From 9be119925a3ecf2dcd0554217114995dce4aae4d Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Louis-F=C3=A9lix=20Nothias?= <louis-felix.nothias@cnrs.fr>
Date: Fri, 26 Jun 2026 17:21:45 -0300
Subject: [PATCH 1/3] feat(tools): per-tool YAML license enrichment (#4)

Propagate license_tier/license/license_detection from tools_index.json into
the 909 tools/<slug>.yaml LinkML records, schema-correctly.

- scripts/enrich_tool_yaml.py: tier_map(tools_index) -> per-slug license rows;
  enrich(collection_dir) joins by slug and writes the three fields right after
  schema_version (idempotent, _yaml_dump style-preserving, no git/network).
- asb_skill_bundle.yaml: vendor the LinkML schema at repo root (where
  validate.yml gate 1 expects it) and add optional license_tier/license/
  license_detection slots to the ASBTool class + a LicenseTierEnum
  {open,noncommercial,restricted}. Verified: ASBTool instances with the new
  fields validate clean and an invalid tier is rejected; the gate's result on
  collection.yaml is unchanged.
- check_tools_index.check_collection: cross-check each tools/<slug>.yaml
  license_tier == its tools_index license_tier (tools without a yaml skipped).
- Ran on collections/metabolomics/v2: 909 enriched, 0 mismatches
  (511 open / 389 restricted / 9 noncommercial); re-run is a byte-stable no-op.

Tests: 19 new (enrich + cross-check), full suite 397 passed.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 asb_skill_bundle.yaml                         | 639 ++++++++++++++++++
 .../v2/tools/10-5281-zenodo-4680579.yaml      |   3 +
 .../metabolomics/v2/tools/adam-optimizer.yaml |   3 +
 collections/metabolomics/v2/tools/adap.yaml   |   3 +
 .../v2/tools/adviselipidomics.yaml            |   3 +
 collections/metabolomics/v2/tools/aer.yaml    |   3 +
 collections/metabolomics/v2/tools/aerith.yaml |   3 +
 .../agilent-1290-infinity-uhplc-system.yaml   |   3 +
 ...-6550-ifunnel-q-tof-mass-spectrometer.yaml |   3 +
 .../v2/tools/agilent-masshunter.yaml          |   3 +
 .../v2/tools/agilent-q-tof-uhplc-hrms-ms.yaml |   3 +
 .../v2/tools/agilent-unknowns-analysis.yaml   |   3 +
 .../metabolomics/v2/tools/airdpro-v5.yaml     |   3 +
 .../metabolomics/v2/tools/airdpro-v6.yaml     |   3 +
 .../metabolomics/v2/tools/alphatims.yaml      |   3 +
 .../metabolomics/v2/tools/alvadesc.yaml       |   3 +
 .../metabolomics/v2/tools/amanida.yaml        |   3 +
 .../metabolomics/v2/tools/anaconda.yaml       |   3 +
 .../metabolomics/v2/tools/ann-solo.yaml       |   3 +
 collections/metabolomics/v2/tools/annome.yaml |   3 +
 .../metabolomics/v2/tools/antismash.yaml      |   3 +
 .../v2/tools/apache-maven-3-8.yaml            |   3 +
 .../metabolomics/v2/tools/appveyor.yaml       |   3 +
 collections/metabolomics/v2/tools/arrow.yaml  |   3 +
 .../metabolomics/v2/tools/asap-ms.yaml        |   3 +
 ...nctions-module-nn-cluster-by-mz-seeds.yaml |   3 +
 ...ild-grid-by-centroiding-bin-track-mzs.yaml |   3 +
 .../v2/tools/asari-peaks-module.yaml          |   3 +
 collections/metabolomics/v2/tools/asari.yaml  |   3 +
 .../metabolomics/v2/tools/ase-ani.yaml        |   3 +
 collections/metabolomics/v2/tools/asics.yaml  |   3 +
 .../v2/tools/assign-hierarchy.yaml            |   3 +
 .../metabolomics/v2/tools/autoccs.yaml        |   3 +
 .../metabolomics/v2/tools/autotuner.yaml      |   3 +
 collections/metabolomics/v2/tools/avir-r.yaml |   3 +
 .../metabolomics/v2/tools/aws-cli.yaml        |   3 +
 collections/metabolomics/v2/tools/bago.yaml   |   3 +
 collections/metabolomics/v2/tools/bam.yaml    |   3 +
 collections/metabolomics/v2/tools/bart.yaml   |   3 +
 .../metabolomics/v2/tools/base64enc.yaml      |   3 +
 .../v2/tools/basicevaluationengine.yaml       |   3 +
 .../benjamini-hochberg-fdr-correction.yaml    |   3 +
 .../metabolomics/v2/tools/big-scape.yaml      |   3 +
 .../metabolomics/v2/tools/big-slice.yaml      |   3 +
 .../metabolomics/v2/tools/bigscape.yaml       |   3 +
 .../metabolomics/v2/tools/biobase.yaml        |   3 +
 .../metabolomics/v2/tools/biocmanager.yaml    |   3 +
 .../metabolomics/v2/tools/bioconda.yaml       |   3 +
 .../metabolomics/v2/tools/bioconductor.yaml   |   3 +
 .../metabolomics/v2/tools/biocparallel.yaml   |   3 +
 .../v2/tools/bioinformatic-toolbox.yaml       |   3 +
 .../metabolomics/v2/tools/biosynfoni.yaml     |   3 +
 .../metabolomics/v2/tools/biotransformer.yaml |   3 +
 .../v2/tools/biotransformerapi.yaml           |   3 +
 .../metabolomics/v2/tools/biotranslator.yaml  |   3 +
 .../v2/tools/bitterpredict-m.yaml             |   3 +
 .../metabolomics/v2/tools/bitterpredict.yaml  |   3 +
 collections/metabolomics/v2/tools/black.yaml  |   3 +
 collections/metabolomics/v2/tools/blast.yaml  |   3 +
 collections/metabolomics/v2/tools/bmxp.yaml   |   3 +
 collections/metabolomics/v2/tools/bokeh.yaml  |   3 +
 .../metabolomics/v2/tools/bridgedb.yaml       |   3 +
 .../v2/tools/bruker-q-tof-uhplc-hrms-ms.yaml  |   3 +
 .../metabolomics/v2/tools/bruker-solarix.yaml |   3 +
 collections/metabolomics/v2/tools/c.yaml      |   3 +
 .../metabolomics/v2/tools/calculator.yaml     |   3 +
 collections/metabolomics/v2/tools/camera.yaml |   3 +
 .../canonical-correlation-analysis-cca.yaml   |   3 +
 .../metabolomics/v2/tools/canopus.yaml        |   3 +
 .../metabolomics/v2/tools/cardinal.yaml       |   3 +
 .../metabolomics/v2/tools/cardinalio.yaml     |   3 +
 collections/metabolomics/v2/tools/caret.yaml  |   3 +
 .../metabolomics/v2/tools/casanovo.yaml       |   3 +
 .../cca-canonical-correlation-analysis.yaml   |   3 +
 .../metabolomics/v2/tools/centwave.yaml       |   3 +
 collections/metabolomics/v2/tools/cfm-id.yaml |   3 +
 collections/metabolomics/v2/tools/cfmid.yaml  |   3 +
 ...kyline-i-agree-to-the-vendor-licenses.yaml |   3 +
 collections/metabolomics/v2/tools/chebi.yaml  |   3 +
 .../v2/tools/chem-spectra-app.yaml            |   3 +
 .../metabolomics/v2/tools/chemecho.yaml       |   3 +
 .../v2/tools/chemicalmixturefrommzml.yaml     |   3 +
 .../tools/chemistry-development-kit-cdk.yaml  |   3 +
 .../metabolomics/v2/tools/chemminer.yaml      |   3 +
 .../metabolomics/v2/tools/chemparse.yaml      |   3 +
 .../metabolomics/v2/tools/chemprop-ir.yaml    |   3 +
 .../metabolomics/v2/tools/chemprop.yaml       |   3 +
 .../metabolomics/v2/tools/chemspider.yaml     |   3 +
 collections/metabolomics/v2/tools/cir.yaml    |   3 +
 .../metabolomics/v2/tools/classyfire.yaml     |   3 +
 .../metabolomics/v2/tools/cliquems.yaml       |   3 +
 .../metabolomics/v2/tools/clumsid.yaml        |   3 +
 .../metabolomics/v2/tools/clumsiddata.yaml    |   3 +
 .../v2/tools/clusterprofiler.yaml             |   3 +
 ...apy-for-optgpsampler-uniform-sampling.yaml |   3 +
 .../tools/cobrapy-optgpsampler-algorithm.yaml |   3 +
 .../metabolomics/v2/tools/cobrapy.yaml        |   3 +
 .../metabolomics/v2/tools/coconut.yaml        |   3 +
 .../v2/tools/cohen-s-kappa-metric.yaml        |   3 +
 .../v2/tools/color-jitter-augmentation.yaml   |   3 +
 collections/metabolomics/v2/tools/combat.yaml |   3 +
 collections/metabolomics/v2/tools/commit.yaml |   3 +
 .../metabolomics/v2/tools/commons-math3.yaml  |   3 +
 .../metabolomics/v2/tools/comparador.yaml     |   3 +
 .../metabolomics/v2/tools/comparems2.yaml     |   3 +
 .../metabolomics/v2/tools/complexheatmap.yaml |   3 +
 .../v2/tools/compound-discoverer.yaml         |   3 +
 collections/metabolomics/v2/tools/conda.yaml  |   3 +
 .../v2/tools/consensus-clustering.yaml        |   3 +
 ...based-stoichiometric-metabolic-models.yaml |   3 +
 .../v2/tools/converterbuilder.yaml            |   3 +
 .../convolutional-neural-network-cnn.yaml     |   3 +
 .../tools/convolutional-neural-network.yaml   |   3 +
 .../metabolomics/v2/tools/cordbat.yaml        |   3 +
 collections/metabolomics/v2/tools/corems.yaml |   3 +
 .../tools/cosine-neutral-loss-repository.yaml |   3 +
 .../v2/tools/cosine-neutral-loss.yaml         |   3 +
 .../metabolomics/v2/tools/cox-nnet.yaml       |   3 +
 collections/metabolomics/v2/tools/cox-ph.yaml |   3 +
 collections/metabolomics/v2/tools/cpat.yaml   |   3 +
 collections/metabolomics/v2/tools/crest.yaml  |   3 +
 .../metabolomics/v2/tools/csi-fingerid.yaml   |   3 +
 collections/metabolomics/v2/tools/cts.yaml    |   3 +
 .../metabolomics/v2/tools/cuda-toolkit.yaml   |   3 +
 collections/metabolomics/v2/tools/cuda.yaml   |   3 +
 collections/metabolomics/v2/tools/cudnn.yaml  |   3 +
 collections/metabolomics/v2/tools/curl.yaml   |   3 +
 .../metabolomics/v2/tools/cyclobranch.yaml    |   3 +
 .../metabolomics/v2/tools/cypreact.yaml       |   3 +
 .../metabolomics/v2/tools/cyproduct.yaml      |   3 +
 .../metabolomics/v2/tools/cytoscape-js.yaml   |   3 +
 .../metabolomics/v2/tools/cytoscape.yaml      |   3 +
 collections/metabolomics/v2/tools/d3-js.yaml  |   3 +
 .../metabolomics/v2/tools/data-table.yaml     |   3 +
 collections/metabolomics/v2/tools/dbdipy.yaml |   3 +
 collections/metabolomics/v2/tools/dbnorm.yaml |   3 +
 ...or-equivalent-tree-based-ml-framework.yaml |   3 +
 .../metabolomics/v2/tools/decometdia.yaml     |   3 +
 .../metabolomics/v2/tools/deepmass2.yaml      |   3 +
 collections/metabolomics/v2/tools/deimos.yaml |   3 +
 .../metabolomics/v2/tools/deoptim.yaml        |   3 +
 .../metabolomics/v2/tools/depthcharge.yaml    |   3 +
 .../metabolomics/v2/tools/dereplicator.yaml   |   3 +
 collections/metabolomics/v2/tools/deseq2.yaml |   3 +
 .../metabolomics/v2/tools/devtools.yaml       |   3 +
 collections/metabolomics/v2/tools/dgl.yaml    |   3 +
 collections/metabolomics/v2/tools/di-ms.yaml  |   3 +
 collections/metabolomics/v2/tools/dia-nn.yaml |   3 +
 .../metabolomics/v2/tools/diffspectra.yaml    |   3 +
 .../metabolomics/v2/tools/dimorphite-dl.yaml  |   3 +
 collections/metabolomics/v2/tools/django.yaml |   3 +
 .../metabolomics/v2/tools/docker-compose.yaml |   3 +
 .../v2/tools/docker-desktop-for-mac.yaml      |   3 +
 ...build-docker-inspect-docker-system-df.yaml |   3 +
 .../metabolomics/v2/tools/docker-engine.yaml  |   3 +
 collections/metabolomics/v2/tools/docker.yaml |   3 +
 ...le-multi-stage-build-with-target-flag.yaml |   3 +
 .../metabolomics/v2/tools/doparallel.yaml     |   3 +
 collections/metabolomics/v2/tools/dplyr.yaml  |   3 +
 collections/metabolomics/v2/tools/dropms.yaml |   3 +
 .../v2/tools/drugbank-extraction-py.yaml      |   3 +
 .../metabolomics/v2/tools/drugbank.yaml       |   3 +
 collections/metabolomics/v2/tools/dures.yaml  |   3 +
 .../metabolomics/v2/tools/dynaconf.yaml       |   3 +
 .../v2/tools/dynamic-time-warping-dtw.yaml    |   3 +
 .../metabolomics/v2/tools/dynamictreecut.yaml |   3 +
 collections/metabolomics/v2/tools/edger.yaml  |   3 +
 collections/metabolomics/v2/tools/eflux.yaml  |   3 +
 .../v2/tools/elastic-net-regression.yaml      |   3 +
 .../metabolomics/v2/tools/elastic-net.yaml    |   3 +
 .../metabolomics/v2/tools/elemcor.yaml        |   3 +
 .../metabolomics/v2/tools/elementtree.yaml    |   3 +
 .../metabolomics/v2/tools/email-service.yaml  |   3 +
 .../metabolomics/v2/tools/emperor.yaml        |   3 +
 collections/metabolomics/v2/tools/enpkg.yaml  |   3 +
 .../metabolomics/v2/tools/entropy-search.yaml |   3 +
 ...ry-model-code-and-pre-trained-weights.yaml |   3 +
 .../metabolomics/v2/tools/envipat.yaml        |   3 +
 .../metabolomics/v2/tools/environment.yaml    |   3 +
 .../metabolomics/v2/tools/excalibur.yaml      |   3 +
 .../metabolomics/v2/tools/expressionset.yaml  |   3 +
 .../metabolomics/v2/tools/factoextra.yaml     |   3 +
 collections/metabolomics/v2/tools/falcon.yaml |   3 +
 collections/metabolomics/v2/tools/fastqc.yaml |   3 +
 .../v2/tools/featurefindermetabo.yaml         |   3 +
 collections/metabolomics/v2/tools/fella.yaml  |   3 +
 collections/metabolomics/v2/tools/fgsea.yaml  |   3 +
 collections/metabolomics/v2/tools/fiddle.yaml |   3 +
 .../metabolomics/v2/tools/figshare.yaml       |   3 +
 .../v2/tools/filtering-augmentation.yaml      |   3 +
 collections/metabolomics/v2/tools/fimo.yaml   |   3 +
 .../v2/tools/fisher-s-exact-test.yaml         |   3 +
 collections/metabolomics/v2/tools/flake8.yaml |   3 +
 collections/metabolomics/v2/tools/flask.yaml  |   3 +
 .../tools/flux-variability-analysis-fva.yaml  |   3 +
 .../v2/tools/flux-variability-analysis.yaml   |   3 +
 collections/metabolomics/v2/tools/fmcsr.yaml  |   3 +
 collections/metabolomics/v2/tools/fnicm.yaml  |   3 +
 .../metabolomics/v2/tools/foodmasst.yaml      |   3 +
 .../metabolomics/v2/tools/formularity.yaml    |   3 +
 collections/metabolomics/v2/tools/freda.yaml  |   3 +
 .../metabolomics/v2/tools/future-apply.yaml   |   3 +
 collections/metabolomics/v2/tools/future.yaml |   3 +
 .../v2/tools/galaxy-genomics-framework.yaml   |   3 +
 collections/metabolomics/v2/tools/galaxy.yaml |   3 +
 collections/metabolomics/v2/tools/gcims.yaml  |   3 +
 collections/metabolomics/v2/tools/gensim.yaml |   3 +
 .../v2/tools/geodesic-interpolate.yaml        |   3 +
 collections/metabolomics/v2/tools/george.yaml |   3 +
 .../metabolomics/v2/tools/get-models-sh.yaml  |   3 +
 .../v2/tools/get-precmz-prodmz.yaml           |   3 +
 .../metabolomics/v2/tools/getfeatistics.yaml  |   3 +
 collections/metabolomics/v2/tools/ggplot.yaml |   3 +
 .../metabolomics/v2/tools/ggplot2.yaml        |   3 +
 collections/metabolomics/v2/tools/git.yaml    |   3 +
 .../github-actions-workflow-ci-build-yml.yaml |   3 +
 .../metabolomics/v2/tools/github-actions.yaml |   3 +
 ...b-com-bittremieux-cosine-neutral-loss.yaml |   3 +
 .../v2/tools/github-com-hassounlab-esp.yaml   |   3 +
 .../github-com-jlichtarge-pcaglasso.yaml      |   3 +
 .../github-com-wanluliulab-spatialmeta.yaml   |   3 +
 .../v2/tools/github-com-zsspython-lagf.yaml   |   3 +
 .../v2/tools/github-kbseah-mass2adduct.yaml   |   3 +
 collections/metabolomics/v2/tools/github.yaml |   3 +
 collections/metabolomics/v2/tools/gitlab.yaml |   3 +
 collections/metabolomics/v2/tools/gleams.yaml |   3 +
 .../metabolomics/v2/tools/gnps-gc.yaml        |   3 +
 .../gnps-lcms-visualization-dashboard.yaml    |   3 +
 .../metabolomics/v2/tools/gnps-masst.yaml     |   3 +
 .../v2/tools/gnps-molecular-networking.yaml   |   3 +
 .../v2/tools/gnps-spectral-libraries.yaml     |   3 +
 ...ctral-networking-molecular-networking.yaml |   3 +
 collections/metabolomics/v2/tools/gnps.yaml   |   3 +
 collections/metabolomics/v2/tools/gnps2.yaml  |   3 +
 .../metabolomics/v2/tools/gnuplot.yaml        |   3 +
 .../metabolomics/v2/tools/google-chrome.yaml  |   3 +
 .../metabolomics/v2/tools/google-colab.yaml   |   3 +
 .../v2/tools/google-colaboratory.yaml         |   3 +
 ...ework-pytorch-geometric-or-equivalent.yaml |   3 +
 .../v2/tools/graphical-time-warping-gtw.yaml  |   3 +
 .../metabolomics/v2/tools/graphormer.yaml     |   3 +
 collections/metabolomics/v2/tools/grid.yaml   |   3 +
 .../metabolomics/v2/tools/gunicorn.yaml       |   3 +
 collections/metabolomics/v2/tools/gx-fba.yaml |   3 +
 collections/metabolomics/v2/tools/h2o.yaml    |   3 +
 .../metabolomics/v2/tools/h5py-2-7-1.yaml     |   3 +
 collections/metabolomics/v2/tools/h5py.yaml   |   3 +
 collections/metabolomics/v2/tools/hacca.yaml  |   3 +
 .../metabolomics/v2/tools/hassounlab-bam.yaml |   3 +
 ...r-library-h5py-h5netcdf-or-equivalent.yaml |   3 +
 collections/metabolomics/v2/tools/hdf5.yaml   |   3 +
 .../metabolomics/v2/tools/hdf5plugin.yaml     |   3 +
 ...g-euclidean-distance-complete-linkage.yaml |   3 +
 .../v2/tools/hineslab-moccal.yaml             |   3 +
 collections/metabolomics/v2/tools/hmdb-4.yaml |   3 +
 collections/metabolomics/v2/tools/hmdb.yaml   |   3 +
 .../metabolomics/v2/tools/hnswlib.yaml        |   3 +
 .../metabolomics/v2/tools/homebrew.yaml       |   3 +
 collections/metabolomics/v2/tools/hruv.yaml   |   3 +
 collections/metabolomics/v2/tools/html.yaml   |   3 +
 .../metabolomics/v2/tools/htseq-v-0-6-1.yaml  |   3 +
 ...https-doi-org-10-5281-zenodo-11243781.yaml |   3 +
 ...ttps-github-com-emosca-cnr-margherita.yaml |   3 +
 .../https-github-com-sdrogers-nplinker.yaml   |   3 +
 .../https-github-com-shuzhao-li-asari.yaml    |   3 +
 .../v2/tools/hugging-face-transformers.yaml   |   3 +
 .../tools/human-metabolome-database-hmdb.yaml |   3 +
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 .../metabolomics/v2/tools/i-van-krevelen.yaml |   3 +
 .../metabolomics/v2/tools/iceberg-model.yaml  |   3 +
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 collections/metabolomics/v2/tools/idsm.yaml   |   3 +
 collections/metabolomics/v2/tools/igraph.yaml |   3 +
 .../v2/tools/image-processing-toolbox.yaml    |   3 +
 collections/metabolomics/v2/tools/impute.yaml |   3 +
 .../metabolomics/v2/tools/imzml-writer.yaml   |   3 +
 .../v2/tools/independentmassspectrometer.yaml |   3 +
 .../v2/tools/injectiondesign.yaml             |   3 +
 ...-dependent-missing-value-augmentation.yaml |   3 +
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 collections/metabolomics/v2/tools/joblib.yaml |   3 +
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 .../metabolomics/v2/tools/kaleido.yaml        |   3 +
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 collections/metabolomics/v2/tools/kegg.yaml   |   3 +
 .../metabolomics/v2/tools/keggrest.yaml       |   3 +
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 collections/metabolomics/v2/tools/keras.yaml  |   3 +
 collections/metabolomics/v2/tools/khipu.yaml  |   3 +
 collections/metabolomics/v2/tools/knime.yaml  |   3 +
 collections/metabolomics/v2/tools/knitr.yaml  |   3 +
 .../metabolomics/v2/tools/largemetabo.yaml    |   3 +
 .../latent-dirichlet-allocation-lda.yaml      |   3 +
 .../metabolomics/v2/tools/lcmsworld.yaml      |   3 +
 .../lda-latent-dirichlet-allocation.yaml      |   3 +
 .../metabolomics/v2/tools/lib2nist.yaml       |   3 +
 .../metabolomics/v2/tools/lilikoi-v2-0.yaml   |   3 +
 collections/metabolomics/v2/tools/limma.yaml  |   3 +
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 .../metabolomics/v2/tools/lipidlynxx.yaml     |   3 +
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 914 files changed, 3717 insertions(+)
 create mode 100644 asb_skill_bundle.yaml
 create mode 100644 scripts/enrich_tool_yaml.py
 create mode 100644 tests/test_enrich_tool_yaml.py

diff --git a/asb_skill_bundle.yaml b/asb_skill_bundle.yaml
new file mode 100644
index 000000000..85d1a7b17
--- /dev/null
+++ b/asb_skill_bundle.yaml
@@ -0,0 +1,639 @@
+id: https://w3id.org/holobiomicslab/asb-schema/skill-bundle/v0.2
+name: asb_skill_bundle_v0_2
+description: >-
+  LinkML schema for SciTask Skill Bundle v0.1 — a versioned, curated description of
+  one reusable computational skill identified across multiple papers. Each bundle
+  contains a human-readable skill description and 12 structured sidecars.
+
+license: CC-BY-4.0
+version: "0.2.0"
+
+prefixes:
+  linkml:   https://w3id.org/linkml/
+  asb:      https://w3id.org/holobiomicslab/asb-schema/
+  asbskill: https://w3id.org/holobiomicslab/asb-skill/
+  schema:   http://schema.org/
+  dcterms:  http://purl.org/dc/terms/
+  pplan:    http://purl.org/net/p-plan#
+  prov:     http://www.w3.org/ns/prov#
+  EDAM:     http://edamontology.org/
+  rocrate:  https://w3id.org/ro/crate#
+
+imports:
+  - linkml:types
+
+default_prefix: asb
+default_range: string
+
+# ---------------------------------------------------------------------------
+# Classes
+# ---------------------------------------------------------------------------
+
+classes:
+
+  ToolRecord:
+    description: >-
+      A tool referenced in a Skill Bundle's tools.json sidecar.
+    attributes:
+      tool_name:
+        description: Tool name (e.g. matchms, scikit-learn)
+        range: string
+        required: true
+        annotations:
+          importance: must_have
+        close_mappings:
+          - EDAM:operation_0004
+      canonical_url:
+        description: Canonical URL (GitHub, bio.tools, PyPI, etc.)
+        range: uri
+        annotations:
+          importance: should_have
+        close_mappings:
+          - schema:codeRepository
+      version:
+        description: Version string used or recommended
+        range: string
+        annotations:
+          importance: should_have
+        close_mappings:
+          - schema:softwareVersion
+      tool_description:
+        description: Short description of the tool
+        range: string
+        annotations:
+          importance: should_have
+        exact_mappings:
+          - schema:description
+      edam_topics:
+        description: EDAM topic IRIs for this tool
+        range: uri
+        multivalued: true
+        annotations:
+          importance: nice_to_have
+        exact_mappings:
+          - EDAM:topic_0003
+
+  PaperReference:
+    description: A reference to a source paper that contributed to this skill bundle.
+    attributes:
+      doi:
+        description: DOI of the paper
+        range: string
+        annotations:
+          importance: should_have
+        exact_mappings:
+          - schema:identifier
+      title:
+        description: Title of the paper
+        range: string
+        annotations:
+          importance: must_have
+        exact_mappings:
+          - schema:name
+      relevance:
+        description: Short note on the relevance of this paper to the skill
+        range: string
+        annotations:
+          importance: nice_to_have
+        close_mappings:
+          - schema:description
+      task_ids:
+        description: task_id values from this paper that surfaced this skill
+        range: string
+        multivalued: true
+        annotations:
+          importance: nice_to_have
+        close_mappings:
+          - dcterms:isPartOf
+
+  MergeAuditRecord:
+    description: >-
+      Per-merge audit record documenting alias deduplication decisions.
+      Surfaces the data ``corpus_artifacts._semantic_dedup`` already records
+      so dedup decisions are queryable and citable (IDEAS-E / spec §11).
+    attributes:
+      alias:
+        description: Original skill label before deduplication
+        range: string
+        required: true
+        annotations:
+          importance: must_have
+        close_mappings:
+          - schema:alternateName
+      target_slug:
+        description: Canonical slug this alias was merged into
+        range: string
+        required: true
+        annotations:
+          importance: must_have
+        exact_mappings:
+          - schema:identifier
+      jaccard_score:
+        description: Token-set Jaccard similarity score used for the merge decision
+        range: float
+        annotations:
+          importance: should_have
+        close_mappings:
+          - schema:value
+      embedding_cosine:
+        description: Cosine similarity of MiniLM embeddings (when semantic dedup ran)
+        range: float
+        annotations:
+          importance: should_have
+        close_mappings:
+          - schema:value
+      edam_match:
+        description: True when both records share an EDAM operation IRI
+        range: boolean
+        annotations:
+          importance: nice_to_have
+        close_mappings:
+          - schema:sameAs
+      llm_judge_verdict:
+        description: Free-form judgement string from an LLM dedup judge (if used)
+        range: string
+        annotations:
+          importance: nice_to_have
+        close_mappings:
+          - schema:description
+      method:
+        description: Deduplication method (e.g. token_set_jaccard, semantic_embed, llm_judge)
+        range: string
+        annotations:
+          importance: should_have
+        close_mappings:
+          - prov:wasGeneratedBy
+      decision:
+        description: Final merge decision
+        range: MergeDecisionEnum
+        required: true
+        annotations:
+          importance: must_have
+        close_mappings:
+          - prov:wasInfluencedBy
+      decided_at:
+        description: When the merge decision was recorded (ISO 8601)
+        range: datetime
+        annotations:
+          importance: should_have
+        close_mappings:
+          - prov:generatedAtTime
+      decided_by:
+        description: Agent or person that made the decision (e.g. "agent:dedup", "orcid:0000-...")
+        range: string
+        annotations:
+          importance: should_have
+        close_mappings:
+          - prov:wasAttributedTo
+
+  SkillBundle:
+    description: >-
+      A versioned, curated description of one reusable computational skill
+      identified across multiple papers. Contains a human-readable skill
+      description and 12 structured sidecars (papers, parameters, failure modes,
+      tools, environments, links, etc.).
+    tree_root: true
+    slots:
+      - slug
+      - skill_name
+      - skill_description
+      - when_to_use
+      - skill_tools
+      - edam_topics
+      - edam_operation
+      - scripts
+      - skill_kb_path
+      - bundle_dir
+      - bundle_version
+      - source_task_ids
+      - source_papers
+      - merged_aliases
+      - merged_alias_records
+
+  ASBSkill:
+    description: >-
+      Collection-time aggregated skill record — the deduplicated, paper-grounded
+      scientific competency surfaced by ``corpus_artifacts.collect_skills`` at
+      release time. Distinct from ``SkillBundle`` which is the per-capsule
+      artifact. Mirrors the Python dataclass at agentic_science_builder.schemas.ASBSkill
+      (renamed from SciSkill in Plan 2a / ASB-runtime).
+    slots:
+      - slug
+      - skill_name
+      - description
+      - when_to_use
+      - related_tools
+      - source_task_ids
+      - source_paper_doi
+      - source_paper_title
+      - source_papers
+      - merged_aliases
+      - merged_alias_records
+      - edam_operation
+      - edam_topics
+      - kb_path
+      - bundle_dir
+
+  ASBTool:
+    description: >-
+      Collection-time aggregated tool record — the deduplicated, paper-grounded
+      software-tool reference surfaced by ``corpus_artifacts.collect_tools``.
+      Mirrors the Python dataclass at agentic_science_builder.schemas.ASBTool
+      (renamed from SciTool in Plan 2a / ASB-runtime).
+    slots:
+      - slug
+      - tool_name
+      - canonical_url
+      - related_skills
+      - source_task_ids
+      - source_paper_doi
+      - source_paper_title
+      - evidence_spans
+      - version_used
+      - install
+      - resolution_attempts
+      - edam_operation
+      - edam_topics
+      - bio_tools_id
+      - license_tier
+      - license
+      - license_detection
+
+  ToolAffordance:
+    description: >-
+      W3C WoT ActionAffordance-aligned mixin (IDEAS-F / spec §15).
+      RESERVED for v1 — slot definitions exist but no ASB class consumes
+      them yet. When the ecosystem standardises on WoT for executable
+      tools, ASBTool (or an ExecutableTool subclass) will inherit from
+      this mixin without breaking existing instances.
+    mixin: true
+    slots:
+      - input_schema
+      - output_schema
+      - precondition
+      - effect
+      - side_effect_free
+
+# ---------------------------------------------------------------------------
+# Slots
+# ---------------------------------------------------------------------------
+
+slots:
+
+  slug:
+    description: >-
+      Lowercase, hyphen-separated unique identifier for this skill bundle
+      (e.g. spectral-similarity-scoring)
+    range: string
+    required: true
+    annotations:
+      importance: must_have
+    exact_mappings:
+      - schema:identifier
+
+  skill_name:
+    description: Human-readable canonical name of the skill
+    range: string
+    required: true
+    annotations:
+      importance: must_have
+    exact_mappings:
+      - schema:name
+
+  skill_description:
+    description: Full description of the skill's purpose and scope
+    range: string
+    annotations:
+      importance: must_have
+    exact_mappings:
+      - schema:description
+
+  when_to_use:
+    description: Guidance on when and how to apply this skill
+    range: string
+    annotations:
+      importance: should_have
+    close_mappings:
+      - pplan:Plan
+
+  skill_tools:
+    description: Tool records for tools associated with this skill
+    range: ToolRecord
+    multivalued: true
+    annotations:
+      importance: must_have
+    close_mappings:
+      - EDAM:operation_0004
+
+  edam_topics:
+    description: EDAM topic IRIs for this skill (e.g. http://edamontology.org/topic_3172)
+    range: uri
+    multivalued: true
+    annotations:
+      importance: should_have
+    exact_mappings:
+      - EDAM:topic_0003
+
+  edam_operation:
+    description: Primary EDAM operation IRI for this skill (e.g. http://edamontology.org/operation_3799)
+    range: uri
+    annotations:
+      importance: should_have
+    exact_mappings:
+      - EDAM:operation_0004
+
+  scripts:
+    description: >-
+      Paths to embedded script chunks from linked GitHub repositories
+      (line-range copies, not full clones)
+    range: string
+    multivalued: true
+    annotations:
+      importance: nice_to_have
+    exact_mappings:
+      - prov:atLocation
+
+  skill_kb_path:
+    description: Relative path to the skill's knowledge base entry file (e.g. docs/skill_name.md)
+    range: string
+    annotations:
+      importance: nice_to_have
+    exact_mappings:
+      - prov:atLocation
+
+  bundle_dir:
+    description: Absolute path to the offline skill knowledge base bundle directory
+    range: string
+    annotations:
+      importance: nice_to_have
+    exact_mappings:
+      - prov:atLocation
+
+  bundle_version:
+    description: Version of this skill bundle (e.g. 0.1.0)
+    range: string
+    required: true
+    annotations:
+      importance: must_have
+    close_mappings:
+      - schema:version
+
+  source_task_ids:
+    description: task_id values of the SciTask Cards from which this skill was extracted
+    range: string
+    multivalued: true
+    annotations:
+      importance: should_have
+    close_mappings:
+      - dcterms:isPartOf
+
+  source_papers:
+    description: Structured references to papers that contributed to this bundle
+    range: PaperReference
+    multivalued: true
+    annotations:
+      importance: should_have
+    close_mappings:
+      - dcterms:source
+
+  merged_aliases:
+    description: Original labels of skills merged into this canonical entry
+    range: string
+    multivalued: true
+    annotations:
+      importance: nice_to_have
+    close_mappings:
+      - schema:alternateName
+
+  merged_alias_records:
+    description: Per-merge audit records documenting alias deduplication decisions
+    range: MergeAuditRecord
+    multivalued: true
+    annotations:
+      importance: nice_to_have
+    close_mappings:
+      - prov:wasGeneratedBy
+
+  description:
+    description: >-
+      Retrieval-key description for an ASBSkill. Discipline-constrained
+      (IDEAS-D / spec §5): 50–300 chars, leads with "Use when …", no marketing
+      tokens. The CI gate in asb-skill-collections additionally enforces the
+      banned-token list at release time.
+    range: string
+    required: true
+    minimum_value: 50
+    maximum_value: 300
+    pattern: "^[Uu]se when .+"
+    annotations:
+      importance: must_have
+      banned_tokens:
+        - revolutionary
+        - cutting-edge
+        - best-in-class
+        - powerful
+        - amazing
+        - state-of-the-art
+        - groundbreaking
+    exact_mappings:
+      - schema:description
+
+  related_tools:
+    description: Canonical URLs / slugs of tools used by this skill
+    range: string
+    multivalued: true
+    annotations:
+      importance: should_have
+    close_mappings:
+      - EDAM:operation_0004
+
+  source_paper_doi:
+    description: Primary source paper DOI (flat field, complements source_papers[])
+    range: string
+    annotations:
+      importance: should_have
+    exact_mappings:
+      - schema:identifier
+
+  source_paper_title:
+    description: Primary source paper title (flat field, complements source_papers[])
+    range: string
+    annotations:
+      importance: nice_to_have
+    exact_mappings:
+      - schema:name
+
+  kb_path:
+    description: Relative path to the skill's knowledge-base entry file
+    range: string
+    annotations:
+      importance: nice_to_have
+    exact_mappings:
+      - prov:atLocation
+
+  tool_name:
+    description: Tool name (mirrors ToolRecord.tool_name; used by ASBTool)
+    range: string
+    required: true
+    annotations:
+      importance: must_have
+    close_mappings:
+      - schema:name
+
+  canonical_url:
+    description: Canonical URL for the tool (GitHub, bio.tools, PyPI, etc.)
+    range: uri
+    annotations:
+      importance: should_have
+    close_mappings:
+      - schema:codeRepository
+
+  related_skills:
+    description: Slugs of ASBSkill records that reference this tool
+    range: string
+    multivalued: true
+    annotations:
+      importance: should_have
+    close_mappings:
+      - dcterms:isPartOf
+
+  evidence_spans:
+    description: Verbatim quotes from source papers anchoring this tool reference
+    range: string
+    multivalued: true
+    annotations:
+      importance: should_have
+    close_mappings:
+      - prov:wasDerivedFrom
+
+  version_used:
+    description: Version string actually used in the source paper(s)
+    range: string
+    annotations:
+      importance: nice_to_have
+    close_mappings:
+      - schema:softwareVersion
+
+  install:
+    description: Install metadata dict (conda / pip / docker / etc.) produced by tool_resolver
+    range: string
+    annotations:
+      importance: nice_to_have
+    close_mappings:
+      - schema:installUrl
+
+  resolution_attempts:
+    description: Audit list of resolver attempts (each entry a dict; serialized as JSON)
+    range: string
+    multivalued: true
+    annotations:
+      importance: nice_to_have
+    close_mappings:
+      - prov:wasGeneratedBy
+
+  bio_tools_id:
+    description: >-
+      bio.tools identifier for this tool (IDEAS-G). Reserved slot for the
+      future bio.tools federation work; not populated in v1.
