Getting it into your agent
One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.
npx skills add bigbio/sdrf-skills --skill sdrf-celllinegit clone --depth 1 https://github.com/bigbio/sdrf-skillsWrote this? Show the measurements
A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.
[](https://agentmods.dev/skills/bigbio/sdrf-skills/sdrf-cellline)<a href="https://agentmods.dev/skills/bigbio/sdrf-skills/sdrf-cellline"><img src="https://agentmods.dev/badge/skills/bigbio/sdrf-skills/sdrf-cellline/github.svg" alt="Measured on agentmods" height="20"></a>Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.
<a href="https://agentmods.dev/skills/bigbio/sdrf-skills/sdrf-cellline"><img src="https://agentmods.dev/badge/skills/bigbio/sdrf-skills/sdrf-cellline.svg" alt="Reviewed on agentmods" width="80" height="20"></a>- NVIDIA SkillSpector warn
SkillSpector: 6 findings, up to medium
These are SkillSpector’s own severities. On a checked sample its high-severity flags on skills were ~96% false positives — a documented command, a public API, a “never do X” rule — so we show them as a caution to read, not a verdict. Why →
- medium Data Exfiltration · line 22 Data is being sent to an external URL. This could be legitimate telemetry or data exfiltration. Manual review is recommended.Fix: Verify the destination URL is trusted and necessary. Remove or replace with documented APIs. Ensure no secrets, tokens, or PII are transmitted.
- medium Data Exfiltration · line 23 Data is being sent to an external URL. This could be legitimate telemetry or data exfiltration. Manual review is recommended.Fix: Verify the destination URL is trusted and necessary. Remove or replace with documented APIs. Ensure no secrets, tokens, or PII are transmitted.
- medium Data Exfiltration · line 93 Data is being sent to an external URL. This could be legitimate telemetry or data exfiltration. Manual review is recommended.Fix: Verify the destination URL is trusted and necessary. Remove or replace with documented APIs. Ensure no secrets, tokens, or PII are transmitted.
- medium Data Exfiltration · line 96 Data is being sent to an external URL. This could be legitimate telemetry or data exfiltration. Manual review is recommended.Fix: Verify the destination URL is trusted and necessary. Remove or replace with documented APIs. Ensure no secrets, tokens, or PII are transmitted.
- medium Data Exfiltration · line 97 Data is being sent to an external URL. This could be legitimate telemetry or data exfiltration. Manual review is recommended.Fix: Verify the destination URL is trusted and necessary. Remove or replace with documented APIs. Ensure no secrets, tokens, or PII are transmitted.
- medium Data Exfiltration · line 100 Data is being sent to an external URL. This could be legitimate telemetry or data exfiltration. Manual review is recommended.Fix: Verify the destination URL is trusted and necessary. Remove or replace with documented APIs. Ensure no secrets, tokens, or PII are transmitted.
What it costs to keep this loaded
Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.
| Model | Per session | Once invoked |
|---|---|---|
| Fable 5.1 | $0.00082 | $0.04111 |
| Opus 5 | $0.00041 | $0.02056 |
| Sonnet 5 | $0.00016 | $0.00822 |
| Haiku 4.5 | $0.00008 | $0.00411 |
Grade A, and why
sdrf-cellline scanned grade A with 1 finding against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 4d ago.
A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.
Makes network callslowCapability
Not a fault in itself. Listed so you know the mod talks to something, and to what.
curl -sSLO https://ftp.expasy.org/databases/cellosaurus/cellosaurus.txt How it starts
The opening of the file, as written. The whole thing — 317 lines — stays where its author put it; the contents beside it link to each section on GitHub.
SDRF Cell Line Annotation
You are translating cell line identity into the SDRF columns required by the
cell-lines template. The source of truth is Cellosaurus (SIB / Expasy) —
it is not hosted on EBI OLS, so this skill queries Cellosaurus directly. OLS
is still used for the target ontologies the SDRF columns reference
(NCBITaxon, MONDO, UBERON, HANCESTRO, CLO/BTO/EFO). This skill encodes the
rules for the translation — it does not ship a local database.
