tooluniverse-electron-microscopy

Search and analyze electron microscopy data — cryo-EM density maps (EMDB), fitted atomic models (PDB), raw micrograph datasets (EMPIAR), and cryo-electron tomography volumes (CryoET Data Portal). Use for finding 3D structural data on a protein/complex, comparing experimental EM resolution to AlphaFold confidence, and accessing raw EM data for re-processing.

Quality

73%

Does it follow best practices?

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Securityby

Low

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tessl review fix ./plugin/skills/tooluniverse-electron-microscopy/SKILL.md

Quality

Content

63%Weight 40%Scale 1-5

Reviews the quality of instructions and guidance provided to agents. Good implementation is clear, handles edge cases, and produces reliable results.

A thorough, well-structured pipeline document with concrete tool signatures and a clear phased workflow, weakened mainly by didactic conceptual primers and a monolithic single-file layout with no progressive disclosure via bundle files.

Suggestions

Trim general-background primers (TEM/cryo-EM/SEM resolution explanations) that Claude already knows, keeping only the domain-specific resolution-interpretation thresholds.

Move the IDR tool catalog and/or per-phase tool signatures into separate reference files under references/ and link to them from SKILL.md to improve progressive disclosure.

Add at least one runnable EM tool call example in the tu.run_tool(...) form shown for IDR, so the EM phases reach copy-paste-ready actionability.

Dimension	Reasoning	Score
Conciseness	Mostly efficient tool documentation, but conceptual primers Claude already knows (TEM vs cryo-EM vs SEM resolution, general EM background) and verbose resolution tables add unnecessary explanation, matching anchor 3.	3 / 5
Actionability	Each phase lists concrete tools with exact input/output signatures and threshold-based guidance (cross-correlation > 0.7, FSC 0.143), and one IDR example is copy-paste-ready; the gap is that EM tool calls are shown as signatures rather than runnable tu.run_tool(...) examples, matching anchor 4.	4 / 5
Workflow Clarity	An explicit 8-phase pipeline with an ASCII flow diagram, per-phase numbered workflows, edge-case fallbacks, and a quality checklist gives a clear sequence with most checkpoints present; validation loops are advisory rather than enforced, so anchor 4 not 5.	4 / 5
Progressive Disclosure	No bundle files exist (references/scripts/assets absent) and all content is inlined in a ~290-line SKILL.md with good section headers but no one-level-deep file references, so content that could be externalized (e.g. the IDR tool catalog, per-phase signatures) stays inline, matching anchor 3.	3 / 5
	Total	14 / 20 Passed

Description

83%Weight 40%Scale 1-5

Based on the skill's description, can an agent find and select it at the right time? Clear, specific descriptions lead to better discovery.

A strong description that clearly states what the skill does and when to use it, with concrete trigger conditions and named databases. Minor gaps in action distinctiveness and verbatim synonym coverage keep specificity and trigger quality at 4 rather than 5.

Dimension	Reasoning	Score
Specificity	Names multiple concrete actions (search/analyze, find 3D structural data, compare EM resolution to AlphaFold, access raw data for re-processing), but they overlap somewhat and 'analyze' stays abstract, so it sits at anchor 4 rather than 5.	4 / 5
Completeness	Explicitly answers both what (Search and analyze electron microscopy data across named databases) and when (a 'Use for ...' clause listing three concrete trigger conditions), matching the anchor-5 example.	5 / 5
Trigger Term Quality	Good coverage of database names (EMDB, PDB, EMPIAR, CryoET Data Portal) and natural domain terms (cryo-EM, EM resolution, AlphaFold, raw micrograph) that users would say, missing only a few synonyms/verbatim phrasings, matching anchor 4.	4 / 5
Distinctiveness Conflict Risk	Strongly distinctive EM niche with named databases, but PDB/AlphaFold are shared with sibling skills and the description itself does not state the scope boundary (that lives in the body), so minor overlap risk remains at anchor 4.	4 / 5
	Total	17 / 20 Passed

Validation

100%

Warnings & errors only

Checks the skill against the spec for correct structure and formatting. All validation checks must pass before discovery and implementation can be scored.

Validation — 16 / 16 Passed

Validation for skill structure

No warnings or errors.

Repository: mims-harvard/ToolUniverse
Path: plugin/skills/tooluniverse-electron-microscopy/SKILL.md
Commit: 1b02920

Reviewed: 1 day ago

Table of Contents

Discovery Implementation Validation

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