ArticleBiotech (Basel (Switzerland))2022
Bio-Strings: A Relational Database Data-Type for Dealing with Large Biosequences.
Article in Biotech (Basel (Switzerland)), 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed.
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- Plastic additives enrich diverse bacterial communities which show the hallmarks of plastic degradation.Sustainable microbiology · 2026Article
- Taxonomic description of cyanobacteria from extreme habitats through genome-based classification.Frontiers in microbiology · 2026Article
- Evolutionary Process Underlying Receptor Gene Expansion and Cellular Divergence of Olfactory Sensory Neurons in Honeybees.Molecular biology and evolution · 2025Article
- "Paraxenoviridae", a putative family of ubiquitous marine bacteriophages with double-stranded RNA genomes.bioRxiv : the preprint server for biology · 2025Article
- mRNA stability fine-tunes gene expression in the developing cortex to control neurogenesis.PLoS biology · 2025Article
- "Paraxenoviridae", a putative family of globally distributed marine bacteriophages with double-stranded RNA genomes.The ISME journal · 2025Article
- A Machine Learning Pipeline to Screen Large In Vivo Molecular Data to Curate Disease Signatures of High Translational Potential.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Amino acid influx via LAT1 regulates iron demand and sensitivity to PPMX-T003 of aggressive natural killer cell leukemia.Leukemia · 2024Article
- Centralized and Federated Models for the Analysis of Clinical Data.Annual review of biomedical data science · 2024Review
- Protocol for fast clonal family inference and analysis from large-scale B cell receptor repertoire sequencing data.STAR protocols · 2024Article
- LAFEM: A Scoring Model to Evaluate Functional Landscape of Lysine Acetylome.Molecular & cellular proteomics : MCP · 2024Article
- Validation of deep amplicon sequencing of Dicrocoelium in small ruminants from Northern regions of Pakistan.PloS one · 2024Article
- Article
- aenmd: annotating escape from nonsense-mediated decay for transcripts with protein-truncating variants.Bioinformatics (Oxford, England) · 2023Article
- Sin3a Associated Protein 130kDa, sap130, plays an evolutionary conserved role in zebrafish heart development.bioRxiv : the preprint server for biology · 2023Article
- aenmd: Annotating escape from nonsense-mediated decay for transcripts with protein-truncating variants.bioRxiv : the preprint server for biology · 2023Article
- Sin3a associated protein 130 kDa, sap130, plays an evolutionary conserved role in zebrafish heart development.Frontiers in cell and developmental biology · 2023Article
Corrections and comments
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Authors and funding
8 authors.
Funding
Abstract
DNA sequencers output a large set of very long biological data strings that we should persist in databases rather than basic text file systems. Many different data models and database management systems (DBMS) may deal with both storage and efficiency issues regarding genomic datasets. Specifically, there is a need for handling strings with variable sizes while keeping their biological meaning. Relational database management systems (RDBMS) provide several data types that could be further explored for the genomics context. Besides, they enforce integrity, consistency, and enable good abstractions for more conventional data. We propose the relational text data type to represent and manipulate biological sequences and their derivatives. We present a logical schema for representing the core biological information, which may be inferred from a given biological conceptual data schema and the corresponding function manipulations. We implement and evaluate these stored functions into an actual RDBMS for both efficacy and efficiency. We show that it is possible to enforce basic and complex requirements for the genomic domain. We claim that the well-established relational text data type in RDBMS may appropriately handle the representation and persistency of biological sequences. We base our approach on the idea of domain-specific abstract data types that can store data with semantically defined functions while hiding those details from non-technical end-users.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.