Omilayers: a Python package for efficient data management to support multi-omic analysis
Abstract Multi-omic integration involves the management of diverse omic datasets. Conducting an effective analysis of these datasets necessitates a data management system that meets a specific set of requirements, such as rapid storage and retrieval of data with varying numbers of features and mixed...
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| Format: | Article |
| Language: | English |
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BMC
2025-02-01
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| Series: | BMC Bioinformatics |
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| Online Access: | https://doi.org/10.1186/s12859-025-06067-7 |
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| _version_ | 1823861577380528128 |
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| author | Dimitrios Kioroglou |
| author_facet | Dimitrios Kioroglou |
| author_sort | Dimitrios Kioroglou |
| collection | DOAJ |
| description | Abstract Multi-omic integration involves the management of diverse omic datasets. Conducting an effective analysis of these datasets necessitates a data management system that meets a specific set of requirements, such as rapid storage and retrieval of data with varying numbers of features and mixed data-types, ensurance of reliable and secure database transactions, extension of stored data row and column-wise and facilitation of data distribution. SQLite and DuckDB are embedded databases that fulfil these requirements. However, they utilize the structured query language (SQL) that hinders their implementation by the uninitiated user, and complicates their use in repetitive tasks due to the necessity of writing SQL queries. This study offers Omilayers, a Python package that encapsulates these two databases and exposes a subset of their functionality that is geared towards frequent and repetitive analytical procedures. Synthetic data were used to demonstrate the use of Omilayers and compare the performance of SQLite and DuckDB. |
| format | Article |
| id | doaj-art-936094483d204f969d8d56e8630257aa |
| institution | Kabale University |
| issn | 1471-2105 |
| language | English |
| publishDate | 2025-02-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Bioinformatics |
| spelling | doaj-art-936094483d204f969d8d56e8630257aa2025-02-09T12:57:00ZengBMCBMC Bioinformatics1471-21052025-02-0126111110.1186/s12859-025-06067-7Omilayers: a Python package for efficient data management to support multi-omic analysisDimitrios Kioroglou0Integrative Genomics Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA)Abstract Multi-omic integration involves the management of diverse omic datasets. Conducting an effective analysis of these datasets necessitates a data management system that meets a specific set of requirements, such as rapid storage and retrieval of data with varying numbers of features and mixed data-types, ensurance of reliable and secure database transactions, extension of stored data row and column-wise and facilitation of data distribution. SQLite and DuckDB are embedded databases that fulfil these requirements. However, they utilize the structured query language (SQL) that hinders their implementation by the uninitiated user, and complicates their use in repetitive tasks due to the necessity of writing SQL queries. This study offers Omilayers, a Python package that encapsulates these two databases and exposes a subset of their functionality that is geared towards frequent and repetitive analytical procedures. Synthetic data were used to demonstrate the use of Omilayers and compare the performance of SQLite and DuckDB.https://doi.org/10.1186/s12859-025-06067-7Multi-omicsData managementDatabasesPython |
| spellingShingle | Dimitrios Kioroglou Omilayers: a Python package for efficient data management to support multi-omic analysis BMC Bioinformatics Multi-omics Data management Databases Python |
| title | Omilayers: a Python package for efficient data management to support multi-omic analysis |
| title_full | Omilayers: a Python package for efficient data management to support multi-omic analysis |
| title_fullStr | Omilayers: a Python package for efficient data management to support multi-omic analysis |
| title_full_unstemmed | Omilayers: a Python package for efficient data management to support multi-omic analysis |
| title_short | Omilayers: a Python package for efficient data management to support multi-omic analysis |
| title_sort | omilayers a python package for efficient data management to support multi omic analysis |
| topic | Multi-omics Data management Databases Python |
| url | https://doi.org/10.1186/s12859-025-06067-7 |
| work_keys_str_mv | AT dimitrioskioroglou omilayersapythonpackageforefficientdatamanagementtosupportmultiomicanalysis |