ASB Skill Collections

Curated, evidence-grounded skill and software-tool collections for scientific
AI agents, generated by the AgenticScienceBuilder
(ASB) pipeline. Each skill is distilled from a peer-reviewed method paper and its
public code repository, anchored to verbatim evidence, EDAM-annotated, and gated
for licensing/PII before release.

This is a community effort, initiated at the Dagstuhl Seminar Computational
Metabolomics (26181,
26–30 April 2026).

This release — metabolomics-v0.1.0 (preliminary):
collections/metabolomics/v2 — 5,865 skills
across 909 tools distilled from 568 papers, for computational
metabolomics — predominantly LC-MS/MS, but also LC-MS, GC-MS,
mass-spectrometry imaging, ion mobility and lipidomics, with some NMR and
multi-omics / statistics / pathway tools.

Artifacts in this release

Only ASB-Skills and ASB-Tools are published now; the benchmark and capsule
layers follow (see PROVENANCE.md).

Structure & roadmap

asb-skill-collections is a multi-domain marketplace — it hosts ASB-generated skill
collections for any scientific domain, organized by provenance (ASB-generated), not by
field, so the repo name and marketplace stay domain-agnostic as new domains are added:

collections/<domain>/<version>/    # full collection per domain   (e.g. metabolomics/v2)
packs/<domain>/<technique>/        # lighter per-technique subsets (e.g. metabolomics/lc-ms)

Each domain ships a full plugin (<domain>) plus per-technique packs (<domain>-<technique>).
Metabolomics is the first released collection; proteomics, transcriptomics, epigenomics and
further domains follow under the same layout — no rename, just new entries under
collections/ + marketplace.json.

📦 Install

[!TIP]
Fastest path — two lines in Claude Code: the full collection, or a lighter per-technique pack.

🚀 Claude Code (native plugin)

/plugin marketplace add HolobiomicsLab/asb-skill-collections
/plugin install metabolomics@asb-skill-collections          # full collection (5,865 skills)

🧩 Lighter per-technique packs — load only what you need

/plugin install metabolomics-lc-ms@asb-skill-collections    # also: gc-ms, nmr, ms-imaging,
                                                            # ion-mobility, ce-ms,
                                                            # direct-infusion, ms-generic

[!NOTE]
Packs overlap (a multi-technique skill appears in several) — install one full plugin or a few packs, not both. See packs/metabolomics/.

🌐 Web UI — Claude · ChatGPT · Mistral

No CLI: upload the search indexes +
the few skills you need as the assistant's knowledge (Claude Projects, ChatGPT
Custom GPT/Project, Mistral Agent/Library) and paste a routing instruction —
step-by-step in USAGE.md.

🤖 Any other agent / IDE

The collection is plain Markdown + JSON — point your
agent at collections/metabolomics/v2/ and read the indexes. See
AGENTS.md.

🌍 Install beyond Claude Code

Other agent runtimes have no /plugin install. Use the bundled asbb CLI from a
local clone to materialize a pack into the runtime's own location.

git clone https://github.com/HolobiomicsLab/asb-skill-collections.git
cd asb-skill-collections
python3 -m scripts.asbb_cli install --list-runtimes      # see all targets

Skill-native runtimes (read SKILL.md directly):

# Codex + Copilot CLI + Gemini CLI all share ~/.agents/skills — one install:
python3 -m scripts.asbb_cli install metabolomics-lc-ms --runtime agents

# Or a specific home: --runtime codex | copilot | gemini
# Vendor into a project for Claude Code: --runtime claude  (add --user for ~/.claude)

Rules/instruction IDEs (a SKILL.md is rendered into their format — run from
the target project):

python3 -m scripts.asbb_cli install metabolomics-lc-ms --runtime cursor          # .cursor/rules/*.mdc
python3 -m scripts.asbb_cli install metabolomics-lc-ms --runtime cline           # .clinerules/*.md
python3 -m scripts.asbb_cli install metabolomics-lc-ms --runtime vscode-copilot  # .github/instructions/*.instructions.md

Anything else (pi, Antigravity, or a runtime without a preset):

python3 -m scripts.asbb_cli install metabolomics-lc-ms --dest ~/some/skills/dir

Skill-native installs symlink by default (a git pull in the clone updates
them); add --copy for a self-contained copy. --dry-run previews, --force
overwrites unmanaged files, and asbb uninstall <pack> --runtime <id> cleanly
removes exactly what was installed (tracked in ~/.asbb/installed.json).

For Claude Code, the plugin marketplace above remains the recommended path.

Use

Search → apply → ground. Find a skill via skills_index.json (by EDAM IRI,
tool name, or keyword) or tools_index.json; read its SKILL.md and follow the
procedure; then optionally ground it against the source paper/repo to verify a
parameter or claim — see the 🔎 Grounding (Perspicacité) section below.
Requirements (libraries, per-skill tool deps) are in USAGE §0.

