/cross-reference

name: cross-reference
description: Cross-reference ENCODE data with PubMed, bioRxiv, ClinicalTrials.gov, Open Targets, GTEx, ClinVar, GWAS Catalog, gnomAD, Ensembl, and other scientific databases. Use when the user wants to find publications, preprints, or clinical trials related to ENCODE experiments, chain ENCODE data with other scientific MCP servers, or build translational pipelines from genomic data to clinical application.

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 disease-relevant ENCODE data (e.g., pancreatic tissue data for diabetes trials) 2. Use `encode_get_references` to find linked NCT IDs 3. Search ClinicalTrials.gov for trials targeting the same genes/proteins as ENCODE experiments 4. Link relevant trial NCT IDs to experiments using `encode_link_reference`

ENCODE + Open Targets

1. Identify ENCODE ChIP-seq or CRISPR screen targets of interest 2. Resolve gene symbols to Ensembl Gene IDs via `search_entities` 3. Query Open Targets for disease associations, tractability, and drug candidates 4. Chain from ENCODE functional data to therapeutic hypotheses

ENCODE + GTEx

1. Find ENCODE regulatory experiments in a tissue of interest 2. Annotate peaks with nearest genes using GENCODE annotations 3. Query GTEx for expression of those genes in the matching tissue 4. Validate that putative regulatory elements sit near actively transcribed genes

ENCODE + GWAS Catalog + ClinVar

1. Obtain trait-associated variants from the GWAS Catalog 2. Check clinical significance in ClinVar 3. Intersect variant coordinates with ENCODE peak files and cCREs 4. Determine whether disease-associated variants fall in regulatory elements

ENCODE + Consensus (Academic Search)

1. Search for high-quality research papers about ENCODE targets (H3K27me3, CTCF, etc.) 2. Find systematic reviews and meta-analyses relevant to ENCODE data types 3. Cross-validate ENCODE quality metrics against published benchmarks

ENCODE + GEO

1. Check ENCODE experiment `dbxrefs` for GEO accessions (format: `GEO:GSExxxxx`) 2. Search GEO E-utilities for complementary datasets in the same tissue/assay 3. Link GEO accessions to tracked experiments using `encode_link_reference` 4. See `geo-connector` skill for detailed GEO API usage

ENCODE + SRA

Raw sequencing reads for ENCODE experiments are deposited in NCBI SRA. GEO records link to SRA via E-utilities `elink`. For reprocessing ENCODE data or accessing raw reads not on the ENCODE Portal, query SRA via:

curl "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=gds&db=sra&id=GDS_UID&tool=encode_mcp&email=YOUR_EMAIL"

ENCODE + Ensembl

Use the Ensembl REST API to cross-reference ENCODE targets and regulatory elements with Ensembl annotations. See `ensembl-annotation` skill for VEP, Regulatory Build, and gene lookup endpoints.

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Identifier Format Quick Reference

| Identifier | Format | Example | Database | MCP Tool / Skill | |---|---|---|---|---| | PMID | numeric string | "35486828" | PubMed | `get_article_metadata` | | DOI | 10.xxxx/... | "10.1038/s41586-020-2493-4" | CrossRef | `convert_article_ids` | | NCT ID | NCT + 8 digits | "NCT04567890" | ClinicalTrials.gov | `get_trial_details` | | GEO Series | GSE + digits | "GSE123456" | GEO/NCBI | `geo-connector` skill | | GEO Sample | GSM + digits | "GSM1234567" | GEO/NCBI | `geo-connector` skill | | bioRxiv DOI | 10.1101/YYYY.MM.DD.xxx | "10.1101/2024.06.15.598765" | bioRxiv | `get_preprint` | | ENCODE Experiment | ENCSR + 6 alphanum | "ENCSR123ABC" | ENCODE | `encode_get_experiment` | | ENCODE File | ENCFF + 6 alphanum | "ENCFF001AAA" | ENCODE | `encode_get_file_info` | | Ensembl Gene | ENSG + 11 digits | "ENSG00000102974" | Ensembl | `ensembl-annotation` skill | | Ensembl Transcript | ENST + 11 digits | "ENST00000264010" | Ensembl | `ensembl-annotation` skill | | SRA Study | SRP + digits | "SRP123456" | SRA/NCBI | E-utilities | | SRA Run | SRR + digits | "SRR1234567" | SRA/NCBI | E-utilities | | ROR ID | 9 chars | "021nxhr62" | ROR | `search_by_funder` | | ChEMBL ID | CHEMBL + digits | "CHEMBL25" | Open Targets | `search_entities` | | rsID | rs + digits | "rs7903146" | dbSNP/ClinVar | `clinvar-annotation` skill | | ClinVar Accession | RCV + digits | "RCV000012345" | ClinVar | `clinvar-annotation` skill | | JASPAR Matrix | MA + digits + version | "MA0139.1" | JASPAR | `jaspar-motifs` skill |

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Code Examples

1. PubMed: "Find the original paper for this ENCODE experiment and link it"

Step 1: Track the experiment to extract publications