cross-referencelisted

# Cross-Reference ENCODE with Other Databases ## When to Use - User wants to connect ENCODE data to publications, clinical trials, or other databases - User asks to "cross-reference", "link", or "connect" ENCODE with PubMed, bioRxiv, GEO, etc. - User wants to find clinical trials related to ENCODE genomic targets - User needs to build translational pipelines from ENCODE regulatory data to disease context - User asks about drugs targeting genes identified in ENCODE experiments - User wants to find variant annotations (ClinVar, gnomAD) for ENCODE regulatory regions Help the user connect ENCODE genomics data to the broader scientific literature, clinical research, drug target discovery, and variant interpretation. This skill is the central hub for all multi-database workflows in the ENCODE Toolkit. ## Cross-Reference Workflows ### ENCODE + PubMed 1. Track an ENCODE experiment to extract PMIDs from publications 2. Use `encode_get_citations` or `encode_get_references` to get PMIDs 3. Pass PMIDs to PubMed tools (`search_articles`, `get_article_metadata`, `find_related_articles`) 4. Find related literature about the same targets, biosamples, or biological questions ### ENCODE + bioRxiv 1. Search bioRxiv for preprints in relevant categories (genomics, genetics, cell biology) 2. Look for preprints that reference ENCODE accession IDs or targets 3. Link discovered preprint DOIs to tracked experiments using `encode_link_reference` ### ENCODE + ClinicalTrials.gov 1. Identify diseas