+    range: string
+    annotations:
+      importance: nice_to_have
+    close_mappings:
+      - schema:identifier
+
+  license_tier:
+    description: >-
+      Consumer-facing license tier for this tool, rolled up most-restrictively
+      across its source papers/repos (open / noncommercial / restricted). The
+      same value carried in tools_index.json; propagated into tools/<slug>.yaml
+      by scripts/enrich_tool_yaml.py.
+    range: LicenseTierEnum
+    annotations:
+      importance: should_have
+    close_mappings:
+      - schema:license
+
+  license:
+    description: >-
+      Detected SPDX-ish license identifier for the tool's primary repo
+      (e.g. MIT, GPL-2.0, CC-BY-NC-4.0); null when undetected.
+    range: string
+    annotations:
+      importance: nice_to_have
+    exact_mappings:
+      - schema:license
+
+  license_detection:
+    description: >-
+      How the license was detected (e.g. github-api, readme-llm, none) — audit
+      trail for the license_tier rollup.
+    range: string
+    annotations:
+      importance: nice_to_have
+    close_mappings:
+      - prov:wasGeneratedBy
+
+  input_schema:
+    description: JSON Schema describing the tool's input payload (WoT ActionAffordance.input)
+    range: string
+    annotations:
+      importance: nice_to_have
+    close_mappings:
+      - schema:potentialAction
+
+  output_schema:
+    description: JSON Schema describing the tool's output payload (WoT ActionAffordance.output)
+    range: string
+    annotations:
+      importance: nice_to_have
+    close_mappings:
+      - schema:potentialAction
+
+  precondition:
+    description: Free-form precondition (e.g. "requires CUDA 12.x") — WoT-style affordance hint
+    range: string
+    annotations:
+      importance: nice_to_have
+    close_mappings:
+      - prov:wasInfluencedBy
+
+  effect:
+    description: Free-form effect description for downstream agents
+    range: string
+    annotations:
+      importance: nice_to_have
+    close_mappings:
+      - prov:generated
+
+  side_effect_free:
+    description: True when invoking the tool has no observable side effects (pure function)
+    range: boolean
+    annotations:
+      importance: nice_to_have
+    close_mappings:
+      - schema:propertyID
+
+enums:
+  MergeDecisionEnum:
+    description: Possible outcomes recorded by a MergeAuditRecord
+    permissible_values:
+      auto_merge:
+        description: Auto-merged above the auto threshold
+      manual_merge:
+        description: Manually merged by a curator
+      kept_separate:
+        description: Reviewed and explicitly kept as distinct entries
+      needs_review:
+        description: Pending human review
+
+  LicenseTierEnum:
+    description: >-
+      Consumer-facing license tier, orthogonal to open-access status. Governs
+      acknowledgement / link-only handling for tools and skills.
+    permissible_values:
+      open:
+        description: Permissive / open license — freely reusable
+      noncommercial:
+        description: Noncommercial-only license (e.g. CC-BY-NC) — requires acknowledgement
+      restricted:
+        description: Restricted or undetected license — link-only, conservative default
diff --git a/collections/metabolomics/v2/tools/10-5281-zenodo-4680579.yaml b/collections/metabolomics/v2/tools/10-5281-zenodo-4680579.yaml
index cd8494989..2f53423e2 100644
--- a/collections/metabolomics/v2/tools/10-5281-zenodo-4680579.yaml
+++ b/collections/metabolomics/v2/tools/10-5281-zenodo-4680579.yaml
@@ -10,3 +10,6 @@ derived_from:
 source_repos:
 - NPLinker/nplinker
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
diff --git a/collections/metabolomics/v2/tools/adam-optimizer.yaml b/collections/metabolomics/v2/tools/adam-optimizer.yaml
index 1c18e2a4a..9056dff9c 100644
--- a/collections/metabolomics/v2/tools/adam-optimizer.yaml
+++ b/collections/metabolomics/v2/tools/adam-optimizer.yaml
@@ -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
diff --git a/collections/metabolomics/v2/tools/adap.yaml b/collections/metabolomics/v2/tools/adap.yaml
index cf6a1c0ce..b3b233239 100644
--- a/collections/metabolomics/v2/tools/adap.yaml
+++ b/collections/metabolomics/v2/tools/adap.yaml
@@ -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
diff --git a/collections/metabolomics/v2/tools/adviselipidomics.yaml b/collections/metabolomics/v2/tools/adviselipidomics.yaml
index e9a95c993..cc17b9034 100644
--- a/collections/metabolomics/v2/tools/adviselipidomics.yaml
+++ b/collections/metabolomics/v2/tools/adviselipidomics.yaml
@@ -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
diff --git a/collections/metabolomics/v2/tools/aer.yaml b/collections/metabolomics/v2/tools/aer.yaml
index 84a3d3fe6..d9bb20f3a 100644
--- a/collections/metabolomics/v2/tools/aer.yaml
+++ b/collections/metabolomics/v2/tools/aer.yaml
@@ -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
diff --git a/collections/metabolomics/v2/tools/aerith.yaml b/collections/metabolomics/v2/tools/aerith.yaml
index bc38add1c..b8ce154e5 100644
--- a/collections/metabolomics/v2/tools/aerith.yaml
+++ b/collections/metabolomics/v2/tools/aerith.yaml
@@ -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
diff --git a/collections/metabolomics/v2/tools/agilent-1290-infinity-uhplc-system.yaml b/collections/metabolomics/v2/tools/agilent-1290-infinity-uhplc-system.yaml
index 1a085ccde..476ad3d44 100644
--- a/collections/metabolomics/v2/tools/agilent-1290-infinity-uhplc-system.yaml
+++ b/collections/metabolomics/v2/tools/agilent-1290-infinity-uhplc-system.yaml
@@ -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
diff --git a/collections/metabolomics/v2/tools/agilent-6550-ifunnel-q-tof-mass-spectrometer.yaml b/collections/metabolomics/v2/tools/agilent-6550-ifunnel-q-tof-mass-spectrometer.yaml
index 9789bdab6..4bfdf7d7c 100644
--- a/collections/metabolomics/v2/tools/agilent-6550-ifunnel-q-tof-mass-spectrometer.yaml
+++ b/collections/metabolomics/v2/tools/agilent-6550-ifunnel-q-tof-mass-spectrometer.yaml
@@ -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
diff --git a/collections/metabolomics/v2/tools/agilent-masshunter.yaml b/collections/metabolomics/v2/tools/agilent-masshunter.yaml
index 27995245e..55d3cad24 100644
--- a/collections/metabolomics/v2/tools/agilent-masshunter.yaml
+++ b/collections/metabolomics/v2/tools/agilent-masshunter.yaml
@@ -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
diff --git a/collections/metabolomics/v2/tools/agilent-q-tof-uhplc-hrms-ms.yaml b/collections/metabolomics/v2/tools/agilent-q-tof-uhplc-hrms-ms.yaml
index 58abe0f1c..d797d9537 100644
--- a/collections/metabolomics/v2/tools/agilent-q-tof-uhplc-hrms-ms.yaml
+++ b/collections/metabolomics/v2/tools/agilent-q-tof-uhplc-hrms-ms.yaml
@@ -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
diff --git a/collections/metabolomics/v2/tools/agilent-unknowns-analysis.yaml b/collections/metabolomics/v2/tools/agilent-unknowns-analysis.yaml
index 99b719b7b..70f75435d 100644
--- a/collections/metabolomics/v2/tools/agilent-unknowns-analysis.yaml
+++ b/collections/metabolomics/v2/tools/agilent-unknowns-analysis.yaml
@@ -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
diff --git a/collections/metabolomics/v2/tools/airdpro-v5.yaml b/collections/metabolomics/v2/tools/airdpro-v5.yaml
index 6373cb6e3..7477aab5b 100644
--- a/collections/metabolomics/v2/tools/airdpro-v5.yaml
+++ b/collections/metabolomics/v2/tools/airdpro-v5.yaml
@@ -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
diff --git a/collections/metabolomics/v2/tools/airdpro-v6.yaml b/collections/metabolomics/v2/tools/airdpro-v6.yaml
index 6fb3f6f26..acbae7a76 100644
--- a/collections/metabolomics/v2/tools/airdpro-v6.yaml
+++ b/collections/metabolomics/v2/tools/airdpro-v6.yaml
@@ -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
diff --git a/collections/metabolomics/v2/tools/alphatims.yaml b/collections/metabolomics/v2/tools/alphatims.yaml
index 9a42a11cf..3cda323a3 100644
--- a/collections/metabolomics/v2/tools/alphatims.yaml
+++ b/collections/metabolomics/v2/tools/alphatims.yaml
@@ -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
diff --git a/collections/metabolomics/v2/tools/alvadesc.yaml b/collections/metabolomics/v2/tools/alvadesc.yaml
index 1744322f9..0725e9518 100644
--- a/collections/metabolomics/v2/tools/alvadesc.yaml
+++ b/collections/metabolomics/v2/tools/alvadesc.yaml
@@ -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
diff --git a/collections/metabolomics/v2/tools/amanida.yaml b/collections/metabolomics/v2/tools/amanida.yaml
index 7e3a8a5a3..6fabed829 100644
--- a/collections/metabolomics/v2/tools/amanida.yaml
+++ b/collections/metabolomics/v2/tools/amanida.yaml
@@ -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
diff --git a/collections/metabolomics/v2/tools/anaconda.yaml b/collections/metabolomics/v2/tools/anaconda.yaml
index acb2be1d2..8c80c5231 100644
--- a/collections/metabolomics/v2/tools/anaconda.yaml
+++ b/collections/metabolomics/v2/tools/anaconda.yaml
@@ -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
diff --git a/collections/metabolomics/v2/tools/ann-solo.yaml b/collections/metabolomics/v2/tools/ann-solo.yaml
index 8b8df4df4..afb8e4400 100644
--- a/collections/metabolomics/v2/tools/ann-solo.yaml
+++ b/collections/metabolomics/v2/tools/ann-solo.yaml
@@ -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
diff --git a/collections/metabolomics/v2/tools/annome.yaml b/collections/metabolomics/v2/tools/annome.yaml
index e79db68d9..b907e6d32 100644
--- a/collections/metabolomics/v2/tools/annome.yaml
+++ b/collections/metabolomics/v2/tools/annome.yaml
@@ -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
diff --git a/collections/metabolomics/v2/tools/antismash.yaml b/collections/metabolomics/v2/tools/antismash.yaml
index eb7cf959e..26d7045a1 100644
--- a/collections/metabolomics/v2/tools/antismash.yaml
+++ b/collections/metabolomics/v2/tools/antismash.yaml
@@ -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
diff --git a/collections/metabolomics/v2/tools/apache-maven-3-8.yaml b/collections/metabolomics/v2/tools/apache-maven-3-8.yaml
index d1155ee2e..9339a3363 100644
--- a/collections/metabolomics/v2/tools/apache-maven-3-8.yaml
+++ b/collections/metabolomics/v2/tools/apache-maven-3-8.yaml
@@ -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
diff --git a/collections/metabolomics/v2/tools/appveyor.yaml b/collections/metabolomics/v2/tools/appveyor.yaml
index f4aba7e8a..310859f8c 100644
--- a/collections/metabolomics/v2/tools/appveyor.yaml
+++ b/collections/metabolomics/v2/tools/appveyor.yaml
@@ -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
diff --git a/collections/metabolomics/v2/tools/arrow.yaml b/collections/metabolomics/v2/tools/arrow.yaml
index be5442a9f..b2ded0d6f 100644
--- a/collections/metabolomics/v2/tools/arrow.yaml
+++ b/collections/metabolomics/v2/tools/arrow.yaml
@@ -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
diff --git a/collections/metabolomics/v2/tools/asap-ms.yaml b/collections/metabolomics/v2/tools/asap-ms.yaml
index 50d831400..442253dbd 100644
--- a/collections/metabolomics/v2/tools/asap-ms.yaml
+++ b/collections/metabolomics/v2/tools/asap-ms.yaml
@@ -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
diff --git a/collections/metabolomics/v2/tools/asari-mass-functions-module-nn-cluster-by-mz-seeds.yaml b/collections/metabolomics/v2/tools/asari-mass-functions-module-nn-cluster-by-mz-seeds.yaml
index 69ec85c24..a6460e022 100644
--- a/collections/metabolomics/v2/tools/asari-mass-functions-module-nn-cluster-by-mz-seeds.yaml
+++ b/collections/metabolomics/v2/tools/asari-mass-functions-module-nn-cluster-by-mz-seeds.yaml
@@ -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
diff --git a/collections/metabolomics/v2/tools/asari-massgrid-class-build-grid-sample-wise-add-sample-build-grid-by-centroiding-bin-track-mzs.yaml b/collections/metabolomics/v2/tools/asari-massgrid-class-build-grid-sample-wise-add-sample-build-grid-by-centroiding-bin-track-mzs.yaml
index c65fe1c57..f70cf213d 100644
--- a/collections/metabolomics/v2/tools/asari-massgrid-class-build-grid-sample-wise-add-sample-build-grid-by-centroiding-bin-track-mzs.yaml
+++ b/collections/metabolomics/v2/tools/asari-massgrid-class-build-grid-sample-wise-add-sample-build-grid-by-centroiding-bin-track-mzs.yaml
@@ -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
diff --git a/collections/metabolomics/v2/tools/asari-peaks-module.yaml b/collections/metabolomics/v2/tools/asari-peaks-module.yaml
index d268193ad..2feb2c814 100644
--- a/collections/metabolomics/v2/tools/asari-peaks-module.yaml
+++ b/collections/metabolomics/v2/tools/asari-peaks-module.yaml
@@ -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
diff --git a/collections/metabolomics/v2/tools/asari.yaml b/collections/metabolomics/v2/tools/asari.yaml
index bfadb0045..299bd4690 100644
--- a/collections/metabolomics/v2/tools/asari.yaml
+++ b/collections/metabolomics/v2/tools/asari.yaml
@@ -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
diff --git a/collections/metabolomics/v2/tools/ase-ani.yaml b/collections/metabolomics/v2/tools/ase-ani.yaml
index ac58274f7..62f366aac 100644
--- a/collections/metabolomics/v2/tools/ase-ani.yaml
+++ b/collections/metabolomics/v2/tools/ase-ani.yaml
@@ -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
diff --git a/collections/metabolomics/v2/tools/asics.yaml b/collections/metabolomics/v2/tools/asics.yaml
index 6d40c7378..66009a679 100644
--- a/collections/metabolomics/v2/tools/asics.yaml
+++ b/collections/metabolomics/v2/tools/asics.yaml
@@ -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
diff --git a/collections/metabolomics/v2/tools/assign-hierarchy.yaml b/collections/metabolomics/v2/tools/assign-hierarchy.yaml
index 7ca99887b..bf6166c32 100644
--- a/collections/metabolomics/v2/tools/assign-hierarchy.yaml
+++ b/collections/metabolomics/v2/tools/assign-hierarchy.yaml
@@ -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
diff --git a/collections/metabolomics/v2/tools/autoccs.yaml b/collections/metabolomics/v2/tools/autoccs.yaml
index 39133790c..af8695014 100644
--- a/collections/metabolomics/v2/tools/autoccs.yaml
+++ b/collections/metabolomics/v2/tools/autoccs.yaml
@@ -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
diff --git a/collections/metabolomics/v2/tools/autotuner.yaml b/collections/metabolomics/v2/tools/autotuner.yaml
index 1ab9516ed..12c2036e6 100644
--- a/collections/metabolomics/v2/tools/autotuner.yaml
+++ b/collections/metabolomics/v2/tools/autotuner.yaml
@@ -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
diff --git a/collections/metabolomics/v2/tools/avir-r.yaml b/collections/metabolomics/v2/tools/avir-r.yaml
index 508c46630..2e03013b1 100644
--- a/collections/metabolomics/v2/tools/avir-r.yaml
+++ b/collections/metabolomics/v2/tools/avir-r.yaml
@@ -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
diff --git a/collections/metabolomics/v2/tools/aws-cli.yaml b/collections/metabolomics/v2/tools/aws-cli.yaml
index 1695c93d5..edadfaad9 100644
--- a/collections/metabolomics/v2/tools/aws-cli.yaml
+++ b/collections/metabolomics/v2/tools/aws-cli.yaml
@@ -9,3 +9,6 @@ derived_from:
 source_repos:
 - meowcat/MSNovelist
 schema_version: 0.2.0
+license_tier: open
+license: AGPL-3.0
+license_detection: github-api
diff --git a/collections/metabolomics/v2/tools/bago.yaml b/collections/metabolomics/v2/tools/bago.yaml
index 25d7ae017..837aba27d 100644
--- a/collections/metabolomics/v2/tools/bago.yaml
+++ b/collections/metabolomics/v2/tools/bago.yaml
@@ -11,6 +11,9 @@ derived_from:
 source_repos:
 - huaxuyu/bago
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - CE-MS
diff --git a/collections/metabolomics/v2/tools/bam.yaml b/collections/metabolomics/v2/tools/bam.yaml
index d2384f4e2..5f5f522ed 100644
--- a/collections/metabolomics/v2/tools/bam.yaml
+++ b/collections/metabolomics/v2/tools/bam.yaml
@@ -6,6 +6,9 @@ derived_from:
 - doi: 10.1021/acs.analchem.4c01565
   title: bam
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - NMR
diff --git a/collections/metabolomics/v2/tools/bart.yaml b/collections/metabolomics/v2/tools/bart.yaml
index 64383fcb0..7d96920cc 100644
--- a/collections/metabolomics/v2/tools/bart.yaml
+++ b/collections/metabolomics/v2/tools/bart.yaml
@@ -9,5 +9,8 @@ derived_from:
 source_repos:
 - OpenDFM/MS-BART
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - mass-spectrometry
diff --git a/collections/metabolomics/v2/tools/base64enc.yaml b/collections/metabolomics/v2/tools/base64enc.yaml
index c6c9f08db..9f3baa8c1 100644
--- a/collections/metabolomics/v2/tools/base64enc.yaml
+++ b/collections/metabolomics/v2/tools/base64enc.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - yufree/mzrtsim
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/basicevaluationengine.yaml b/collections/metabolomics/v2/tools/basicevaluationengine.yaml
index d7dbfc3df..7d22775a6 100644
--- a/collections/metabolomics/v2/tools/basicevaluationengine.yaml
+++ b/collections/metabolomics/v2/tools/basicevaluationengine.yaml
@@ -10,6 +10,9 @@ derived_from:
 source_repos:
 - Wang-Bioinformatics-Lab/ModiFinder_base
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: file-present-unclassified
 techniques:
 - LC-MS
 - ion-mobility-MS
diff --git a/collections/metabolomics/v2/tools/benjamini-hochberg-fdr-correction.yaml b/collections/metabolomics/v2/tools/benjamini-hochberg-fdr-correction.yaml
index 71db944a0..58b9586ff 100644
--- a/collections/metabolomics/v2/tools/benjamini-hochberg-fdr-correction.yaml
+++ b/collections/metabolomics/v2/tools/benjamini-hochberg-fdr-correction.yaml
@@ -6,3 +6,6 @@ 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
diff --git a/collections/metabolomics/v2/tools/big-scape.yaml b/collections/metabolomics/v2/tools/big-scape.yaml
index ef3e1ada6..64761391d 100644
--- a/collections/metabolomics/v2/tools/big-scape.yaml
+++ b/collections/metabolomics/v2/tools/big-scape.yaml
@@ -12,6 +12,9 @@ derived_from:
 source_repos:
 - NPLinker/nplinker
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - CE-MS
diff --git a/collections/metabolomics/v2/tools/big-slice.yaml b/collections/metabolomics/v2/tools/big-slice.yaml
index 92442e4d3..faed2e7be 100644
--- a/collections/metabolomics/v2/tools/big-slice.yaml
+++ b/collections/metabolomics/v2/tools/big-slice.yaml
@@ -10,3 +10,6 @@ derived_from:
 source_repos:
 - medema-group/bigslice
 schema_version: 0.2.0
+license_tier: open
+license: AGPL-3.0
+license_detection: github-api
diff --git a/collections/metabolomics/v2/tools/bigscape.yaml b/collections/metabolomics/v2/tools/bigscape.yaml
index 3b8cd2576..359cb0bf3 100644
--- a/collections/metabolomics/v2/tools/bigscape.yaml
+++ b/collections/metabolomics/v2/tools/bigscape.yaml
@@ -12,5 +12,8 @@ derived_from:
 source_repos:
 - NPLinker/nplinker
 schema_version: 0.2.0
+license_tier: open
+license: Apache-2.0
+license_detection: github-api
 techniques:
 - LC-MS
diff --git a/collections/metabolomics/v2/tools/biobase.yaml b/collections/metabolomics/v2/tools/biobase.yaml
index f3b560fd2..ad7b9bbb6 100644
--- a/collections/metabolomics/v2/tools/biobase.yaml
+++ b/collections/metabolomics/v2/tools/biobase.yaml
@@ -13,6 +13,9 @@ source_repos:
 - antonvsdata/notame
 - idrblab/NOREVA;
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - mass-spectrometry
diff --git a/collections/metabolomics/v2/tools/biocmanager.yaml b/collections/metabolomics/v2/tools/biocmanager.yaml
index b8a6bccfb..83c300202 100644
--- a/collections/metabolomics/v2/tools/biocmanager.yaml
+++ b/collections/metabolomics/v2/tools/biocmanager.yaml
@@ -13,6 +13,9 @@ source_repos:
 - idrblab/NOREVA;
 - kilgain/MassSpec
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/bioconda.yaml b/collections/metabolomics/v2/tools/bioconda.yaml
index 10f0e4ee8..e17367d67 100644
--- a/collections/metabolomics/v2/tools/bioconda.yaml
+++ b/collections/metabolomics/v2/tools/bioconda.yaml
@@ -6,5 +6,8 @@ derived_from:
 - doi: 10.1021/acs.jproteome.8b00717
   title: pyteomics
 schema_version: 0.2.0
+license_tier: open
+license: Apache-2.0
+license_detection: github-api
 techniques:
 - LC-MS
diff --git a/collections/metabolomics/v2/tools/bioconductor.yaml b/collections/metabolomics/v2/tools/bioconductor.yaml
index 85c301360..9e1ba8d77 100644
--- a/collections/metabolomics/v2/tools/bioconductor.yaml
+++ b/collections/metabolomics/v2/tools/bioconductor.yaml
@@ -32,6 +32,9 @@ source_repos:
 - sneumann/xcms
 - xdomingoal/erah-devel
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - CE-MS
diff --git a/collections/metabolomics/v2/tools/biocparallel.yaml b/collections/metabolomics/v2/tools/biocparallel.yaml
index 238c05dd4..c5efdefa1 100644
--- a/collections/metabolomics/v2/tools/biocparallel.yaml
+++ b/collections/metabolomics/v2/tools/biocparallel.yaml
@@ -10,6 +10,9 @@ derived_from:
 source_repos:
 - kuwisdelu/Cardinal
 schema_version: 0.2.0
+license_tier: open
+license: Artistic-2.0
+license_detection: github-api
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/bioinformatic-toolbox.yaml b/collections/metabolomics/v2/tools/bioinformatic-toolbox.yaml
index 219049689..eb3ce0341 100644
--- a/collections/metabolomics/v2/tools/bioinformatic-toolbox.yaml
+++ b/collections/metabolomics/v2/tools/bioinformatic-toolbox.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - AdrianHaun/AriumMS
 schema_version: 0.2.0
+license_tier: open
+license: BSD-3-Clause
+license_detection: github-api
 techniques:
 - LC-MS
 - CE-MS
diff --git a/collections/metabolomics/v2/tools/biosynfoni.yaml b/collections/metabolomics/v2/tools/biosynfoni.yaml
index 05f03c872..7d7f94628 100644
--- a/collections/metabolomics/v2/tools/biosynfoni.yaml
+++ b/collections/metabolomics/v2/tools/biosynfoni.yaml
@@ -10,3 +10,6 @@ derived_from:
 source_repos:
 - lucinamay/biosynfoni
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
diff --git a/collections/metabolomics/v2/tools/biotransformer.yaml b/collections/metabolomics/v2/tools/biotransformer.yaml
index 1d6c07e10..01fd7d8cc 100644
--- a/collections/metabolomics/v2/tools/biotransformer.yaml
+++ b/collections/metabolomics/v2/tools/biotransformer.yaml
@@ -17,6 +17,9 @@ source_repos:
 - https://bitbucket.org/wishartlab/biotransformer3.0jar.git
 - rickhelmus/patRoon
 schema_version: 0.2.0
+license_tier: noncommercial
+license: Academic use free; commercial use/redistribution by permission of the authors (Wishart Lab). Env. module data CC-BY-NC-SA (enviPath/EAWAG).
+license_detection: null
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/biotransformerapi.yaml b/collections/metabolomics/v2/tools/biotransformerapi.yaml
index 06a1c41ae..444f1dbe0 100644
--- a/collections/metabolomics/v2/tools/biotransformerapi.yaml
+++ b/collections/metabolomics/v2/tools/biotransformerapi.yaml
@@ -9,3 +9,6 @@ derived_from:
 source_repos:
 - Le0nT1/CyProduct
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
diff --git a/collections/metabolomics/v2/tools/biotranslator.yaml b/collections/metabolomics/v2/tools/biotranslator.yaml
index 3487442c0..c92108f63 100644
--- a/collections/metabolomics/v2/tools/biotranslator.yaml
+++ b/collections/metabolomics/v2/tools/biotranslator.yaml
@@ -9,3 +9,6 @@ derived_from:
 source_repos:
 - ASAGlab/MOI--An-integrated-solution-for-omics-analyses
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
diff --git a/collections/metabolomics/v2/tools/bitterpredict-m.yaml b/collections/metabolomics/v2/tools/bitterpredict-m.yaml
index a79aec30c..7346fe7ff 100644
--- a/collections/metabolomics/v2/tools/bitterpredict-m.yaml
+++ b/collections/metabolomics/v2/tools/bitterpredict-m.yaml
@@ -6,3 +6,6 @@ derived_from:
 - doi: 10.1021/acs.jafc.3c09767
   title: bittermass
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
diff --git a/collections/metabolomics/v2/tools/bitterpredict.yaml b/collections/metabolomics/v2/tools/bitterpredict.yaml
index b02fb4dfe..d5ec1bb6b 100644
--- a/collections/metabolomics/v2/tools/bitterpredict.yaml
+++ b/collections/metabolomics/v2/tools/bitterpredict.yaml
@@ -6,3 +6,6 @@ derived_from:
 - doi: 10.1021/acs.jafc.3c09767
   title: bittermass
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
diff --git a/collections/metabolomics/v2/tools/black.yaml b/collections/metabolomics/v2/tools/black.yaml
index ccc82aa25..7410e7c17 100644
--- a/collections/metabolomics/v2/tools/black.yaml
+++ b/collections/metabolomics/v2/tools/black.yaml
@@ -13,5 +13,8 @@ source_repos:
 - SysMedOs/LipidLynxX
 - medema-group/BiG-SCAPE
 schema_version: 0.2.0
+license_tier: open
+license: AGPL-3.0
+license_detection: github-api
 techniques:
 - mass-spectrometry
diff --git a/collections/metabolomics/v2/tools/blast.yaml b/collections/metabolomics/v2/tools/blast.yaml
index b37ee453a..d161a4821 100644
--- a/collections/metabolomics/v2/tools/blast.yaml
+++ b/collections/metabolomics/v2/tools/blast.yaml
@@ -9,5 +9,8 @@ derived_from:
 source_repos:
 - mibig-secmet/mibig-json
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
diff --git a/collections/metabolomics/v2/tools/bmxp.yaml b/collections/metabolomics/v2/tools/bmxp.yaml
index 2c746b1ee..a83bf04bb 100644
--- a/collections/metabolomics/v2/tools/bmxp.yaml
+++ b/collections/metabolomics/v2/tools/bmxp.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - broadinstitute/bmxp
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: license-file
 techniques:
 - LC-MS
 - ion-mobility-MS
diff --git a/collections/metabolomics/v2/tools/bokeh.yaml b/collections/metabolomics/v2/tools/bokeh.yaml
index 939dad0a9..a6727ae8a 100644
--- a/collections/metabolomics/v2/tools/bokeh.yaml
+++ b/collections/metabolomics/v2/tools/bokeh.yaml
@@ -16,6 +16,9 @@ derived_from:
 source_repos:
 - Roestlab/massdash
 schema_version: 0.2.0
+license_tier: open
+license: BSD-3-Clause
+license_detection: github-api
 techniques:
 - LC-MS
 - ion-mobility-MS
diff --git a/collections/metabolomics/v2/tools/bridgedb.yaml b/collections/metabolomics/v2/tools/bridgedb.yaml
index fad92da19..c6d33b26f 100644
--- a/collections/metabolomics/v2/tools/bridgedb.yaml
+++ b/collections/metabolomics/v2/tools/bridgedb.yaml
@@ -11,6 +11,9 @@ derived_from:
 source_repos:
 - RECETOX/MSMetaEnhancer
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
 techniques:
 - LC-MS
 - mass-spectrometry
diff --git a/collections/metabolomics/v2/tools/bruker-q-tof-uhplc-hrms-ms.yaml b/collections/metabolomics/v2/tools/bruker-q-tof-uhplc-hrms-ms.yaml
index da8e1d7e8..3762de007 100644
--- a/collections/metabolomics/v2/tools/bruker-q-tof-uhplc-hrms-ms.yaml
+++ b/collections/metabolomics/v2/tools/bruker-q-tof-uhplc-hrms-ms.yaml
@@ -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
diff --git a/collections/metabolomics/v2/tools/bruker-solarix.yaml b/collections/metabolomics/v2/tools/bruker-solarix.yaml
index cf176ab7d..f5ee56116 100644
--- a/collections/metabolomics/v2/tools/bruker-solarix.yaml
+++ b/collections/metabolomics/v2/tools/bruker-solarix.yaml
@@ -6,5 +6,8 @@ derived_from:
 - doi: 10.5281/zenodo.14009575
   title: corems
 schema_version: 0.2.0
+license_tier: open
+license: BSD-2-Clause
+license_detection: github-api
 techniques:
 - mass-spectrometry
diff --git a/collections/metabolomics/v2/tools/c.yaml b/collections/metabolomics/v2/tools/c.yaml
index ce893eff0..c30b5d8ea 100644
--- a/collections/metabolomics/v2/tools/c.yaml
+++ b/collections/metabolomics/v2/tools/c.yaml
@@ -4,3 +4,6 @@ evidence_spans:
 - // A small example demonstrating the basic usage of OpenTIMS in C++.