🔎 Grounding (Perspicacité)

Skills carry distilled procedure; to verify an exact parameter, threshold, or claim,
ground a skill against the paper it was distilled from. Grounding is optional and
additive — every skill works without it — and ships inside every plugin and pack.

It's powered by Perspicacité —
Holobiomics Lab's local-first scientific literature-RAG engine. Two backends, KB-primary
with a serverless fallback:

• kb (Perspicacité) — RAG over the source paper's full text + supplementary
  information, persistent and citable. The per-paper KB (asb-paper-<doi>) is auto-created
  and ingested on first use via the MCP tools ensure_kb / ground_paper.
• local (serverless) — no server: git clone the skill's source repo + best-effort
  open-access paper, then read the files directly.

Use it

• In Claude Code: run /ground on the skill in play — it installs + queries the
  source KB, or falls back to a local clone when no server is running.
• Anywhere: call the bundled bin/perspicacite_kb_bind.py (prepare / query / local).

[!TIP]
Recommended before you act on a numeric parameter, threshold, or quantitative claim —
it's the difference between "the skill says ~5 ppm" and "the paper specifies 5 ppm."

The kb backend needs a reachable Perspicacité (PERSPICACITE_BASE, default
http://127.0.0.1:8000); the local backend needs only git + network. Full guide:
USAGE.md §4.

What's in the collection

_{The LC-MS view of the collection (the metabolomics-lc-ms pack): papers → ASB → EDAM-typed skills, routed by Perspicacité. The full release spans 5,865 skills across all techniques.}

The default entry point is skills/_router/SKILL.md.

For a description of the collection's content (technique & EDAM-topic breakdown)
and how it was selected (sources, inclusion/exclusion criteria, grounding,
gating), see ABOUT.md.

How it was generated

The exact ASB build command and the mixed-model routing (Opus 4.8 for
outline/card-revision, Haiku 4.5 for the rest, OpenAI embeddings) are documented
in PROVENANCE.md, recorded per build
in build_manifest.json. The raw per-paper ASB capsules and the benchmark
layer (full end-to-end traceability) will be released later.

Attribution & citation

If you use this collection, cite both the collection and the original
paper behind each skill you use (attribution.original_doi).

• Collection authors (Zenodo, see CITATION.cff):
  AgenticScienceBuilder Community, Louis-Félix Nothias, HolobiomicsLab.cnrs.fr, MetaboLinkAI.net.
• Per-skill roles (in each SKILL.md attribution: block): generator
  (the ASB pipeline) · curators (who modify/validate — none yet) · promoter
  (suggests use — Louis-Félix Nothias) · sponsor (paid the API cost — CNRS &
  Université Côte d'Azur) · original_doi (source paper).
• Zenodo DOI: 10.5281/zenodo.20794027.

Funding & acknowledgements

This collaborative project was initiated at the Dagstuhl Seminar Computational
Metabolomics (26181,
26–30 April 2026), and we thank the seminar's participants and organizers.
API generation costs for this collection were sponsored by CNRS and
Université Côte d'Azur. Built with the AgenticScienceBuilder pipeline and
grounded with Perspicacité (Holobiomics Lab).

📚 Sources & provenance

Skills are distilled from peer-reviewed method papers anchored to the
computational metabolomics review series (Misra → Enveda). See
governance/SOURCES.md for the source inventory and the
scientific inclusion criteria, and governance/CONTENT_POLICY.md
for the legal/open-access policy.

Suggest or annotate a paper: see
Contributing → Propose or annotate a paper.

License

Dual-licensed, by layer (see LICENSING.md):

• Code (scripts, tooling) — Apache-2.0.
• Collection content (skill descriptions, tool records, structured metadata) —
  CC-BY-4.0 (as stamped in every SKILL.md, collection.yaml, CITATION.cff).
• Verbatim quotations from source papers (evidence_spans) — minimal,
  attributed, under fair-use / quotation right; a rights holder may request removal.

Maintainers & contributing

Maintained by Holobiomics Lab — see
MAINTAINERS.md. Curator workflow: CONTRIBUTING.md;
conflict-of-interest policy: COI_POLICY.md. All governance & policy
docs now live in governance/.

Other collections

collections/ also contains epigenomics/v1, transcriptomics/v1, and the
earlier metabolomics/v1. These are staged/internal and not part of this
release — only metabolomics/v2 is published via the plugin.

Status & caveats

• Zenodo DOI — 10.5281/zenodo.20794027.
• w3id.org/holobiomicslab/… IRIs — reserved identifiers that do not
  resolve yet (the redirect is not live); treat as stable names, not links.
• HuggingFace mirror & leaderboard — planned, not yet live.
• Benchmark / capsules — to be released later.