Cellosaurus access
| Mode | Endpoint / file | Notes |
|---|---|---|
| Web (browse) | https://www.cellosaurus.org/<CVCL_id> |
Human-readable record. |
| REST API (JSON) | https://api.cellosaurus.org/cell-line/<CVCL_id>?format=json |
Single-entry fetch; preferred for accession lookups. |
| REST search | https://api.cellosaurus.org/search/cell-line?q=<query>&format=json |
Free-text / field-qualified search (id:HeLa, sy:HeLa-S3). |
| Bulk download | https://ftp.expasy.org/databases/cellosaurus/cellosaurus.txt (flat) https://ftp.expasy.org/databases/cellosaurus/cellosaurus.obo (OBO) https://ftp.expasy.org/databases/cellosaurus/cellosaurus.xml (XML) |
Offline / batch use only. Re-download monthly to stay current. |
Use the REST API by default. Drop to the bulk file only when the user asks for offline mode or needs to enrich many SDRFs in one pass.
When to Use
- A single cell line lookup ("What is HeLa?" / "Look up CVCL_0030").
- Enriching an SDRF where
characteristics[cell line]is filled but the Cellosaurus-derivable columns (organism, disease, sampling site, sex, ancestry, age, developmental stage, cellosaurus accession/name) are blank, generic, or inconsistent. - Resolving ambiguous cell line names raised by
/sdrf-skills:sdrf-annotate,/sdrf-skills:sdrf-validate, or/sdrf-skills:sdrf-fix.
For pure ontology-term lookup unrelated to cell lines, use /sdrf-skills:sdrf-knowledge.
Step 0: Identify the cell-lines template requirements
Always read the template first — column names, requirement levels, and target ontologies must come from the spec, never from memory.
What this file has done since we first saw it
Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.
- 4d ago Changed · -1 tokens per session dde13c54bae0
- 10d ago First seen · 317 lines · 83 tokens per session scan A 85afb85b4f52
sdrf-cellline is a skill published in the GitHub repository bigbio/sdrf-skills (18 stars, last pushed 4d ago), licensed MIT. It adds 82 tokens to every session and 4,111 once invoked, about $0.0004 per session on Opus 5. A static security scan graded it A with 1 finding (makes network calls). No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-30.
Other skills, from other repositories
uniprot-query
Query UniProt database for protein sequences, metadata, and search by criteria. Use this skill when: (1) Looking up protein information by UniProt accession ID, (2) Searching proteins by gene name, organism, function, or disease, (3) Retrieving comprehensive protein metadata including domains, PTMs, and annotations.
proteomics-de
Load when computing two-group differential protein abundance (group2 vs group1, log2FC + p-value + BH-adjusted FDR) via Welch t-test, equal-variance t-test, or Mann-Whitney on a wide protein × sample CSV. Skip when you need multi-condition DE (run pairwise contrasts manually); label-based TMT linear-mixed models.
proteomics-enrichment
Load when running over-representation analysis (ORA) on a list of proteins via Fisher's exact test against a built-in 8-pathway DEMO dictionary, with BH-FDR correction. Skip when needing a real pathway database (this skill is demo-only) (use bulkrna-enrichment); rank-based GSEA.
proteomics-ptm
Load when summarising PTM sites (phosphorylation, acetylation, ubiquitination, etc.) from a per-site CSV — site-class assignment (Olsen et al. Class I/II/III by localizationprobability), per-PTM-type counts, amino-acid distribution, sites-per-protein. Skip when raw spectra are the input; you only need protein-level…
proteomics-quantification
Load when computing per-protein abundance from a peptide / PSM table via LFQ (intensity summation), iBAQ (intensity / tryptic peptide count), or spectral counting (PSMs per protein). Skip when the input is already protein-level (use proteomics-ms-qc); label-based TMT / iTRAQ workflows (search upstream first).
proteomics-structural
Load when summarising cross-linking MS (XL-MS) results — intra/inter-protein link split, optional FDR filtering, distance-constraint validation against a per-crosslinker (DSS / BS3 / EDC / DSSO / DSBU) max distance. Skip when raw spectra are the input (run XlinkX / pLink / xiSEARCH first); no XL-MS experiment was…