HolobiomicsLab · lfnothias · Jun 26, 2026 · Jun 26, 2026 · Jun 26, 2026 · Jun 26, 2026
@@ -1,6 +1,6 @@
 ---
-description: Synthesize a workflow-level super-skill from a pipeline seed — cluster the sub-skills, identify the canonical ordered pipeline, write the orchestration, tier it synthetic/super/hold, and stage a reviewable proposal PR (you never auto-merge — a maintainer merges after open curation).
-argument-hint: "[pipeline-name] [short-description] [collection-dir]"
+description: Synthesize a workflow-level super-skill from a pipeline seed — cluster the sub-skills, identify the canonical ordered pipeline, write the orchestration, tier it synthetic (or literature when grounded in a review DOI) / super / hold, and stage a reviewable proposal PR (you never auto-merge — a maintainer merges after open curation).
+argument-hint: "[pipeline-name] [short-description] [collection-dir] [--review-doi DOI]"
 ---
 You are auto-creating a **super-skill** — a workflow-level meta-skill that
 orchestrates several existing sub-skills (e.g. "molecular networking") — and
@@ -24,8 +24,12 @@ model), [`governance/PROVENANCE_TIERS.md`](../../../../governance/PROVENANCE_TIE
 meta-skills — this command generalizes them into a synthesizable, openly-curated rail.
 
 Inputs: `$ARGUMENTS` — the pipeline `name` (required), a short `description` of what
-the pipeline does (required), and the collection dir (default
-`collections/metabolomics/v2`).
+the pipeline does (required), the collection dir (default
+`collections/metabolomics/v2`), and an optional `--review-doi <DOI>`. Pass
+`--review-doi` **only** when the canonical pipeline is grounded in a real **review
+article** (a survey/tutorial that defines these stages): it flips the staged origin
+from `synthetic` (derived from the orchestrated skills) to `literature` (the review
+DOI is the source) — see step 4. Default (no review DOI) stays `synthetic`.
 
 Steps:
 
@@ -77,17 +81,23 @@ Steps:
      its source). This is genuine synthesis — write the real workflow, cite real
      slugs, don't fabricate.
 
-4. **Assemble the frontmatter (synthetic / super / hold).** Use the synthesizer's
-   `meta_frontmatter` — it reuses `normalize_skill.normalized_frontmatter` then
-   layers the super-skill invariants (`metadata.skill_kind="super"`,
+4. **Assemble the frontmatter (super / hold; synthetic or literature).** Use the
+   synthesizer's `meta_frontmatter` — it reuses `normalize_skill.normalized_frontmatter`
+   then layers the super-skill invariants (`metadata.skill_kind="super"`,
    `metadata.orchestrates`, `metadata.synthesized_from`), mirrors `related_skills`
-   onto the orchestrated slugs, and sets `provenance_tier="synthetic"`,
-   `status="hold"`:
+   onto the orchestrated slugs, and sets `status="hold"`. The origin depends on
+   whether you pass a **review DOI**:
+   - **default (no `review_doi`)** → `provenance_tier="synthetic"` (the pipeline is
+     derived from the orchestrated skills);
+   - **`review_doi="<DOI>"`** → `provenance_tier="literature"`, with
+     `metadata.dois=[<DOI>]` and `derived_from=[{doi:<DOI>}]` (the pipeline is grounded
+     in that review article). Only pass it for a real review/survey you can cite — the
+     proposals gate enforces *literature ⇒ ≥1 doi*; never fabricate a DOI.
    ```python
    from scripts.synthesize_meta_skill import meta_frontmatter
 
    orchestrates    = ["<stage-1-slug>", "<stage-2-slug>", ...]   # curated, ordered, real
-   synthesized_from = orchestrates + ["doi:10...."]              # sub-slugs (+ review DOIs if any)
+   synthesized_from = list(orchestrates)                         # the source sub-skill slugs
    tools_used       = ["<tool-slug>", ...]                       # from cluster["tools"]
 
    fm = meta_frontmatter(
@@ -97,6 +107,7 @@ Steps:
        synthesized_from=synthesized_from,
        tools_used=tools_used,
        license_tier="open",            # set from LICENSE_TIERS.md / the grounded tools
+       review_doi=None,                # or "10.xxxx/..." → literature-tier (review-grounded)
    )
    ```
 
