asb-skill-collections

<p align="center"> <img src="assets/asb-logo.png" alt="AgenticScienceBuilder logo" width="120"> </p> # ASB Skill Collections [](collections/metabolomics/v2) [](collections/metabolomics/v2/skills_index.json) [](collections/metabolomics/v2/tools_index.json) [](LICENSE) [](LICENSING.md) [](https://doi.org/10.5281/zenodo.20794027) Curated, **evidence-grounded** skill and software-tool collections for scientific AI agents, generated by the [AgenticScienceBuilder](https://github.com/HolobiomicsLab/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](https://www.dagstuhl.de/en/seminars/seminar-calendar/seminar-details/26181), 26–30 April 2026). <p align="center"> <img src="assets/asb-overview.png" alt="ASB pipeline: real research papers → ASB → domain benchmark (skills · tools · data) → agents evaluated → community validates, with a domain/community-defined feedback loop" width="640"> </p> > **This release — `metabolomics-v0.1.0` (preliminary):** > [`collections/metabolomics/v2`](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 | Artifact | Status | |---|---| | **ASB-Skills** — evidence-grounded procedural skills | ✅ **released** | | **ASB-Tools** — deduplicated software-tool records (EDAM + DOIs) | ✅ **released** | | **ASB-Benchmark** — per-paper tasks + claim-retrieval test sets | ⏳ to be released soon | | **ASB-Capsules** — raw per-paper ASB pipeline outputs (full traceability) | ⏳ to be released soon | Only **ASB-Skills** and **ASB-Tools** are published now; the benchmark and capsule layers follow (see [PROVENANCE.md](collections/metabolomics/v2/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) ```bash /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 ```bash /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/](packs/metabolomics/README.md). ### 🌐 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](collections/metabolomics/v2/USAGE.md#chat-assistants-via-the-web-ui-claude--chatgpt--mistral). ### 🤖 Any other agent / IDE The collection is plain Markdown + JSON — point your agent at `collections/metabolomics/v2/` and read the indexes. See [AGENTS.md](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. ```bash 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): ```bash # 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): ```bash 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): ```bash 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](collections/metabolomics/v2/USAGE.md). ## 🔎 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](https://github.com/HolobiomicsLab/Perspicacite-AI)** — 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](collections/metabolomics/v2/USAGE.md). ## What's in the collection <p align="center"> <img src="assets/metabolomics-skills-collection.png" alt="Metabolomics skill collection schematic: peer-reviewed papers → ASB → EDAM-typed, deduplicated skills routed via Perspicacité (EDAM filter + skill KB, search_skill_kb) to a Mimosa agent, spanning the untargeted LC-MS/MS workflow and wrapping community tools (GNPS, XCMS, matchms, MS-DIAL, MZmine, SIRIUS, spec2vec)" width="760"> </p> <p align="center">_{The LC-MS view of the collection (the <code>metabolomics-lc-ms</code> pack): papers → ASB → EDAM-typed skills, routed by Perspicacité. The full release spans 5,865 skills across all techniques.}</p> | File | Contents | |---|---| | `skills/<slug>/SKILL.md` | one evidence-grounded skill each (frontmatter: EDAM IRIs, `derived_from` DOIs, `evidence_spans`, `tools`, `attribution`) | | `tools/<slug>.yaml` | deduplicated software-tool records with EDAM + source DOIs | | `skills_index.json` / `tools_index.json` | machine search indexes | | `kb_bundle.json` | skill → source-paper KB slugs **+ `repo_urls`** (grounding map) | | `bin/perspicacite_kb_bind.py` · `commands/ground.md` · `GROUNDING.md` | packaged grounding — the binder, the `/ground` command, and a how-to (shipped in every plugin & pack) | | `collection.yaml` · `corpus.yaml` | collection record · per-paper access basis (`repo-oa`) | | `CITATION.cff` · `PROVENANCE.md` · `gate_report.json` | citation · how it was generated · release-gate verdict | 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](collections/metabolomics/v2/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](collections/metabolomics/v2/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`](collections/metabolomics/v2/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](https://doi.org/10.5281/zenodo.20794027). ## Funding & acknowledgements This collaborative project was initiated at the Dagstuhl Seminar **Computational Metabolomics** ([26181](https://www.dagstuhl.de/en/seminars/seminar-calendar/seminar-details/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`](governance/SOURCES.md) for the source inventory and the scientific inclusion criteria, and [`governance/CONTENT_POLICY.md`](governance/CONTENT_POLICY.md) for the legal/open-access policy. **Suggest or annotate a paper:** see [Contributing → Propose or annotate a paper](.github/CONTRIBUTING.md#propose-or-annotate-a-paper). ## License Dual-licensed, by layer (see [LICENSING.md](LICENSING.md)): - **Code** (scripts, tooling) — [Apache-2.0](LICENSE). - **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](https://github.com/HolobiomicsLab) — see [MAINTAINERS.md](governance/MAINTAINERS.md). Curator workflow: [CONTRIBUTING.md](.github/CONTRIBUTING.md); conflict-of-interest policy: [COI_POLICY.md](governance/COI_POLICY.md). All governance & policy docs now live in [`governance/`](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](https://doi.org/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.