 - '`OpenTIMS` is a C++ library'
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: null
diff --git a/collections/metabolomics/v2/tools/calculator.yaml b/collections/metabolomics/v2/tools/calculator.yaml
index 5305e7898..7cf4acc90 100644
--- a/collections/metabolomics/v2/tools/calculator.yaml
+++ b/collections/metabolomics/v2/tools/calculator.yaml
@@ -9,3 +9,6 @@ derived_from:
 source_repos:
 - djdt/pewpew
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
diff --git a/collections/metabolomics/v2/tools/camera.yaml b/collections/metabolomics/v2/tools/camera.yaml
index ebb52c5d6..fa8d73974 100644
--- a/collections/metabolomics/v2/tools/camera.yaml
+++ b/collections/metabolomics/v2/tools/camera.yaml
@@ -13,6 +13,9 @@ source_repos:
 - LinShuhaiLAB/LipidIN
 - b2slab/mWISE
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/canonical-correlation-analysis-cca.yaml b/collections/metabolomics/v2/tools/canonical-correlation-analysis-cca.yaml
index bd350bf81..17cb19884 100644
--- a/collections/metabolomics/v2/tools/canonical-correlation-analysis-cca.yaml
+++ b/collections/metabolomics/v2/tools/canonical-correlation-analysis-cca.yaml
@@ -6,6 +6,9 @@ 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
diff --git a/collections/metabolomics/v2/tools/canopus.yaml b/collections/metabolomics/v2/tools/canopus.yaml
index 92c39cd3d..cfbf45486 100644
--- a/collections/metabolomics/v2/tools/canopus.yaml
+++ b/collections/metabolomics/v2/tools/canopus.yaml
@@ -15,6 +15,9 @@ source_repos:
 - luigiquiros/inventa
 - sirius-ms/sirius
 schema_version: 0.2.0
+license_tier: open
+license: AGPL-3.0
+license_detection: github-api
 techniques:
 - LC-MS
 - CE-MS
diff --git a/collections/metabolomics/v2/tools/cardinal.yaml b/collections/metabolomics/v2/tools/cardinal.yaml
index 70b517490..232ead9be 100644
--- a/collections/metabolomics/v2/tools/cardinal.yaml
+++ b/collections/metabolomics/v2/tools/cardinal.yaml
@@ -21,6 +21,9 @@ source_repos:
 - kuwisdelu/Cardinal
 - swinnenteam/LipidQMap
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: file-present-unclassified
 techniques:
 - LC-MS
 - CE-MS
diff --git a/collections/metabolomics/v2/tools/cardinalio.yaml b/collections/metabolomics/v2/tools/cardinalio.yaml
index 31aa610ff..f3ebcdf5f 100644
--- a/collections/metabolomics/v2/tools/cardinalio.yaml
+++ b/collections/metabolomics/v2/tools/cardinalio.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - kuwisdelu/Cardinal
 schema_version: 0.2.0
+license_tier: open
+license: Artistic-2.0
+license_detection: github-api
 techniques:
 - MS-imaging
 - mass-spectrometry
diff --git a/collections/metabolomics/v2/tools/caret.yaml b/collections/metabolomics/v2/tools/caret.yaml
index a9d5ebb20..ba12d9ddb 100644
--- a/collections/metabolomics/v2/tools/caret.yaml
+++ b/collections/metabolomics/v2/tools/caret.yaml
@@ -14,5 +14,8 @@ source_repos:
 - KelseyChetnik/MetaClean
 - slfan2013/SERDA
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
diff --git a/collections/metabolomics/v2/tools/casanovo.yaml b/collections/metabolomics/v2/tools/casanovo.yaml
index 7d2429dba..41fcb7d8b 100644
--- a/collections/metabolomics/v2/tools/casanovo.yaml
+++ b/collections/metabolomics/v2/tools/casanovo.yaml
@@ -10,6 +10,9 @@ derived_from:
 source_repos:
 - Noble-Lab/casanovo
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - MS-imaging
diff --git a/collections/metabolomics/v2/tools/cca-canonical-correlation-analysis.yaml b/collections/metabolomics/v2/tools/cca-canonical-correlation-analysis.yaml
index c0454db31..be7ed1c69 100644
--- a/collections/metabolomics/v2/tools/cca-canonical-correlation-analysis.yaml
+++ b/collections/metabolomics/v2/tools/cca-canonical-correlation-analysis.yaml
@@ -6,3 +6,6 @@ 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
diff --git a/collections/metabolomics/v2/tools/centwave.yaml b/collections/metabolomics/v2/tools/centwave.yaml
index e7eec7854..d1b576801 100644
--- a/collections/metabolomics/v2/tools/centwave.yaml
+++ b/collections/metabolomics/v2/tools/centwave.yaml
@@ -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
diff --git a/collections/metabolomics/v2/tools/cfm-id.yaml b/collections/metabolomics/v2/tools/cfm-id.yaml
index c4d1cedbb..5fe5e72dd 100644
--- a/collections/metabolomics/v2/tools/cfm-id.yaml
+++ b/collections/metabolomics/v2/tools/cfm-id.yaml
@@ -19,6 +19,9 @@ source_repos:
 - beherasan/MS2Compound
 - https://gitlab.com/nexs-metabolomics/projects/dna_adductomics_database.git
 schema_version: 0.2.0
+license_tier: restricted
+license: no license found (verified 2026-06-24)
+license_detection: null
 techniques:
 - LC-MS
 - MS-imaging
diff --git a/collections/metabolomics/v2/tools/cfmid.yaml b/collections/metabolomics/v2/tools/cfmid.yaml
index 80f0104bd..03c9b9a17 100644
--- a/collections/metabolomics/v2/tools/cfmid.yaml
+++ b/collections/metabolomics/v2/tools/cfmid.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - aaronma2020/MSGO
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/chambm-pwiz-skyline-i-agree-to-the-vendor-licenses.yaml b/collections/metabolomics/v2/tools/chambm-pwiz-skyline-i-agree-to-the-vendor-licenses.yaml
index fccb47ee2..6bc1aeaf6 100644
--- a/collections/metabolomics/v2/tools/chambm-pwiz-skyline-i-agree-to-the-vendor-licenses.yaml
+++ b/collections/metabolomics/v2/tools/chambm-pwiz-skyline-i-agree-to-the-vendor-licenses.yaml
@@ -9,5 +9,8 @@ derived_from:
 source_repos:
 - VIU-Metabolomics/imzML_Writer
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
 techniques:
 - mass-spectrometry
diff --git a/collections/metabolomics/v2/tools/chebi.yaml b/collections/metabolomics/v2/tools/chebi.yaml
index a938181b4..f4cc28ed7 100644
--- a/collections/metabolomics/v2/tools/chebi.yaml
+++ b/collections/metabolomics/v2/tools/chebi.yaml
@@ -9,5 +9,8 @@ derived_from:
 source_repos:
 - privrja/MassSpecBlocks
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
 techniques:
 - mass-spectrometry
diff --git a/collections/metabolomics/v2/tools/chem-spectra-app.yaml b/collections/metabolomics/v2/tools/chem-spectra-app.yaml
index cb513d370..b72a0b696 100644
--- a/collections/metabolomics/v2/tools/chem-spectra-app.yaml
+++ b/collections/metabolomics/v2/tools/chem-spectra-app.yaml
@@ -9,5 +9,8 @@ derived_from:
 source_repos:
 - ComPlat/chem-spectra-app
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
 techniques:
 - NMR
diff --git a/collections/metabolomics/v2/tools/chemecho.yaml b/collections/metabolomics/v2/tools/chemecho.yaml
index 5c714d63f..b03bf8177 100644
--- a/collections/metabolomics/v2/tools/chemecho.yaml
+++ b/collections/metabolomics/v2/tools/chemecho.yaml
@@ -9,5 +9,8 @@ derived_from:
 source_repos:
 - biorack/chemecho
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
diff --git a/collections/metabolomics/v2/tools/chemicalmixturefrommzml.yaml b/collections/metabolomics/v2/tools/chemicalmixturefrommzml.yaml
index 1a66b2998..daf072a58 100644
--- a/collections/metabolomics/v2/tools/chemicalmixturefrommzml.yaml
+++ b/collections/metabolomics/v2/tools/chemicalmixturefrommzml.yaml
@@ -6,5 +6,8 @@ derived_from:
 - doi: 10.1021/acs.analchem.0c03895
   title: Rapid Development of Improved Data-Dependent Acquisition Strategies
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
diff --git a/collections/metabolomics/v2/tools/chemistry-development-kit-cdk.yaml b/collections/metabolomics/v2/tools/chemistry-development-kit-cdk.yaml
index 85d91fd50..ed7fe7fea 100644
--- a/collections/metabolomics/v2/tools/chemistry-development-kit-cdk.yaml
+++ b/collections/metabolomics/v2/tools/chemistry-development-kit-cdk.yaml
@@ -10,6 +10,9 @@ derived_from:
 source_repos:
 - NPLinker/nplinker
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - mass-spectrometry
diff --git a/collections/metabolomics/v2/tools/chemminer.yaml b/collections/metabolomics/v2/tools/chemminer.yaml
index 4d8e9acfe..ec0c2a297 100644
--- a/collections/metabolomics/v2/tools/chemminer.yaml
+++ b/collections/metabolomics/v2/tools/chemminer.yaml
@@ -7,6 +7,9 @@ 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
diff --git a/collections/metabolomics/v2/tools/chemparse.yaml b/collections/metabolomics/v2/tools/chemparse.yaml
index dff46077d..a33ab574b 100644
--- a/collections/metabolomics/v2/tools/chemparse.yaml
+++ b/collections/metabolomics/v2/tools/chemparse.yaml
@@ -11,5 +11,8 @@ derived_from:
 source_repos:
 - FanzhouKong/spectral_denoising
 schema_version: 0.2.0
+license_tier: open
+license: Apache-2.0
+license_detection: github-api
 techniques:
 - LC-MS
diff --git a/collections/metabolomics/v2/tools/chemprop-ir.yaml b/collections/metabolomics/v2/tools/chemprop-ir.yaml
index f4be51548..7f89b2fa7 100644
--- a/collections/metabolomics/v2/tools/chemprop-ir.yaml
+++ b/collections/metabolomics/v2/tools/chemprop-ir.yaml
@@ -6,5 +6,8 @@ derived_from:
 - doi: 10.1021/acs.jcim.1c00055
   title: Chemprop-IR
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
 techniques:
 - NMR
diff --git a/collections/metabolomics/v2/tools/chemprop.yaml b/collections/metabolomics/v2/tools/chemprop.yaml
index 6df657088..5a03f391f 100644
--- a/collections/metabolomics/v2/tools/chemprop.yaml
+++ b/collections/metabolomics/v2/tools/chemprop.yaml
@@ -6,6 +6,9 @@ derived_from:
 - doi: 10.1021/acs.jcim.1c00055
   title: Chemprop-IR
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
 techniques:
 - LC-MS
 - NMR
diff --git a/collections/metabolomics/v2/tools/chemspider.yaml b/collections/metabolomics/v2/tools/chemspider.yaml
index 5699df38b..2dd4b6f03 100644
--- a/collections/metabolomics/v2/tools/chemspider.yaml
+++ b/collections/metabolomics/v2/tools/chemspider.yaml
@@ -9,5 +9,8 @@ derived_from:
 source_repos:
 - privrja/MassSpecBlocks
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
 techniques:
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/cir.yaml b/collections/metabolomics/v2/tools/cir.yaml
index a27df3531..5801f4f4c 100644
--- a/collections/metabolomics/v2/tools/cir.yaml
+++ b/collections/metabolomics/v2/tools/cir.yaml
@@ -11,6 +11,9 @@ derived_from:
 source_repos:
 - RECETOX/MSMetaEnhancer
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
 techniques:
 - LC-MS
 - mass-spectrometry
diff --git a/collections/metabolomics/v2/tools/classyfire.yaml b/collections/metabolomics/v2/tools/classyfire.yaml
index 21f601e0c..245f278bc 100644
--- a/collections/metabolomics/v2/tools/classyfire.yaml
+++ b/collections/metabolomics/v2/tools/classyfire.yaml
@@ -14,6 +14,9 @@ source_repos:
 - michaelwitting/RepoRT
 - zquinlan/concise
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
 techniques:
 - LC-MS
 - mass-spectrometry
diff --git a/collections/metabolomics/v2/tools/cliquems.yaml b/collections/metabolomics/v2/tools/cliquems.yaml
index d50274228..cf6b043e7 100644
--- a/collections/metabolomics/v2/tools/cliquems.yaml
+++ b/collections/metabolomics/v2/tools/cliquems.yaml
@@ -10,5 +10,8 @@ derived_from:
 source_repos:
 - b2slab/mWISE
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
diff --git a/collections/metabolomics/v2/tools/clumsid.yaml b/collections/metabolomics/v2/tools/clumsid.yaml
index 06686a9f4..52b29441f 100644
--- a/collections/metabolomics/v2/tools/clumsid.yaml
+++ b/collections/metabolomics/v2/tools/clumsid.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - LeaveMeNotTonight/CMDN
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - CE-MS
diff --git a/collections/metabolomics/v2/tools/clumsiddata.yaml b/collections/metabolomics/v2/tools/clumsiddata.yaml
index 7970e2be6..e029310bd 100644
--- a/collections/metabolomics/v2/tools/clumsiddata.yaml
+++ b/collections/metabolomics/v2/tools/clumsiddata.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - LeaveMeNotTonight/CMDN
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - CE-MS
diff --git a/collections/metabolomics/v2/tools/clusterprofiler.yaml b/collections/metabolomics/v2/tools/clusterprofiler.yaml
index a19abe4b6..211d8f248 100644
--- a/collections/metabolomics/v2/tools/clusterprofiler.yaml
+++ b/collections/metabolomics/v2/tools/clusterprofiler.yaml
@@ -13,6 +13,9 @@ source_repos:
 - ASAGlab/MOI--An-integrated-solution-for-omics-analyses
 - emosca-cnr/margheRita
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - CE-MS
diff --git a/collections/metabolomics/v2/tools/cobrapy-for-optgpsampler-uniform-sampling.yaml b/collections/metabolomics/v2/tools/cobrapy-for-optgpsampler-uniform-sampling.yaml
index e2c9a24ac..3e5f40bda 100644
--- a/collections/metabolomics/v2/tools/cobrapy-for-optgpsampler-uniform-sampling.yaml
+++ b/collections/metabolomics/v2/tools/cobrapy-for-optgpsampler-uniform-sampling.yaml
@@ -6,3 +6,6 @@ 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
diff --git a/collections/metabolomics/v2/tools/cobrapy-optgpsampler-algorithm.yaml b/collections/metabolomics/v2/tools/cobrapy-optgpsampler-algorithm.yaml
index 022ee4dab..3f4805693 100644
--- a/collections/metabolomics/v2/tools/cobrapy-optgpsampler-algorithm.yaml
+++ b/collections/metabolomics/v2/tools/cobrapy-optgpsampler-algorithm.yaml
@@ -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
diff --git a/collections/metabolomics/v2/tools/cobrapy.yaml b/collections/metabolomics/v2/tools/cobrapy.yaml
index 66fd1f433..a25a6b701 100644
--- a/collections/metabolomics/v2/tools/cobrapy.yaml
+++ b/collections/metabolomics/v2/tools/cobrapy.yaml
@@ -8,5 +8,8 @@ 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
diff --git a/collections/metabolomics/v2/tools/coconut.yaml b/collections/metabolomics/v2/tools/coconut.yaml
index 7770dee53..251ac9a21 100644
--- a/collections/metabolomics/v2/tools/coconut.yaml
+++ b/collections/metabolomics/v2/tools/coconut.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - privrja/MassSpecBlocks
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
 techniques:
 - LC-MS
 - mass-spectrometry
diff --git a/collections/metabolomics/v2/tools/cohen-s-kappa-metric.yaml b/collections/metabolomics/v2/tools/cohen-s-kappa-metric.yaml
index d9c8b1aac..009452a8d 100644
--- a/collections/metabolomics/v2/tools/cohen-s-kappa-metric.yaml
+++ b/collections/metabolomics/v2/tools/cohen-s-kappa-metric.yaml
@@ -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
diff --git a/collections/metabolomics/v2/tools/color-jitter-augmentation.yaml b/collections/metabolomics/v2/tools/color-jitter-augmentation.yaml
index eefe8e501..de64083db 100644
--- a/collections/metabolomics/v2/tools/color-jitter-augmentation.yaml
+++ b/collections/metabolomics/v2/tools/color-jitter-augmentation.yaml
@@ -6,5 +6,8 @@ derived_from:
 - doi: 10.1021/acs.analchem.3c05002
   title: deepion
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - MS-imaging
diff --git a/collections/metabolomics/v2/tools/combat.yaml b/collections/metabolomics/v2/tools/combat.yaml
index d6b6bd4d9..91770aa98 100644
--- a/collections/metabolomics/v2/tools/combat.yaml
+++ b/collections/metabolomics/v2/tools/combat.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - ShinyFabio/ADViSELipidomics
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
 techniques:
 - LC-MS
 - CE-MS
diff --git a/collections/metabolomics/v2/tools/commit.yaml b/collections/metabolomics/v2/tools/commit.yaml
index ccf5c27f9..51d05c84c 100644
--- a/collections/metabolomics/v2/tools/commit.yaml
+++ b/collections/metabolomics/v2/tools/commit.yaml
@@ -7,3 +7,6 @@ derived_from:
 - doi: 10.1371/journal.pcbi.1009906
   title: COMMIT
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
diff --git a/collections/metabolomics/v2/tools/commons-math3.yaml b/collections/metabolomics/v2/tools/commons-math3.yaml
index 846135e87..7a1efb01e 100644
--- a/collections/metabolomics/v2/tools/commons-math3.yaml
+++ b/collections/metabolomics/v2/tools/commons-math3.yaml
@@ -10,6 +10,9 @@ derived_from:
 source_repos:
 - rformassspectrometry/Spectra
 schema_version: 0.2.0
+license_tier: open
+license: Artistic-2.0
+license_detection: readme-llm
 techniques:
 - LC-MS
 - NMR
diff --git a/collections/metabolomics/v2/tools/comparador.yaml b/collections/metabolomics/v2/tools/comparador.yaml
index bea891cb8..89987f46c 100644
--- a/collections/metabolomics/v2/tools/comparador.yaml
+++ b/collections/metabolomics/v2/tools/comparador.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - pnnl/IonToolPack
 schema_version: 0.2.0
+license_tier: open
+license: BSD-2-Clause
+license_detection: github-api
 techniques:
 - LC-MS
 - direct-infusion-MS
diff --git a/collections/metabolomics/v2/tools/comparems2.yaml b/collections/metabolomics/v2/tools/comparems2.yaml
index 15bba6c53..da24c6087 100644
--- a/collections/metabolomics/v2/tools/comparems2.yaml
+++ b/collections/metabolomics/v2/tools/comparems2.yaml
@@ -9,5 +9,8 @@ derived_from:
 source_repos:
 - 524D/compareMS2
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
 techniques:
 - LC-MS
diff --git a/collections/metabolomics/v2/tools/complexheatmap.yaml b/collections/metabolomics/v2/tools/complexheatmap.yaml
index 96dfd89c2..9312dde7d 100644
--- a/collections/metabolomics/v2/tools/complexheatmap.yaml
+++ b/collections/metabolomics/v2/tools/complexheatmap.yaml
@@ -15,6 +15,9 @@ source_repos:
 - ASAGlab/MOI--An-integrated-solution-for-omics-analyses
 - emosca-cnr/margheRita
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - ion-mobility-MS
diff --git a/collections/metabolomics/v2/tools/compound-discoverer.yaml b/collections/metabolomics/v2/tools/compound-discoverer.yaml
index 673536bf6..eb1b965f8 100644
--- a/collections/metabolomics/v2/tools/compound-discoverer.yaml
+++ b/collections/metabolomics/v2/tools/compound-discoverer.yaml
@@ -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
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/conda.yaml b/collections/metabolomics/v2/tools/conda.yaml
index aaf241be8..fccade2e1 100644
--- a/collections/metabolomics/v2/tools/conda.yaml
+++ b/collections/metabolomics/v2/tools/conda.yaml
@@ -46,6 +46,9 @@ source_repos:
 - yuxuanliao/PACCS
 - zxguocsu/GCMSFormer
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/consensus-clustering.yaml b/collections/metabolomics/v2/tools/consensus-clustering.yaml
index c1deba22a..182040b7d 100644
--- a/collections/metabolomics/v2/tools/consensus-clustering.yaml
+++ b/collections/metabolomics/v2/tools/consensus-clustering.yaml
@@ -6,3 +6,6 @@ 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
diff --git a/collections/metabolomics/v2/tools/constraint-based-stoichiometric-metabolic-models.yaml b/collections/metabolomics/v2/tools/constraint-based-stoichiometric-metabolic-models.yaml
index 8c519b003..b260f7a66 100644
--- a/collections/metabolomics/v2/tools/constraint-based-stoichiometric-metabolic-models.yaml
+++ b/collections/metabolomics/v2/tools/constraint-based-stoichiometric-metabolic-models.yaml
@@ -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
diff --git a/collections/metabolomics/v2/tools/converterbuilder.yaml b/collections/metabolomics/v2/tools/converterbuilder.yaml
index 2f2ca0e51..f5f49fad9 100644
--- a/collections/metabolomics/v2/tools/converterbuilder.yaml
+++ b/collections/metabolomics/v2/tools/converterbuilder.yaml
@@ -9,5 +9,8 @@ derived_from:
 source_repos:
 - RECETOX/MSMetaEnhancer
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
 techniques:
 - mass-spectrometry
diff --git a/collections/metabolomics/v2/tools/convolutional-neural-network-cnn.yaml b/collections/metabolomics/v2/tools/convolutional-neural-network-cnn.yaml
index 9589f875b..ad97aed56 100644
--- a/collections/metabolomics/v2/tools/convolutional-neural-network-cnn.yaml
+++ b/collections/metabolomics/v2/tools/convolutional-neural-network-cnn.yaml
@@ -12,6 +12,9 @@ derived_from:
 source_repos:
 - massspecdl/ChemEmbed
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - NMR
diff --git a/collections/metabolomics/v2/tools/convolutional-neural-network.yaml b/collections/metabolomics/v2/tools/convolutional-neural-network.yaml
index 469292507..6e7b61a7a 100644
--- a/collections/metabolomics/v2/tools/convolutional-neural-network.yaml
+++ b/collections/metabolomics/v2/tools/convolutional-neural-network.yaml
@@ -6,5 +6,8 @@ derived_from:
 - doi: 10.1021/acscentsci.4c01132
   title: NMR2Struct
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
 techniques:
 - NMR
diff --git a/collections/metabolomics/v2/tools/cordbat.yaml b/collections/metabolomics/v2/tools/cordbat.yaml
index 516e23b4a..853a292aa 100644
--- a/collections/metabolomics/v2/tools/cordbat.yaml
+++ b/collections/metabolomics/v2/tools/cordbat.yaml
@@ -9,5 +9,8 @@ derived_from:
 source_repos:
 - BorchLab/CordBat
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: file-present-unclassified
 techniques:
 - mass-spectrometry
diff --git a/collections/metabolomics/v2/tools/corems.yaml b/collections/metabolomics/v2/tools/corems.yaml
index 86dad4377..9de34481e 100644
--- a/collections/metabolomics/v2/tools/corems.yaml
+++ b/collections/metabolomics/v2/tools/corems.yaml
@@ -9,6 +9,9 @@ derived_from:
 - doi: 10.5281/zenodo.14009575
   title: corems
 schema_version: 0.2.0
+license_tier: open
+license: BSD-2-Clause
+license_detection: github-api
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/cosine-neutral-loss-repository.yaml b/collections/metabolomics/v2/tools/cosine-neutral-loss-repository.yaml
index 14a5c7644..68bd10f6c 100644
--- a/collections/metabolomics/v2/tools/cosine-neutral-loss-repository.yaml
+++ b/collections/metabolomics/v2/tools/cosine-neutral-loss-repository.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - bittremieux/cosine_neutral_loss
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: null
 techniques:
 - LC-MS
 - CE-MS
diff --git a/collections/metabolomics/v2/tools/cosine-neutral-loss.yaml b/collections/metabolomics/v2/tools/cosine-neutral-loss.yaml
index 77796f849..ad3cd9317 100644
--- a/collections/metabolomics/v2/tools/cosine-neutral-loss.yaml
+++ b/collections/metabolomics/v2/tools/cosine-neutral-loss.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - bittremieux/cosine_neutral_loss
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: null
 techniques:
 - LC-MS
 - CE-MS
diff --git a/collections/metabolomics/v2/tools/cox-nnet.yaml b/collections/metabolomics/v2/tools/cox-nnet.yaml
index 0555627ea..364ed690e 100644
--- a/collections/metabolomics/v2/tools/cox-nnet.yaml
+++ b/collections/metabolomics/v2/tools/cox-nnet.yaml
@@ -9,5 +9,8 @@ derived_from:
 source_repos:
 - lanagarmire/lilikoi2
 schema_version: 0.2.0
+license_tier: open
+license: GPL-3.0
+license_detection: github-api
 techniques:
 - LC-MS
diff --git a/collections/metabolomics/v2/tools/cox-ph.yaml b/collections/metabolomics/v2/tools/cox-ph.yaml
index eb7682c25..2366d5351 100644
--- a/collections/metabolomics/v2/tools/cox-ph.yaml
+++ b/collections/metabolomics/v2/tools/cox-ph.yaml
@@ -9,5 +9,8 @@ derived_from:
 source_repos:
 - lanagarmire/lilikoi2
 schema_version: 0.2.0
+license_tier: open
+license: GPL-3.0
+license_detection: github-api
 techniques:
 - LC-MS
diff --git a/collections/metabolomics/v2/tools/cpat.yaml b/collections/metabolomics/v2/tools/cpat.yaml
index ccd8b744e..88113b9d8 100644
--- a/collections/metabolomics/v2/tools/cpat.yaml
+++ b/collections/metabolomics/v2/tools/cpat.yaml
@@ -9,3 +9,6 @@ derived_from:
 source_repos:
 - ASAGlab/MOI--An-integrated-solution-for-omics-analyses
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
diff --git a/collections/metabolomics/v2/tools/crest.yaml b/collections/metabolomics/v2/tools/crest.yaml
index 695cc52f0..d956b9162 100644
--- a/collections/metabolomics/v2/tools/crest.yaml
+++ b/collections/metabolomics/v2/tools/crest.yaml
@@ -10,6 +10,9 @@ derived_from:
 source_repos:
 - grimme-lab/QCxMS2
 schema_version: 0.2.0
+license_tier: open
+license: LGPL-3.0
+license_detection: github-api
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/csi-fingerid.yaml b/collections/metabolomics/v2/tools/csi-fingerid.yaml
index 1bc012668..55030b854 100644
--- a/collections/metabolomics/v2/tools/csi-fingerid.yaml
+++ b/collections/metabolomics/v2/tools/csi-fingerid.yaml
@@ -11,6 +11,9 @@ derived_from:
 source_repos:
 - sirius-ms/sirius
 schema_version: 0.2.0
+license_tier: open
+license: AGPL-3.0
+license_detection: github-api
 techniques:
 - LC-MS
 - CE-MS
diff --git a/collections/metabolomics/v2/tools/cts.yaml b/collections/metabolomics/v2/tools/cts.yaml
index 3c7899450..cca8890eb 100644
--- a/collections/metabolomics/v2/tools/cts.yaml
+++ b/collections/metabolomics/v2/tools/cts.yaml
@@ -15,6 +15,9 @@ source_repos:
 - RECETOX/MSMetaEnhancer
 - rickhelmus/patRoon
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/cuda-toolkit.yaml b/collections/metabolomics/v2/tools/cuda-toolkit.yaml
index 1ff198e6f..1feda6c6d 100644
--- a/collections/metabolomics/v2/tools/cuda-toolkit.yaml
+++ b/collections/metabolomics/v2/tools/cuda-toolkit.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - Noble-Lab/casanovo
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - MS-imaging
diff --git a/collections/metabolomics/v2/tools/cuda.yaml b/collections/metabolomics/v2/tools/cuda.yaml
index 34ff9258b..8792091a1 100644
--- a/collections/metabolomics/v2/tools/cuda.yaml
+++ b/collections/metabolomics/v2/tools/cuda.yaml
@@ -23,6 +23,9 @@ source_repos:
 - sword-nan/SpecEmbedding
 - wh-xu/Hyper-Spec
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - CE-MS
diff --git a/collections/metabolomics/v2/tools/cudnn.yaml b/collections/metabolomics/v2/tools/cudnn.yaml
index 49ad252bb..875804d24 100644
--- a/collections/metabolomics/v2/tools/cudnn.yaml
+++ b/collections/metabolomics/v2/tools/cudnn.yaml
@@ -10,3 +10,6 @@ derived_from:
 source_repos:
 - chensaian/TransG-Net
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
diff --git a/collections/metabolomics/v2/tools/curl.yaml b/collections/metabolomics/v2/tools/curl.yaml
index 0fe9a606f..138a0b170 100644
--- a/collections/metabolomics/v2/tools/curl.yaml
+++ b/collections/metabolomics/v2/tools/curl.yaml
@@ -9,5 +9,8 @@ derived_from:
 source_repos:
 - ComPlat/chem-spectra-app
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
 techniques:
 - NMR
diff --git a/collections/metabolomics/v2/tools/cyclobranch.yaml b/collections/metabolomics/v2/tools/cyclobranch.yaml
index ec20f9089..fc9782587 100644
--- a/collections/metabolomics/v2/tools/cyclobranch.yaml
+++ b/collections/metabolomics/v2/tools/cyclobranch.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - privrja/MassSpecBlocks
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
 techniques:
 - LC-MS
 - CE-MS
diff --git a/collections/metabolomics/v2/tools/cypreact.yaml b/collections/metabolomics/v2/tools/cypreact.yaml
index a1ba61578..c10a1df82 100644
--- a/collections/metabolomics/v2/tools/cypreact.yaml
+++ b/collections/metabolomics/v2/tools/cypreact.yaml
@@ -10,3 +10,6 @@ derived_from:
 source_repos:
 - https://bitbucket.org/Leon_Ti/cypreact.git
 schema_version: 0.2.0
+license_tier: restricted
+license: no LICENSE file found (verified 2026-06-24)
+license_detection: null
diff --git a/collections/metabolomics/v2/tools/cyproduct.yaml b/collections/metabolomics/v2/tools/cyproduct.yaml
index 20089d322..d9092e2f2 100644
--- a/collections/metabolomics/v2/tools/cyproduct.yaml
+++ b/collections/metabolomics/v2/tools/cyproduct.yaml
@@ -9,3 +9,6 @@ derived_from:
 source_repos:
 - Le0nT1/CyProduct
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
diff --git a/collections/metabolomics/v2/tools/cytoscape-js.yaml b/collections/metabolomics/v2/tools/cytoscape-js.yaml
index 7e003ad3d..afe80d3fc 100644
--- a/collections/metabolomics/v2/tools/cytoscape-js.yaml
+++ b/collections/metabolomics/v2/tools/cytoscape-js.yaml
@@ -9,3 +9,6 @@ derived_from:
 source_repos:
 - dgrapov/MetaMapR
 schema_version: 0.2.0
+license_tier: open
+license: AGPL-3.0
+license_detection: license-file
diff --git a/collections/metabolomics/v2/tools/cytoscape.yaml b/collections/metabolomics/v2/tools/cytoscape.yaml
index 57108b93c..39cf56b24 100644
--- a/collections/metabolomics/v2/tools/cytoscape.yaml
+++ b/collections/metabolomics/v2/tools/cytoscape.yaml
@@ -25,6 +25,9 @@ source_repos:
 - Karnovsky-Lab/DNEA
 - lanagarmire/lilikoi2
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: file-present-unclassified
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/d3-js.yaml b/collections/metabolomics/v2/tools/d3-js.yaml
index 0aa977182..39a4f9695 100644
--- a/collections/metabolomics/v2/tools/d3-js.yaml
+++ b/collections/metabolomics/v2/tools/d3-js.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - Wang-Bioinformatics-Lab/NetworkFamily_MultipleAlignment_Website
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: file-present-unclassified
 techniques:
 - LC-MS
 - mass-spectrometry
diff --git a/collections/metabolomics/v2/tools/data-table.yaml b/collections/metabolomics/v2/tools/data-table.yaml
index 6084f5755..43b00cac7 100644
--- a/collections/metabolomics/v2/tools/data-table.yaml
+++ b/collections/metabolomics/v2/tools/data-table.yaml
@@ -14,6 +14,9 @@ source_repos:
 - BalunasLab/mpact
 - BiosystemEngineeringLab-IITB/dures
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: file-present-unclassified
 techniques:
 - LC-MS
 - CE-MS
diff --git a/collections/metabolomics/v2/tools/dbdipy.yaml b/collections/metabolomics/v2/tools/dbdipy.yaml
index 03198a8ac..96e8daa31 100644
--- a/collections/metabolomics/v2/tools/dbdipy.yaml
+++ b/collections/metabolomics/v2/tools/dbdipy.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - leopold-weidner/DBDIpy
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: readme-llm
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/dbnorm.yaml b/collections/metabolomics/v2/tools/dbnorm.yaml
index c2321791a..8e37abc38 100644
--- a/collections/metabolomics/v2/tools/dbnorm.yaml
+++ b/collections/metabolomics/v2/tools/dbnorm.yaml
@@ -10,3 +10,6 @@ derived_from:
 source_repos:
 - NBDZ/dbnorm
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
diff --git a/collections/metabolomics/v2/tools/decision-tree-classifier-scikit-learn-or-equivalent-tree-based-ml-framework.yaml b/collections/metabolomics/v2/tools/decision-tree-classifier-scikit-learn-or-equivalent-tree-based-ml-framework.yaml
index f885e897d..33e44acb8 100644
--- a/collections/metabolomics/v2/tools/decision-tree-classifier-scikit-learn-or-equivalent-tree-based-ml-framework.yaml
+++ b/collections/metabolomics/v2/tools/decision-tree-classifier-scikit-learn-or-equivalent-tree-based-ml-framework.yaml
@@ -9,5 +9,8 @@ derived_from:
 source_repos:
 - biorack/chemecho
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
diff --git a/collections/metabolomics/v2/tools/decometdia.yaml b/collections/metabolomics/v2/tools/decometdia.yaml
index e72c40f78..a8dd13be7 100644
--- a/collections/metabolomics/v2/tools/decometdia.yaml
+++ b/collections/metabolomics/v2/tools/decometdia.yaml
@@ -9,5 +9,8 @@ derived_from:
 source_repos:
 - ZhuMSLab/DecoMetDIA
 schema_version: 0.2.0
+license_tier: noncommercial
+license: CC-BY-NC-ND-4.0
+license_detection: readme-llm
 techniques:
 - LC-MS
diff --git a/collections/metabolomics/v2/tools/deepmass2.yaml b/collections/metabolomics/v2/tools/deepmass2.yaml
index ea28e2d60..c610b9ac1 100644
--- a/collections/metabolomics/v2/tools/deepmass2.yaml
+++ b/collections/metabolomics/v2/tools/deepmass2.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - hcji/DeepMASS2_Data_Processing
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - ion-mobility-MS
diff --git a/collections/metabolomics/v2/tools/deimos.yaml b/collections/metabolomics/v2/tools/deimos.yaml
index bfa528591..a8b83bdf3 100644
--- a/collections/metabolomics/v2/tools/deimos.yaml
+++ b/collections/metabolomics/v2/tools/deimos.yaml
@@ -8,6 +8,9 @@ derived_from:
 - doi: 10.1021/acs.analchem.1c05017
   title: deimos
 schema_version: 0.2.0
+license_tier: open
+license: BSD-3-Clause
+license_detection: github-api
 techniques:
 - LC-MS
 - direct-infusion-MS
diff --git a/collections/metabolomics/v2/tools/deoptim.yaml b/collections/metabolomics/v2/tools/deoptim.yaml
index bd72d2fc2..93eebf691 100644
--- a/collections/metabolomics/v2/tools/deoptim.yaml
+++ b/collections/metabolomics/v2/tools/deoptim.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - BiosystemEngineeringLab-IITB/dures
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: file-present-unclassified
 techniques:
 - LC-MS
 - CE-MS
diff --git a/collections/metabolomics/v2/tools/depthcharge.yaml b/collections/metabolomics/v2/tools/depthcharge.yaml
index a8f2d8919..5721e3ea3 100644
--- a/collections/metabolomics/v2/tools/depthcharge.yaml
+++ b/collections/metabolomics/v2/tools/depthcharge.yaml
@@ -10,6 +10,9 @@ derived_from:
 source_repos:
 - Noble-Lab/casanovo
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - MS-imaging
diff --git a/collections/metabolomics/v2/tools/dereplicator.yaml b/collections/metabolomics/v2/tools/dereplicator.yaml
index 31a359cc0..2f7727086 100644
--- a/collections/metabolomics/v2/tools/dereplicator.yaml
+++ b/collections/metabolomics/v2/tools/dereplicator.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - ablab/npdtools
 schema_version: 0.2.0
+license_tier: open
+license: Apache-2.0
+license_detection: readme-llm
 techniques:
 - LC-MS
 - direct-infusion-MS
diff --git a/collections/metabolomics/v2/tools/deseq2.yaml b/collections/metabolomics/v2/tools/deseq2.yaml
index 9979760b2..bf719eca7 100644
--- a/collections/metabolomics/v2/tools/deseq2.yaml
+++ b/collections/metabolomics/v2/tools/deseq2.yaml
@@ -10,3 +10,6 @@ derived_from:
 source_repos:
 - ASAGlab/MOI--An-integrated-solution-for-omics-analyses
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
