cross-reference skillA
cross-reference is agent-read markdown (skill) from ammawla/encode-toolkit: 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..
Indexed from public GitHub and served as immutable, content-addressed versions. Install it pinned to an exact SHA-256 with the mdr CLI, and every file is verified against the hash recorded here before it reaches your agent. The deterministic audit below grades the latest version, and the same file always earns the same grade.
What the file says
# 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 …
Read the whole file at its exact version.
How to install
mdr add ammawla/encode-toolkit/cross-reference@git:20260312.665e731mdr add ammawla/encode-toolkit/cross-reference@sha256:47382b7a44c5054bPin to a label to follow the author's releases, or to a sha256 to freeze the exact bytes forever. Either way the resolved hash is written to mdr.lock, and mdr install reproduces it on any machine.
[](https://markdownregistry.com/a/art_qk6dt2b34sisthbw)
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Versions
Audit of the latest version
- pass: Frontmatter block present
- pass: Frontmatter declares a name
- pass: Frontmatter declares a description
- pass: Size between 200 bytes and 200 KB (35265 bytes)
- pass: No zero-width or bidi control characters
- pass: No instruction hidden inside an HTML comment
- pass: No link to an exfiltration or paste host
- pass: No credential-shaped string
- pass: No instruction to send local credentials anywhere
- pass: No text hidden with inline styles
- pass: No prompt-injection phrasing
- pass: No curl or wget piped into a shell
- pass: No recursive delete of root, home or parent
- pass: No instruction to read or print local credentials
- pass: No base64 blob over 200 characters
- pass: No link to a raw IP address
- pass: No script tag
Source
ammawla/encode-toolkit · 20 stars · license AGPL-3.0 · pushed 2026-09-21 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_qk6dt2b34sisthbw GET https://markdownregistry.com/api/v1/resolve?ref=ammawla/encode-toolkit/cross-reference GET https://markdownregistry.com/api/v1/blob/47382b7a44c5054b8f873ae6777d58c56286fc9bc22a82b676862f23e195039b
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