About this Research Topic
Please note that Systems Microbiology does not consider descriptive studies solely based on amplicon (e.g., 16S rRNA) profiles, unless accompanied by a clear hypothesis and experimentation, and provide insight into the microbiological system or process being studied.
The field of plasmid research has garnered significant attention due to the critical role plasmids play in microbial genetics, including metabolism, virulence, and antibiotic resistance. Plasmids, as extrachromosomal DNA elements, facilitate horizontal gene transfer among bacteria, contributing to rapid bacterial evolution and gene flow in various environments. Despite the availability of extensive plasmid sequence data in primary databases like the International Nucleotide Sequence Database Collaboration (INSDC), these resources often suffer from poor organization and annotation. Recent advancements have led to the development of secondary plasmid databases that incorporate metadata from primary sources. However, these databases and associated bioinformatics tools still face challenges such as data incompleteness, bias, and inaccurate annotations. Addressing these issues requires a combination of expert knowledge, experimental validation, and meticulous manual curation to enhance the reliability and utility of plasmid databases.
This research topic aims to advance the development of high-quality plasmid databases and precision bioinformatics tools. The primary objectives include identifying and addressing the limitations of current plasmid databases, proposing innovative solutions, and providing experimental evidence to support database improvements. Specific questions to be explored include: What are the main sources of data bias in existing plasmid databases? How can manual curation and experimental validation improve the accuracy of plasmid annotations? What new tools and algorithms can be developed to enhance plasmid identification and classification?
To gather further insights into the development and enhancement of plasmid databases, we welcome articles addressing, but not limited to, the following themes:
- Discussing problems of the current plasmid databases and tools
- Experimental evidence for (re)construction of plasmid databases
- New databases, tools, and algorithms
- Plasmid classification
- Gene Ontology
By focusing on these themes, we aim to foster a comprehensive understanding of plasmid diversity and functionality, ultimately contributing to advancements in microbial ecology, medical research, and genetic engineering.
The field of plasmid research has garnered significant attention due to the critical role plasmids play in microbial genetics, including metabolism, virulence, and antibiotic resistance. Plasmids, as extrachromosomal DNA elements, facilitate horizontal gene transfer among bacteria, contributing to rapid bacterial evolution and gene flow in various environments. Despite the availability of extensive plasmid sequence data in primary databases like the International Nucleotide Sequence Database Collaboration (INSDC), these resources often suffer from poor organization and annotation. Recent advancements have led to the development of secondary plasmid databases that incorporate metadata from primary sources. However, these databases and associated bioinformatics tools still face challenges such as data incompleteness, bias, and inaccurate annotations. Addressing these issues requires a combination of expert knowledge, experimental validation, and meticulous manual curation to enhance the reliability and utility of plasmid databases.
This research topic aims to advance the development of high-quality plasmid databases and precision bioinformatics tools. The primary objectives include identifying and addressing the limitations of current plasmid databases, proposing innovative solutions, and providing experimental evidence to support database improvements. Specific questions to be explored include: What are the main sources of data bias in existing plasmid databases? How can manual curation and experimental validation improve the accuracy of plasmid annotations? What new tools and algorithms can be developed to enhance plasmid identification and classification?
To gather further insights into the development and enhancement of plasmid databases, we welcome articles addressing, but not limited to, the following themes:
- Discussing problems of the current plasmid databases and tools
- Experimental evidence for (re)construction of plasmid databases
- New databases, tools, and algorithms
- Plasmid classification
- Gene Ontology
By focusing on these themes, we aim to foster a comprehensive understanding of plasmid diversity and functionality, ultimately contributing to advancements in microbial ecology, medical research, and genetic engineering.
Keywords: Plasmid, Database, Metadata, Experimental evidence, Computational tools
Important Note: All contributions to this Research Topic must be within the scope of the section and journal to which they are submitted, as defined in their mission statements. Frontiers reserves the right to guide an out-of-scope manuscript to a more suitable section or journal at any stage of peer review.