diff --git a/collections/metabolomics/v2/tools/devtools.yaml b/collections/metabolomics/v2/tools/devtools.yaml
index 56c64d227..136e7cec4 100644
--- a/collections/metabolomics/v2/tools/devtools.yaml
+++ b/collections/metabolomics/v2/tools/devtools.yaml
@@ -31,6 +31,9 @@ source_repos:
 - kilgain/MassSpec
 - komorowskilab/MetaFetcheR
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/dgl.yaml b/collections/metabolomics/v2/tools/dgl.yaml
index e7e61c091..5c032695e 100644
--- a/collections/metabolomics/v2/tools/dgl.yaml
+++ b/collections/metabolomics/v2/tools/dgl.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - HopkinsLaboratory/Graphormer-RT
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - ion-mobility-MS
diff --git a/collections/metabolomics/v2/tools/di-ms.yaml b/collections/metabolomics/v2/tools/di-ms.yaml
index 1f5d426a2..d4a794ec7 100644
--- a/collections/metabolomics/v2/tools/di-ms.yaml
+++ b/collections/metabolomics/v2/tools/di-ms.yaml
@@ -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
diff --git a/collections/metabolomics/v2/tools/dia-nn.yaml b/collections/metabolomics/v2/tools/dia-nn.yaml
index 74ef8deeb..76212d810 100644
--- a/collections/metabolomics/v2/tools/dia-nn.yaml
+++ b/collections/metabolomics/v2/tools/dia-nn.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - Roestlab/massdash
 schema_version: 0.2.0
+license_tier: open
+license: BSD-3-Clause
+license_detection: github-api
 techniques:
 - LC-MS
 - ion-mobility-MS
diff --git a/collections/metabolomics/v2/tools/diffspectra.yaml b/collections/metabolomics/v2/tools/diffspectra.yaml
index 906a1c564..aabc467fa 100644
--- a/collections/metabolomics/v2/tools/diffspectra.yaml
+++ b/collections/metabolomics/v2/tools/diffspectra.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - AzureLeon1/DiffSpectra
 schema_version: 0.2.0
+license_tier: open
+license: Apache-2.0
+license_detection: github-api
 techniques:
 - NMR
 - mass-spectrometry
diff --git a/collections/metabolomics/v2/tools/dimorphite-dl.yaml b/collections/metabolomics/v2/tools/dimorphite-dl.yaml
index a724c426f..a6f25efca 100644
--- a/collections/metabolomics/v2/tools/dimorphite-dl.yaml
+++ b/collections/metabolomics/v2/tools/dimorphite-dl.yaml
@@ -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
diff --git a/collections/metabolomics/v2/tools/django.yaml b/collections/metabolomics/v2/tools/django.yaml
index 1e380160b..0024a8bb6 100644
--- a/collections/metabolomics/v2/tools/django.yaml
+++ b/collections/metabolomics/v2/tools/django.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - RTKlab-BYU/MSConnect
 schema_version: 0.2.0
+license_tier: open
+license: Apache-2.0
+license_detection: github-api
 techniques:
 - LC-MS
 - mass-spectrometry
diff --git a/collections/metabolomics/v2/tools/docker-compose.yaml b/collections/metabolomics/v2/tools/docker-compose.yaml
index 4d691139c..015d38deb 100644
--- a/collections/metabolomics/v2/tools/docker-compose.yaml
+++ b/collections/metabolomics/v2/tools/docker-compose.yaml
@@ -11,6 +11,9 @@ derived_from:
 source_repos:
 - mwang87/NP-Classifier
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
 techniques:
 - ion-mobility-MS
 - mass-spectrometry
diff --git a/collections/metabolomics/v2/tools/docker-desktop-for-mac.yaml b/collections/metabolomics/v2/tools/docker-desktop-for-mac.yaml
index aac8503a3..86c22b15f 100644
--- a/collections/metabolomics/v2/tools/docker-desktop-for-mac.yaml
+++ b/collections/metabolomics/v2/tools/docker-desktop-for-mac.yaml
@@ -9,6 +9,9 @@ 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:
 - ion-mobility-MS
 - mass-spectrometry
diff --git a/collections/metabolomics/v2/tools/docker-docker-build-docker-inspect-docker-system-df.yaml b/collections/metabolomics/v2/tools/docker-docker-build-docker-inspect-docker-system-df.yaml
index 308559ed8..f7085f14e 100644
--- a/collections/metabolomics/v2/tools/docker-docker-build-docker-inspect-docker-system-df.yaml
+++ b/collections/metabolomics/v2/tools/docker-docker-build-docker-inspect-docker-system-df.yaml
@@ -6,3 +6,6 @@ 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
diff --git a/collections/metabolomics/v2/tools/docker-engine.yaml b/collections/metabolomics/v2/tools/docker-engine.yaml
index 3de5b3f8b..96f1e3ca3 100644
--- a/collections/metabolomics/v2/tools/docker-engine.yaml
+++ b/collections/metabolomics/v2/tools/docker-engine.yaml
@@ -6,6 +6,9 @@ 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:
 - ion-mobility-MS
 - mass-spectrometry
diff --git a/collections/metabolomics/v2/tools/docker.yaml b/collections/metabolomics/v2/tools/docker.yaml
index 78be47e41..d24aa726a 100644
--- a/collections/metabolomics/v2/tools/docker.yaml
+++ b/collections/metabolomics/v2/tools/docker.yaml
@@ -63,6 +63,9 @@ source_repos:
 - vdhooftcompmet/MS2LDA
 - volvox292/mass2smiles
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/dockerfile-multi-stage-build-with-target-flag.yaml b/collections/metabolomics/v2/tools/dockerfile-multi-stage-build-with-target-flag.yaml
index 5ea302648..5cc42c023 100644
--- a/collections/metabolomics/v2/tools/dockerfile-multi-stage-build-with-target-flag.yaml
+++ b/collections/metabolomics/v2/tools/dockerfile-multi-stage-build-with-target-flag.yaml
@@ -6,3 +6,6 @@ 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
diff --git a/collections/metabolomics/v2/tools/doparallel.yaml b/collections/metabolomics/v2/tools/doparallel.yaml
index 2e7858b88..3bee214eb 100644
--- a/collections/metabolomics/v2/tools/doparallel.yaml
+++ b/collections/metabolomics/v2/tools/doparallel.yaml
@@ -9,5 +9,8 @@ derived_from:
 source_repos:
 - antonvsdata/notame
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
diff --git a/collections/metabolomics/v2/tools/dplyr.yaml b/collections/metabolomics/v2/tools/dplyr.yaml
index d7c615f80..f2f935c46 100644
--- a/collections/metabolomics/v2/tools/dplyr.yaml
+++ b/collections/metabolomics/v2/tools/dplyr.yaml
@@ -23,6 +23,9 @@ source_repos:
 - SydneyBioX/hRUV
 - kilgain/MassSpec
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: file-present-unclassified
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/dropms.yaml b/collections/metabolomics/v2/tools/dropms.yaml
index 8f0da2271..ae94e9cd7 100644
--- a/collections/metabolomics/v2/tools/dropms.yaml
+++ b/collections/metabolomics/v2/tools/dropms.yaml
@@ -6,6 +6,9 @@ derived_from:
 - doi: 10.1186/s40168-023-01476-3
   title: MetaboDirect
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/drugbank-extraction-py.yaml b/collections/metabolomics/v2/tools/drugbank-extraction-py.yaml
index 95bc9c14d..d7be27321 100644
--- a/collections/metabolomics/v2/tools/drugbank-extraction-py.yaml
+++ b/collections/metabolomics/v2/tools/drugbank-extraction-py.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - corinnabrungs/msn_tree_library
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
 techniques:
 - GC-MS
 - mass-spectrometry
diff --git a/collections/metabolomics/v2/tools/drugbank.yaml b/collections/metabolomics/v2/tools/drugbank.yaml
index 71a9c75f3..e8982472d 100644
--- a/collections/metabolomics/v2/tools/drugbank.yaml
+++ b/collections/metabolomics/v2/tools/drugbank.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - daniellyz/meRgeION2
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - CE-MS
diff --git a/collections/metabolomics/v2/tools/dures.yaml b/collections/metabolomics/v2/tools/dures.yaml
index 512d7468f..465306a95 100644
--- a/collections/metabolomics/v2/tools/dures.yaml
+++ b/collections/metabolomics/v2/tools/dures.yaml
@@ -9,5 +9,8 @@ derived_from:
 source_repos:
 - BiosystemEngineeringLab-IITB/dures
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: file-present-unclassified
 techniques:
 - LC-MS
diff --git a/collections/metabolomics/v2/tools/dynaconf.yaml b/collections/metabolomics/v2/tools/dynaconf.yaml
index 92b9a5fd6..87855e704 100644
--- a/collections/metabolomics/v2/tools/dynaconf.yaml
+++ b/collections/metabolomics/v2/tools/dynaconf.yaml
@@ -9,5 +9,8 @@ derived_from:
 source_repos:
 - NPLinker/nplinker
 schema_version: 0.2.0
+license_tier: open
+license: Apache-2.0
+license_detection: github-api
 techniques:
 - LC-MS
diff --git a/collections/metabolomics/v2/tools/dynamic-time-warping-dtw.yaml b/collections/metabolomics/v2/tools/dynamic-time-warping-dtw.yaml
index 4a8c9165e..bdfdc1591 100644
--- a/collections/metabolomics/v2/tools/dynamic-time-warping-dtw.yaml
+++ b/collections/metabolomics/v2/tools/dynamic-time-warping-dtw.yaml
@@ -9,5 +9,8 @@ derived_from:
 source_repos:
 - ChiungTingWu/ncGTW
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
diff --git a/collections/metabolomics/v2/tools/dynamictreecut.yaml b/collections/metabolomics/v2/tools/dynamictreecut.yaml
index e792dfe40..76ba14cd9 100644
--- a/collections/metabolomics/v2/tools/dynamictreecut.yaml
+++ b/collections/metabolomics/v2/tools/dynamictreecut.yaml
@@ -10,6 +10,9 @@ derived_from:
 source_repos:
 - cbroeckl/RAMClustR
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/edger.yaml b/collections/metabolomics/v2/tools/edger.yaml
index e26f8d2d5..87d86022c 100644
--- a/collections/metabolomics/v2/tools/edger.yaml
+++ b/collections/metabolomics/v2/tools/edger.yaml
@@ -15,5 +15,8 @@ source_repos:
 - ASAGlab/MOI--An-integrated-solution-for-omics-analyses
 - ShinyFabio/ADViSELipidomics
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
 techniques:
 - mass-spectrometry
diff --git a/collections/metabolomics/v2/tools/eflux.yaml b/collections/metabolomics/v2/tools/eflux.yaml
index 02a49f5db..2176997b4 100644
--- a/collections/metabolomics/v2/tools/eflux.yaml
+++ b/collections/metabolomics/v2/tools/eflux.yaml
@@ -7,5 +7,8 @@ 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
diff --git a/collections/metabolomics/v2/tools/elastic-net-regression.yaml b/collections/metabolomics/v2/tools/elastic-net-regression.yaml
index ecf8cb7a7..d54c68d15 100644
--- a/collections/metabolomics/v2/tools/elastic-net-regression.yaml
+++ b/collections/metabolomics/v2/tools/elastic-net-regression.yaml
@@ -6,3 +6,6 @@ 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
diff --git a/collections/metabolomics/v2/tools/elastic-net.yaml b/collections/metabolomics/v2/tools/elastic-net.yaml
index d59898d7a..6c377865a 100644
--- a/collections/metabolomics/v2/tools/elastic-net.yaml
+++ b/collections/metabolomics/v2/tools/elastic-net.yaml
@@ -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
 - NMR
diff --git a/collections/metabolomics/v2/tools/elemcor.yaml b/collections/metabolomics/v2/tools/elemcor.yaml
index 65fb9bdf5..6bcfb8de5 100644
--- a/collections/metabolomics/v2/tools/elemcor.yaml
+++ b/collections/metabolomics/v2/tools/elemcor.yaml
@@ -10,6 +10,9 @@ derived_from:
 source_repos:
 - 4dsoftware/elemcor
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
 techniques:
 - LC-MS
 - NMR
diff --git a/collections/metabolomics/v2/tools/elementtree.yaml b/collections/metabolomics/v2/tools/elementtree.yaml
index 59d049bbe..f04d8d9f0 100644
--- a/collections/metabolomics/v2/tools/elementtree.yaml
+++ b/collections/metabolomics/v2/tools/elementtree.yaml
@@ -6,5 +6,8 @@ derived_from:
 - doi: 10.1093/bioinformatics/bty046
   title: pymzml
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
 techniques:
 - mass-spectrometry
diff --git a/collections/metabolomics/v2/tools/email-service.yaml b/collections/metabolomics/v2/tools/email-service.yaml
index 3c5971848..d330671d5 100644
--- a/collections/metabolomics/v2/tools/email-service.yaml
+++ b/collections/metabolomics/v2/tools/email-service.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - czbiohub-sf/Rapid-QC-MS
 schema_version: 0.2.0
+license_tier: open
+license: BSD-3-Clause
+license_detection: license-file
 techniques:
 - LC-MS
 - CE-MS
diff --git a/collections/metabolomics/v2/tools/emperor.yaml b/collections/metabolomics/v2/tools/emperor.yaml
index fa15eda2d..cada9acff 100644
--- a/collections/metabolomics/v2/tools/emperor.yaml
+++ b/collections/metabolomics/v2/tools/emperor.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - mwang87/ReDU-MS2-Documentation
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - CE-MS
diff --git a/collections/metabolomics/v2/tools/enpkg.yaml b/collections/metabolomics/v2/tools/enpkg.yaml
index 893fb2413..1b2ac79f4 100644
--- a/collections/metabolomics/v2/tools/enpkg.yaml
+++ b/collections/metabolomics/v2/tools/enpkg.yaml
@@ -6,5 +6,8 @@ derived_from:
 - doi: 10.1021/acscentsci.3c00800
   title: A Sample-Centric and Knowledge-Driven Computational Framework for Natural Products Drug Discovery
 schema_version: 0.2.0
+license_tier: open
+license: GPL-3.0
+license_detection: github-api
 techniques:
 - LC-MS
diff --git a/collections/metabolomics/v2/tools/entropy-search.yaml b/collections/metabolomics/v2/tools/entropy-search.yaml
index 41e3af1ab..19d4fba4a 100644
--- a/collections/metabolomics/v2/tools/entropy-search.yaml
+++ b/collections/metabolomics/v2/tools/entropy-search.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - YuanyueLi/FlashEntropySearch
 schema_version: 0.2.0
+license_tier: open
+license: Apache-2.0
+license_detection: github-api
 techniques:
 - LC-MS
 - mass-spectrometry
diff --git a/collections/metabolomics/v2/tools/enveda-ccs-prediction-repository-model-code-and-pre-trained-weights.yaml b/collections/metabolomics/v2/tools/enveda-ccs-prediction-repository-model-code-and-pre-trained-weights.yaml
index 82bf2d1b7..968b7bd67 100644
--- a/collections/metabolomics/v2/tools/enveda-ccs-prediction-repository-model-code-and-pre-trained-weights.yaml
+++ b/collections/metabolomics/v2/tools/enveda-ccs-prediction-repository-model-code-and-pre-trained-weights.yaml
@@ -6,5 +6,8 @@ derived_from:
 - doi: 10.1186/s13321-024-00899-w
   title: mol2ccs
 schema_version: 0.2.0
+license_tier: open
+license: GPL-2.0
+license_detection: github-api
 techniques:
 - ion-mobility-MS
diff --git a/collections/metabolomics/v2/tools/envipat.yaml b/collections/metabolomics/v2/tools/envipat.yaml
index 87e6f4fb0..8c0a0ea2a 100644
--- a/collections/metabolomics/v2/tools/envipat.yaml
+++ b/collections/metabolomics/v2/tools/envipat.yaml
@@ -13,6 +13,9 @@ source_repos:
 - YasinEl/mzRAPP
 - jcapelladesto/isoSCAN
 schema_version: 0.2.0
+license_tier: open
+license: GPL-3.0
+license_detection: github-api
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/environment.yaml b/collections/metabolomics/v2/tools/environment.yaml
index ff4d95b9d..94ae45da5 100644
--- a/collections/metabolomics/v2/tools/environment.yaml
+++ b/collections/metabolomics/v2/tools/environment.yaml
@@ -6,5 +6,8 @@ derived_from:
 - doi: 10.1021/acs.analchem.0c03895
   title: Rapid Development of Improved Data-Dependent Acquisition Strategies
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
diff --git a/collections/metabolomics/v2/tools/excalibur.yaml b/collections/metabolomics/v2/tools/excalibur.yaml
index 68ce8ca4f..a02523bca 100644
--- a/collections/metabolomics/v2/tools/excalibur.yaml
+++ b/collections/metabolomics/v2/tools/excalibur.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - 98104781/LSG
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - CE-MS
diff --git a/collections/metabolomics/v2/tools/expressionset.yaml b/collections/metabolomics/v2/tools/expressionset.yaml
index ddcffa8ea..7206db502 100644
--- a/collections/metabolomics/v2/tools/expressionset.yaml
+++ b/collections/metabolomics/v2/tools/expressionset.yaml
@@ -9,5 +9,8 @@ derived_from:
 source_repos:
 - antonvsdata/notame
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
diff --git a/collections/metabolomics/v2/tools/factoextra.yaml b/collections/metabolomics/v2/tools/factoextra.yaml
index c5e1678df..ebcddbebb 100644
--- a/collections/metabolomics/v2/tools/factoextra.yaml
+++ b/collections/metabolomics/v2/tools/factoextra.yaml
@@ -9,5 +9,8 @@ derived_from:
 source_repos:
 - LargeMetabo/LargeMetabo
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - mass-spectrometry
diff --git a/collections/metabolomics/v2/tools/falcon.yaml b/collections/metabolomics/v2/tools/falcon.yaml
index ebad7a081..ee70fdbe5 100644
--- a/collections/metabolomics/v2/tools/falcon.yaml
+++ b/collections/metabolomics/v2/tools/falcon.yaml
@@ -6,6 +6,9 @@ derived_from:
 - doi: 10.1002/rcm.9153
   title: Large‐scale tandem mass spectrum clustering using fast nearest neighbor searching
 schema_version: 0.2.0
+license_tier: open
+license: BSD-3-Clause
+license_detection: github-api
 techniques:
 - LC-MS
 - ion-mobility-MS
diff --git a/collections/metabolomics/v2/tools/fastqc.yaml b/collections/metabolomics/v2/tools/fastqc.yaml
index adb8aa840..2102cc16d 100644
--- a/collections/metabolomics/v2/tools/fastqc.yaml
+++ b/collections/metabolomics/v2/tools/fastqc.yaml
@@ -10,3 +10,6 @@ derived_from:
 source_repos:
 - ASAGlab/MOI--An-integrated-solution-for-omics-analyses
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
diff --git a/collections/metabolomics/v2/tools/featurefindermetabo.yaml b/collections/metabolomics/v2/tools/featurefindermetabo.yaml
index 840aa0adb..a0682b310 100644
--- a/collections/metabolomics/v2/tools/featurefindermetabo.yaml
+++ b/collections/metabolomics/v2/tools/featurefindermetabo.yaml
@@ -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
diff --git a/collections/metabolomics/v2/tools/fella.yaml b/collections/metabolomics/v2/tools/fella.yaml
index 5a053a30d..19c489912 100644
--- a/collections/metabolomics/v2/tools/fella.yaml
+++ b/collections/metabolomics/v2/tools/fella.yaml
@@ -9,5 +9,8 @@ derived_from:
 source_repos:
 - b2slab/mWISE
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
diff --git a/collections/metabolomics/v2/tools/fgsea.yaml b/collections/metabolomics/v2/tools/fgsea.yaml
index 95ab251ad..42e813c74 100644
--- a/collections/metabolomics/v2/tools/fgsea.yaml
+++ b/collections/metabolomics/v2/tools/fgsea.yaml
@@ -9,5 +9,8 @@ derived_from:
 source_repos:
 - biodatalab/enrichmet
 schema_version: 0.2.0
+license_tier: open
+license: AGPL-3.0
+license_detection: github-api
 techniques:
 - LC-MS
diff --git a/collections/metabolomics/v2/tools/fiddle.yaml b/collections/metabolomics/v2/tools/fiddle.yaml
index b469d1159..17f47ebe9 100644
--- a/collections/metabolomics/v2/tools/fiddle.yaml
+++ b/collections/metabolomics/v2/tools/fiddle.yaml
@@ -6,6 +6,9 @@ derived_from:
 - doi: 10.1038/s41467-025-66060-9
   title: fiddle
 schema_version: 0.2.0
+license_tier: open
+license: Apache-2.0
+license_detection: github-api
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/figshare.yaml b/collections/metabolomics/v2/tools/figshare.yaml
index 5eebf010a..5f3ee84e7 100644
--- a/collections/metabolomics/v2/tools/figshare.yaml
+++ b/collections/metabolomics/v2/tools/figshare.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - sword-nan/SpecEmbedding
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - MS-imaging
diff --git a/collections/metabolomics/v2/tools/filtering-augmentation.yaml b/collections/metabolomics/v2/tools/filtering-augmentation.yaml
index 258fca32c..28e9b66bf 100644
--- a/collections/metabolomics/v2/tools/filtering-augmentation.yaml
+++ b/collections/metabolomics/v2/tools/filtering-augmentation.yaml
@@ -6,5 +6,8 @@ derived_from:
 - doi: 10.1021/acs.analchem.3c05002
   title: deepion
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - MS-imaging
diff --git a/collections/metabolomics/v2/tools/fimo.yaml b/collections/metabolomics/v2/tools/fimo.yaml
index 3dd6b3d0f..0e2d5fafa 100644
--- a/collections/metabolomics/v2/tools/fimo.yaml
+++ b/collections/metabolomics/v2/tools/fimo.yaml
@@ -9,3 +9,6 @@ derived_from:
 source_repos:
 - ASAGlab/MOI--An-integrated-solution-for-omics-analyses
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
diff --git a/collections/metabolomics/v2/tools/fisher-s-exact-test.yaml b/collections/metabolomics/v2/tools/fisher-s-exact-test.yaml
index 1f2a1f9b7..a94ae23ff 100644
--- a/collections/metabolomics/v2/tools/fisher-s-exact-test.yaml
+++ b/collections/metabolomics/v2/tools/fisher-s-exact-test.yaml
@@ -9,5 +9,8 @@ derived_from:
 source_repos:
 - biodatalab/enrichmet
 schema_version: 0.2.0
+license_tier: open
+license: AGPL-3.0
+license_detection: github-api
 techniques:
 - LC-MS
diff --git a/collections/metabolomics/v2/tools/flake8.yaml b/collections/metabolomics/v2/tools/flake8.yaml
index 96394c586..9452b1518 100644
--- a/collections/metabolomics/v2/tools/flake8.yaml
+++ b/collections/metabolomics/v2/tools/flake8.yaml
@@ -9,5 +9,8 @@ derived_from:
 source_repos:
 - medema-group/BiG-SCAPE
 schema_version: 0.2.0
+license_tier: open
+license: AGPL-3.0
+license_detection: github-api
 techniques:
 - LC-MS
diff --git a/collections/metabolomics/v2/tools/flask.yaml b/collections/metabolomics/v2/tools/flask.yaml
index ac8f5c6c5..95ec4e8b5 100644
--- a/collections/metabolomics/v2/tools/flask.yaml
+++ b/collections/metabolomics/v2/tools/flask.yaml
@@ -10,6 +10,9 @@ derived_from:
 source_repos:
 - ComPlat/chem-spectra-app
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
 techniques:
 - LC-MS
 - MS-imaging
diff --git a/collections/metabolomics/v2/tools/flux-variability-analysis-fva.yaml b/collections/metabolomics/v2/tools/flux-variability-analysis-fva.yaml
index 57da39115..89af3e447 100644
--- a/collections/metabolomics/v2/tools/flux-variability-analysis-fva.yaml
+++ b/collections/metabolomics/v2/tools/flux-variability-analysis-fva.yaml
@@ -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
diff --git a/collections/metabolomics/v2/tools/flux-variability-analysis.yaml b/collections/metabolomics/v2/tools/flux-variability-analysis.yaml
index e4429e15c..03b8b3a67 100644
--- a/collections/metabolomics/v2/tools/flux-variability-analysis.yaml
+++ b/collections/metabolomics/v2/tools/flux-variability-analysis.yaml
@@ -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
diff --git a/collections/metabolomics/v2/tools/fmcsr.yaml b/collections/metabolomics/v2/tools/fmcsr.yaml
index 63ab54477..6f8bfe256 100644
--- a/collections/metabolomics/v2/tools/fmcsr.yaml
+++ b/collections/metabolomics/v2/tools/fmcsr.yaml
@@ -7,6 +7,9 @@ derived_from:
 - doi: 10.1371/journal.pone.0306202
   title: uafr
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - GC-MS
 - NMR
diff --git a/collections/metabolomics/v2/tools/fnicm.yaml b/collections/metabolomics/v2/tools/fnicm.yaml
index 5beb759c4..3188deae2 100644
--- a/collections/metabolomics/v2/tools/fnicm.yaml
+++ b/collections/metabolomics/v2/tools/fnicm.yaml
@@ -9,3 +9,6 @@ derived_from:
 source_repos:
 - LiQi94/FNICM
 schema_version: 0.2.0
+license_tier: open
+license: AFL-3.0
+license_detection: github-api
diff --git a/collections/metabolomics/v2/tools/foodmasst.yaml b/collections/metabolomics/v2/tools/foodmasst.yaml
index 15f8a922a..024a3943d 100644
--- a/collections/metabolomics/v2/tools/foodmasst.yaml
+++ b/collections/metabolomics/v2/tools/foodmasst.yaml
@@ -11,6 +11,9 @@ derived_from:
 source_repos:
 - mwang87/MASST
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - MS-imaging
diff --git a/collections/metabolomics/v2/tools/formularity.yaml b/collections/metabolomics/v2/tools/formularity.yaml
index d3819d6e0..08de2e3c5 100644
--- a/collections/metabolomics/v2/tools/formularity.yaml
+++ b/collections/metabolomics/v2/tools/formularity.yaml
@@ -7,6 +7,9 @@ derived_from:
 - doi: 10.1186/s40168-023-01476-3
   title: MetaboDirect
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
 techniques:
 - LC-MS
 - direct-infusion-MS
diff --git a/collections/metabolomics/v2/tools/freda.yaml b/collections/metabolomics/v2/tools/freda.yaml
index 99b255a7a..ab94a7bae 100644
--- a/collections/metabolomics/v2/tools/freda.yaml
+++ b/collections/metabolomics/v2/tools/freda.yaml
@@ -6,6 +6,9 @@ derived_from:
 - doi: 10.1186/s40168-023-01476-3
   title: MetaboDirect
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/future-apply.yaml b/collections/metabolomics/v2/tools/future-apply.yaml
index ab9fdfbde..ade2a1952 100644
--- a/collections/metabolomics/v2/tools/future-apply.yaml
+++ b/collections/metabolomics/v2/tools/future-apply.yaml
@@ -6,6 +6,9 @@ derived_from:
 - doi: 10.1021/acs.analchem.2c05389
   title: mspcompiler
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: file-present-unclassified
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/future.yaml b/collections/metabolomics/v2/tools/future.yaml
index 93a1b2cd5..0d792c71a 100644
--- a/collections/metabolomics/v2/tools/future.yaml
+++ b/collections/metabolomics/v2/tools/future.yaml
@@ -6,6 +6,9 @@ derived_from:
 - doi: 10.1021/acs.analchem.2c05389
   title: mspcompiler
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: file-present-unclassified
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/galaxy-genomics-framework.yaml b/collections/metabolomics/v2/tools/galaxy-genomics-framework.yaml
index f2d5e2ea2..8e53b2aa8 100644
--- a/collections/metabolomics/v2/tools/galaxy-genomics-framework.yaml
+++ b/collections/metabolomics/v2/tools/galaxy-genomics-framework.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - secimTools/SECIMTools
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
 techniques:
 - LC-MS
 - mass-spectrometry
diff --git a/collections/metabolomics/v2/tools/galaxy.yaml b/collections/metabolomics/v2/tools/galaxy.yaml
index bf2fca689..1be5924e2 100644
--- a/collections/metabolomics/v2/tools/galaxy.yaml
+++ b/collections/metabolomics/v2/tools/galaxy.yaml
@@ -13,6 +13,9 @@ source_repos:
 - Viant-Metabolomics/Galaxy-M
 - wanchanglin/ionflow
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - CE-MS
diff --git a/collections/metabolomics/v2/tools/gcims.yaml b/collections/metabolomics/v2/tools/gcims.yaml
index 88ec26faa..370e698d6 100644
--- a/collections/metabolomics/v2/tools/gcims.yaml
+++ b/collections/metabolomics/v2/tools/gcims.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - sipss/GCIMS
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: file-present-unclassified
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/gensim.yaml b/collections/metabolomics/v2/tools/gensim.yaml
index b517ca591..689501840 100644
--- a/collections/metabolomics/v2/tools/gensim.yaml
+++ b/collections/metabolomics/v2/tools/gensim.yaml
@@ -16,6 +16,9 @@ source_repos:
 - Qiong-Yang/FastEI
 - vdhooftcompmet/MS2LDA
 schema_version: 0.2.0
+license_tier: open
+license: Apache-2.0
+license_detection: github-api
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/geodesic-interpolate.yaml b/collections/metabolomics/v2/tools/geodesic-interpolate.yaml
index 17c70dbde..717e812c2 100644
--- a/collections/metabolomics/v2/tools/geodesic-interpolate.yaml
+++ b/collections/metabolomics/v2/tools/geodesic-interpolate.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - grimme-lab/QCxMS2
 schema_version: 0.2.0
+license_tier: open
+license: LGPL-3.0
+license_detection: github-api
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/george.yaml b/collections/metabolomics/v2/tools/george.yaml
index a1d40217e..7d52d215c 100644
--- a/collections/metabolomics/v2/tools/george.yaml
+++ b/collections/metabolomics/v2/tools/george.yaml
@@ -10,6 +10,9 @@ derived_from:
 source_repos:
 - jcapelladesto/geoRge
 schema_version: 0.2.0
+license_tier: open
+license: GPL-3.0
+license_detection: github-api
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/get-models-sh.yaml b/collections/metabolomics/v2/tools/get-models-sh.yaml
index 08cf0ae70..b1155016d 100644
--- a/collections/metabolomics/v2/tools/get-models-sh.yaml
+++ b/collections/metabolomics/v2/tools/get-models-sh.yaml
@@ -6,3 +6,6 @@ derived_from:
 - doi: 10.1021/acs.jnatprod.1c00399
   title: npclassifier
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
diff --git a/collections/metabolomics/v2/tools/get-precmz-prodmz.yaml b/collections/metabolomics/v2/tools/get-precmz-prodmz.yaml
index e0c2f9686..49dbc3851 100644
--- a/collections/metabolomics/v2/tools/get-precmz-prodmz.yaml
+++ b/collections/metabolomics/v2/tools/get-precmz-prodmz.yaml
@@ -9,5 +9,8 @@ derived_from:
 source_repos:
 - kslynn128171/MRMQuant
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
diff --git a/collections/metabolomics/v2/tools/getfeatistics.yaml b/collections/metabolomics/v2/tools/getfeatistics.yaml
index 052740862..6a348e32e 100644
--- a/collections/metabolomics/v2/tools/getfeatistics.yaml
+++ b/collections/metabolomics/v2/tools/getfeatistics.yaml
@@ -10,6 +10,9 @@ 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
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/ggplot.yaml b/collections/metabolomics/v2/tools/ggplot.yaml
index c666534b5..03d4e9751 100644
--- a/collections/metabolomics/v2/tools/ggplot.yaml
+++ b/collections/metabolomics/v2/tools/ggplot.yaml
@@ -9,5 +9,8 @@ derived_from:
 source_repos:
 - BalunasLab/mpact
 schema_version: 0.2.0
+license_tier: open
+license: GPL-2.0
+license_detection: github-api
 techniques:
 - LC-MS
diff --git a/collections/metabolomics/v2/tools/ggplot2.yaml b/collections/metabolomics/v2/tools/ggplot2.yaml
index b0b8c4e13..3c8460313 100644
--- a/collections/metabolomics/v2/tools/ggplot2.yaml
+++ b/collections/metabolomics/v2/tools/ggplot2.yaml
@@ -50,6 +50,9 @@ source_repos:
 - kilgain/MassSpec
 - wesleyburr/subMaldi
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: file-present-unclassified
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/git.yaml b/collections/metabolomics/v2/tools/git.yaml
index c8ff0dfc4..2741c649e 100644
--- a/collections/metabolomics/v2/tools/git.yaml
+++ b/collections/metabolomics/v2/tools/git.yaml
@@ -39,6 +39,9 @@ source_repos:
 - zhanghailiangcsu/MSBERT
 - zhanghailiangcsu/MWFormer
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: file-present-unclassified
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/github-actions-workflow-ci-build-yml.yaml b/collections/metabolomics/v2/tools/github-actions-workflow-ci-build-yml.yaml
index 815198b19..5a503546a 100644
--- a/collections/metabolomics/v2/tools/github-actions-workflow-ci-build-yml.yaml
+++ b/collections/metabolomics/v2/tools/github-actions-workflow-ci-build-yml.yaml
@@ -9,3 +9,6 @@ derived_from:
 source_repos:
 - fermo-metabolomics/FERMO
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
diff --git a/collections/metabolomics/v2/tools/github-actions.yaml b/collections/metabolomics/v2/tools/github-actions.yaml
index 4019bcb44..e7cb5820f 100644
--- a/collections/metabolomics/v2/tools/github-actions.yaml
+++ b/collections/metabolomics/v2/tools/github-actions.yaml
@@ -29,6 +29,9 @@ source_repos:
 - iomega/ms2query
 - systemsomicslab/MsdialWorkbench
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - CE-MS
diff --git a/collections/metabolomics/v2/tools/github-com-bittremieux-cosine-neutral-loss.yaml b/collections/metabolomics/v2/tools/github-com-bittremieux-cosine-neutral-loss.yaml
index 5840c12e8..24accdc23 100644
--- a/collections/metabolomics/v2/tools/github-com-bittremieux-cosine-neutral-loss.yaml
+++ b/collections/metabolomics/v2/tools/github-com-bittremieux-cosine-neutral-loss.yaml
@@ -9,5 +9,8 @@ derived_from:
 source_repos:
 - bittremieux/cosine_neutral_loss
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: null
 techniques:
 - CE-MS
diff --git a/collections/metabolomics/v2/tools/github-com-hassounlab-esp.yaml b/collections/metabolomics/v2/tools/github-com-hassounlab-esp.yaml
index 6eeb2b187..5d44b9374 100644
--- a/collections/metabolomics/v2/tools/github-com-hassounlab-esp.yaml
+++ b/collections/metabolomics/v2/tools/github-com-hassounlab-esp.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - HassounLab/ESP
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/github-com-jlichtarge-pcaglasso.yaml b/collections/metabolomics/v2/tools/github-com-jlichtarge-pcaglasso.yaml
index e894d9f5b..d02d0b965 100644
--- a/collections/metabolomics/v2/tools/github-com-jlichtarge-pcaglasso.yaml
+++ b/collections/metabolomics/v2/tools/github-com-jlichtarge-pcaglasso.yaml
@@ -9,3 +9,6 @@ derived_from:
 source_repos:
 - jlichtarge/pcaGLASSO
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
diff --git a/collections/metabolomics/v2/tools/github-com-wanluliulab-spatialmeta.yaml b/collections/metabolomics/v2/tools/github-com-wanluliulab-spatialmeta.yaml
index eef9ccab5..c9dfe91ed 100644
--- a/collections/metabolomics/v2/tools/github-com-wanluliulab-spatialmeta.yaml
+++ b/collections/metabolomics/v2/tools/github-com-wanluliulab-spatialmeta.yaml
@@ -9,3 +9,6 @@ derived_from:
 source_repos:
 - WanluLiuLab/SpatialMETA
 schema_version: 0.2.0
+license_tier: open
+license: BSD-3-Clause
+license_detection: github-api
diff --git a/collections/metabolomics/v2/tools/github-com-zsspython-lagf.yaml b/collections/metabolomics/v2/tools/github-com-zsspython-lagf.yaml
index 29063554d..a0c662f66 100644
--- a/collections/metabolomics/v2/tools/github-com-zsspython-lagf.yaml
+++ b/collections/metabolomics/v2/tools/github-com-zsspython-lagf.yaml
@@ -10,3 +10,6 @@ derived_from:
 source_repos:
 - zsspython/LAGF
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
diff --git a/collections/metabolomics/v2/tools/github-kbseah-mass2adduct.yaml b/collections/metabolomics/v2/tools/github-kbseah-mass2adduct.yaml
index 17959747c..502273c7c 100644
--- a/collections/metabolomics/v2/tools/github-kbseah-mass2adduct.yaml
+++ b/collections/metabolomics/v2/tools/github-kbseah-mass2adduct.yaml
@@ -6,3 +6,6 @@ derived_from:
 - doi: 10.1021/acs.analchem.0c04720
   title: Determination of Abundant Metabolite Matrix Adducts Illuminates the Dark Metabolome of MALDI-Mass Spectrometry Imaging Datasets
 schema_version: 0.2.0
+license_tier: open
+license: GPL-3.0
+license_detection: github-api
diff --git a/collections/metabolomics/v2/tools/github.yaml b/collections/metabolomics/v2/tools/github.yaml
