970&biblioteca=vazio&busca=64970&qFacets=64970reponame:AINFOinstname:Instituto Nacional de Investigación Agropecuariainstacron:Instituto Nacional de Investigación Agropecuariaenenginfo:eu-repo/semantics/openAccessAcceso abiertooai:redi.anii.org.uy:20.500.12381/49502026-02-10T17:37:28Z |
| spellingShingle | SMARTER-database: a tool to integrate SNP array datasets for sheep and goat breeds. COZZI, P. Animal and Plant Sciences Bioinformatics Animal Genetics SISTEMA GANADERO EXTENSIVO - INIA SMARTER-database |
| status_str | publishedVersion |
| title | SMARTER-database: a tool to integrate SNP array datasets for sheep and goat breeds. |
| title_full | SMARTER-database: a tool to integrate SNP array datasets for sheep and goat breeds. |
| title_fullStr | SMARTER-database: a tool to integrate SNP array datasets for sheep and goat breeds. |
| title_full_unstemmed | SMARTER-database: a tool to integrate SNP array datasets for sheep and goat breeds. |
| title_short | SMARTER-database: a tool to integrate SNP array datasets for sheep and goat breeds. |
| title_sort | SMARTER-database: a tool to integrate SNP array datasets for sheep and goat breeds. |
| topic | Animal and Plant Sciences Bioinformatics Animal Genetics SISTEMA GANADERO EXTENSIVO - INIA SMARTER-database |
| url | https://ainfo.inia.uy/consulta/busca?b=pc&id=64970&biblioteca=vazio&busca=64970&qFacets=64970 |