publication-trust skillA
publication-trust is agent-read markdown (skill) from ammawla/encode-toolkit: Assess the scientific integrity and trustworthiness of publications before relying on their findings. Use this skill whenever evaluating a paper for a workflow, citing a study, building an analysis on published methods, or when a user asks about the reliability of a study. Checks for formal retractions, corrections, expressions of concern, and — critically — informal contradictions where subsequent studies failed to reproduce key findings. Integrates with PubMed, bioRxiv, and Consensus to provid.
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
# Publication Trust Assessment Evaluate the scientific integrity and reliability of publications before building analyses on their findings. ## When to Use - User wants to evaluate the reliability and reproducibility of a genomics publication - User asks about "publication quality", "reproducibility", "trust assessment", or "paper evaluation" - User needs to check if a paper follows ENCODE data standards and best practices - User wants to verify that cited datasets, tools, and methods meet community standards - Example queries: "is this paper's ChIP-seq analysis trustworthy?", "evaluate the methods in this genomics paper", "check if this study follows ENCODE standards" ## Why This Matters Not all published findings are reliable. Problems range from formal retractions (data fabrication, image manipulation) to informal contradictions where independent groups fail to reproduce key claims. In genomics and computational biology, building pipelines or analyses on unreliable findings wastes resources and propagates errors. **The problem is not always obvious.** Formal retractions are rare compared to the number of problematic papers. More commonly: …
Read the whole file at its exact version.
How to install
mdr add ammawla/encode-toolkit/publication-trust@git:20260920.6050003mdr add ammawla/encode-toolkit/publication-trust@sha256:0f6e2afe92a176b9Pin 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_3amqy5su5cx2pt2l)
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Versions
| version | committed | commit | size | audit | |
|---|---|---|---|---|---|
| git:20260920.6050003 latest | 2026-09-20 | 6050003 | 19,912 B | A | view · diff |
| git:20260312.be32706 | 2026-03-12 | be32706 | 18,646 B | A | view |
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 (19912 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_3amqy5su5cx2pt2l GET https://markdownregistry.com/api/v1/resolve?ref=ammawla/encode-toolkit/publication-trust GET https://markdownregistry.com/api/v1/blob/0f6e2afe92a176b948bf77d0a1ec0bdec3724cb9a75c581a3619c65027dd747e
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