index b4c66f3af..e495a6421 100644
--- a/collections/metabolomics/v2/tools/github.yaml
+++ b/collections/metabolomics/v2/tools/github.yaml
@@ -174,6 +174,9 @@ source_repos:
 - xdomingoal/erah-devel
 - zhangxiang1205/CorrDIA
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - CE-MS
diff --git a/collections/metabolomics/v2/tools/gitlab.yaml b/collections/metabolomics/v2/tools/gitlab.yaml
index 2d1523f1a..2136629ed 100644
--- a/collections/metabolomics/v2/tools/gitlab.yaml
+++ b/collections/metabolomics/v2/tools/gitlab.yaml
@@ -10,6 +10,9 @@ source_repos:
 - hcji/TarMet
 - tidymass/tidymass
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: file-present-unclassified
 techniques:
 - LC-MS
 - CE-MS
diff --git a/collections/metabolomics/v2/tools/gleams.yaml b/collections/metabolomics/v2/tools/gleams.yaml
index b5bfe2cc1..12092219d 100644
--- a/collections/metabolomics/v2/tools/gleams.yaml
+++ b/collections/metabolomics/v2/tools/gleams.yaml
@@ -10,5 +10,8 @@ derived_from:
 source_repos:
 - bittremieux-lab/GLEAMS
 schema_version: 0.2.0
+license_tier: open
+license: BSD-3-Clause
+license_detection: github-api
 techniques:
 - LC-MS
diff --git a/collections/metabolomics/v2/tools/gnps-gc.yaml b/collections/metabolomics/v2/tools/gnps-gc.yaml
index 5fdce66ab..6267ea0a7 100644
--- a/collections/metabolomics/v2/tools/gnps-gc.yaml
+++ b/collections/metabolomics/v2/tools/gnps-gc.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - bittremieux/GNPS_GC
 schema_version: 0.2.0
+license_tier: open
+license: BSD-3-Clause
+license_detection: github-api
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/gnps-lcms-visualization-dashboard.yaml b/collections/metabolomics/v2/tools/gnps-lcms-visualization-dashboard.yaml
index b226e6515..fe2aa00bb 100644
--- a/collections/metabolomics/v2/tools/gnps-lcms-visualization-dashboard.yaml
+++ b/collections/metabolomics/v2/tools/gnps-lcms-visualization-dashboard.yaml
@@ -10,6 +10,9 @@ derived_from:
 source_repos:
 - Wang-Bioinformatics-Lab/GNPS_LCMSDashboard
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: file-present-unclassified
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/gnps-masst.yaml b/collections/metabolomics/v2/tools/gnps-masst.yaml
index a59b92fea..ee7762303 100644
--- a/collections/metabolomics/v2/tools/gnps-masst.yaml
+++ b/collections/metabolomics/v2/tools/gnps-masst.yaml
@@ -11,6 +11,9 @@ derived_from:
 source_repos:
 - mwang87/MASST
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - CE-MS
diff --git a/collections/metabolomics/v2/tools/gnps-molecular-networking.yaml b/collections/metabolomics/v2/tools/gnps-molecular-networking.yaml
index 8993cc671..a76404ab3 100644
--- a/collections/metabolomics/v2/tools/gnps-molecular-networking.yaml
+++ b/collections/metabolomics/v2/tools/gnps-molecular-networking.yaml
@@ -9,5 +9,8 @@ derived_from:
 source_repos:
 - mwang87/MetabolomicsSpectrumResolver
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
 techniques:
 - LC-MS
diff --git a/collections/metabolomics/v2/tools/gnps-spectral-libraries.yaml b/collections/metabolomics/v2/tools/gnps-spectral-libraries.yaml
index 02d69b398..2ef956059 100644
--- a/collections/metabolomics/v2/tools/gnps-spectral-libraries.yaml
+++ b/collections/metabolomics/v2/tools/gnps-spectral-libraries.yaml
@@ -9,5 +9,8 @@ derived_from:
 source_repos:
 - mwang87/MetabolomicsSpectrumResolver
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
 techniques:
 - LC-MS
diff --git a/collections/metabolomics/v2/tools/gnps-spectral-networking-molecular-networking.yaml b/collections/metabolomics/v2/tools/gnps-spectral-networking-molecular-networking.yaml
index 29892e772..ec7ccf067 100644
--- a/collections/metabolomics/v2/tools/gnps-spectral-networking-molecular-networking.yaml
+++ b/collections/metabolomics/v2/tools/gnps-spectral-networking-molecular-networking.yaml
@@ -9,5 +9,8 @@ derived_from:
 source_repos:
 - ablab/npdtools
 schema_version: 0.2.0
+license_tier: open
+license: Apache-2.0
+license_detection: readme-llm
 techniques:
 - LC-MS
diff --git a/collections/metabolomics/v2/tools/gnps.yaml b/collections/metabolomics/v2/tools/gnps.yaml
index 25e0a1b30..d438f174c 100644
--- a/collections/metabolomics/v2/tools/gnps.yaml
+++ b/collections/metabolomics/v2/tools/gnps.yaml
@@ -55,6 +55,9 @@ source_repos:
 - sneumann/xcms
 - zquinlan/concise
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/gnps2.yaml b/collections/metabolomics/v2/tools/gnps2.yaml
index 6f14abe27..8d26e25f6 100644
--- a/collections/metabolomics/v2/tools/gnps2.yaml
+++ b/collections/metabolomics/v2/tools/gnps2.yaml
@@ -17,6 +17,9 @@ source_repos:
 - Wang-Bioinformatics-Lab/GNPS2_Workflows
 - mwang87/ReDU-MS2-Documentation
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - MS-imaging
diff --git a/collections/metabolomics/v2/tools/gnuplot.yaml b/collections/metabolomics/v2/tools/gnuplot.yaml
index d4ba0f6fc..dec9337ce 100644
--- a/collections/metabolomics/v2/tools/gnuplot.yaml
+++ b/collections/metabolomics/v2/tools/gnuplot.yaml
@@ -10,3 +10,6 @@ derived_from:
 source_repos:
 - matteogiulietti/LipidOne
 schema_version: 0.2.0
+license_tier: open
+license: BSD-2-Clause
+license_detection: readme-llm
diff --git a/collections/metabolomics/v2/tools/google-chrome.yaml b/collections/metabolomics/v2/tools/google-chrome.yaml
index b17c8d3b7..0931c6ab3 100644
--- a/collections/metabolomics/v2/tools/google-chrome.yaml
+++ b/collections/metabolomics/v2/tools/google-chrome.yaml
@@ -9,5 +9,8 @@ derived_from:
 source_repos:
 - lidawei1975/colmarvista
 schema_version: 0.2.0
+license_tier: open
+license: GPL-3.0
+license_detection: github-api
 techniques:
 - NMR
diff --git a/collections/metabolomics/v2/tools/google-colab.yaml b/collections/metabolomics/v2/tools/google-colab.yaml
index ab1b8d741..b2b3cf129 100644
--- a/collections/metabolomics/v2/tools/google-colab.yaml
+++ b/collections/metabolomics/v2/tools/google-colab.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - alexandrovteam/SpaceM
 schema_version: 0.2.0
+license_tier: open
+license: Apache-2.0
+license_detection: github-api
 techniques:
 - LC-MS
 - MS-imaging
diff --git a/collections/metabolomics/v2/tools/google-colaboratory.yaml b/collections/metabolomics/v2/tools/google-colaboratory.yaml
index 9b64737bc..9f913cab6 100644
--- a/collections/metabolomics/v2/tools/google-colaboratory.yaml
+++ b/collections/metabolomics/v2/tools/google-colaboratory.yaml
@@ -9,5 +9,8 @@ derived_from:
 source_repos:
 - facundof2016/CCSP2.0
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - ion-mobility-MS
diff --git a/collections/metabolomics/v2/tools/graph-neural-network-gnn-framework-pytorch-geometric-or-equivalent.yaml b/collections/metabolomics/v2/tools/graph-neural-network-gnn-framework-pytorch-geometric-or-equivalent.yaml
index 7dc8c804d..f696b05db 100644
--- a/collections/metabolomics/v2/tools/graph-neural-network-gnn-framework-pytorch-geometric-or-equivalent.yaml
+++ b/collections/metabolomics/v2/tools/graph-neural-network-gnn-framework-pytorch-geometric-or-equivalent.yaml
@@ -6,3 +6,6 @@ derived_from:
 - doi: 10.1186/s13321-024-00899-w
   title: mol2ccs
 schema_version: 0.2.0
+license_tier: open
+license: GPL-2.0
+license_detection: github-api
diff --git a/collections/metabolomics/v2/tools/graphical-time-warping-gtw.yaml b/collections/metabolomics/v2/tools/graphical-time-warping-gtw.yaml
index b7c809534..8106f4208 100644
--- a/collections/metabolomics/v2/tools/graphical-time-warping-gtw.yaml
+++ b/collections/metabolomics/v2/tools/graphical-time-warping-gtw.yaml
@@ -9,5 +9,8 @@ derived_from:
 source_repos:
 - ChiungTingWu/ncGTW
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
diff --git a/collections/metabolomics/v2/tools/graphormer.yaml b/collections/metabolomics/v2/tools/graphormer.yaml
index dc33a9d78..97693b140 100644
--- a/collections/metabolomics/v2/tools/graphormer.yaml
+++ b/collections/metabolomics/v2/tools/graphormer.yaml
@@ -9,5 +9,8 @@ derived_from:
 source_repos:
 - HopkinsLaboratory/Graphormer-RT
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
diff --git a/collections/metabolomics/v2/tools/grid.yaml b/collections/metabolomics/v2/tools/grid.yaml
index 29453b405..4cecb9ee8 100644
--- a/collections/metabolomics/v2/tools/grid.yaml
+++ b/collections/metabolomics/v2/tools/grid.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - LeaveMeNotTonight/CMDN
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - CE-MS
diff --git a/collections/metabolomics/v2/tools/gunicorn.yaml b/collections/metabolomics/v2/tools/gunicorn.yaml
index e928332af..1e157c1a3 100644
--- a/collections/metabolomics/v2/tools/gunicorn.yaml
+++ b/collections/metabolomics/v2/tools/gunicorn.yaml
@@ -10,5 +10,8 @@ derived_from:
 source_repos:
 - ComPlat/chem-spectra-app
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
 techniques:
 - NMR
diff --git a/collections/metabolomics/v2/tools/gx-fba.yaml b/collections/metabolomics/v2/tools/gx-fba.yaml
index e3c0f7fa0..027befc37 100644
--- a/collections/metabolomics/v2/tools/gx-fba.yaml
+++ b/collections/metabolomics/v2/tools/gx-fba.yaml
@@ -7,5 +7,8 @@ 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
diff --git a/collections/metabolomics/v2/tools/h2o.yaml b/collections/metabolomics/v2/tools/h2o.yaml
index 0a6988c37..3e55301d6 100644
--- a/collections/metabolomics/v2/tools/h2o.yaml
+++ b/collections/metabolomics/v2/tools/h2o.yaml
@@ -9,5 +9,8 @@ derived_from:
 source_repos:
 - lanagarmire/lilikoi2
 schema_version: 0.2.0
+license_tier: open
+license: GPL-3.0
+license_detection: github-api
 techniques:
 - LC-MS
diff --git a/collections/metabolomics/v2/tools/h5py-2-7-1.yaml b/collections/metabolomics/v2/tools/h5py-2-7-1.yaml
index ce0069f0b..5ab0b0503 100644
--- a/collections/metabolomics/v2/tools/h5py-2-7-1.yaml
+++ b/collections/metabolomics/v2/tools/h5py-2-7-1.yaml
@@ -9,5 +9,8 @@ derived_from:
 source_repos:
 - wabdelmoula/massNet
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - MS-imaging
diff --git a/collections/metabolomics/v2/tools/h5py.yaml b/collections/metabolomics/v2/tools/h5py.yaml
index 84832e091..c3f5b77c2 100644
--- a/collections/metabolomics/v2/tools/h5py.yaml
+++ b/collections/metabolomics/v2/tools/h5py.yaml
@@ -25,6 +25,9 @@ source_repos:
 - bioinfo-ibms-pumc/SMART
 - wabdelmoula/massNet
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - direct-infusion-MS
diff --git a/collections/metabolomics/v2/tools/hacca.yaml b/collections/metabolomics/v2/tools/hacca.yaml
index 96a95fb79..139f2dcd6 100644
--- a/collections/metabolomics/v2/tools/hacca.yaml
+++ b/collections/metabolomics/v2/tools/hacca.yaml
@@ -9,5 +9,8 @@ derived_from:
 source_repos:
 - LittleLittleCloud/haCCA
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: file-present-unclassified
 techniques:
 - MS-imaging
diff --git a/collections/metabolomics/v2/tools/hassounlab-bam.yaml b/collections/metabolomics/v2/tools/hassounlab-bam.yaml
index 49dc00ac1..47714c4e7 100644
--- a/collections/metabolomics/v2/tools/hassounlab-bam.yaml
+++ b/collections/metabolomics/v2/tools/hassounlab-bam.yaml
@@ -6,5 +6,8 @@ derived_from:
 - doi: 10.1021/acs.analchem.4c01565
   title: bam
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
diff --git a/collections/metabolomics/v2/tools/hdf5-reader-writer-library-h5py-h5netcdf-or-equivalent.yaml b/collections/metabolomics/v2/tools/hdf5-reader-writer-library-h5py-h5netcdf-or-equivalent.yaml
index 3036d887f..a8c76f1ac 100644
--- a/collections/metabolomics/v2/tools/hdf5-reader-writer-library-h5py-h5netcdf-or-equivalent.yaml
+++ b/collections/metabolomics/v2/tools/hdf5-reader-writer-library-h5py-h5netcdf-or-equivalent.yaml
@@ -9,5 +9,8 @@ derived_from:
 source_repos:
 - swinnenteam/LipidQMap
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: file-present-unclassified
 techniques:
 - MS-imaging
diff --git a/collections/metabolomics/v2/tools/hdf5.yaml b/collections/metabolomics/v2/tools/hdf5.yaml
index 59870056c..cbc478aeb 100644
--- a/collections/metabolomics/v2/tools/hdf5.yaml
+++ b/collections/metabolomics/v2/tools/hdf5.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - PNNL-m-q/mza
 schema_version: 0.2.0
+license_tier: open
+license: BSD-2-Clause
+license_detection: github-api
 techniques:
 - LC-MS
 - ion-mobility-MS
diff --git a/collections/metabolomics/v2/tools/hdf5plugin.yaml b/collections/metabolomics/v2/tools/hdf5plugin.yaml
index 84e36a662..6d21c8d5a 100644
--- a/collections/metabolomics/v2/tools/hdf5plugin.yaml
+++ b/collections/metabolomics/v2/tools/hdf5plugin.yaml
@@ -12,6 +12,9 @@ derived_from:
 source_repos:
 - PNNL-m-q/mzapy
 schema_version: 0.2.0
+license_tier: open
+license: BSD-2-Clause
+license_detection: github-api
 techniques:
 - LC-MS
 - ion-mobility-MS
diff --git a/collections/metabolomics/v2/tools/hierarchical-clustering-euclidean-distance-complete-linkage.yaml b/collections/metabolomics/v2/tools/hierarchical-clustering-euclidean-distance-complete-linkage.yaml
index 307db53e6..4031ed10d 100644
--- a/collections/metabolomics/v2/tools/hierarchical-clustering-euclidean-distance-complete-linkage.yaml
+++ b/collections/metabolomics/v2/tools/hierarchical-clustering-euclidean-distance-complete-linkage.yaml
@@ -6,3 +6,6 @@ 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
diff --git a/collections/metabolomics/v2/tools/hineslab-moccal.yaml b/collections/metabolomics/v2/tools/hineslab-moccal.yaml
index fecdd797d..8f46d20d4 100644
--- a/collections/metabolomics/v2/tools/hineslab-moccal.yaml
+++ b/collections/metabolomics/v2/tools/hineslab-moccal.yaml
@@ -6,6 +6,9 @@ derived_from:
 - doi: 10.1021/acs.analchem.3c04290
   title: moccal
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
 techniques:
 - CE-MS
 - ion-mobility-MS
diff --git a/collections/metabolomics/v2/tools/hmdb-4.yaml b/collections/metabolomics/v2/tools/hmdb-4.yaml
index f8fcddb38..9b8631563 100644
--- a/collections/metabolomics/v2/tools/hmdb-4.yaml
+++ b/collections/metabolomics/v2/tools/hmdb-4.yaml
@@ -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
 - CE-MS
diff --git a/collections/metabolomics/v2/tools/hmdb.yaml b/collections/metabolomics/v2/tools/hmdb.yaml
index 462ac30cc..7e6cbab69 100644
--- a/collections/metabolomics/v2/tools/hmdb.yaml
+++ b/collections/metabolomics/v2/tools/hmdb.yaml
@@ -11,6 +11,9 @@ derived_from:
 source_repos:
 - griquelme/tidyms
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/hnswlib.yaml b/collections/metabolomics/v2/tools/hnswlib.yaml
index e40ca3e5d..4e50427d5 100644
--- a/collections/metabolomics/v2/tools/hnswlib.yaml
+++ b/collections/metabolomics/v2/tools/hnswlib.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - Qiong-Yang/FastEI
 schema_version: 0.2.0
+license_tier: open
+license: Apache-2.0
+license_detection: github-api
 techniques:
 - LC-MS
 - mass-spectrometry
diff --git a/collections/metabolomics/v2/tools/homebrew.yaml b/collections/metabolomics/v2/tools/homebrew.yaml
index a3ec9797b..3b5f891b7 100644
--- a/collections/metabolomics/v2/tools/homebrew.yaml
+++ b/collections/metabolomics/v2/tools/homebrew.yaml
@@ -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
diff --git a/collections/metabolomics/v2/tools/hruv.yaml b/collections/metabolomics/v2/tools/hruv.yaml
index 2652b1e4f..b244c4bdf 100644
--- a/collections/metabolomics/v2/tools/hruv.yaml
+++ b/collections/metabolomics/v2/tools/hruv.yaml
@@ -10,6 +10,9 @@ derived_from:
 source_repos:
 - SydneyBioX/hRUV
 schema_version: 0.2.0
+license_tier: open
+license: GPL-3.0
+license_detection: github-api
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/html.yaml b/collections/metabolomics/v2/tools/html.yaml
index b00d22399..e0a44e11b 100644
--- a/collections/metabolomics/v2/tools/html.yaml
+++ b/collections/metabolomics/v2/tools/html.yaml
@@ -9,5 +9,8 @@ derived_from:
 source_repos:
 - RTKlab-BYU/MSConnect
 schema_version: 0.2.0
+license_tier: open
+license: Apache-2.0
+license_detection: github-api
 techniques:
 - mass-spectrometry
diff --git a/collections/metabolomics/v2/tools/htseq-v-0-6-1.yaml b/collections/metabolomics/v2/tools/htseq-v-0-6-1.yaml
index ce168cde5..819977301 100644
--- a/collections/metabolomics/v2/tools/htseq-v-0-6-1.yaml
+++ b/collections/metabolomics/v2/tools/htseq-v-0-6-1.yaml
@@ -7,5 +7,8 @@ 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
diff --git a/collections/metabolomics/v2/tools/https-doi-org-10-5281-zenodo-11243781.yaml b/collections/metabolomics/v2/tools/https-doi-org-10-5281-zenodo-11243781.yaml
index e8de24c49..0977dcb5d 100644
--- a/collections/metabolomics/v2/tools/https-doi-org-10-5281-zenodo-11243781.yaml
+++ b/collections/metabolomics/v2/tools/https-doi-org-10-5281-zenodo-11243781.yaml
@@ -10,3 +10,6 @@ derived_from:
 source_repos:
 - emosca-cnr/margheRita
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
diff --git a/collections/metabolomics/v2/tools/https-github-com-emosca-cnr-margherita.yaml b/collections/metabolomics/v2/tools/https-github-com-emosca-cnr-margherita.yaml
index bb90f0306..7329c40c2 100644
--- a/collections/metabolomics/v2/tools/https-github-com-emosca-cnr-margherita.yaml
+++ b/collections/metabolomics/v2/tools/https-github-com-emosca-cnr-margherita.yaml
@@ -11,3 +11,6 @@ derived_from:
 source_repos:
 - emosca-cnr/margheRita
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
diff --git a/collections/metabolomics/v2/tools/https-github-com-sdrogers-nplinker.yaml b/collections/metabolomics/v2/tools/https-github-com-sdrogers-nplinker.yaml
index 7f34c96f0..7794e198f 100644
--- a/collections/metabolomics/v2/tools/https-github-com-sdrogers-nplinker.yaml
+++ b/collections/metabolomics/v2/tools/https-github-com-sdrogers-nplinker.yaml
@@ -9,3 +9,6 @@ derived_from:
 source_repos:
 - NPLinker/nplinker
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
diff --git a/collections/metabolomics/v2/tools/https-github-com-shuzhao-li-asari.yaml b/collections/metabolomics/v2/tools/https-github-com-shuzhao-li-asari.yaml
index d036e6a41..793ba45a9 100644
--- a/collections/metabolomics/v2/tools/https-github-com-shuzhao-li-asari.yaml
+++ b/collections/metabolomics/v2/tools/https-github-com-shuzhao-li-asari.yaml
@@ -11,3 +11,6 @@ derived_from:
 source_repos:
 - shuzhao-li-lab/asari
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: file-present-unclassified
diff --git a/collections/metabolomics/v2/tools/hugging-face-transformers.yaml b/collections/metabolomics/v2/tools/hugging-face-transformers.yaml
index 62688b066..5155b19a5 100644
--- a/collections/metabolomics/v2/tools/hugging-face-transformers.yaml
+++ b/collections/metabolomics/v2/tools/hugging-face-transformers.yaml
@@ -9,5 +9,8 @@ derived_from:
 source_repos:
 - OpenDFM/MS-BART
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - mass-spectrometry
diff --git a/collections/metabolomics/v2/tools/human-metabolome-database-hmdb.yaml b/collections/metabolomics/v2/tools/human-metabolome-database-hmdb.yaml
index f6169a532..f7c8edcb5 100644
--- a/collections/metabolomics/v2/tools/human-metabolome-database-hmdb.yaml
+++ b/collections/metabolomics/v2/tools/human-metabolome-database-hmdb.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - Leo-Cheng-Lab/ROIAL-NMR
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/hyperspec.yaml b/collections/metabolomics/v2/tools/hyperspec.yaml
index a5a04647a..fb75e10d2 100644
--- a/collections/metabolomics/v2/tools/hyperspec.yaml
+++ b/collections/metabolomics/v2/tools/hyperspec.yaml
@@ -10,6 +10,9 @@ derived_from:
 source_repos:
 - wh-xu/Hyper-Spec
 schema_version: 0.2.0
+license_tier: open
+license: BSD-3-Clause
+license_detection: github-api
 techniques:
 - LC-MS
 - NMR
diff --git a/collections/metabolomics/v2/tools/i-van-krevelen.yaml b/collections/metabolomics/v2/tools/i-van-krevelen.yaml
index e4a89096c..8eff1b720 100644
--- a/collections/metabolomics/v2/tools/i-van-krevelen.yaml
+++ b/collections/metabolomics/v2/tools/i-van-krevelen.yaml
@@ -6,6 +6,9 @@ derived_from:
 - doi: 10.1186/s40168-023-01476-3
   title: MetaboDirect
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/iceberg-model.yaml b/collections/metabolomics/v2/tools/iceberg-model.yaml
index b5d5f4204..3610bd419 100644
--- a/collections/metabolomics/v2/tools/iceberg-model.yaml
+++ b/collections/metabolomics/v2/tools/iceberg-model.yaml
@@ -9,3 +9,6 @@ derived_from:
 source_repos:
 - samgoldman97/ms-pred
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
diff --git a/collections/metabolomics/v2/tools/iceberg-webui.yaml b/collections/metabolomics/v2/tools/iceberg-webui.yaml
index 981ee83d8..46ea6c083 100644
--- a/collections/metabolomics/v2/tools/iceberg-webui.yaml
+++ b/collections/metabolomics/v2/tools/iceberg-webui.yaml
@@ -11,6 +11,9 @@ derived_from:
 source_repos:
 - samgoldman97/ms-pred
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/iceberg.yaml b/collections/metabolomics/v2/tools/iceberg.yaml
index bfd0b0a12..525fd10df 100644
--- a/collections/metabolomics/v2/tools/iceberg.yaml
+++ b/collections/metabolomics/v2/tools/iceberg.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - samgoldman97/ms-pred
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/idsl-csa.yaml b/collections/metabolomics/v2/tools/idsl-csa.yaml
index 799a0bbae..6c320d030 100644
--- a/collections/metabolomics/v2/tools/idsl-csa.yaml
+++ b/collections/metabolomics/v2/tools/idsl-csa.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - idslme/IDSL.CSA
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
 techniques:
 - LC-MS
 - CE-MS
diff --git a/collections/metabolomics/v2/tools/idsl-ipa.yaml b/collections/metabolomics/v2/tools/idsl-ipa.yaml
index 9f7df6fd1..8ea5cf403 100644
--- a/collections/metabolomics/v2/tools/idsl-ipa.yaml
+++ b/collections/metabolomics/v2/tools/idsl-ipa.yaml
@@ -13,6 +13,9 @@ source_repos:
 - idslme/IDSL.IPA
 - idslme/IDSL.UFA
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/idsl-ufa.yaml b/collections/metabolomics/v2/tools/idsl-ufa.yaml
index e74047945..5e99e2072 100644
--- a/collections/metabolomics/v2/tools/idsl-ufa.yaml
+++ b/collections/metabolomics/v2/tools/idsl-ufa.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - idslme/IDSL.UFA
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/idsm.yaml b/collections/metabolomics/v2/tools/idsm.yaml
index 6d152e817..f3f3f9f82 100644
--- a/collections/metabolomics/v2/tools/idsm.yaml
+++ b/collections/metabolomics/v2/tools/idsm.yaml
@@ -11,6 +11,9 @@ derived_from:
 source_repos:
 - RECETOX/MSMetaEnhancer
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
 techniques:
 - LC-MS
 - mass-spectrometry
diff --git a/collections/metabolomics/v2/tools/igraph.yaml b/collections/metabolomics/v2/tools/igraph.yaml
index 5738d0c64..5cf432e18 100644
--- a/collections/metabolomics/v2/tools/igraph.yaml
+++ b/collections/metabolomics/v2/tools/igraph.yaml
@@ -20,6 +20,9 @@ source_repos:
 - b2slab/mWISE
 - biodatalab/enrichmet
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - CE-MS
diff --git a/collections/metabolomics/v2/tools/image-processing-toolbox.yaml b/collections/metabolomics/v2/tools/image-processing-toolbox.yaml
index f1def35e5..1eb336367 100644
--- a/collections/metabolomics/v2/tools/image-processing-toolbox.yaml
+++ b/collections/metabolomics/v2/tools/image-processing-toolbox.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - AdrianHaun/AriumMS
 schema_version: 0.2.0
+license_tier: open
+license: BSD-3-Clause
+license_detection: github-api
 techniques:
 - LC-MS
 - CE-MS
diff --git a/collections/metabolomics/v2/tools/impute.yaml b/collections/metabolomics/v2/tools/impute.yaml
index c003a1151..2f9531544 100644
--- a/collections/metabolomics/v2/tools/impute.yaml
+++ b/collections/metabolomics/v2/tools/impute.yaml
@@ -8,3 +8,6 @@ derived_from:
 source_repos:
 - idrblab/NOREVA;
 schema_version: 0.2.0
+license_tier: open
+license: GPL-3.0
+license_detection: github-api
diff --git a/collections/metabolomics/v2/tools/imzml-writer.yaml b/collections/metabolomics/v2/tools/imzml-writer.yaml
index 96af78280..7ec833750 100644
--- a/collections/metabolomics/v2/tools/imzml-writer.yaml
+++ b/collections/metabolomics/v2/tools/imzml-writer.yaml
@@ -10,6 +10,9 @@ derived_from:
 source_repos:
 - VIU-Metabolomics/imzML_Writer
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
 techniques:
 - MS-imaging
 - mass-spectrometry
diff --git a/collections/metabolomics/v2/tools/independentmassspectrometer.yaml b/collections/metabolomics/v2/tools/independentmassspectrometer.yaml
index fa78b26ff..689956414 100644
--- a/collections/metabolomics/v2/tools/independentmassspectrometer.yaml
+++ b/collections/metabolomics/v2/tools/independentmassspectrometer.yaml
@@ -6,5 +6,8 @@ derived_from:
 - doi: 10.1021/acs.analchem.0c03895
   title: Rapid Development of Improved Data-Dependent Acquisition Strategies
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
diff --git a/collections/metabolomics/v2/tools/injectiondesign.yaml b/collections/metabolomics/v2/tools/injectiondesign.yaml
index eefcec384..e2827f652 100644
--- a/collections/metabolomics/v2/tools/injectiondesign.yaml
+++ b/collections/metabolomics/v2/tools/injectiondesign.yaml
@@ -9,5 +9,8 @@ derived_from:
 source_repos:
 - CSi-Studio/InjectionDesign
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: file-present-unclassified
 techniques:
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/intensity-dependent-missing-value-augmentation.yaml b/collections/metabolomics/v2/tools/intensity-dependent-missing-value-augmentation.yaml
index 59754c634..5cb937642 100644
--- a/collections/metabolomics/v2/tools/intensity-dependent-missing-value-augmentation.yaml
+++ b/collections/metabolomics/v2/tools/intensity-dependent-missing-value-augmentation.yaml
@@ -6,5 +6,8 @@ derived_from:
 - doi: 10.1021/acs.analchem.3c05002
   title: deepion
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - MS-imaging
diff --git a/collections/metabolomics/v2/tools/interactiveplotter.yaml b/collections/metabolomics/v2/tools/interactiveplotter.yaml
index e8b45e006..97ac9fa82 100644
--- a/collections/metabolomics/v2/tools/interactiveplotter.yaml
+++ b/collections/metabolomics/v2/tools/interactiveplotter.yaml
@@ -9,5 +9,8 @@ derived_from:
 source_repos:
 - Roestlab/massdash
 schema_version: 0.2.0
+license_tier: open
+license: BSD-3-Clause
+license_detection: github-api
 techniques:
 - LC-MS
diff --git a/collections/metabolomics/v2/tools/interactivetwodimensionplotter.yaml b/collections/metabolomics/v2/tools/interactivetwodimensionplotter.yaml
index 5bdaf8da9..a460310c3 100644
--- a/collections/metabolomics/v2/tools/interactivetwodimensionplotter.yaml
+++ b/collections/metabolomics/v2/tools/interactivetwodimensionplotter.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - Roestlab/massdash
 schema_version: 0.2.0
+license_tier: open
+license: BSD-3-Clause
+license_detection: github-api
 techniques:
 - LC-MS
 - ion-mobility-MS
diff --git a/collections/metabolomics/v2/tools/interpretmsspectrum.yaml b/collections/metabolomics/v2/tools/interpretmsspectrum.yaml
index 6021a5be9..22fa9a2c2 100644
--- a/collections/metabolomics/v2/tools/interpretmsspectrum.yaml
+++ b/collections/metabolomics/v2/tools/interpretmsspectrum.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - cbroeckl/RAMClustR
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/iokr.yaml b/collections/metabolomics/v2/tools/iokr.yaml
index b0ee4ce76..4de8f6fb5 100644
--- a/collections/metabolomics/v2/tools/iokr.yaml
+++ b/collections/metabolomics/v2/tools/iokr.yaml
@@ -9,5 +9,8 @@ derived_from:
 source_repos:
 - NPLinker/nplinker
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
diff --git a/collections/metabolomics/v2/tools/ion-identity.yaml b/collections/metabolomics/v2/tools/ion-identity.yaml
index 73187c58b..be9d38229 100644
--- a/collections/metabolomics/v2/tools/ion-identity.yaml
+++ b/collections/metabolomics/v2/tools/ion-identity.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - luigiquiros/inventa
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
 techniques:
 - LC-MS
 - NMR
diff --git a/collections/metabolomics/v2/tools/ionflow.yaml b/collections/metabolomics/v2/tools/ionflow.yaml
index 5c11c25bb..3d0113cc1 100644
--- a/collections/metabolomics/v2/tools/ionflow.yaml
+++ b/collections/metabolomics/v2/tools/ionflow.yaml
@@ -9,3 +9,6 @@ derived_from:
 source_repos:
 - wanchanglin/ionflow
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
diff --git a/collections/metabolomics/v2/tools/iontoolpack.yaml b/collections/metabolomics/v2/tools/iontoolpack.yaml
index d1d2759a8..b93f5e73d 100644
--- a/collections/metabolomics/v2/tools/iontoolpack.yaml
+++ b/collections/metabolomics/v2/tools/iontoolpack.yaml
@@ -10,6 +10,9 @@ derived_from:
 source_repos:
 - pnnl/IonToolPack
 schema_version: 0.2.0
+license_tier: open
+license: BSD-2-Clause
+license_detection: github-api
 techniques:
 - LC-MS
 - direct-infusion-MS
diff --git a/collections/metabolomics/v2/tools/ipapy2.yaml b/collections/metabolomics/v2/tools/ipapy2.yaml
index 6f3fa2fbc..7a666fa10 100644
--- a/collections/metabolomics/v2/tools/ipapy2.yaml
+++ b/collections/metabolomics/v2/tools/ipapy2.yaml
@@ -9,5 +9,8 @@ derived_from:
 source_repos:
 - francescodc87/ipaPy2
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
 techniques:
 - LC-MS
diff --git a/collections/metabolomics/v2/tools/ipbhalle-metfragweb.yaml b/collections/metabolomics/v2/tools/ipbhalle-metfragweb.yaml
index 7e7da13ca..8e0dabc4f 100644
--- a/collections/metabolomics/v2/tools/ipbhalle-metfragweb.yaml
+++ b/collections/metabolomics/v2/tools/ipbhalle-metfragweb.yaml
@@ -6,5 +6,8 @@ derived_from:
 - doi: 10.1186/s13321-016-0115-9
   title: MetFrag
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - mass-spectrometry
diff --git a/collections/metabolomics/v2/tools/ipresto.yaml b/collections/metabolomics/v2/tools/ipresto.yaml
index 8366bec01..d813378e4 100644
--- a/collections/metabolomics/v2/tools/ipresto.yaml
+++ b/collections/metabolomics/v2/tools/ipresto.yaml
@@ -9,3 +9,6 @@ derived_from:
 source_repos:
 - https://git.wur.nl/bioinformatics/iPRESTO.git
 schema_version: 0.2.0
+license_tier: open
+license: AGPL-3.0
+license_detection: null
diff --git a/collections/metabolomics/v2/tools/isfrag.yaml b/collections/metabolomics/v2/tools/isfrag.yaml
index 88e097629..104aba8a1 100644
--- a/collections/metabolomics/v2/tools/isfrag.yaml
+++ b/collections/metabolomics/v2/tools/isfrag.yaml
@@ -10,5 +10,8 @@ derived_from:
 source_repos:
 - HuanLab/ISFrag
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
 techniques:
 - LC-MS
diff --git a/collections/metabolomics/v2/tools/isoformswitchanalyzer.yaml b/collections/metabolomics/v2/tools/isoformswitchanalyzer.yaml
index da1a5b7e7..9c4785969 100644
--- a/collections/metabolomics/v2/tools/isoformswitchanalyzer.yaml
+++ b/collections/metabolomics/v2/tools/isoformswitchanalyzer.yaml
@@ -9,3 +9,6 @@ derived_from:
 source_repos:
 - ASAGlab/MOI--An-integrated-solution-for-omics-analyses
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
diff --git a/collections/metabolomics/v2/tools/isofusion.yaml b/collections/metabolomics/v2/tools/isofusion.yaml
index 9dc1da5e3..3e9c3def8 100644
--- a/collections/metabolomics/v2/tools/isofusion.yaml
+++ b/collections/metabolomics/v2/tools/isofusion.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - xfcui/IsoFusion
 schema_version: 0.2.0
+license_tier: open
+license: GPL-3.0
+license_detection: github-api
 techniques:
 - LC-MS
 - CE-MS
diff --git a/collections/metabolomics/v2/tools/isopairfinder.yaml b/collections/metabolomics/v2/tools/isopairfinder.yaml
index d0d3c5944..51c27e797 100644
--- a/collections/metabolomics/v2/tools/isopairfinder.yaml
+++ b/collections/metabolomics/v2/tools/isopairfinder.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - kilgain/MassSpec
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/isoscan.yaml b/collections/metabolomics/v2/tools/isoscan.yaml
index 688c4101e..8336354fa 100644
--- a/collections/metabolomics/v2/tools/isoscan.yaml
+++ b/collections/metabolomics/v2/tools/isoscan.yaml
@@ -10,6 +10,9 @@ derived_from:
 source_repos:
 - jcapelladesto/isoSCAN
 schema_version: 0.2.0
+license_tier: open
+license: GPL-3.0
+license_detection: github-api
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/java-21.yaml b/collections/metabolomics/v2/tools/java-21.yaml
index e502fdcd4..ca268569b 100644
--- a/collections/metabolomics/v2/tools/java-21.yaml
+++ b/collections/metabolomics/v2/tools/java-21.yaml
@@ -6,5 +6,8 @@ derived_from:
 - doi: 10.1186/s13321-016-0115-9
   title: MetFrag
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - mass-spectrometry
diff --git a/collections/metabolomics/v2/tools/java.yaml b/collections/metabolomics/v2/tools/java.yaml
index 1966f82fb..ef2a770bb 100644
--- a/collections/metabolomics/v2/tools/java.yaml
+++ b/collections/metabolomics/v2/tools/java.yaml
@@ -13,5 +13,8 @@ source_repos:
 - Le0nT1/CyProduct
 - simeoni-biolab/MetNet
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
diff --git a/collections/metabolomics/v2/tools/javafx-24.yaml b/collections/metabolomics/v2/tools/javafx-24.yaml
index 8924b0b0d..c3deb8617 100644
--- a/collections/metabolomics/v2/tools/javafx-24.yaml
+++ b/collections/metabolomics/v2/tools/javafx-24.yaml
@@ -8,6 +8,9 @@ derived_from:
 - doi: 10.1038/s41587-023-01690-2
   title: mzmine3
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/javascript.yaml b/collections/metabolomics/v2/tools/javascript.yaml
index e3ecc653e..867419ca2 100644
--- a/collections/metabolomics/v2/tools/javascript.yaml
+++ b/collections/metabolomics/v2/tools/javascript.yaml
@@ -9,5 +9,8 @@ derived_from:
