biocontext-knowledge-queries

To annotate a list of differentially expressed genes, you can batch query UniProt functions, Reactome pathways, GO terms, and PanglaoDB markers. The Skill normalizes species and identifiers while applying rate-limit aware external API calls to retrieve integrated biomedical annotations.

Yes, you can validate cell type markers using PanglaoDB for mouse datasets. The Skill supports marker validation across human, mouse, zebrafish, and rat datasets by querying PanglaoDB alongside other integrated biomedical knowledge sources.

Yes, this Skill supports OpenTargets GraphQL queries for drug-disease association exploration. It integrates OpenTargets data access to help researchers retrieve target associations and explore drug-disease relationships programmatically.

To perform batch annotation without hitting external API timeouts, the Skill provides rate-limit aware external API calls and troubleshooting guidance for query formats. It supports batch annotation workflows to enrich DEG lists while managing integration issues across 49 biomedical data sources.

The best way to retrieve protein structures and literature for a specific gene is to query AlphaFold for structures and Europe PMC for literature within a single workflow. The Skill unifies access to these resources to consolidate protein function lookup and literature retrieval.

Species codes causing errors during gene annotation often result from unnormalized identifiers or incorrect query formats. The Skill provides species and identifier normalization along with troubleshooting guidance for species codes, timeouts, and query formats to reduce common integration issues.