@@ -134,9 +145,10 @@ Steps:
    ```
 
 7. **Validate what was staged** with the same gate CI runs — it enforces the
-   synthetic/super invariants (`synthesized_from` non-empty; `skill_kind ∈
-   {skill,super}`; for `super`, `orchestrates` non-empty and **every** orchestrated
-   slug resolves in `skills_index.json`), so the PR is green before any push:
+   provenance + super invariants (synthetic ⇒ `synthesized_from` non-empty;
+   literature ⇒ ≥1 `dois`; `skill_kind ∈ {skill,super}`; for `super`, `orchestrates`
+   non-empty and **every** orchestrated slug resolves in `skills_index.json`), so the
+   PR is green before any push:
    ```bash
    python -m scripts.check_proposals "<collection-dir>"
    ```

@@ -10,3 +10,6 @@ derived_from:
 source_repos:
 - NPLinker/nplinker
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
@@ -7,6 +7,9 @@ derived_from:
 - doi: 10.1371/journal.pcbi.1009021
   title: 'MiMeNet: Exploring microbiome-metabolome relationships using neural networks'
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
 techniques:
 - LC-MS
 - GC-MS

@@ -6,5 +6,8 @@ derived_from:
 - doi: 10.1021/acs.analchem.1c02687
   title: 'SLAW: A Scalable and Self-Optimizing Processing Workflow for Untargeted LC-MS'
 schema_version: 0.2.0
+license_tier: open
+license: GPL-2.0
+license_detection: github-api
 techniques:
 - LC-MS
@@ -10,6 +10,9 @@ derived_from:
 source_repos:
 - ShinyFabio/ADViSELipidomics
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
 techniques:
 - LC-MS
 - mass-spectrometry
@@ -9,5 +9,8 @@ derived_from:
 source_repos:
 - FrigerioGianfranco/GetFeatistics
 schema_version: 0.2.0
+license_tier: open
+license: GPL-3.0
+license_detection: github-api
 techniques:
 - LC-MS
@@ -10,6 +10,9 @@ derived_from:
 source_repos:
 - thepanlab/Aerith
 schema_version: 0.2.0
+license_tier: open
+license: GPL-3.0
+license_detection: github-api
 techniques:
 - LC-MS
 - ion-mobility-MS

@@ -6,5 +6,8 @@ derived_from:
 - doi: 10.1371/journal.pcbi.1009337
   title: 'INTEGRATE: Model-based multi-omics data integration to characterize multi-level metabolic regulation'
 schema_version: 0.2.0
+license_tier: open
+license: GPL-3.0
+license_detection: github-api
 techniques:
 - LC-MS
@@ -6,5 +6,8 @@ derived_from:
 - doi: 10.1371/journal.pcbi.1009337
   title: 'INTEGRATE: Model-based multi-omics data integration to characterize multi-level metabolic regulation'
 schema_version: 0.2.0
+license_tier: open
+license: GPL-3.0
+license_detection: github-api
 techniques:
 - LC-MS
@@ -11,6 +11,9 @@ derived_from:
 source_repos:
 - PNNL-Comp-Mass-Spec/PNNL-PreProcessor
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - GC-MS

@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - GarrettLab-UF/LipidMatch
 schema_version: 0.2.0
+license_tier: open
+license: CC-BY-4.0
+license_detection: license-file
 techniques:
 - LC-MS
 - direct-infusion-MS
@@ -6,6 +6,9 @@ derived_from:
 - doi: 10.1371/journal.pone.0306202
   title: uafr
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - GC-MS

