publication-trust SKILL.md skillA
This file is byte-identical to the first copy the registry indexed. Same content hash, so the same checks give both the same grade.
publication-trust from ammawla/encode-toolkit is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.
mdr add ammawla/encode-toolkit/publication-trust@git:20260920.6050003Pins git:20260920.6050003 in mdr.lock. Pin the fingerprint instead.
- Audit grade
- A, 17 of 17 checks passed
- Kind
- SKILL.md skill
- Repository
- ammawla/encode-toolkit
- Path
skills/publication-trust/SKILL.md- Versions recorded
- 2
- Latest version
- git:20260920.6050003, committed Sep 20, 2026
- First version recorded
- Mar 8, 2026
- Size
- 19,912 bytes
- Repository stars
- 21
- License
- AGPL-3.0
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…
Collected from public GitHub. Every version is saved exactly as it was and never changes. Install it at an exact version with the mdr tool, and every file is checked before it reaches your agent. The main file is checked against the SHA-256 fingerprint recorded here, and the others against the fingerprints GitHub keeps for its source commit. The automatic checks below grade the latest version, and the same checks always give the same file 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@sha256:0f6e2afe92a176b9The line at the top of this page pins the label git:20260920.6050003, which is what most people want. This one pins the sha256 fingerprint of the contents instead, so it survives a label being moved. Either way the exact version is written to mdr.lock, and mdr install downloads and checks those contents again, so it installs them exactly or stops with an error.
[](https://markdownregistry.com/a/art_yc3yi6uxoiltmth3)
1 badge image fetches in 30 days. What the badge shows.
Versions
The registry has recorded 2 versions of this file, between Mar 8, 2026 and Sep 20, 2026, about one every 196 days.
| version | committed | commit | size | audit | |
|---|---|---|---|---|---|
| git:20260920.6050003 latest | 2026-09-20 | 6050003 | 19,912 B | A | view · diff |
| git:20260308.ca46af5 | 2026-03-08 | ca46af5 | 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 · 21 stars · license AGPL-3.0 · pushed 2026-09-27 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_yc3yi6uxoiltmth3 GET https://markdownregistry.com/api/v1/resolve?ref=ammawla/encode-toolkit/publication-trust GET https://markdownregistry.com/api/v1/blob/0f6e2afe92a176b948bf77d0a1ec0bdec3724cb9a75c581a3619c65027dd747e
Your AI assistant does the legwork. You hear about the deals worth your word. Hand yours the standing instructions at modelranch.com and it joins the network that reads files like this one.
Guides: the SKILL.md format and its required fields · what to check before you install a skill · how to pin a skill to an exact version · where to find agent skills · keeping a team on the same skills · which agent file does what.
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