 source_repos:
 - RTKlab-BYU/MSConnect
 schema_version: 0.2.0
+license_tier: open
+license: Apache-2.0
+license_detection: github-api
 techniques:
 - mass-spectrometry
diff --git a/collections/metabolomics/v2/tools/javax-faces-2-2-12-jar.yaml b/collections/metabolomics/v2/tools/javax-faces-2-2-12-jar.yaml
index 193f68468..7ec367ee4 100644
--- a/collections/metabolomics/v2/tools/javax-faces-2-2-12-jar.yaml
+++ b/collections/metabolomics/v2/tools/javax-faces-2-2-12-jar.yaml
@@ -10,3 +10,6 @@ derived_from:
 source_repos:
 - albertogilf/ceuMassMediator
 schema_version: 0.2.0
+license_tier: open
+license: GPL-3.0
+license_detection: github-api
diff --git a/collections/metabolomics/v2/tools/jdk-25.yaml b/collections/metabolomics/v2/tools/jdk-25.yaml
index dea484e87..307ef1822 100644
--- a/collections/metabolomics/v2/tools/jdk-25.yaml
+++ b/collections/metabolomics/v2/tools/jdk-25.yaml
@@ -8,6 +8,9 @@ derived_from:
 - doi: 10.1038/s41587-023-01690-2
   title: mzmine3
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/jfreechart.yaml b/collections/metabolomics/v2/tools/jfreechart.yaml
index 2bdcf9a5d..da3ca2a7a 100644
--- a/collections/metabolomics/v2/tools/jfreechart.yaml
+++ b/collections/metabolomics/v2/tools/jfreechart.yaml
@@ -10,6 +10,9 @@ derived_from:
 source_repos:
 - rformassspectrometry/Spectra
 schema_version: 0.2.0
+license_tier: open
+license: Artistic-2.0
+license_detection: readme-llm
 techniques:
 - LC-MS
 - NMR
diff --git a/collections/metabolomics/v2/tools/jms.yaml b/collections/metabolomics/v2/tools/jms.yaml
index 1ef6c34ec..1fe19d5bb 100644
--- a/collections/metabolomics/v2/tools/jms.yaml
+++ b/collections/metabolomics/v2/tools/jms.yaml
@@ -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
 - CE-MS
diff --git a/collections/metabolomics/v2/tools/joblib.yaml b/collections/metabolomics/v2/tools/joblib.yaml
index 403a55179..61dd1d4d7 100644
--- a/collections/metabolomics/v2/tools/joblib.yaml
+++ b/collections/metabolomics/v2/tools/joblib.yaml
@@ -14,6 +14,9 @@ source_repos:
 - ablab/npdtools
 - zsspython/LAGF
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - direct-infusion-MS
diff --git a/collections/metabolomics/v2/tools/jopt-simple.yaml b/collections/metabolomics/v2/tools/jopt-simple.yaml
index f517be61a..e9ceb406c 100644
--- a/collections/metabolomics/v2/tools/jopt-simple.yaml
+++ b/collections/metabolomics/v2/tools/jopt-simple.yaml
@@ -10,6 +10,9 @@ derived_from:
 source_repos:
 - rformassspectrometry/Spectra
 schema_version: 0.2.0
+license_tier: open
+license: Artistic-2.0
+license_detection: readme-llm
 techniques:
 - LC-MS
 - NMR
diff --git a/collections/metabolomics/v2/tools/jorhelp-docker-image.yaml b/collections/metabolomics/v2/tools/jorhelp-docker-image.yaml
index 09c54e545..7860e154d 100644
--- a/collections/metabolomics/v2/tools/jorhelp-docker-image.yaml
+++ b/collections/metabolomics/v2/tools/jorhelp-docker-image.yaml
@@ -9,3 +9,6 @@ derived_from:
 source_repos:
 - xfcui/IsoFusion
 schema_version: 0.2.0
+license_tier: open
+license: GPL-3.0
+license_detection: github-api
diff --git a/collections/metabolomics/v2/tools/jpa-r-package.yaml b/collections/metabolomics/v2/tools/jpa-r-package.yaml
index eaaac1270..74ab4c26b 100644
--- a/collections/metabolomics/v2/tools/jpa-r-package.yaml
+++ b/collections/metabolomics/v2/tools/jpa-r-package.yaml
@@ -9,3 +9,6 @@ derived_from:
 source_repos:
 - HuanLab/JPA
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
diff --git a/collections/metabolomics/v2/tools/jpa.yaml b/collections/metabolomics/v2/tools/jpa.yaml
index a7a5a57fb..ac7f32732 100644
--- a/collections/metabolomics/v2/tools/jpa.yaml
+++ b/collections/metabolomics/v2/tools/jpa.yaml
@@ -10,6 +10,9 @@ derived_from:
 source_repos:
 - HuanLab/JPA
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
 techniques:
 - LC-MS
 - NMR
diff --git a/collections/metabolomics/v2/tools/jsonschema.yaml b/collections/metabolomics/v2/tools/jsonschema.yaml
index 234609f59..7013724a5 100644
--- a/collections/metabolomics/v2/tools/jsonschema.yaml
+++ b/collections/metabolomics/v2/tools/jsonschema.yaml
@@ -11,6 +11,9 @@ derived_from:
 source_repos:
 - MoseleyBioinformaticsLab/mwtab
 schema_version: 0.2.0
+license_tier: open
+license: BSD-3-Clause-Clear
+license_detection: github-api
 techniques:
 - NMR
 - mass-spectrometry
diff --git a/collections/metabolomics/v2/tools/jupyter-lab.yaml b/collections/metabolomics/v2/tools/jupyter-lab.yaml
index 8a294c6a7..2a98d1f25 100644
--- a/collections/metabolomics/v2/tools/jupyter-lab.yaml
+++ b/collections/metabolomics/v2/tools/jupyter-lab.yaml
@@ -9,5 +9,8 @@ derived_from:
 source_repos:
 - facundof2016/CCSP2.0
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - ion-mobility-MS
diff --git a/collections/metabolomics/v2/tools/jupyter-notebook.yaml b/collections/metabolomics/v2/tools/jupyter-notebook.yaml
index f550eb1c5..d0b57aa5c 100644
--- a/collections/metabolomics/v2/tools/jupyter-notebook.yaml
+++ b/collections/metabolomics/v2/tools/jupyter-notebook.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - kevinmildau/msFeaST
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
 techniques:
 - LC-MS
 - mass-spectrometry
diff --git a/collections/metabolomics/v2/tools/jupyter-notebooks.yaml b/collections/metabolomics/v2/tools/jupyter-notebooks.yaml
index 0c954f7ad..a981a2a06 100644
--- a/collections/metabolomics/v2/tools/jupyter-notebooks.yaml
+++ b/collections/metabolomics/v2/tools/jupyter-notebooks.yaml
@@ -6,6 +6,9 @@ derived_from:
 - doi: 10.1021/acs.analchem.3c04444
   title: specxplore
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
 techniques:
 - LC-MS
 - NMR
diff --git a/collections/metabolomics/v2/tools/jupyter.yaml b/collections/metabolomics/v2/tools/jupyter.yaml
index 3c0ecfa19..b34a07909 100644
--- a/collections/metabolomics/v2/tools/jupyter.yaml
+++ b/collections/metabolomics/v2/tools/jupyter.yaml
@@ -15,6 +15,9 @@ derived_from:
 source_repos:
 - griquelme/tidyms
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - CE-MS
diff --git a/collections/metabolomics/v2/tools/kableextra.yaml b/collections/metabolomics/v2/tools/kableextra.yaml
index 93578e67e..31c161e2a 100644
--- a/collections/metabolomics/v2/tools/kableextra.yaml
+++ b/collections/metabolomics/v2/tools/kableextra.yaml
@@ -6,5 +6,8 @@ derived_from:
 - doi: 10.1021/acs.analchem.5c00567
   title: Automated Integration and Quality Assessment of Chromatographic Peaks in LC–MS-Based Metabolomics and Lipidomics Using TARDIS
 schema_version: 0.2.0
+license_tier: open
+license: GPL-3.0
+license_detection: github-api
 techniques:
 - LC-MS
diff --git a/collections/metabolomics/v2/tools/kaleido.yaml b/collections/metabolomics/v2/tools/kaleido.yaml
index 97314c832..de0918df7 100644
--- a/collections/metabolomics/v2/tools/kaleido.yaml
+++ b/collections/metabolomics/v2/tools/kaleido.yaml
@@ -9,3 +9,6 @@ derived_from:
 source_repos:
 - pmartR/PMart_ShinyApp
 schema_version: 0.2.0
+license_tier: open
+license: BSD-2-Clause
+license_detection: github-api
diff --git a/collections/metabolomics/v2/tools/kegg-database.yaml b/collections/metabolomics/v2/tools/kegg-database.yaml
index dcb0db834..52f4f4b02 100644
--- a/collections/metabolomics/v2/tools/kegg-database.yaml
+++ b/collections/metabolomics/v2/tools/kegg-database.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - b2slab/mWISE
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - direct-infusion-MS
diff --git a/collections/metabolomics/v2/tools/kegg.yaml b/collections/metabolomics/v2/tools/kegg.yaml
index 021b0cbae..c7a4d1c27 100644
--- a/collections/metabolomics/v2/tools/kegg.yaml
+++ b/collections/metabolomics/v2/tools/kegg.yaml
@@ -13,6 +13,9 @@ source_repos:
 - biodatalab/enrichmet
 - simeoni-biolab/MetNet
 schema_version: 0.2.0
+license_tier: open
+license: AGPL-3.0
+license_detection: github-api
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/keggrest.yaml b/collections/metabolomics/v2/tools/keggrest.yaml
index 07fc5edb3..22287f6c0 100644
--- a/collections/metabolomics/v2/tools/keggrest.yaml
+++ b/collections/metabolomics/v2/tools/keggrest.yaml
@@ -17,6 +17,9 @@ source_repos:
 - biodatalab/enrichmet
 - connor-reid-tiffany/Omu
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/keras-2-2-0.yaml b/collections/metabolomics/v2/tools/keras-2-2-0.yaml
index ae096c77c..4c9006572 100644
--- a/collections/metabolomics/v2/tools/keras-2-2-0.yaml
+++ b/collections/metabolomics/v2/tools/keras-2-2-0.yaml
@@ -9,3 +9,6 @@ derived_from:
 source_repos:
 - wabdelmoula/massNet
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
diff --git a/collections/metabolomics/v2/tools/keras.yaml b/collections/metabolomics/v2/tools/keras.yaml
index 037f241ac..a38e8e355 100644
--- a/collections/metabolomics/v2/tools/keras.yaml
+++ b/collections/metabolomics/v2/tools/keras.yaml
@@ -27,6 +27,9 @@ source_repos:
 - slfan2013/SERDA
 - wabdelmoula/massNet
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: file-present-unclassified
 techniques:
 - LC-MS
 - CE-MS
diff --git a/collections/metabolomics/v2/tools/khipu.yaml b/collections/metabolomics/v2/tools/khipu.yaml
index ef14b9ab5..200a749f4 100644
--- a/collections/metabolomics/v2/tools/khipu.yaml
+++ b/collections/metabolomics/v2/tools/khipu.yaml
@@ -16,6 +16,9 @@ source_repos:
 - shuzhao-li-lab/asari
 - shuzhao-li-lab/khipu
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: file-present-unclassified
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/knime.yaml b/collections/metabolomics/v2/tools/knime.yaml
index 62c824034..f5175decc 100644
--- a/collections/metabolomics/v2/tools/knime.yaml
+++ b/collections/metabolomics/v2/tools/knime.yaml
@@ -15,6 +15,9 @@ source_repos:
 - MolecularCartography/Optimus
 - OpenMS/OpenMS
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: file-present-unclassified
 techniques:
 - LC-MS
 - CE-MS
diff --git a/collections/metabolomics/v2/tools/knitr.yaml b/collections/metabolomics/v2/tools/knitr.yaml
index d69724a4f..729da24db 100644
--- a/collections/metabolomics/v2/tools/knitr.yaml
+++ b/collections/metabolomics/v2/tools/knitr.yaml
@@ -12,6 +12,9 @@ derived_from:
 source_repos:
 - MRCIEU/metaboprep
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: file-present-unclassified
 techniques:
 - LC-MS
 - ion-mobility-MS
diff --git a/collections/metabolomics/v2/tools/largemetabo.yaml b/collections/metabolomics/v2/tools/largemetabo.yaml
index 3bcf6e771..7fed7d190 100644
--- a/collections/metabolomics/v2/tools/largemetabo.yaml
+++ b/collections/metabolomics/v2/tools/largemetabo.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - LargeMetabo/LargeMetabo
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/latent-dirichlet-allocation-lda.yaml b/collections/metabolomics/v2/tools/latent-dirichlet-allocation-lda.yaml
index 0ecf0a182..237a73760 100644
--- a/collections/metabolomics/v2/tools/latent-dirichlet-allocation-lda.yaml
+++ b/collections/metabolomics/v2/tools/latent-dirichlet-allocation-lda.yaml
@@ -10,6 +10,9 @@ derived_from:
 source_repos:
 - vdhooftcompmet/MS2LDA
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/lcmsworld.yaml b/collections/metabolomics/v2/tools/lcmsworld.yaml
index 5027a27af..290c3c658 100644
--- a/collections/metabolomics/v2/tools/lcmsworld.yaml
+++ b/collections/metabolomics/v2/tools/lcmsworld.yaml
@@ -9,5 +9,8 @@ derived_from:
 source_repos:
 - PGB-LIV/lcmsWorld
 schema_version: 0.2.0
+license_tier: open
+license: AGPL-3.0
+license_detection: github-api
 techniques:
 - LC-MS
diff --git a/collections/metabolomics/v2/tools/lda-latent-dirichlet-allocation.yaml b/collections/metabolomics/v2/tools/lda-latent-dirichlet-allocation.yaml
index bda017336..0e78332b3 100644
--- a/collections/metabolomics/v2/tools/lda-latent-dirichlet-allocation.yaml
+++ b/collections/metabolomics/v2/tools/lda-latent-dirichlet-allocation.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - HassounLab/ESP
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/lib2nist.yaml b/collections/metabolomics/v2/tools/lib2nist.yaml
index f462680cc..fa98ebf2a 100644
--- a/collections/metabolomics/v2/tools/lib2nist.yaml
+++ b/collections/metabolomics/v2/tools/lib2nist.yaml
@@ -6,6 +6,9 @@ derived_from:
 - doi: 10.1021/acs.analchem.2c05389
   title: mspcompiler
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: file-present-unclassified
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/lilikoi-v2-0.yaml b/collections/metabolomics/v2/tools/lilikoi-v2-0.yaml
index e595d3365..faaae3ede 100644
--- a/collections/metabolomics/v2/tools/lilikoi-v2-0.yaml
+++ b/collections/metabolomics/v2/tools/lilikoi-v2-0.yaml
@@ -10,6 +10,9 @@ derived_from:
 source_repos:
 - lanagarmire/lilikoi2
 schema_version: 0.2.0
+license_tier: open
+license: GPL-3.0
+license_detection: github-api
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/limma.yaml b/collections/metabolomics/v2/tools/limma.yaml
index 5a8a23621..6eaecbcb8 100644
--- a/collections/metabolomics/v2/tools/limma.yaml
+++ b/collections/metabolomics/v2/tools/limma.yaml
@@ -25,6 +25,9 @@ source_repos:
 - idrblab/NOREVA;
 - sneumann/xcms
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: file-present-unclassified
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/lipid-map.yaml b/collections/metabolomics/v2/tools/lipid-map.yaml
index 3732ef532..60827fb64 100644
--- a/collections/metabolomics/v2/tools/lipid-map.yaml
+++ b/collections/metabolomics/v2/tools/lipid-map.yaml
@@ -6,6 +6,9 @@ derived_from:
 - doi: 10.1371/journal.pcbi.1011912
   title: Common data models to streamline metabolomics processing and annotation, and implementation in a Python pipeline
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: license-file
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/lipid-maps.yaml b/collections/metabolomics/v2/tools/lipid-maps.yaml
index 3b333f3bf..a3c7e9cad 100644
--- a/collections/metabolomics/v2/tools/lipid-maps.yaml
+++ b/collections/metabolomics/v2/tools/lipid-maps.yaml
@@ -9,6 +9,9 @@ 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
diff --git a/collections/metabolomics/v2/tools/lipidlynxx.yaml b/collections/metabolomics/v2/tools/lipidlynxx.yaml
index b4642e09b..5162075d1 100644
--- a/collections/metabolomics/v2/tools/lipidlynxx.yaml
+++ b/collections/metabolomics/v2/tools/lipidlynxx.yaml
@@ -9,3 +9,6 @@ derived_from:
 source_repos:
 - SysMedOs/LipidLynxX
 schema_version: 0.2.0
+license_tier: open
+license: GPL-3.0
+license_detection: github-api
diff --git a/collections/metabolomics/v2/tools/lipidmatch.yaml b/collections/metabolomics/v2/tools/lipidmatch.yaml
index b46bdc9e6..fba83f402 100644
--- a/collections/metabolomics/v2/tools/lipidmatch.yaml
+++ b/collections/metabolomics/v2/tools/lipidmatch.yaml
@@ -14,6 +14,9 @@ source_repos:
 - GarrettLab-UF/LipidMatch
 - InnovativeOmics/Core-Match
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/lipidqmap.yaml b/collections/metabolomics/v2/tools/lipidqmap.yaml
index bd7903517..d7a0462e8 100644
--- a/collections/metabolomics/v2/tools/lipidqmap.yaml
+++ b/collections/metabolomics/v2/tools/lipidqmap.yaml
@@ -11,6 +11,9 @@ derived_from:
 source_repos:
 - swinnenteam/LipidQMap
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: file-present-unclassified
 techniques:
 - LC-MS
 - direct-infusion-MS
diff --git a/collections/metabolomics/v2/tools/lipidr.yaml b/collections/metabolomics/v2/tools/lipidr.yaml
index 219906cc7..34aca988a 100644
--- a/collections/metabolomics/v2/tools/lipidr.yaml
+++ b/collections/metabolomics/v2/tools/lipidr.yaml
@@ -11,6 +11,9 @@ derived_from:
 source_repos:
 - ahmohamed/lipidr
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: file-present-unclassified
 techniques:
 - LC-MS
 - mass-spectrometry
diff --git a/collections/metabolomics/v2/tools/lipidsearch.yaml b/collections/metabolomics/v2/tools/lipidsearch.yaml
index 947010f70..0c99dcd21 100644
--- a/collections/metabolomics/v2/tools/lipidsearch.yaml
+++ b/collections/metabolomics/v2/tools/lipidsearch.yaml
@@ -9,6 +9,9 @@ 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
diff --git a/collections/metabolomics/v2/tools/lipidspace.yaml b/collections/metabolomics/v2/tools/lipidspace.yaml
index 267d443a1..a50c71255 100644
--- a/collections/metabolomics/v2/tools/lipidspace.yaml
+++ b/collections/metabolomics/v2/tools/lipidspace.yaml
@@ -9,3 +9,6 @@ derived_from:
 source_repos:
 - lifs-tools/lipidspace
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
diff --git a/collections/metabolomics/v2/tools/lipoclean.yaml b/collections/metabolomics/v2/tools/lipoclean.yaml
index 8bf43ec56..382fe185a 100644
--- a/collections/metabolomics/v2/tools/lipoclean.yaml
+++ b/collections/metabolomics/v2/tools/lipoclean.yaml
@@ -6,6 +6,9 @@ derived_from:
 - doi: 10.1021/acs.analchem.4c04040
   title: lipoclean
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
 techniques:
 - LC-MS
 - ion-mobility-MS
diff --git a/collections/metabolomics/v2/tools/liquid.yaml b/collections/metabolomics/v2/tools/liquid.yaml
index 324d2b3d7..0883dfa7e 100644
--- a/collections/metabolomics/v2/tools/liquid.yaml
+++ b/collections/metabolomics/v2/tools/liquid.yaml
@@ -9,6 +9,9 @@ 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
diff --git a/collections/metabolomics/v2/tools/lme4.yaml b/collections/metabolomics/v2/tools/lme4.yaml
index 1bb5bdb89..56a15e166 100644
--- a/collections/metabolomics/v2/tools/lme4.yaml
+++ b/collections/metabolomics/v2/tools/lme4.yaml
@@ -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
diff --git a/collections/metabolomics/v2/tools/local-code-artifact.yaml b/collections/metabolomics/v2/tools/local-code-artifact.yaml
index a1ed49335..2072f12ce 100644
--- a/collections/metabolomics/v2/tools/local-code-artifact.yaml
+++ b/collections/metabolomics/v2/tools/local-code-artifact.yaml
@@ -7,3 +7,6 @@ derived_from:
 source_repos:
 - CNIC-Proteomics/TurboPutative
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
diff --git a/collections/metabolomics/v2/tools/lotus-database.yaml b/collections/metabolomics/v2/tools/lotus-database.yaml
index 293e003df..ba6e89837 100644
--- a/collections/metabolomics/v2/tools/lotus-database.yaml
+++ b/collections/metabolomics/v2/tools/lotus-database.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - luigiquiros/inventa
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
 techniques:
 - LC-MS
 - ion-mobility-MS
diff --git a/collections/metabolomics/v2/tools/lowess.yaml b/collections/metabolomics/v2/tools/lowess.yaml
index 0ff7af58e..a886883f2 100644
--- a/collections/metabolomics/v2/tools/lowess.yaml
+++ b/collections/metabolomics/v2/tools/lowess.yaml
@@ -9,5 +9,8 @@ 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
diff --git a/collections/metabolomics/v2/tools/lsg-lipid-spectrum-generator.yaml b/collections/metabolomics/v2/tools/lsg-lipid-spectrum-generator.yaml
index cf4d9429d..2a040a406 100644
--- a/collections/metabolomics/v2/tools/lsg-lipid-spectrum-generator.yaml
+++ b/collections/metabolomics/v2/tools/lsg-lipid-spectrum-generator.yaml
@@ -9,5 +9,8 @@ derived_from:
 source_repos:
 - 98104781/LSG
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
diff --git a/collections/metabolomics/v2/tools/lsg.yaml b/collections/metabolomics/v2/tools/lsg.yaml
index 73b18d364..82da103d9 100644
--- a/collections/metabolomics/v2/tools/lsg.yaml
+++ b/collections/metabolomics/v2/tools/lsg.yaml
@@ -10,6 +10,9 @@ derived_from:
 source_repos:
 - 98104781/LSG
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - CE-MS
diff --git a/collections/metabolomics/v2/tools/madbyte.yaml b/collections/metabolomics/v2/tools/madbyte.yaml
index bb079abd4..ee54f7472 100644
--- a/collections/metabolomics/v2/tools/madbyte.yaml
+++ b/collections/metabolomics/v2/tools/madbyte.yaml
@@ -9,5 +9,8 @@ derived_from:
 source_repos:
 - liningtonlab/madbyte
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
 techniques:
 - NMR
diff --git a/collections/metabolomics/v2/tools/mag-mass2motif-annotation-guidance.yaml b/collections/metabolomics/v2/tools/mag-mass2motif-annotation-guidance.yaml
index 4c02a56d9..6833c31e8 100644
--- a/collections/metabolomics/v2/tools/mag-mass2motif-annotation-guidance.yaml
+++ b/collections/metabolomics/v2/tools/mag-mass2motif-annotation-guidance.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - vdhooftcompmet/MS2LDA
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
 techniques:
 - LC-MS
 - mass-spectrometry
diff --git a/collections/metabolomics/v2/tools/mag.yaml b/collections/metabolomics/v2/tools/mag.yaml
index 160adfe5d..c102d5652 100644
--- a/collections/metabolomics/v2/tools/mag.yaml
+++ b/collections/metabolomics/v2/tools/mag.yaml
@@ -9,5 +9,8 @@ derived_from:
 source_repos:
 - vdhooftcompmet/MS2LDA
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
 techniques:
 - LC-MS
diff --git a/collections/metabolomics/v2/tools/magma.yaml b/collections/metabolomics/v2/tools/magma.yaml
index d2eb9896f..5954a343b 100644
--- a/collections/metabolomics/v2/tools/magma.yaml
+++ b/collections/metabolomics/v2/tools/magma.yaml
@@ -7,6 +7,9 @@ derived_from:
 - doi: 10.5702/massspectrometry.S0033
   title: magma
 schema_version: 0.2.0
+license_tier: open
+license: Apache-2.0
+license_detection: github-api
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/magrittr.yaml b/collections/metabolomics/v2/tools/magrittr.yaml
index 43c26880f..7dd367564 100644
--- a/collections/metabolomics/v2/tools/magrittr.yaml
+++ b/collections/metabolomics/v2/tools/magrittr.yaml
@@ -14,6 +14,9 @@ source_repos:
 - BiosystemEngineeringLab-IITB/dures
 - krumsieklab/maplet
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: file-present-unclassified
 techniques:
 - LC-MS
 - CE-MS
diff --git a/collections/metabolomics/v2/tools/make.yaml b/collections/metabolomics/v2/tools/make.yaml
index c41805e60..9ee37a9e2 100644
--- a/collections/metabolomics/v2/tools/make.yaml
+++ b/collections/metabolomics/v2/tools/make.yaml
@@ -13,6 +13,9 @@ source_repos:
 - eugenemel/maven
 - lotusnprod/lotus-processor
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - mass-spectrometry
diff --git a/collections/metabolomics/v2/tools/mamsi-mamsistructsearch.yaml b/collections/metabolomics/v2/tools/mamsi-mamsistructsearch.yaml
index a004d30f0..c78182dd4 100644
--- a/collections/metabolomics/v2/tools/mamsi-mamsistructsearch.yaml
+++ b/collections/metabolomics/v2/tools/mamsi-mamsistructsearch.yaml
@@ -6,6 +6,9 @@ derived_from:
 - doi: 10.1371/journal.pcbi.1011814
   title: 'PathIntegrate: Multivariate modelling approaches for pathway-based multi-omics data integration'
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/mamsistructsearch.yaml b/collections/metabolomics/v2/tools/mamsistructsearch.yaml
index f9815b437..1909b280f 100644
--- a/collections/metabolomics/v2/tools/mamsistructsearch.yaml
+++ b/collections/metabolomics/v2/tools/mamsistructsearch.yaml
@@ -6,6 +6,9 @@ derived_from:
 - doi: 10.1371/journal.pcbi.1011814
   title: 'PathIntegrate: Multivariate modelling approaches for pathway-based multi-omics data integration'
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - direct-infusion-MS
diff --git a/collections/metabolomics/v2/tools/mann-whitney-u-test.yaml b/collections/metabolomics/v2/tools/mann-whitney-u-test.yaml
index b6fbf51fd..30a6ae283 100644
--- a/collections/metabolomics/v2/tools/mann-whitney-u-test.yaml
+++ b/collections/metabolomics/v2/tools/mann-whitney-u-test.yaml
@@ -7,5 +7,8 @@ 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
diff --git a/collections/metabolomics/v2/tools/manual-expert-review.yaml b/collections/metabolomics/v2/tools/manual-expert-review.yaml
index 1eab45d90..357a88719 100644
--- a/collections/metabolomics/v2/tools/manual-expert-review.yaml
+++ b/collections/metabolomics/v2/tools/manual-expert-review.yaml
@@ -8,6 +8,9 @@ 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: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - ion-mobility-MS
diff --git a/collections/metabolomics/v2/tools/maplet.yaml b/collections/metabolomics/v2/tools/maplet.yaml
index 5180e97c8..63bd5c911 100644
--- a/collections/metabolomics/v2/tools/maplet.yaml
+++ b/collections/metabolomics/v2/tools/maplet.yaml
@@ -9,3 +9,6 @@ derived_from:
 source_repos:
 - krumsieklab/maplet
 schema_version: 0.2.0
+license_tier: open
+license: GPL-3.0
+license_detection: github-api
diff --git a/collections/metabolomics/v2/tools/margherita.yaml b/collections/metabolomics/v2/tools/margherita.yaml
index e044e0217..4afd37b15 100644
--- a/collections/metabolomics/v2/tools/margherita.yaml
+++ b/collections/metabolomics/v2/tools/margherita.yaml
@@ -11,6 +11,9 @@ derived_from:
 source_repos:
 - emosca-cnr/margheRita
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - mass-spectrometry
diff --git a/collections/metabolomics/v2/tools/mariadb-10.yaml b/collections/metabolomics/v2/tools/mariadb-10.yaml
index 7a6d9ba53..4359c43bb 100644
--- a/collections/metabolomics/v2/tools/mariadb-10.yaml
+++ b/collections/metabolomics/v2/tools/mariadb-10.yaml
@@ -9,5 +9,8 @@ derived_from:
 source_repos:
 - privrja/MassSpecBlocks
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
 techniques:
 - mass-spectrometry
diff --git a/collections/metabolomics/v2/tools/marr.yaml b/collections/metabolomics/v2/tools/marr.yaml
index 8f1c34231..0ba363f61 100644
--- a/collections/metabolomics/v2/tools/marr.yaml
+++ b/collections/metabolomics/v2/tools/marr.yaml
@@ -10,6 +10,9 @@ derived_from:
 source_repos:
 - Ghoshlab/marr
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - mass-spectrometry
diff --git a/collections/metabolomics/v2/tools/mascot-generic-format-mgf.yaml b/collections/metabolomics/v2/tools/mascot-generic-format-mgf.yaml
index ec106b258..af74202ca 100644
--- a/collections/metabolomics/v2/tools/mascot-generic-format-mgf.yaml
+++ b/collections/metabolomics/v2/tools/mascot-generic-format-mgf.yaml
@@ -9,3 +9,6 @@ derived_from:
 source_repos:
 - beherasan/MS2Compound
 schema_version: 0.2.0
+license_tier: open
+license: CC-BY-4.0
+license_detection: github-api
diff --git a/collections/metabolomics/v2/tools/mass-functions-nn-cluster-by-mz-seeds.yaml b/collections/metabolomics/v2/tools/mass-functions-nn-cluster-by-mz-seeds.yaml
index 94b222c1f..4bf56c7df 100644
--- a/collections/metabolomics/v2/tools/mass-functions-nn-cluster-by-mz-seeds.yaml
+++ b/collections/metabolomics/v2/tools/mass-functions-nn-cluster-by-mz-seeds.yaml
@@ -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
 - direct-infusion-MS
diff --git a/collections/metabolomics/v2/tools/mass-query-language-massql.yaml b/collections/metabolomics/v2/tools/mass-query-language-massql.yaml
index 689fe1ea2..d6ce79573 100644
--- a/collections/metabolomics/v2/tools/mass-query-language-massql.yaml
+++ b/collections/metabolomics/v2/tools/mass-query-language-massql.yaml
@@ -9,5 +9,8 @@ derived_from:
 source_repos:
 - biorack/chemecho
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
diff --git a/collections/metabolomics/v2/tools/mass2adduct.yaml b/collections/metabolomics/v2/tools/mass2adduct.yaml
index bba622b1d..672305ae3 100644
--- a/collections/metabolomics/v2/tools/mass2adduct.yaml
+++ b/collections/metabolomics/v2/tools/mass2adduct.yaml
@@ -10,6 +10,9 @@ derived_from:
 - doi: 10.1021/acs.analchem.0c04720
   title: Determination of Abundant Metabolite Matrix Adducts Illuminates the Dark Metabolome of MALDI-Mass Spectrometry Imaging Datasets
 schema_version: 0.2.0
+license_tier: open
+license: GPL-3.0
+license_detection: github-api
 techniques:
 - LC-MS
 - CE-MS
diff --git a/collections/metabolomics/v2/tools/mass2chem.yaml b/collections/metabolomics/v2/tools/mass2chem.yaml
index 0c25ea1ae..9ed65ac26 100644
--- a/collections/metabolomics/v2/tools/mass2chem.yaml
+++ b/collections/metabolomics/v2/tools/mass2chem.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - shuzhao-li-lab/khipu
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: file-present-unclassified
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/massbank-web-validator.yaml b/collections/metabolomics/v2/tools/massbank-web-validator.yaml
index 3f131fe94..4fd4d288d 100644
--- a/collections/metabolomics/v2/tools/massbank-web-validator.yaml
+++ b/collections/metabolomics/v2/tools/massbank-web-validator.yaml
@@ -9,5 +9,8 @@ derived_from:
 source_repos:
 - MassBank/MassBank-data
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - mass-spectrometry
diff --git a/collections/metabolomics/v2/tools/massbank-web.yaml b/collections/metabolomics/v2/tools/massbank-web.yaml
index 6e6824a7f..40c2b3dc3 100644
--- a/collections/metabolomics/v2/tools/massbank-web.yaml
+++ b/collections/metabolomics/v2/tools/massbank-web.yaml
@@ -9,3 +9,6 @@ derived_from:
 source_repos:
 - MassBank/MassBank-data
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
diff --git a/collections/metabolomics/v2/tools/massbank.yaml b/collections/metabolomics/v2/tools/massbank.yaml
index 1ff199471..e3e783123 100644
--- a/collections/metabolomics/v2/tools/massbank.yaml
+++ b/collections/metabolomics/v2/tools/massbank.yaml
@@ -16,6 +16,9 @@ source_repos:
 - mwang87/MetabolomicsSpectrumResolver
 - xdomingoal/erah-devel
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/masscube.yaml b/collections/metabolomics/v2/tools/masscube.yaml
index 7d7a4d82a..2cd732724 100644
--- a/collections/metabolomics/v2/tools/masscube.yaml
+++ b/collections/metabolomics/v2/tools/masscube.yaml
@@ -10,6 +10,9 @@ derived_from:
 source_repos:
 - huaxuyu/masscube
 schema_version: 0.2.0
+license_tier: noncommercial
+license: CC-BY-NC-4.0
+license_detection: license-file
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/massdash-loaders-resultsloader.yaml b/collections/metabolomics/v2/tools/massdash-loaders-resultsloader.yaml
index c291059db..e57cfd211 100644
--- a/collections/metabolomics/v2/tools/massdash-loaders-resultsloader.yaml
+++ b/collections/metabolomics/v2/tools/massdash-loaders-resultsloader.yaml
@@ -9,5 +9,8 @@ derived_from:
 source_repos:
 - Roestlab/massdash
 schema_version: 0.2.0
+license_tier: open
+license: BSD-3-Clause
+license_detection: github-api
 techniques:
 - LC-MS
diff --git a/collections/metabolomics/v2/tools/massdash-peakpickers-mrmtransitiongrouppicker.yaml b/collections/metabolomics/v2/tools/massdash-peakpickers-mrmtransitiongrouppicker.yaml
index 2149ec125..df44c8bd2 100644
--- a/collections/metabolomics/v2/tools/massdash-peakpickers-mrmtransitiongrouppicker.yaml
+++ b/collections/metabolomics/v2/tools/massdash-peakpickers-mrmtransitiongrouppicker.yaml
@@ -9,5 +9,8 @@ derived_from:
 source_repos:
 - Roestlab/massdash
 schema_version: 0.2.0
+license_tier: open
+license: BSD-3-Clause
+license_detection: github-api
 techniques:
 - LC-MS
diff --git a/collections/metabolomics/v2/tools/massdash-peakpickers-pymrmtransitiongrouppicker.yaml b/collections/metabolomics/v2/tools/massdash-peakpickers-pymrmtransitiongrouppicker.yaml
index 4d2b913bc..822a72e54 100644
--- a/collections/metabolomics/v2/tools/massdash-peakpickers-pymrmtransitiongrouppicker.yaml
+++ b/collections/metabolomics/v2/tools/massdash-peakpickers-pymrmtransitiongrouppicker.yaml
@@ -9,5 +9,8 @@ derived_from:
 source_repos:
 - Roestlab/massdash
 schema_version: 0.2.0
+license_tier: open
+license: BSD-3-Clause
+license_detection: github-api
 techniques:
 - LC-MS
diff --git a/collections/metabolomics/v2/tools/massdash-plotting-interactiveplotter.yaml b/collections/metabolomics/v2/tools/massdash-plotting-interactiveplotter.yaml
index 54babd9d0..6ec044514 100644
--- a/collections/metabolomics/v2/tools/massdash-plotting-interactiveplotter.yaml
+++ b/collections/metabolomics/v2/tools/massdash-plotting-interactiveplotter.yaml
@@ -9,5 +9,8 @@ derived_from:
 source_repos:
 - Roestlab/massdash
 schema_version: 0.2.0
+license_tier: open
+license: BSD-3-Clause
+license_detection: github-api
 techniques:
 - LC-MS
diff --git a/collections/metabolomics/v2/tools/massdash-structs-featuremap.yaml b/collections/metabolomics/v2/tools/massdash-structs-featuremap.yaml
index b9d3dd74e..afd9c0c97 100644
--- a/collections/metabolomics/v2/tools/massdash-structs-featuremap.yaml
+++ b/collections/metabolomics/v2/tools/massdash-structs-featuremap.yaml
@@ -9,5 +9,8 @@ derived_from:
 source_repos:
 - Roestlab/massdash
 schema_version: 0.2.0
+license_tier: open
+license: BSD-3-Clause
+license_detection: github-api
 techniques:
 - LC-MS
diff --git a/collections/metabolomics/v2/tools/massdash.yaml b/collections/metabolomics/v2/tools/massdash.yaml
index e8b67bff9..cdd00e7ec 100644
--- a/collections/metabolomics/v2/tools/massdash.yaml
+++ b/collections/metabolomics/v2/tools/massdash.yaml
@@ -11,6 +11,9 @@ derived_from:
 source_repos:
 - Roestlab/massdash
 schema_version: 0.2.0
+license_tier: open
+license: BSD-3-Clause
+license_detection: github-api
 techniques:
 - LC-MS
 - ion-mobility-MS
diff --git a/collections/metabolomics/v2/tools/masshunter-profinder.yaml b/collections/metabolomics/v2/tools/masshunter-profinder.yaml
index b787611bb..ff57af800 100644
--- a/collections/metabolomics/v2/tools/masshunter-profinder.yaml
+++ b/collections/metabolomics/v2/tools/masshunter-profinder.yaml
@@ -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
diff --git a/collections/metabolomics/v2/tools/massive.yaml b/collections/metabolomics/v2/tools/massive.yaml
index 42998d564..ab5f7d5f2 100644
--- a/collections/metabolomics/v2/tools/massive.yaml
+++ b/collections/metabolomics/v2/tools/massive.yaml
@@ -10,6 +10,9 @@ derived_from:
 source_repos:
 - mwang87/ReDU-MS2-Documentation
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - CE-MS
diff --git a/collections/metabolomics/v2/tools/massql.yaml b/collections/metabolomics/v2/tools/massql.yaml