@@ -7,6 +7,9 @@ derived_from:
 - doi: 10.1186/s12859-021-04490-0
   title: aird
 schema_version: 0.2.0
+license_tier: open
+license: MulanPSL-2.0
+license_detection: github-api
 techniques:
 - LC-MS
 - ion-mobility-MS

@@ -7,6 +7,9 @@ derived_from:
 - doi: 10.1186/s12859-021-04490-0
   title: aird
 schema_version: 0.2.0
+license_tier: open
+license: MulanPSL-2.0
+license_detection: github-api
 techniques:
 - LC-MS
 - ion-mobility-MS

@@ -7,6 +7,9 @@ derived_from:
 - doi: 10.1021/acs.jproteome.4c00873
   title: pyopenmsviz
 schema_version: 0.2.0
+license_tier: open
+license: BSD-3-Clause
+license_detection: github-api
 techniques:
 - LC-MS
 - ion-mobility-MS

@@ -6,6 +6,9 @@ derived_from:
 - doi: 10.1186/s13321-022-00613-8
   title: Probabilistic metabolite annotation using retention time prediction and meta-learned projections
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - mass-spectrometry
@@ -9,5 +9,8 @@ derived_from:
 source_repos:
 - mariallr/amanida
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - mass-spectrometry
@@ -26,6 +26,9 @@ source_repos:
 - zhanghailiangcsu/MSBERT
 - zhanghailiangcsu/MWFormer
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - GC-MS

@@ -10,6 +10,9 @@ derived_from:
 source_repos:
 - bittremieux-lab/ANN-SoLo
 schema_version: 0.2.0
+license_tier: open
+license: Apache-2.0
+license_detection: github-api
 techniques:
 - LC-MS
 - CE-MS

@@ -9,5 +9,8 @@ derived_from:
 source_repos:
 - chrboku/AnnoMe
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
 techniques:
 - LC-MS
@@ -22,6 +22,9 @@ source_repos:
 - NPLinker/nplinker
 - ablab/npdtools
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - direct-infusion-MS

@@ -7,3 +7,6 @@ derived_from:
 - doi: 10.1186/s13321-016-0115-9
   title: MetFrag
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
@@ -9,3 +9,6 @@ derived_from:
 source_repos:
 - eugenemel/maven
 schema_version: 0.2.0
+license_tier: open
+license: GPL-3.0
+license_detection: github-api
@@ -7,6 +7,9 @@ derived_from:
 - doi: 10.1021/acs.jproteome.5c00435
   title: 'mzPeak: Designing a Scalable, Interoperable, and Future-Ready Mass Spectrometry Data Format'
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - mass-spectrometry
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - Katherine00689/RapidMass
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - direct-infusion-MS
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - shuzhao-li-lab/asari
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: file-present-unclassified
 techniques:
 - LC-MS
 - GC-MS
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - shuzhao-li-lab/asari
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: file-present-unclassified
 techniques:
 - LC-MS
 - GC-MS
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - shuzhao-li-lab/asari
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: file-present-unclassified
 techniques:
 - LC-MS
 - GC-MS

@@ -13,6 +13,9 @@ derived_from:
 source_repos:
 - shuzhao-li-lab/asari
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: file-present-unclassified
 techniques:
 - LC-MS
 - GC-MS

@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - DasSusanta/snakemake_ccs
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - ion-mobility-MS

@@ -9,5 +9,8 @@ derived_from:
 source_repos:
 - GaelleLefort/ASICS
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - NMR
@@ -9,5 +9,8 @@ derived_from:
 source_repos:
 - connor-reid-tiffany/Omu
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - NMR
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - PNNL-Comp-Mass-Spec/AutoCCS
 schema_version: 0.2.0
+license_tier: open
+license: BSD-2-Clause
+license_detection: github-api
 techniques:
 - LC-MS
 - ion-mobility-MS
@@ -9,5 +9,8 @@ derived_from:
 source_repos:
 - KujawinskiLaboratory/Autotuner
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
 techniques:
 - mass-spectrometry
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - HuanLab/AVIR
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
 techniques:
 - LC-MS
 - GC-MS