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eqtl-catalogue-region-fetch

Fetch a region of cis-eQTL summary statistics from EBI eQTL Catalogue v7+ via tabix-on-FTP. Use when an agent needs eQTL beta / SE / p-value for every variant in a window around a gene's TSS for one specific dataset (study × tissue × quantification method). Input: dataset_id, chromosome, start, end, optional molecular_trait_id. Output: harmonised TSV slice.

Quality

87%

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SKILL.md
Quality
Evals
Security

Quality

Content

77%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 well-structured, highly actionable single-file skill whose domain-specific gotchas and validation documentation are excellent. Its main weaknesses are verbosity (padded gotcha paragraphs, inline full citations, time-sensitive probe statistics and dates) and a monolithic structure that inlines detail which belongs in separate reference files.

Suggestions

Trim Gotchas 6 and 8 into short rule statements and move the supporting measurements (probe counts, per-dataset disagreement tallies, cache-key history) into a references/gotcha-details.md file.

Move the full Sun 2018 citation out of the 'Do NOT fire when' bullet into the existing Citations section, keeping only the actionable guidance (pass molecular_trait_id for QTD000584, use ukb-ppp-region-fetch for UKB-PPP) inline.

Replace time-sensitive inline dates (HTTP 410 since September 2026, probed 2026-09-13, measured 2026-10-22) with version-stable statements or collect them in a 'deprecated / upstream status' section, and split the example-output block into an examples/ reference file.

DimensionReasoningScore

Conciseness

The core content (gotchas on strand-aware cis-windows, ALT-effect beta, duplicate-rsid collapsing) is genuinely non-obvious domain knowledge, but several passages are heavily padded: a full inline citation for Sun 2018 (doi, PMID, author list) in the Trigger section, cache-probing statistics ('33 of 758 probed 2026-09-13', 'measured 2026-10-22, 0 of 468 repeated keys disagreed (82 in the SORT1 QTD000276 window, 311 in QTD000609, 75 in QTD000269 .cc)'), and time-sensitive dates (HTTP 410 'since September 2026') not placed in a deprecated section, which the rubric explicitly penalizes. Gotchas 6 and 8 are 200+ word run-on paragraphs that could be tightened substantially.

3 / 5

Actionability

The CLI Reference gives copy-paste-ready commands covering standard usage, the bundled demo, demo listing, and the ClawBio runner variant, plus a concrete JSON config schema and realistic example output (manifest.yaml, variants.tsv, collapsed_rows.tsv, report.md). Fully executable guidance with specific examples covering the common cases.

5 / 5

Workflow Clarity

The 5-step workflow (resolve dataset_id -> pick region -> tabix range fetch -> filter by molecular_trait_id -> write outputs) is clearly sequenced with concrete commands, and validation is explicit and thorough: every row is checked against the 19 expected columns with EQTLCatalogueSchemaError naming the file and bad row, the CLI exits 2 and writes nothing on failure, duplicate-stat conflicts raise EQTLCatalogueDuplicateRowConflict, and the invariant 'n_variants + len(collapsed) == n_rows_read is checked, not assumed'. No validation cap applies.

5 / 5

Progressive Disclosure

Sections are well-organized with clear headers, but everything lives in one ~186-line monolithic SKILL.md: the enormous Gotcha 6 and 8 paragraphs, the full example-output dumps, and the citation detail are content that clearly belongs in separate reference files. Referenced bundle paths (data/dataset_index_r7.tsv, examples/input.json, eqtl_catalogue_region_fetch.py) are not present in the bundle to verify, and no dedicated reference files carry any of the detail.

3 / 5

Total

16

/

20

Passed

Description

92%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 model description: third-person, concise, concrete about the mechanism (tabix-on-FTP), explicit about both what it does and when to use it, and sharply scoped to one dataset-level regional fetch with a stated input/output contract. The only minor gap is a few natural trigger synonyms.

DimensionReasoningScore

Specificity

'Fetch a region of cis-eQTL summary statistics from EBI eQTL Catalogue v7+ via tabix-on-FTP' plus enumerated inputs (dataset_id, chromosome, start, end, optional molecular_trait_id) and a concrete output ('harmonised TSV slice') gives multiple specific concrete actions with comprehensive coverage. Not 4: there are no gaps — the mechanism, the per-variant fields (beta / SE / p-value), and the input/output contract are all stated.

5 / 5

Completeness

Both 'what' ('Fetch a region of cis-eQTL summary statistics... via tabix-on-FTP') and 'when' ('Use when an agent needs eQTL beta / SE / p-value for every variant in a window around a gene's TSS for one specific dataset') are explicitly and concretely answered, with the input/output contract on top. Not 4: the 'when' clause is fully explicit, not merely present.

5 / 5

Trigger Term Quality

Strong domain-natural terms ('cis-eQTL', 'eQTL Catalogue', 'eQTL beta / SE / p-value', 'window around a gene's TSS', 'study × tissue × quantification method') that a bioinformatician would naturally say, but common variations like 'eQTLs for a gene', 'summary stats', 'colocalisation', or cohort names like 'GTEx' are missing. Not 3: keyword coverage goes well beyond 'some relevant keywords'; not 5: a few natural synonyms are absent.

4 / 5

Distinctiveness Conflict Risk

The description carves a clear niche (one dataset, one region, tabix-on-FTP from EBI eQTL Catalogue v7+) that would not fire for sibling skills such as single-variant GTEx Portal lookups, UKB-PPP pQTL fetches, or fine-mapping posteriors. Not 4: overlap risk is minimal because the scope is narrowed to one (study × tissue × quantification method) regional fetch.

5 / 5

Total

19

/

20

Passed

Validation

93%

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

Validation — 15 / 16 Passed

Validation for skill structure

CriteriaDescriptionResult

metadata_field

'metadata' should map string keys to string values

Warning

Total

15

/

16

Passed

Repository

ClawBio/ClawBio

Path

skills/eqtl-catalogue-region-fetch/SKILL.md

Reviewed

Table of Contents

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