index 771b2fca6..5d0330985 100644
--- a/collections/metabolomics/v2/tools/massql.yaml
+++ b/collections/metabolomics/v2/tools/massql.yaml
@@ -17,6 +17,9 @@ source_repos:
 - mwang87/MassQueryLanguage
 - vdhooftcompmet/MS2LDA
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
 techniques:
 - LC-MS
 - mass-spectrometry
diff --git a/collections/metabolomics/v2/tools/massqlab.yaml b/collections/metabolomics/v2/tools/massqlab.yaml
index 1f60da16e..298df507c 100644
--- a/collections/metabolomics/v2/tools/massqlab.yaml
+++ b/collections/metabolomics/v2/tools/massqlab.yaml
@@ -9,5 +9,8 @@ derived_from:
 source_repos:
 - JohnsonDylan/MassQLab
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
 techniques:
 - LC-MS
diff --git a/collections/metabolomics/v2/tools/massspecwavelet.yaml b/collections/metabolomics/v2/tools/massspecwavelet.yaml
index efdf5a63b..55a1398ed 100644
--- a/collections/metabolomics/v2/tools/massspecwavelet.yaml
+++ b/collections/metabolomics/v2/tools/massspecwavelet.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - sneumann/xcms
 schema_version: 0.2.0
+license_tier: open
+license: LGPL-3.0
+license_detection: license-file
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/masst.yaml b/collections/metabolomics/v2/tools/masst.yaml
index a0fef43de..87da053ce 100644
--- a/collections/metabolomics/v2/tools/masst.yaml
+++ b/collections/metabolomics/v2/tools/masst.yaml
@@ -10,6 +10,9 @@ derived_from:
 source_repos:
 - mohimanilab/MASSTplus
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - NMR
diff --git a/collections/metabolomics/v2/tools/matchms.yaml b/collections/metabolomics/v2/tools/matchms.yaml
index 1059232eb..1349c9e44 100644
--- a/collections/metabolomics/v2/tools/matchms.yaml
+++ b/collections/metabolomics/v2/tools/matchms.yaml
@@ -29,6 +29,9 @@ source_repos:
 - matchms/matchms
 - tingxiecsu/CSU-MS2
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/math-distance.yaml b/collections/metabolomics/v2/tools/math-distance.yaml
index d5ad3805f..082a1d38e 100644
--- a/collections/metabolomics/v2/tools/math-distance.yaml
+++ b/collections/metabolomics/v2/tools/math-distance.yaml
@@ -9,3 +9,6 @@ derived_from:
 source_repos:
 - YuanyueLi/SpectralEntropy
 schema_version: 0.2.0
+license_tier: open
+license: Apache-2.0
+license_detection: github-api
diff --git a/collections/metabolomics/v2/tools/matlab-compiler-runtime-8-3.yaml b/collections/metabolomics/v2/tools/matlab-compiler-runtime-8-3.yaml
index c24993691..b77269247 100644
--- a/collections/metabolomics/v2/tools/matlab-compiler-runtime-8-3.yaml
+++ b/collections/metabolomics/v2/tools/matlab-compiler-runtime-8-3.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - Viant-Metabolomics/Galaxy-M
 schema_version: 0.2.0
+license_tier: open
+license: GPL-2.0
+license_detection: github-api
 techniques:
 - LC-MS
 - direct-infusion-MS
diff --git a/collections/metabolomics/v2/tools/matlab-r2024a.yaml b/collections/metabolomics/v2/tools/matlab-r2024a.yaml
index ed8d80f9c..d70af9812 100644
--- a/collections/metabolomics/v2/tools/matlab-r2024a.yaml
+++ b/collections/metabolomics/v2/tools/matlab-r2024a.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - AdrianHaun/AriumMS
 schema_version: 0.2.0
+license_tier: open
+license: BSD-3-Clause
+license_detection: github-api
 techniques:
 - LC-MS
 - CE-MS
diff --git a/collections/metabolomics/v2/tools/matlab.yaml b/collections/metabolomics/v2/tools/matlab.yaml
index 7d5af8a3d..0c184a34d 100644
--- a/collections/metabolomics/v2/tools/matlab.yaml
+++ b/collections/metabolomics/v2/tools/matlab.yaml
@@ -16,6 +16,9 @@ source_repos:
 - KechrisLab/DisCoPad
 - dickinsonlab/DIMPLE-code
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/matplotlib-or-seaborn-for-visualization.yaml b/collections/metabolomics/v2/tools/matplotlib-or-seaborn-for-visualization.yaml
index 7d3f3f3d1..9caddd30d 100644
--- a/collections/metabolomics/v2/tools/matplotlib-or-seaborn-for-visualization.yaml
+++ b/collections/metabolomics/v2/tools/matplotlib-or-seaborn-for-visualization.yaml
@@ -6,5 +6,8 @@ derived_from:
 - doi: 10.1021/acs.analchem.3c05019
   title: 'PS<sup>2</sup>MS: A Deep Learning-Based Prediction System for Identifying New Psychoactive Substances Using Mass Spectrometry'
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - mass-spectrometry
diff --git a/collections/metabolomics/v2/tools/matplotlib.yaml b/collections/metabolomics/v2/tools/matplotlib.yaml
index 8680ff6f1..ba2c90dc0 100644
--- a/collections/metabolomics/v2/tools/matplotlib.yaml
+++ b/collections/metabolomics/v2/tools/matplotlib.yaml
@@ -39,6 +39,9 @@ source_repos:
 - chopralab/CLAW
 - zsspython/LAGF
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/maven-gui.yaml b/collections/metabolomics/v2/tools/maven-gui.yaml
index 128e18efe..b6408c212 100644
--- a/collections/metabolomics/v2/tools/maven-gui.yaml
+++ b/collections/metabolomics/v2/tools/maven-gui.yaml
@@ -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
diff --git a/collections/metabolomics/v2/tools/maxquant.yaml b/collections/metabolomics/v2/tools/maxquant.yaml
index ce734ce61..38a5ef4f5 100644
--- a/collections/metabolomics/v2/tools/maxquant.yaml
+++ b/collections/metabolomics/v2/tools/maxquant.yaml
@@ -10,3 +10,6 @@ derived_from:
 source_repos:
 - fgcz/rawrr
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
diff --git a/collections/metabolomics/v2/tools/mbpls.yaml b/collections/metabolomics/v2/tools/mbpls.yaml
index 08bf01e2d..169d50dfb 100644
--- a/collections/metabolomics/v2/tools/mbpls.yaml
+++ b/collections/metabolomics/v2/tools/mbpls.yaml
@@ -6,5 +6,8 @@ derived_from:
 - doi: 10.1371/journal.pcbi.1011814
   title: 'PathIntegrate: Multivariate modelling approaches for pathway-based multi-omics data integration'
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
diff --git a/collections/metabolomics/v2/tools/mcfnmr.yaml b/collections/metabolomics/v2/tools/mcfnmr.yaml
index 202252d64..b4358b168 100644
--- a/collections/metabolomics/v2/tools/mcfnmr.yaml
+++ b/collections/metabolomics/v2/tools/mcfnmr.yaml
@@ -9,5 +9,8 @@ derived_from:
 source_repos:
 - GeoMetabolomics-ICBM/mcfNMR
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
 techniques:
 - NMR
diff --git a/collections/metabolomics/v2/tools/meister.yaml b/collections/metabolomics/v2/tools/meister.yaml
index ff20e25af..90cac4d7b 100644
--- a/collections/metabolomics/v2/tools/meister.yaml
+++ b/collections/metabolomics/v2/tools/meister.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - richardxie1119/MEISTER
 schema_version: 0.2.0
+license_tier: open
+license: GPL-3.0
+license_detection: github-api
 techniques:
 - LC-MS
 - CE-MS
diff --git a/collections/metabolomics/v2/tools/melonnpan-elastic-net-linear-regression.yaml b/collections/metabolomics/v2/tools/melonnpan-elastic-net-linear-regression.yaml
index 91da6a0a7..c582a01bc 100644
--- a/collections/metabolomics/v2/tools/melonnpan-elastic-net-linear-regression.yaml
+++ b/collections/metabolomics/v2/tools/melonnpan-elastic-net-linear-regression.yaml
@@ -6,3 +6,6 @@ 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
diff --git a/collections/metabolomics/v2/tools/melonnpan.yaml b/collections/metabolomics/v2/tools/melonnpan.yaml
index 43e7d839a..4ad8547bc 100644
--- a/collections/metabolomics/v2/tools/melonnpan.yaml
+++ b/collections/metabolomics/v2/tools/melonnpan.yaml
@@ -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
diff --git a/collections/metabolomics/v2/tools/memo-ms.yaml b/collections/metabolomics/v2/tools/memo-ms.yaml
index bf632b293..e62194358 100644
--- a/collections/metabolomics/v2/tools/memo-ms.yaml
+++ b/collections/metabolomics/v2/tools/memo-ms.yaml
@@ -6,6 +6,9 @@ derived_from:
 - doi: 10.3389/fbinf.2022.842964
   title: memo
 schema_version: 0.2.0
+license_tier: open
+license: GPL-3.0
+license_detection: github-api
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/memo.yaml b/collections/metabolomics/v2/tools/memo.yaml
index 21020857e..dfd3d594f 100644
--- a/collections/metabolomics/v2/tools/memo.yaml
+++ b/collections/metabolomics/v2/tools/memo.yaml
@@ -12,6 +12,9 @@ derived_from:
 source_repos:
 - luigiquiros/inventa
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/mergeion2.yaml b/collections/metabolomics/v2/tools/mergeion2.yaml
index 26c6515ff..c9b785cc9 100644
--- a/collections/metabolomics/v2/tools/mergeion2.yaml
+++ b/collections/metabolomics/v2/tools/mergeion2.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - daniellyz/meRgeION2
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - CE-MS
diff --git a/collections/metabolomics/v2/tools/messes.yaml b/collections/metabolomics/v2/tools/messes.yaml
index 4b5b0135d..f62be61a4 100644
--- a/collections/metabolomics/v2/tools/messes.yaml
+++ b/collections/metabolomics/v2/tools/messes.yaml
@@ -6,6 +6,9 @@ derived_from:
 - doi: 10.3390/metabo11030163
   title: The mwtab Python Library for RESTful Access and Enhanced Quality Control, Deposition, and Curation of the Metabolomics Workbench Data Repository
 schema_version: 0.2.0
+license_tier: open
+license: BSD-3-Clause-Clear
+license_detection: github-api
 techniques:
 - NMR
 - mass-spectrometry
diff --git a/collections/metabolomics/v2/tools/metabcombiner.yaml b/collections/metabolomics/v2/tools/metabcombiner.yaml
index 4f8879fbd..0d758285d 100644
--- a/collections/metabolomics/v2/tools/metabcombiner.yaml
+++ b/collections/metabolomics/v2/tools/metabcombiner.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - hhabra/metabCombiner
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - mass-spectrometry
diff --git a/collections/metabolomics/v2/tools/metaboanalyst.yaml b/collections/metabolomics/v2/tools/metaboanalyst.yaml
index a4d7c04e9..e31b2ba99 100644
--- a/collections/metabolomics/v2/tools/metaboanalyst.yaml
+++ b/collections/metabolomics/v2/tools/metaboanalyst.yaml
@@ -24,6 +24,9 @@ source_repos:
 - cellbiomaths/MInfer
 - scibiome/meteor
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/metaboanalystr.yaml b/collections/metabolomics/v2/tools/metaboanalystr.yaml
index 1dece476a..4ee7bb9ca 100644
--- a/collections/metabolomics/v2/tools/metaboanalystr.yaml
+++ b/collections/metabolomics/v2/tools/metaboanalystr.yaml
@@ -10,6 +10,9 @@ derived_from:
 source_repos:
 - xia-lab/MetaboAnalystR
 schema_version: 0.2.0
+license_tier: open
+license: GPL-3.0
+license_detection: license-file
 techniques:
 - LC-MS
 - CE-MS
diff --git a/collections/metabolomics/v2/tools/metaboannotator.yaml b/collections/metabolomics/v2/tools/metaboannotator.yaml
index 8eafa040e..69911bbb9 100644
--- a/collections/metabolomics/v2/tools/metaboannotator.yaml
+++ b/collections/metabolomics/v2/tools/metaboannotator.yaml
@@ -6,6 +6,9 @@ derived_from:
 - doi: 10.1021/acs.analchem.1c03032
   title: Automated Annotation of Untargeted All-Ion Fragmentation LC–MS Metabolomics Data with MetaboAnnotatoR
 schema_version: 0.2.0
+license_tier: open
+license: GPL-3.0
+license_detection: github-api
 techniques:
 - LC-MS
 - CE-MS
diff --git a/collections/metabolomics/v2/tools/metabocoreutils.yaml b/collections/metabolomics/v2/tools/metabocoreutils.yaml
index 0ba6b54bc..3a8de85d0 100644
--- a/collections/metabolomics/v2/tools/metabocoreutils.yaml
+++ b/collections/metabolomics/v2/tools/metabocoreutils.yaml
@@ -13,6 +13,9 @@ source_repos:
 - LiesaSalzer/MobilityTransformR
 - sneumann/xcms
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/metabodiff.yaml b/collections/metabolomics/v2/tools/metabodiff.yaml
index 9044c5e9d..97bd2b636 100644
--- a/collections/metabolomics/v2/tools/metabodiff.yaml
+++ b/collections/metabolomics/v2/tools/metabodiff.yaml
@@ -11,3 +11,6 @@ derived_from:
 source_repos:
 - andreasmock/MetaboDiff
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
diff --git a/collections/metabolomics/v2/tools/metabodirect.yaml b/collections/metabolomics/v2/tools/metabodirect.yaml
index bff2db6d8..0660564dc 100644
--- a/collections/metabolomics/v2/tools/metabodirect.yaml
+++ b/collections/metabolomics/v2/tools/metabodirect.yaml
@@ -12,6 +12,9 @@ derived_from:
 - doi: 10.1186/s40168-023-01476-3
   title: MetaboDirect
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/metabolabpy.yaml b/collections/metabolomics/v2/tools/metabolabpy.yaml
index 10e851dee..6b378652b 100644
--- a/collections/metabolomics/v2/tools/metabolabpy.yaml
+++ b/collections/metabolomics/v2/tools/metabolabpy.yaml
@@ -9,5 +9,8 @@ derived_from:
 source_repos:
 - ludwigc/metabolabpy
 schema_version: 0.2.0
+license_tier: open
+license: GPL-3.0
+license_detection: github-api
 techniques:
 - NMR
diff --git a/collections/metabolomics/v2/tools/metabolights.yaml b/collections/metabolomics/v2/tools/metabolights.yaml
index 9bae6cfcb..16e1e63d9 100644
--- a/collections/metabolomics/v2/tools/metabolights.yaml
+++ b/collections/metabolomics/v2/tools/metabolights.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - mwang87/MetabolomicsSpectrumResolver
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
 techniques:
 - LC-MS
 - CE-MS
diff --git a/collections/metabolomics/v2/tools/metabolomics-workbench-api.yaml b/collections/metabolomics/v2/tools/metabolomics-workbench-api.yaml
index e89f68dd0..b74f31e7d 100644
--- a/collections/metabolomics/v2/tools/metabolomics-workbench-api.yaml
+++ b/collections/metabolomics/v2/tools/metabolomics-workbench-api.yaml
@@ -9,5 +9,8 @@ derived_from:
 source_repos:
 - ahmohamed/lipidr
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: file-present-unclassified
 techniques:
 - mass-spectrometry
diff --git a/collections/metabolomics/v2/tools/metabolomics-workbench.yaml b/collections/metabolomics/v2/tools/metabolomics-workbench.yaml
index 20c82d172..dd186584c 100644
--- a/collections/metabolomics/v2/tools/metabolomics-workbench.yaml
+++ b/collections/metabolomics/v2/tools/metabolomics-workbench.yaml
@@ -9,5 +9,8 @@ derived_from:
 source_repos:
 - mwang87/MetabolomicsSpectrumResolver
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
 techniques:
 - LC-MS
diff --git a/collections/metabolomics/v2/tools/metaboprep.yaml b/collections/metabolomics/v2/tools/metaboprep.yaml
index db0ebeb18..d70ad472e 100644
--- a/collections/metabolomics/v2/tools/metaboprep.yaml
+++ b/collections/metabolomics/v2/tools/metaboprep.yaml
@@ -11,6 +11,9 @@ derived_from:
 source_repos:
 - MRCIEU/metaboprep
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: file-present-unclassified
 techniques:
 - LC-MS
 - mass-spectrometry
diff --git a/collections/metabolomics/v2/tools/metaboshiny.yaml b/collections/metabolomics/v2/tools/metaboshiny.yaml
index f3adbfed5..42fea16ed 100644
--- a/collections/metabolomics/v2/tools/metaboshiny.yaml
+++ b/collections/metabolomics/v2/tools/metaboshiny.yaml
@@ -11,6 +11,9 @@ derived_from:
 source_repos:
 - joannawolthuis/MetaboShiny
 schema_version: 0.2.0
+license_tier: open
+license: Apache-2.0
+license_detection: github-api
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/metaclean.yaml b/collections/metabolomics/v2/tools/metaclean.yaml
index 3173b40ae..e4bb3132f 100644
--- a/collections/metabolomics/v2/tools/metaclean.yaml
+++ b/collections/metabolomics/v2/tools/metaclean.yaml
@@ -11,5 +11,8 @@ derived_from:
 source_repos:
 - KelseyChetnik/MetaClean
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
diff --git a/collections/metabolomics/v2/tools/metadatamasst.yaml b/collections/metabolomics/v2/tools/metadatamasst.yaml
index c8280b0be..a518da03d 100644
--- a/collections/metabolomics/v2/tools/metadatamasst.yaml
+++ b/collections/metabolomics/v2/tools/metadatamasst.yaml
@@ -11,6 +11,9 @@ derived_from:
 source_repos:
 - mwang87/MASST
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - MS-imaging
diff --git a/collections/metabolomics/v2/tools/metamapr.yaml b/collections/metabolomics/v2/tools/metamapr.yaml
index 057e75af0..ed5fb0a89 100644
--- a/collections/metabolomics/v2/tools/metamapr.yaml
+++ b/collections/metabolomics/v2/tools/metamapr.yaml
@@ -9,3 +9,6 @@ derived_from:
 source_repos:
 - dgrapov/MetaMapR
 schema_version: 0.2.0
+license_tier: open
+license: AGPL-3.0
+license_detection: license-file
diff --git a/collections/metabolomics/v2/tools/metaminer.yaml b/collections/metabolomics/v2/tools/metaminer.yaml
index 9f7f762ba..7f5d0a5b3 100644
--- a/collections/metabolomics/v2/tools/metaminer.yaml
+++ b/collections/metabolomics/v2/tools/metaminer.yaml
@@ -11,6 +11,9 @@ derived_from:
 source_repos:
 - ablab/npdtools
 schema_version: 0.2.0
+license_tier: open
+license: Apache-2.0
+license_detection: readme-llm
 techniques:
 - LC-MS
 - direct-infusion-MS
diff --git a/collections/metabolomics/v2/tools/metams.yaml b/collections/metabolomics/v2/tools/metams.yaml
index ef2bcf5ac..8da4310e6 100644
--- a/collections/metabolomics/v2/tools/metams.yaml
+++ b/collections/metabolomics/v2/tools/metams.yaml
@@ -10,6 +10,9 @@ derived_from:
 source_repos:
 - HuanLab/DaDIA
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/metanet.yaml b/collections/metabolomics/v2/tools/metanet.yaml
index 36053720a..8330e5bc9 100644
--- a/collections/metabolomics/v2/tools/metanet.yaml
+++ b/collections/metabolomics/v2/tools/metanet.yaml
@@ -10,5 +10,8 @@ derived_from:
 source_repos:
 - Asa12138/MetaNet
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - mass-spectrometry
diff --git a/collections/metabolomics/v2/tools/metanorm-r-package.yaml b/collections/metabolomics/v2/tools/metanorm-r-package.yaml
index 061a9b741..62f736458 100644
--- a/collections/metabolomics/v2/tools/metanorm-r-package.yaml
+++ b/collections/metabolomics/v2/tools/metanorm-r-package.yaml
@@ -9,3 +9,6 @@ derived_from:
 source_repos:
 - UGent-LIMET/Metanorm
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
diff --git a/collections/metabolomics/v2/tools/metanorm.yaml b/collections/metabolomics/v2/tools/metanorm.yaml
index f73efd1e4..5a68ff9e6 100644
--- a/collections/metabolomics/v2/tools/metanorm.yaml
+++ b/collections/metabolomics/v2/tools/metanorm.yaml
@@ -9,5 +9,8 @@ derived_from:
 source_repos:
 - UGent-LIMET/Metanorm
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
diff --git a/collections/metabolomics/v2/tools/metaxtract.yaml b/collections/metabolomics/v2/tools/metaxtract.yaml
index 10160c569..567ed63fc 100644
--- a/collections/metabolomics/v2/tools/metaxtract.yaml
+++ b/collections/metabolomics/v2/tools/metaxtract.yaml
@@ -9,5 +9,8 @@ derived_from:
 source_repos:
 - Rappsilber-Laboratory/MetaXtract
 schema_version: 0.2.0
+license_tier: open
+license: Apache-2.0
+license_detection: github-api
 techniques:
 - LC-MS
diff --git a/collections/metabolomics/v2/tools/metcohort.yaml b/collections/metabolomics/v2/tools/metcohort.yaml
index 93fba5ac2..d5bae073a 100644
--- a/collections/metabolomics/v2/tools/metcohort.yaml
+++ b/collections/metabolomics/v2/tools/metcohort.yaml
@@ -10,5 +10,8 @@ derived_from:
 source_repos:
 - JunYang2021/MetCohort
 schema_version: 0.2.0
+license_tier: open
+license: AGPL-3.0
+license_detection: github-api
 techniques:
 - LC-MS
diff --git a/collections/metabolomics/v2/tools/metcorr.yaml b/collections/metabolomics/v2/tools/metcorr.yaml
index ee3fd7df1..e6d04914d 100644
--- a/collections/metabolomics/v2/tools/metcorr.yaml
+++ b/collections/metabolomics/v2/tools/metcorr.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - plyush1993/OUKS
 schema_version: 0.2.0
+license_tier: open
+license: GPL-3.0
+license_detection: github-api
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/metdatamodel.yaml b/collections/metabolomics/v2/tools/metdatamodel.yaml
index 969635695..1efa60a73 100644
--- a/collections/metabolomics/v2/tools/metdatamodel.yaml
+++ b/collections/metabolomics/v2/tools/metdatamodel.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - shuzhao-li-lab/khipu
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: file-present-unclassified
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/metdna2-r-package.yaml b/collections/metabolomics/v2/tools/metdna2-r-package.yaml
index 439c75113..ec57a947d 100644
--- a/collections/metabolomics/v2/tools/metdna2-r-package.yaml
+++ b/collections/metabolomics/v2/tools/metdna2-r-package.yaml
@@ -9,3 +9,6 @@ derived_from:
 source_repos:
 - ZhuMetLab/MetDNA2
 schema_version: 0.2.0
+license_tier: noncommercial
+license: CC-BY-NC-4.0
+license_detection: license-file
diff --git a/collections/metabolomics/v2/tools/meteor.yaml b/collections/metabolomics/v2/tools/meteor.yaml
index 95be20021..167d83a1d 100644
--- a/collections/metabolomics/v2/tools/meteor.yaml
+++ b/collections/metabolomics/v2/tools/meteor.yaml
@@ -10,3 +10,6 @@ derived_from:
 source_repos:
 - scibiome/meteor
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
diff --git a/collections/metabolomics/v2/tools/metfrag.yaml b/collections/metabolomics/v2/tools/metfrag.yaml
index 389789db1..caec4ec32 100644
--- a/collections/metabolomics/v2/tools/metfrag.yaml
+++ b/collections/metabolomics/v2/tools/metfrag.yaml
@@ -25,6 +25,9 @@ source_repos:
 - rickhelmus/patRoon
 - zmahnoor14/MAW
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/metnet.yaml b/collections/metabolomics/v2/tools/metnet.yaml
index 49d83b7c8..df19c0e02 100644
--- a/collections/metabolomics/v2/tools/metnet.yaml
+++ b/collections/metabolomics/v2/tools/metnet.yaml
@@ -10,3 +10,6 @@ derived_from:
 source_repos:
 - simeoni-biolab/MetNet
 schema_version: 0.2.0
+license_tier: open
+license: LGPL-2.1
+license_detection: github-api
diff --git a/collections/metabolomics/v2/tools/metscriber.yaml b/collections/metabolomics/v2/tools/metscriber.yaml
index 56a077e7d..85c5e1636 100644
--- a/collections/metabolomics/v2/tools/metscriber.yaml
+++ b/collections/metabolomics/v2/tools/metscriber.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - ncats/metScribeR
 schema_version: 0.2.0
+license_tier: open
+license: GPL-2.0
+license_detection: github-api
 techniques:
 - LC-MS
 - NMR
diff --git a/collections/metabolomics/v2/tools/mgcv.yaml b/collections/metabolomics/v2/tools/mgcv.yaml
index bb9debcec..5944ac870 100644
--- a/collections/metabolomics/v2/tools/mgcv.yaml
+++ b/collections/metabolomics/v2/tools/mgcv.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - hhabra/metabCombiner
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - mass-spectrometry
diff --git a/collections/metabolomics/v2/tools/mibig.yaml b/collections/metabolomics/v2/tools/mibig.yaml
index 3d5fc55d1..4aabad13e 100644
--- a/collections/metabolomics/v2/tools/mibig.yaml
+++ b/collections/metabolomics/v2/tools/mibig.yaml
@@ -16,6 +16,9 @@ derived_from:
 source_repos:
 - NPLinker/nplinker
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - mass-spectrometry
diff --git a/collections/metabolomics/v2/tools/microbemasst.yaml b/collections/metabolomics/v2/tools/microbemasst.yaml
index 76c58e98a..3f31377c6 100644
--- a/collections/metabolomics/v2/tools/microbemasst.yaml
+++ b/collections/metabolomics/v2/tools/microbemasst.yaml
@@ -11,6 +11,9 @@ derived_from:
 source_repos:
 - mwang87/MASST
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - MS-imaging
diff --git a/collections/metabolomics/v2/tools/microbiomemasst.yaml b/collections/metabolomics/v2/tools/microbiomemasst.yaml
index 4517879b8..bdbf34fbe 100644
--- a/collections/metabolomics/v2/tools/microbiomemasst.yaml
+++ b/collections/metabolomics/v2/tools/microbiomemasst.yaml
@@ -11,6 +11,9 @@ derived_from:
 source_repos:
 - mwang87/MASST
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - MS-imaging
diff --git a/collections/metabolomics/v2/tools/microsoft-visual-c-runtime-x64.yaml b/collections/metabolomics/v2/tools/microsoft-visual-c-runtime-x64.yaml
index 7052b7c70..2b4766dfe 100644
--- a/collections/metabolomics/v2/tools/microsoft-visual-c-runtime-x64.yaml
+++ b/collections/metabolomics/v2/tools/microsoft-visual-c-runtime-x64.yaml
@@ -9,6 +9,9 @@ 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
 - ion-mobility-MS
diff --git a/collections/metabolomics/v2/tools/mimenet.yaml b/collections/metabolomics/v2/tools/mimenet.yaml
index b5f4ea3fc..944130db5 100644
--- a/collections/metabolomics/v2/tools/mimenet.yaml
+++ b/collections/metabolomics/v2/tools/mimenet.yaml
@@ -9,6 +9,9 @@ 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
diff --git a/collections/metabolomics/v2/tools/mimir.yaml b/collections/metabolomics/v2/tools/mimir.yaml
index 6d88c3acc..38b2733f9 100644
--- a/collections/metabolomics/v2/tools/mimir.yaml
+++ b/collections/metabolomics/v2/tools/mimir.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - DanieleBizzarri/MiMIR
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/minems2.yaml b/collections/metabolomics/v2/tools/minems2.yaml
index a18677b8c..85d6382f5 100644
--- a/collections/metabolomics/v2/tools/minems2.yaml
+++ b/collections/metabolomics/v2/tools/minems2.yaml
@@ -6,6 +6,9 @@ derived_from:
 - doi: 10.1186/s13321-025-01051-y
   title: minems2
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: file-present-unclassified
 techniques:
 - LC-MS
 - CE-MS
diff --git a/collections/metabolomics/v2/tools/minfer.yaml b/collections/metabolomics/v2/tools/minfer.yaml
index d8c82d76a..c5ecdd7f7 100644
--- a/collections/metabolomics/v2/tools/minfer.yaml
+++ b/collections/metabolomics/v2/tools/minfer.yaml
@@ -9,3 +9,6 @@ derived_from:
 source_repos:
 - cellbiomaths/MInfer
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
diff --git a/collections/metabolomics/v2/tools/miniconda.yaml b/collections/metabolomics/v2/tools/miniconda.yaml
index 4a6520e46..2e08858d1 100644
--- a/collections/metabolomics/v2/tools/miniconda.yaml
+++ b/collections/metabolomics/v2/tools/miniconda.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - LabLaskin/MSIGen
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
 techniques:
 - CE-MS
 - MS-imaging
diff --git a/collections/metabolomics/v2/tools/mirador.yaml b/collections/metabolomics/v2/tools/mirador.yaml
index 1154e916e..1dfa6a36d 100644
--- a/collections/metabolomics/v2/tools/mirador.yaml
+++ b/collections/metabolomics/v2/tools/mirador.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - pnnl/IonToolPack
 schema_version: 0.2.0
+license_tier: open
+license: BSD-2-Clause
+license_detection: github-api
 techniques:
 - LC-MS
 - direct-infusion-MS
diff --git a/collections/metabolomics/v2/tools/missforest.yaml b/collections/metabolomics/v2/tools/missforest.yaml
index a91732378..30f10f66a 100644
--- a/collections/metabolomics/v2/tools/missforest.yaml
+++ b/collections/metabolomics/v2/tools/missforest.yaml
@@ -9,5 +9,8 @@ derived_from:
 source_repos:
 - antonvsdata/notame
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
diff --git a/collections/metabolomics/v2/tools/mist-cf.yaml b/collections/metabolomics/v2/tools/mist-cf.yaml
index e9f6e48f4..39354aec2 100644
--- a/collections/metabolomics/v2/tools/mist-cf.yaml
+++ b/collections/metabolomics/v2/tools/mist-cf.yaml
@@ -8,6 +8,9 @@ derived_from:
 - doi: 10.1021/acs.jcim.3c01082
   title: 'MIST-CF: Chemical Formula Inference from Tandem Mass Spectra'
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
 techniques:
 - LC-MS
 - MS-imaging
diff --git a/collections/metabolomics/v2/tools/mist.yaml b/collections/metabolomics/v2/tools/mist.yaml
index 254145e6e..686849eb2 100644
--- a/collections/metabolomics/v2/tools/mist.yaml
+++ b/collections/metabolomics/v2/tools/mist.yaml
@@ -12,6 +12,9 @@ derived_from:
 source_repos:
 - samgoldman97/mist
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
 techniques:
 - LC-MS
 - MS-imaging
diff --git a/collections/metabolomics/v2/tools/mixomics.yaml b/collections/metabolomics/v2/tools/mixomics.yaml
index 5304d3d2f..eff442785 100644
--- a/collections/metabolomics/v2/tools/mixomics.yaml
+++ b/collections/metabolomics/v2/tools/mixomics.yaml
@@ -13,6 +13,9 @@ source_repos:
 - DanielQuiroz97/RGCxGC
 - LargeMetabo/LargeMetabo
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/mobilipid.yaml b/collections/metabolomics/v2/tools/mobilipid.yaml
index 189285a05..1a38f2c9c 100644
--- a/collections/metabolomics/v2/tools/mobilipid.yaml
+++ b/collections/metabolomics/v2/tools/mobilipid.yaml
@@ -6,5 +6,8 @@ derived_from:
 - doi: 10.1021/acs.analchem.4c01253
   title: mobilipid
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - ion-mobility-MS
diff --git a/collections/metabolomics/v2/tools/mobilitytransformr.yaml b/collections/metabolomics/v2/tools/mobilitytransformr.yaml
index 80feb4a52..1e8af23a7 100644
--- a/collections/metabolomics/v2/tools/mobilitytransformr.yaml
+++ b/collections/metabolomics/v2/tools/mobilitytransformr.yaml
@@ -10,6 +10,9 @@ derived_from:
 source_repos:
 - LiesaSalzer/MobilityTransformR
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - CE-MS
diff --git a/collections/metabolomics/v2/tools/moccal.yaml b/collections/metabolomics/v2/tools/moccal.yaml
index 7fc9d4034..59f6b81b9 100644
--- a/collections/metabolomics/v2/tools/moccal.yaml
+++ b/collections/metabolomics/v2/tools/moccal.yaml
@@ -6,6 +6,9 @@ derived_from:
 - doi: 10.1021/acs.analchem.3c04290
   title: moccal
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
 techniques:
 - LC-MS
 - CE-MS
diff --git a/collections/metabolomics/v2/tools/mode-shinyapp.yaml b/collections/metabolomics/v2/tools/mode-shinyapp.yaml
index ca64acf7e..0d8455995 100644
--- a/collections/metabolomics/v2/tools/mode-shinyapp.yaml
+++ b/collections/metabolomics/v2/tools/mode-shinyapp.yaml
@@ -9,3 +9,6 @@ derived_from:
 source_repos:
 - pmartR/MODE_ShinyApp
 schema_version: 0.2.0
+license_tier: open
+license: BSD-2-Clause
+license_detection: github-api
diff --git a/collections/metabolomics/v2/tools/modifinder.yaml b/collections/metabolomics/v2/tools/modifinder.yaml
index d067e84d4..0e2eb8130 100644
--- a/collections/metabolomics/v2/tools/modifinder.yaml
+++ b/collections/metabolomics/v2/tools/modifinder.yaml
@@ -11,6 +11,9 @@ derived_from:
 source_repos:
 - Wang-Bioinformatics-Lab/ModiFinder_base
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: file-present-unclassified
 techniques:
 - LC-MS
 - CE-MS
diff --git a/collections/metabolomics/v2/tools/molbar.yaml b/collections/metabolomics/v2/tools/molbar.yaml
index 8fbc0b295..05db0b2c5 100644
--- a/collections/metabolomics/v2/tools/molbar.yaml
+++ b/collections/metabolomics/v2/tools/molbar.yaml
@@ -10,6 +10,9 @@ derived_from:
 source_repos:
 - grimme-lab/QCxMS2
 schema_version: 0.2.0
+license_tier: open
+license: LGPL-3.0
+license_detection: github-api
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/moldiscovery.yaml b/collections/metabolomics/v2/tools/moldiscovery.yaml
index 5e2eb4aaa..d18b10711 100644
--- a/collections/metabolomics/v2/tools/moldiscovery.yaml
+++ b/collections/metabolomics/v2/tools/moldiscovery.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - mohimanilab/molDiscovery
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - MS-imaging
diff --git a/collections/metabolomics/v2/tools/moletrans.yaml b/collections/metabolomics/v2/tools/moletrans.yaml
index 140ae7f7f..607fe1483 100644
--- a/collections/metabolomics/v2/tools/moletrans.yaml
+++ b/collections/metabolomics/v2/tools/moletrans.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - JibaoLiu/MoleTrans
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
 techniques:
 - LC-MS
 - NMR
diff --git a/collections/metabolomics/v2/tools/molmass.yaml b/collections/metabolomics/v2/tools/molmass.yaml
index fd9feebb2..c4ec196e9 100644
--- a/collections/metabolomics/v2/tools/molmass.yaml
+++ b/collections/metabolomics/v2/tools/molmass.yaml
@@ -11,5 +11,8 @@ derived_from:
 source_repos:
 - FanzhouKong/spectral_denoising
 schema_version: 0.2.0
+license_tier: open
+license: Apache-2.0
+license_detection: github-api
 techniques:
 - LC-MS
diff --git a/collections/metabolomics/v2/tools/molnotator.yaml b/collections/metabolomics/v2/tools/molnotator.yaml
index 8eac9c6de..ba27d910e 100644
--- a/collections/metabolomics/v2/tools/molnotator.yaml
+++ b/collections/metabolomics/v2/tools/molnotator.yaml
@@ -10,5 +10,8 @@ derived_from:
 source_repos:
 - ZzakB/MolNotator
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
 techniques:
 - LC-MS
diff --git a/collections/metabolomics/v2/tools/mona.yaml b/collections/metabolomics/v2/tools/mona.yaml
index 469092b18..7fa62feac 100644
--- a/collections/metabolomics/v2/tools/mona.yaml
+++ b/collections/metabolomics/v2/tools/mona.yaml
@@ -8,6 +8,9 @@ derived_from:
 - doi: 10.1021/acs.analchem.2c05389
   title: mspcompiler
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: file-present-unclassified
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/mongodb.yaml b/collections/metabolomics/v2/tools/mongodb.yaml
index 800291049..70ce09bbd 100644
--- a/collections/metabolomics/v2/tools/mongodb.yaml
+++ b/collections/metabolomics/v2/tools/mongodb.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - tyo-nu/MINE-Database
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
 techniques:
 - LC-MS
 - MS-imaging
diff --git a/collections/metabolomics/v2/tools/monte-carlo-dropout.yaml b/collections/metabolomics/v2/tools/monte-carlo-dropout.yaml
index f78c5c523..a8ff3b0ac 100644
--- a/collections/metabolomics/v2/tools/monte-carlo-dropout.yaml
+++ b/collections/metabolomics/v2/tools/monte-carlo-dropout.yaml
@@ -8,5 +8,8 @@ derived_from:
 - doi: 10.1186/s13321-021-00558-4
   title: 'MS2DeepScore: a novel deep learning similarity measure to compare tandem mass spectra'
 schema_version: 0.2.0
+license_tier: open
+license: Apache-2.0
+license_detection: github-api
 techniques:
 - LC-MS
diff --git a/collections/metabolomics/v2/tools/mordred.yaml b/collections/metabolomics/v2/tools/mordred.yaml
index 9365b636e..5f36cf79f 100644
