#36 · Tools & infrastructure

Standardized access layers unify RNA annotation, proteome site and drug-gene data

The shared thread is software that makes existing biological resources programmatically usable rather than generating new predictions. EXTRARNAS is a Java framework that batch-runs multiple RNA annotation tools via Docker and standardizes their outputs into BPSEQ and a new BPSEQE format. Atlantis is a graph-database resource annotating over 11M residues across 20k human proteins with structural and functional sites, linking PDB and AlphaFoldDB. A DGIdb Model Context Protocol server lets LLMs query the drug-gene interaction database via its API, which the authors report improves accurate biomedical answers. What is new is the integration layer: normalizing outputs across tools, linking structural and functional annotations in one graph, and exposing curated knowledge to language-model agents. The items differ in data type and scope, so the common element is interface and integration rather than a shared method.