Integrated Biological Data Collection Platform: An Architecture for Automated Curation of Public Repositories

Introduction In contemporary research, the volume of biological data deposited in public repositories is growing exponentially. The Gene Expression Omnibus (GEO), NCBI Gene, PubMed, and UniProt accumulate thousands of new records daily, including sequences, expression profiles, scientific articles, and functional annotations. On the one hand, this scenario represents a unique opportunity for biomedical research. On the other hand, the diversity of data formats, access protocols, and metadata models creates a significant barrier: each source requires a specific collector, distinct rate-limiting strategies, and its own validation logic. Above all, the lack of standardization in data storage compromises the reproducibility of scientific studies. The need for integrated tools capable of unifying data extraction, curation, and persistence has been widely discussed. In practice, ad hoc solutions such as isolated scripts for individual repositories generate redundant work and make maintenance difficult. First and foremost, it is necessary to establish an architecture that treats data collection as a service rather than a collection of scattered artifacts. This work presents Project 1 of the Integrated Bioinformatics Platform: a containerized Biomedical Data Collector coupled with a Data Lake. Its objective is to provide a REST API capable of triggering asynchronous data collections from the four aforementioned sources, storing immutable raw data in MinIO, and persisting metadata in PostgreSQL, all while ensuring traceability and resilience. Development The system architecture is divided into three main layers. The first is the API and orchestration layer , implemented using FastAPI. Its five endpoints — POST /collections , GET /collections , GET /collections/{id} , GET /collections/{id}/download/{dataset_id} , and GET /health — expose a clean interface for initiating and monitoring collection processes. The second layer is the collector engine , composed of abstract classe