GenomoBase
Year: 2025
Type: article
Abstract: This record contains the source code, input data and curated outputs for GenomoBase, a family-focused database and web server for Genomoviridae. GenomoBase integrates ICTV-based taxonomy, genome annotations, harmonized host and geographic metadata, Serratus-derived metagenomic detections and a curated literature catalogue for all currently recognized Genomoviridae species. The public web instance is available at: https://www.genomobase.org. The archive is organized into two main components: (i) a set of Python scripts for data mining and curation, which build a harmonized Genomoviridae master table, metagenomic metadata JSON and literature catalogue from public resources (ICTV, GenBank/NCBI, Serratus and PubMed/Europe PMC); and (ii) the Django-based web application that uses these curated datasets to power the GenomoBase server (genome browser, BLAST interface, statistics and interactive explorers). Sample input files and the corresponding processed outputs are provided to allow users to fully reproduce the workflow on a test dataset. Contents GenomoBase_Code/ — Django project and application code for the GenomoBase web server (models, views, URLs, templates and configuration files). data_curation_scripts/ — Python scripts for: parsing GenBank files and building the curated Genomoviridae genome/metadata table, enriching Serratus-derived SRA accessions with BioSample/ENA metadata and geocoding locations, constructing the metagenome summary JSON and the literature catalogue. Input_Data/ — Sample input data, including example GenBank files and a list of Serratus-identified SRA runs. Output_Data/ — Curated outputs used by the web server, including the master Excel table, metagenomes_genomobase.json and the literature papers.json. README.md — Detailed documentation on repository structure, software requirements, step-by-step instructions to run the curation scripts and to deploy a local instance of the web application. Together, these resources make the GenomoBase pipeline transparent and reproducible, and enable users to extend or adapt the framework to their own analyses of Genomoviridae or other circular ssDNA virus families. Software components in this record are licensed under the MIT License.Curated datasets (e.g., Genomoviridae master table, metagenome JSON files) are released under the Creative Commons Attribution 4.0 International (CC BY 4.0) license. Users are encouraged to cite the associated GenomoBase article when reusing these resources.
Author: Cardenas-Conejo, Yair
Institution: Universidad de Colima
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: green
OpenAlex ID: W7110963721
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