--- a/collections/metabolomics/v2/tools/mordred.yaml
+++ b/collections/metabolomics/v2/tools/mordred.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - HopkinsLaboratory/Graphormer-RT
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/motifdb.yaml b/collections/metabolomics/v2/tools/motifdb.yaml
index 55e451ac4..7c236fe9c 100644
--- a/collections/metabolomics/v2/tools/motifdb.yaml
+++ b/collections/metabolomics/v2/tools/motifdb.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - vdhooftcompmet/MS2LDA
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
 techniques:
 - LC-MS
 - mass-spectrometry
diff --git a/collections/metabolomics/v2/tools/mozilla-firefox.yaml b/collections/metabolomics/v2/tools/mozilla-firefox.yaml
index be55aeb35..3d61b1864 100644
--- a/collections/metabolomics/v2/tools/mozilla-firefox.yaml
+++ b/collections/metabolomics/v2/tools/mozilla-firefox.yaml
@@ -9,5 +9,8 @@ derived_from:
 source_repos:
 - lidawei1975/colmarvista
 schema_version: 0.2.0
+license_tier: open
+license: GPL-3.0
+license_detection: github-api
 techniques:
 - NMR
diff --git a/collections/metabolomics/v2/tools/mpactr.yaml b/collections/metabolomics/v2/tools/mpactr.yaml
index 72da9d1a4..c10e1378d 100644
--- a/collections/metabolomics/v2/tools/mpactr.yaml
+++ b/collections/metabolomics/v2/tools/mpactr.yaml
@@ -11,6 +11,9 @@ derived_from:
 source_repos:
 - BalunasLab/mpact
 schema_version: 0.2.0
+license_tier: open
+license: GPL-2.0
+license_detection: github-api
 techniques:
 - LC-MS
 - ion-mobility-MS
diff --git a/collections/metabolomics/v2/tools/mrmquant.yaml b/collections/metabolomics/v2/tools/mrmquant.yaml
index 50e551049..3e233ebc6 100644
--- a/collections/metabolomics/v2/tools/mrmquant.yaml
+++ b/collections/metabolomics/v2/tools/mrmquant.yaml
@@ -10,5 +10,8 @@ derived_from:
 source_repos:
 - kslynn128171/MRMQuant
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
diff --git a/collections/metabolomics/v2/tools/mrmtransitiongrouppicker.yaml b/collections/metabolomics/v2/tools/mrmtransitiongrouppicker.yaml
index a45ddd7fc..59580b0fe 100644
--- a/collections/metabolomics/v2/tools/mrmtransitiongrouppicker.yaml
+++ b/collections/metabolomics/v2/tools/mrmtransitiongrouppicker.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - Roestlab/massdash
 schema_version: 0.2.0
+license_tier: open
+license: BSD-3-Clause
+license_detection: github-api
 techniques:
 - LC-MS
 - ion-mobility-MS
diff --git a/collections/metabolomics/v2/tools/mrnannoalgo3-metdna3.yaml b/collections/metabolomics/v2/tools/mrnannoalgo3-metdna3.yaml
index c9d7a3f73..8df8dfcca 100644
--- a/collections/metabolomics/v2/tools/mrnannoalgo3-metdna3.yaml
+++ b/collections/metabolomics/v2/tools/mrnannoalgo3-metdna3.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - ZhuMetLab/MrnAnnoAlgo3
 schema_version: 0.2.0
+license_tier: noncommercial
+license: CC-BY-NC-ND-4.0
+license_detection: readme-llm
 techniques:
 - LC-MS
 - CE-MS
diff --git a/collections/metabolomics/v2/tools/ms-cleanr.yaml b/collections/metabolomics/v2/tools/ms-cleanr.yaml
index 5ecf79206..24c3c3cf0 100644
--- a/collections/metabolomics/v2/tools/ms-cleanr.yaml
+++ b/collections/metabolomics/v2/tools/ms-cleanr.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - eMetaboHUB/MS-CleanR
 schema_version: 0.2.0
+license_tier: open
+license: GPL-3.0
+license_detection: readme-llm
 techniques:
 - LC-MS
 - CE-MS
diff --git a/collections/metabolomics/v2/tools/ms-dial-4.yaml b/collections/metabolomics/v2/tools/ms-dial-4.yaml
index 811af7f95..8b8315d71 100644
--- a/collections/metabolomics/v2/tools/ms-dial-4.yaml
+++ b/collections/metabolomics/v2/tools/ms-dial-4.yaml
@@ -7,6 +7,9 @@ derived_from:
 - doi: 10.1021/acs.analchem.4c04040
   title: lipoclean
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
 techniques:
 - LC-MS
 - ion-mobility-MS
diff --git a/collections/metabolomics/v2/tools/ms-dial-5.yaml b/collections/metabolomics/v2/tools/ms-dial-5.yaml
index ee1e274e4..23f5e1d3c 100644
--- a/collections/metabolomics/v2/tools/ms-dial-5.yaml
+++ b/collections/metabolomics/v2/tools/ms-dial-5.yaml
@@ -6,6 +6,9 @@ derived_from:
 - doi: 10.1021/acs.analchem.4c04040
   title: lipoclean
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
 techniques:
 - LC-MS
 - ion-mobility-MS
diff --git a/collections/metabolomics/v2/tools/ms-dial-or-higher.yaml b/collections/metabolomics/v2/tools/ms-dial-or-higher.yaml
index e762801d0..1e2d1ee70 100644
--- a/collections/metabolomics/v2/tools/ms-dial-or-higher.yaml
+++ b/collections/metabolomics/v2/tools/ms-dial-or-higher.yaml
@@ -9,3 +9,6 @@ derived_from:
 source_repos:
 - eMetaboHUB/MS-CleanR
 schema_version: 0.2.0
+license_tier: open
+license: GPL-3.0
+license_detection: readme-llm
diff --git a/collections/metabolomics/v2/tools/ms-dial-v4-00-or-higher.yaml b/collections/metabolomics/v2/tools/ms-dial-v4-00-or-higher.yaml
index 4a958cf09..6ab07664c 100644
--- a/collections/metabolomics/v2/tools/ms-dial-v4-00-or-higher.yaml
+++ b/collections/metabolomics/v2/tools/ms-dial-v4-00-or-higher.yaml
@@ -10,5 +10,8 @@ derived_from:
 source_repos:
 - eMetaboHUB/MS-CleanR
 schema_version: 0.2.0
+license_tier: open
+license: GPL-3.0
+license_detection: readme-llm
 techniques:
 - LC-MS
diff --git a/collections/metabolomics/v2/tools/ms-dial.yaml b/collections/metabolomics/v2/tools/ms-dial.yaml
index 3ba4a1f1c..c744fe9b5 100644
--- a/collections/metabolomics/v2/tools/ms-dial.yaml
+++ b/collections/metabolomics/v2/tools/ms-dial.yaml
@@ -38,6 +38,9 @@ source_repos:
 - huaxuyu/bago
 - systemsomicslab/MsdialWorkbench
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/ms-distance.yaml b/collections/metabolomics/v2/tools/ms-distance.yaml
index 6cda3713e..b1dfc646c 100644
--- a/collections/metabolomics/v2/tools/ms-distance.yaml
+++ b/collections/metabolomics/v2/tools/ms-distance.yaml
@@ -9,5 +9,8 @@ derived_from:
 source_repos:
 - YuanyueLi/SpectralEntropy
 schema_version: 0.2.0
+license_tier: open
+license: Apache-2.0
+license_detection: github-api
 techniques:
 - LC-MS
diff --git a/collections/metabolomics/v2/tools/ms-entropy.yaml b/collections/metabolomics/v2/tools/ms-entropy.yaml
index 472375663..ed65c5ad3 100644
--- a/collections/metabolomics/v2/tools/ms-entropy.yaml
+++ b/collections/metabolomics/v2/tools/ms-entropy.yaml
@@ -11,5 +11,8 @@ derived_from:
 source_repos:
 - FanzhouKong/spectral_denoising
 schema_version: 0.2.0
+license_tier: open
+license: Apache-2.0
+license_detection: github-api
 techniques:
 - LC-MS
diff --git a/collections/metabolomics/v2/tools/ms-finder.yaml b/collections/metabolomics/v2/tools/ms-finder.yaml
index 0beb309b3..b4d5a3de8 100644
--- a/collections/metabolomics/v2/tools/ms-finder.yaml
+++ b/collections/metabolomics/v2/tools/ms-finder.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - eMetaboHUB/MS-CleanR
 schema_version: 0.2.0
+license_tier: open
+license: GPL-3.0
+license_detection: readme-llm
 techniques:
 - LC-MS
 - CE-MS
diff --git a/collections/metabolomics/v2/tools/ms-pred-iceberg.yaml b/collections/metabolomics/v2/tools/ms-pred-iceberg.yaml
index 676b9c05e..69ba54d20 100644
--- a/collections/metabolomics/v2/tools/ms-pred-iceberg.yaml
+++ b/collections/metabolomics/v2/tools/ms-pred-iceberg.yaml
@@ -9,5 +9,8 @@ derived_from:
 source_repos:
 - samgoldman97/ms-pred
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
 techniques:
 - LC-MS
diff --git a/collections/metabolomics/v2/tools/ms-pred-scarf-model.yaml b/collections/metabolomics/v2/tools/ms-pred-scarf-model.yaml
index 9f2d04c08..caa6ffa84 100644
--- a/collections/metabolomics/v2/tools/ms-pred-scarf-model.yaml
+++ b/collections/metabolomics/v2/tools/ms-pred-scarf-model.yaml
@@ -11,3 +11,6 @@ derived_from:
 source_repos:
 - samgoldman97/ms-pred
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
diff --git a/collections/metabolomics/v2/tools/ms-pred.yaml b/collections/metabolomics/v2/tools/ms-pred.yaml
index 44bddac77..462d7c0cd 100644
--- a/collections/metabolomics/v2/tools/ms-pred.yaml
+++ b/collections/metabolomics/v2/tools/ms-pred.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - samgoldman97/ms-pred
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/ms-rescore.yaml b/collections/metabolomics/v2/tools/ms-rescore.yaml
index 15243faa0..a546a4ee8 100644
--- a/collections/metabolomics/v2/tools/ms-rescore.yaml
+++ b/collections/metabolomics/v2/tools/ms-rescore.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - compomics/ms2rescore
 schema_version: 0.2.0
+license_tier: open
+license: Apache-2.0
+license_detection: github-api
 techniques:
 - LC-MS
 - mass-spectrometry
diff --git a/collections/metabolomics/v2/tools/ms-search.yaml b/collections/metabolomics/v2/tools/ms-search.yaml
index 384faed5c..55b6108fa 100644
--- a/collections/metabolomics/v2/tools/ms-search.yaml
+++ b/collections/metabolomics/v2/tools/ms-search.yaml
@@ -6,6 +6,9 @@ derived_from:
 - doi: 10.1021/acs.analchem.2c05389
   title: mspcompiler
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: file-present-unclassified
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/ms2compound.yaml b/collections/metabolomics/v2/tools/ms2compound.yaml
index 679c13473..8fc563f2c 100644
--- a/collections/metabolomics/v2/tools/ms2compound.yaml
+++ b/collections/metabolomics/v2/tools/ms2compound.yaml
@@ -10,5 +10,8 @@ derived_from:
 source_repos:
 - beherasan/MS2Compound
 schema_version: 0.2.0
+license_tier: open
+license: CC-BY-4.0
+license_detection: github-api
 techniques:
 - LC-MS
diff --git a/collections/metabolomics/v2/tools/ms2deepscore.yaml b/collections/metabolomics/v2/tools/ms2deepscore.yaml
index 49face8e7..b5fc4e31c 100644
--- a/collections/metabolomics/v2/tools/ms2deepscore.yaml
+++ b/collections/metabolomics/v2/tools/ms2deepscore.yaml
@@ -18,6 +18,9 @@ derived_from:
 source_repos:
 - matchms/MS2DeepScore
 schema_version: 0.2.0
+license_tier: open
+license: Apache-2.0
+license_detection: github-api
 techniques:
 - LC-MS
 - CE-MS
diff --git a/collections/metabolomics/v2/tools/ms2lda-preprocessing-generate-corpus.yaml b/collections/metabolomics/v2/tools/ms2lda-preprocessing-generate-corpus.yaml
index 837c0bed6..6dfdaf3f5 100644
--- a/collections/metabolomics/v2/tools/ms2lda-preprocessing-generate-corpus.yaml
+++ b/collections/metabolomics/v2/tools/ms2lda-preprocessing-generate-corpus.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - vdhooftcompmet/MS2LDA
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
 techniques:
 - LC-MS
 - ion-mobility-MS
diff --git a/collections/metabolomics/v2/tools/ms2lda-preprocessing-load-and-clean.yaml b/collections/metabolomics/v2/tools/ms2lda-preprocessing-load-and-clean.yaml
index 757306f2b..2fef55bee 100644
--- a/collections/metabolomics/v2/tools/ms2lda-preprocessing-load-and-clean.yaml
+++ b/collections/metabolomics/v2/tools/ms2lda-preprocessing-load-and-clean.yaml
@@ -10,6 +10,9 @@ derived_from:
 source_repos:
 - vdhooftcompmet/MS2LDA
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
 techniques:
 - LC-MS
 - ion-mobility-MS
diff --git a/collections/metabolomics/v2/tools/ms2lda.yaml b/collections/metabolomics/v2/tools/ms2lda.yaml
index e8f740666..4fbb68b28 100644
--- a/collections/metabolomics/v2/tools/ms2lda.yaml
+++ b/collections/metabolomics/v2/tools/ms2lda.yaml
@@ -23,6 +23,9 @@ source_repos:
 - mwang87/MetabolomicsSpectrumResolver
 - vdhooftcompmet/MS2LDA
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - ion-mobility-MS
diff --git a/collections/metabolomics/v2/tools/ms2mp.yaml b/collections/metabolomics/v2/tools/ms2mp.yaml
index 2f3422617..149ef32eb 100644
--- a/collections/metabolomics/v2/tools/ms2mp.yaml
+++ b/collections/metabolomics/v2/tools/ms2mp.yaml
@@ -9,5 +9,8 @@ derived_from:
 source_repos:
 - ucasaccn/MS2MP
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
diff --git a/collections/metabolomics/v2/tools/ms2query.yaml b/collections/metabolomics/v2/tools/ms2query.yaml
index aa4170ac2..a1e4477df 100644
--- a/collections/metabolomics/v2/tools/ms2query.yaml
+++ b/collections/metabolomics/v2/tools/ms2query.yaml
@@ -10,6 +10,9 @@ derived_from:
 source_repos:
 - iomega/ms2query
 schema_version: 0.2.0
+license_tier: open
+license: Apache-2.0
+license_detection: github-api
 techniques:
 - LC-MS
 - CE-MS
diff --git a/collections/metabolomics/v2/tools/msbackendmgf.yaml b/collections/metabolomics/v2/tools/msbackendmgf.yaml
index ebc8fc6ec..3a8f15867 100644
--- a/collections/metabolomics/v2/tools/msbackendmgf.yaml
+++ b/collections/metabolomics/v2/tools/msbackendmgf.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - sneumann/xcms
 schema_version: 0.2.0
+license_tier: open
+license: LGPL-3.0
+license_detection: license-file
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/msbackendmzr.yaml b/collections/metabolomics/v2/tools/msbackendmzr.yaml
index 9458a96bd..3c6a8ef09 100644
--- a/collections/metabolomics/v2/tools/msbackendmzr.yaml
+++ b/collections/metabolomics/v2/tools/msbackendmzr.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - rformassspectrometry/Spectra
 schema_version: 0.2.0
+license_tier: open
+license: Artistic-2.0
+license_detection: readme-llm
 techniques:
 - LC-MS
 - mass-spectrometry
diff --git a/collections/metabolomics/v2/tools/msconvert-proteowizard.yaml b/collections/metabolomics/v2/tools/msconvert-proteowizard.yaml
index c6d13f4eb..c13119916 100644
--- a/collections/metabolomics/v2/tools/msconvert-proteowizard.yaml
+++ b/collections/metabolomics/v2/tools/msconvert-proteowizard.yaml
@@ -6,6 +6,9 @@ derived_from:
 - doi: 10.1021/acs.analchem.5c00567
   title: Automated Integration and Quality Assessment of Chromatographic Peaks in LC–MS-Based Metabolomics and Lipidomics Using TARDIS
 schema_version: 0.2.0
+license_tier: open
+license: GPL-3.0
+license_detection: github-api
 techniques:
 - LC-MS
 - mass-spectrometry
diff --git a/collections/metabolomics/v2/tools/msconvert.yaml b/collections/metabolomics/v2/tools/msconvert.yaml
index a129158e9..6babcb3c0 100644
--- a/collections/metabolomics/v2/tools/msconvert.yaml
+++ b/collections/metabolomics/v2/tools/msconvert.yaml
@@ -48,6 +48,9 @@ source_repos:
 - guomics-lab/iDIA-QC
 - xfcui/IsoFusion
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/msdata.yaml b/collections/metabolomics/v2/tools/msdata.yaml
index a53948d38..9bc2c52a3 100644
--- a/collections/metabolomics/v2/tools/msdata.yaml
+++ b/collections/metabolomics/v2/tools/msdata.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - LiesaSalzer/MobilityTransformR
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - CE-MS
diff --git a/collections/metabolomics/v2/tools/msdatahub.yaml b/collections/metabolomics/v2/tools/msdatahub.yaml
index 3190cbb78..e663ce64d 100644
--- a/collections/metabolomics/v2/tools/msdatahub.yaml
+++ b/collections/metabolomics/v2/tools/msdatahub.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - sneumann/xcms
 schema_version: 0.2.0
+license_tier: open
+license: LGPL-3.0
+license_detection: license-file
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/msentropy.yaml b/collections/metabolomics/v2/tools/msentropy.yaml
index 604106d51..58d7a2667 100644
--- a/collections/metabolomics/v2/tools/msentropy.yaml
+++ b/collections/metabolomics/v2/tools/msentropy.yaml
@@ -18,6 +18,9 @@ source_repos:
 - YuanyueLi/FlashEntropySearch
 - YuanyueLi/SpectralEntropy
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - CE-MS
diff --git a/collections/metabolomics/v2/tools/msexperiment.yaml b/collections/metabolomics/v2/tools/msexperiment.yaml
index 25cee9d1a..fb1ce8bd5 100644
--- a/collections/metabolomics/v2/tools/msexperiment.yaml
+++ b/collections/metabolomics/v2/tools/msexperiment.yaml
@@ -6,6 +6,9 @@ derived_from:
 - doi: 10.1021/acs.analchem.5c00567
   title: Automated Integration and Quality Assessment of Chromatographic Peaks in LC–MS-Based Metabolomics and Lipidomics Using TARDIS
 schema_version: 0.2.0
+license_tier: open
+license: GPL-3.0
+license_detection: github-api
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/msfeast.yaml b/collections/metabolomics/v2/tools/msfeast.yaml
index 5545bd534..53b850801 100644
--- a/collections/metabolomics/v2/tools/msfeast.yaml
+++ b/collections/metabolomics/v2/tools/msfeast.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - kevinmildau/msFeaST
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
 techniques:
 - LC-MS
 - mass-spectrometry
diff --git a/collections/metabolomics/v2/tools/msfeatures.yaml b/collections/metabolomics/v2/tools/msfeatures.yaml
index c503e0a01..ce68b1ea5 100644
--- a/collections/metabolomics/v2/tools/msfeatures.yaml
+++ b/collections/metabolomics/v2/tools/msfeatures.yaml
@@ -11,6 +11,9 @@ derived_from:
 source_repos:
 - sneumann/xcms
 schema_version: 0.2.0
+license_tier: open
+license: LGPL-3.0
+license_detection: license-file
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/msfiddle.yaml b/collections/metabolomics/v2/tools/msfiddle.yaml
index 4e0814872..82ef51640 100644
--- a/collections/metabolomics/v2/tools/msfiddle.yaml
+++ b/collections/metabolomics/v2/tools/msfiddle.yaml
@@ -6,6 +6,9 @@ derived_from:
 - doi: 10.1038/s41467-025-66060-9
   title: fiddle
 schema_version: 0.2.0
+license_tier: open
+license: Apache-2.0
+license_detection: github-api
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/msfinder.yaml b/collections/metabolomics/v2/tools/msfinder.yaml
index cbd9e58e0..e92308f21 100644
--- a/collections/metabolomics/v2/tools/msfinder.yaml
+++ b/collections/metabolomics/v2/tools/msfinder.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - cbroeckl/RAMClustR
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/msflo.yaml b/collections/metabolomics/v2/tools/msflo.yaml
index d8cb52ec3..a23e49951 100644
--- a/collections/metabolomics/v2/tools/msflo.yaml
+++ b/collections/metabolomics/v2/tools/msflo.yaml
@@ -6,6 +6,9 @@ derived_from:
 - doi: 10.1021/jasms.4c00364
   title: nextflow4msdial
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
 techniques:
 - LC-MS
 - CE-MS
diff --git a/collections/metabolomics/v2/tools/msfragger.yaml b/collections/metabolomics/v2/tools/msfragger.yaml
index b6dce460b..5095cc7af 100644
--- a/collections/metabolomics/v2/tools/msfragger.yaml
+++ b/collections/metabolomics/v2/tools/msfragger.yaml
@@ -9,3 +9,6 @@ derived_from:
 source_repos:
 - laurenfields/MSIght
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
diff --git a/collections/metabolomics/v2/tools/msgo-model.yaml b/collections/metabolomics/v2/tools/msgo-model.yaml
index d083c244e..d50cc9864 100644
--- a/collections/metabolomics/v2/tools/msgo-model.yaml
+++ b/collections/metabolomics/v2/tools/msgo-model.yaml
@@ -9,5 +9,8 @@ derived_from:
 source_repos:
 - aaronma2020/MSGO
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
 techniques:
 - mass-spectrometry
diff --git a/collections/metabolomics/v2/tools/mshub.yaml b/collections/metabolomics/v2/tools/mshub.yaml
index 1aba56ac9..76cadb9a8 100644
--- a/collections/metabolomics/v2/tools/mshub.yaml
+++ b/collections/metabolomics/v2/tools/mshub.yaml
@@ -10,6 +10,9 @@ derived_from:
 source_repos:
 - bittremieux/GNPS_GC
 schema_version: 0.2.0
+license_tier: open
+license: BSD-3-Clause
+license_detection: github-api
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/msi-explorer.yaml b/collections/metabolomics/v2/tools/msi-explorer.yaml
index 3c8efaae3..63894eb3e 100644
--- a/collections/metabolomics/v2/tools/msi-explorer.yaml
+++ b/collections/metabolomics/v2/tools/msi-explorer.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - MMV-Lab/MSI-Explorer
 schema_version: 0.2.0
+license_tier: open
+license: BSD-3-Clause
+license_detection: github-api
 techniques:
 - CE-MS
 - MS-imaging
diff --git a/collections/metabolomics/v2/tools/msigen.yaml b/collections/metabolomics/v2/tools/msigen.yaml
index 285b5f322..764358614 100644
--- a/collections/metabolomics/v2/tools/msigen.yaml
+++ b/collections/metabolomics/v2/tools/msigen.yaml
@@ -10,6 +10,9 @@ derived_from:
 source_repos:
 - LabLaskin/MSIGen
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
 techniques:
 - CE-MS
 - MS-imaging
diff --git a/collections/metabolomics/v2/tools/msmetaenhancer.yaml b/collections/metabolomics/v2/tools/msmetaenhancer.yaml
index 262c10dd5..25cdb825c 100644
--- a/collections/metabolomics/v2/tools/msmetaenhancer.yaml
+++ b/collections/metabolomics/v2/tools/msmetaenhancer.yaml
@@ -13,6 +13,9 @@ derived_from:
 source_repos:
 - RECETOX/MSMetaEnhancer
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
 techniques:
 - LC-MS
 - mass-spectrometry
diff --git a/collections/metabolomics/v2/tools/msmssim.yaml b/collections/metabolomics/v2/tools/msmssim.yaml
index c1fabe2a7..668271651 100644
--- a/collections/metabolomics/v2/tools/msmssim.yaml
+++ b/collections/metabolomics/v2/tools/msmssim.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - LeaveMeNotTonight/CMDN
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - CE-MS
diff --git a/collections/metabolomics/v2/tools/msnbase.yaml b/collections/metabolomics/v2/tools/msnbase.yaml
index b197eb565..35ee94998 100644
--- a/collections/metabolomics/v2/tools/msnbase.yaml
+++ b/collections/metabolomics/v2/tools/msnbase.yaml
@@ -13,6 +13,9 @@ source_repos:
 - LiesaSalzer/MobilityTransformR
 - rformassspectrometry/Spectra
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/msnovelist.yaml b/collections/metabolomics/v2/tools/msnovelist.yaml
index f1d80f983..4ff70464c 100644
--- a/collections/metabolomics/v2/tools/msnovelist.yaml
+++ b/collections/metabolomics/v2/tools/msnovelist.yaml
@@ -16,6 +16,9 @@ source_repos:
 - meowcat/MSNovelist
 - sirius-ms/sirius
 schema_version: 0.2.0
+license_tier: open
+license: AGPL-3.0
+license_detection: github-api
 techniques:
 - LC-MS
 - CE-MS
diff --git a/collections/metabolomics/v2/tools/mspack.yaml b/collections/metabolomics/v2/tools/mspack.yaml
index e9f40884d..ca0798381 100644
--- a/collections/metabolomics/v2/tools/mspack.yaml
+++ b/collections/metabolomics/v2/tools/mspack.yaml
@@ -9,5 +9,8 @@ derived_from:
 source_repos:
 - fhanau/mspack
 schema_version: 0.2.0
+license_tier: open
+license: Apache-2.0
+license_detection: github-api
 techniques:
 - ion-mobility-MS
diff --git a/collections/metabolomics/v2/tools/mspcompiler.yaml b/collections/metabolomics/v2/tools/mspcompiler.yaml
index 2b935fa58..b06fc0d09 100644
--- a/collections/metabolomics/v2/tools/mspcompiler.yaml
+++ b/collections/metabolomics/v2/tools/mspcompiler.yaml
@@ -6,6 +6,9 @@ derived_from:
 - doi: 10.1021/acs.analchem.2c05389
   title: mspcompiler
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: file-present-unclassified
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/msprep.yaml b/collections/metabolomics/v2/tools/msprep.yaml
index b72403d00..5e5598618 100644
--- a/collections/metabolomics/v2/tools/msprep.yaml
+++ b/collections/metabolomics/v2/tools/msprep.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - Ghoshlab/marr
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - mass-spectrometry
diff --git a/collections/metabolomics/v2/tools/msroiaug.yaml b/collections/metabolomics/v2/tools/msroiaug.yaml
index be4770e19..0f3b1ddef 100644
--- a/collections/metabolomics/v2/tools/msroiaug.yaml
+++ b/collections/metabolomics/v2/tools/msroiaug.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - AdrianHaun/AriumMS
 schema_version: 0.2.0
+license_tier: open
+license: BSD-3-Clause
+license_detection: github-api
 techniques:
 - LC-MS
 - CE-MS
diff --git a/collections/metabolomics/v2/tools/mssearchr.yaml b/collections/metabolomics/v2/tools/mssearchr.yaml
index ee065da42..87b7b8218 100644
--- a/collections/metabolomics/v2/tools/mssearchr.yaml
+++ b/collections/metabolomics/v2/tools/mssearchr.yaml
@@ -10,6 +10,9 @@ derived_from:
 source_repos:
 - AndreySamokhin/mssearchr
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: file-present-unclassified
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/msthunder.yaml b/collections/metabolomics/v2/tools/msthunder.yaml
index 73818ae00..eb63e5d98 100644
--- a/collections/metabolomics/v2/tools/msthunder.yaml
+++ b/collections/metabolomics/v2/tools/msthunder.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - LQZ0123/MSThunder
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - NMR
diff --git a/collections/metabolomics/v2/tools/msys2.yaml b/collections/metabolomics/v2/tools/msys2.yaml
index 0160248e1..b8c88d63e 100644
--- a/collections/metabolomics/v2/tools/msys2.yaml
+++ b/collections/metabolomics/v2/tools/msys2.yaml
@@ -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
diff --git a/collections/metabolomics/v2/tools/mtbls2.yaml b/collections/metabolomics/v2/tools/mtbls2.yaml
index ec737d8ab..d069cf23c 100644
--- a/collections/metabolomics/v2/tools/mtbls2.yaml
+++ b/collections/metabolomics/v2/tools/mtbls2.yaml
@@ -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
diff --git a/collections/metabolomics/v2/tools/multiabler.yaml b/collections/metabolomics/v2/tools/multiabler.yaml
index 5af8c2770..9bbe45565 100644
--- a/collections/metabolomics/v2/tools/multiabler.yaml
+++ b/collections/metabolomics/v2/tools/multiabler.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - holab-hku/MultiABLER
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/multiassayexperiment.yaml b/collections/metabolomics/v2/tools/multiassayexperiment.yaml
index f04c4284d..b0e00f437 100644
--- a/collections/metabolomics/v2/tools/multiassayexperiment.yaml
+++ b/collections/metabolomics/v2/tools/multiassayexperiment.yaml
@@ -10,3 +10,6 @@ derived_from:
 source_repos:
 - andreasmock/MetaboDiff
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
diff --git a/collections/metabolomics/v2/tools/multimodalspectraltransformer.yaml b/collections/metabolomics/v2/tools/multimodalspectraltransformer.yaml
index 5a703ff2c..226330f22 100644
--- a/collections/metabolomics/v2/tools/multimodalspectraltransformer.yaml
+++ b/collections/metabolomics/v2/tools/multimodalspectraltransformer.yaml
@@ -9,5 +9,8 @@ derived_from:
 source_repos:
 - mpriessner/MultiModalSpectralTransformer
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
 techniques:
 - NMR
diff --git a/collections/metabolomics/v2/tools/multiprocessing.yaml b/collections/metabolomics/v2/tools/multiprocessing.yaml
index 4343f02b8..9bc49aefb 100644
--- a/collections/metabolomics/v2/tools/multiprocessing.yaml
+++ b/collections/metabolomics/v2/tools/multiprocessing.yaml
@@ -9,3 +9,6 @@ derived_from:
 source_repos:
 - OpenMS/OpenMS
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: file-present-unclassified
diff --git a/collections/metabolomics/v2/tools/multtest.yaml b/collections/metabolomics/v2/tools/multtest.yaml
index 92f630f97..8f2e475cb 100644
--- a/collections/metabolomics/v2/tools/multtest.yaml
+++ b/collections/metabolomics/v2/tools/multtest.yaml
@@ -8,3 +8,6 @@ derived_from:
 source_repos:
 - idrblab/NOREVA;
 schema_version: 0.2.0
+license_tier: open
+license: GPL-3.0
+license_detection: github-api
diff --git a/collections/metabolomics/v2/tools/mwastools.yaml b/collections/metabolomics/v2/tools/mwastools.yaml
index ced597456..28300bc27 100644
--- a/collections/metabolomics/v2/tools/mwastools.yaml
+++ b/collections/metabolomics/v2/tools/mwastools.yaml
@@ -11,6 +11,9 @@ derived_from:
 source_repos:
 - AndreaRMICL/MWASTools
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - NMR
diff --git a/collections/metabolomics/v2/tools/mwise.yaml b/collections/metabolomics/v2/tools/mwise.yaml
index ea48b2700..5e198d733 100644
--- a/collections/metabolomics/v2/tools/mwise.yaml
+++ b/collections/metabolomics/v2/tools/mwise.yaml
@@ -11,5 +11,8 @@ derived_from:
 source_repos:
 - b2slab/mWISE
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
diff --git a/collections/metabolomics/v2/tools/mwtab.yaml b/collections/metabolomics/v2/tools/mwtab.yaml
index cd32e4a80..ead11eb60 100644
--- a/collections/metabolomics/v2/tools/mwtab.yaml
+++ b/collections/metabolomics/v2/tools/mwtab.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - MoseleyBioinformaticsLab/mwtab
 schema_version: 0.2.0
+license_tier: open
+license: BSD-3-Clause-Clear
+license_detection: github-api
 techniques:
 - NMR
 - mass-spectrometry
diff --git a/collections/metabolomics/v2/tools/mysql-8.yaml b/collections/metabolomics/v2/tools/mysql-8.yaml
index abcf48b62..89dc31420 100644
--- a/collections/metabolomics/v2/tools/mysql-8.yaml
+++ b/collections/metabolomics/v2/tools/mysql-8.yaml
@@ -9,5 +9,8 @@ derived_from:
 source_repos:
 - privrja/MassSpecBlocks
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
 techniques:
 - mass-spectrometry
diff --git a/collections/metabolomics/v2/tools/mza.yaml b/collections/metabolomics/v2/tools/mza.yaml
index 4e21745f8..0d2ddd5b8 100644
--- a/collections/metabolomics/v2/tools/mza.yaml
+++ b/collections/metabolomics/v2/tools/mza.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - PNNL-m-q/mza
 schema_version: 0.2.0
+license_tier: open
+license: BSD-2-Clause
+license_detection: github-api
 techniques:
 - LC-MS
 - ion-mobility-MS
diff --git a/collections/metabolomics/v2/tools/mzembed.yaml b/collections/metabolomics/v2/tools/mzembed.yaml
index 124c531aa..9644554ef 100644
--- a/collections/metabolomics/v2/tools/mzembed.yaml
+++ b/collections/metabolomics/v2/tools/mzembed.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - ReviveMed/mzEmbed
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: license-file
 techniques:
 - LC-MS
 - ion-mobility-MS
diff --git a/collections/metabolomics/v2/tools/mzexacto.yaml b/collections/metabolomics/v2/tools/mzexacto.yaml
index c85a00a67..7ed9d520b 100644
--- a/collections/metabolomics/v2/tools/mzexacto.yaml
+++ b/collections/metabolomics/v2/tools/mzexacto.yaml
@@ -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
diff --git a/collections/metabolomics/v2/tools/mzmine-2.yaml b/collections/metabolomics/v2/tools/mzmine-2.yaml
index 06cb859c3..3b269c26e 100644
--- a/collections/metabolomics/v2/tools/mzmine-2.yaml
+++ b/collections/metabolomics/v2/tools/mzmine-2.yaml
@@ -18,6 +18,9 @@ source_repos:
 - idslme/IDSL.IPA
 - mzmine/mzmine2
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/mzmine-3.yaml b/collections/metabolomics/v2/tools/mzmine-3.yaml
index 848a709fe..7263f4f19 100644
--- a/collections/metabolomics/v2/tools/mzmine-3.yaml
+++ b/collections/metabolomics/v2/tools/mzmine-3.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - huaxuyu/bago
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - ion-mobility-MS
diff --git a/collections/metabolomics/v2/tools/mzmine.yaml b/collections/metabolomics/v2/tools/mzmine.yaml
index 2542f94e6..8624bea3b 100644
--- a/collections/metabolomics/v2/tools/mzmine.yaml
+++ b/collections/metabolomics/v2/tools/mzmine.yaml
@@ -36,6 +36,9 @@ source_repos:
 - luigiquiros/inventa
 - mzmine/mzmine2
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/mzmine2.yaml b/collections/metabolomics/v2/tools/mzmine2.yaml
index 2e38202f6..bc60929c7 100644
--- a/collections/metabolomics/v2/tools/mzmine2.yaml
+++ b/collections/metabolomics/v2/tools/mzmine2.yaml
@@ -17,6 +17,9 @@ source_repos:
 - luigiquiros/inventa
 - mzmine/mzmine2
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: license-file
 techniques:
 - LC-MS
 - CE-MS
diff --git a/collections/metabolomics/v2/tools/mzmine3.yaml b/collections/metabolomics/v2/tools/mzmine3.yaml
index cac061e82..ca0f78cf4 100644
--- a/collections/metabolomics/v2/tools/mzmine3.yaml
+++ b/collections/metabolomics/v2/tools/mzmine3.yaml
@@ -14,6 +14,9 @@ source_repos:
 - Functional-Metabolomics-Lab/FBMN-STATS
 - luigiquiros/inventa
 schema_version: 0.2.0
+license_tier: open
+license: BSD-3-Clause
+license_detection: github-api
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/mzmldataloader.yaml b/collections/metabolomics/v2/tools/mzmldataloader.yaml
index c9074f390..1c53bae9a 100644
--- a/collections/metabolomics/v2/tools/mzmldataloader.yaml
+++ b/collections/metabolomics/v2/tools/mzmldataloader.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - Roestlab/massdash
 schema_version: 0.2.0
+license_tier: open
+license: BSD-3-Clause
+license_detection: github-api
 techniques:
 - LC-MS
 - ion-mobility-MS
diff --git a/collections/metabolomics/v2/tools/mzquality.yaml b/collections/metabolomics/v2/tools/mzquality.yaml
index d98715be9..c79f54ff7 100644
--- a/collections/metabolomics/v2/tools/mzquality.yaml
+++ b/collections/metabolomics/v2/tools/mzquality.yaml
@@ -9,6 +9,9 @@ derived_from:
 - doi: 10.1021/jasms.5c00073
   title: mzquality
 schema_version: 0.2.0
+license_tier: open
+license: GPL-3.0
+license_detection: github-api
 techniques:
 - LC-MS
 - mass-spectrometry
diff --git a/collections/metabolomics/v2/tools/mzr.yaml b/collections/metabolomics/v2/tools/mzr.yaml
index 2baecab19..19c5efb8c 100644
--- a/collections/metabolomics/v2/tools/mzr.yaml
+++ b/collections/metabolomics/v2/tools/mzr.yaml
@@ -13,6 +13,9 @@ source_repos:
 - jcapelladesto/isoSCAN
 - thepanlab/Aerith
 schema_version: 0.2.0
+license_tier: open
+license: GPL-3.0
+license_detection: github-api
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/mzrapp.yaml b/collections/metabolomics/v2/tools/mzrapp.yaml
index f1711fa17..9b32d96cc 100644
--- a/collections/metabolomics/v2/tools/mzrapp.yaml
+++ b/collections/metabolomics/v2/tools/mzrapp.yaml
@@ -10,6 +10,9 @@ derived_from:
 source_repos:
 - YasinEl/mzRAPP
 schema_version: 0.2.0
+license_tier: open
+license: GPL-3.0
+license_detection: github-api
 techniques:
 - LC-MS
 - mass-spectrometry
diff --git a/collections/metabolomics/v2/tools/mzrtsim.yaml b/collections/metabolomics/v2/tools/mzrtsim.yaml
index 471412f4d..baebc7190 100644
--- a/collections/metabolomics/v2/tools/mzrtsim.yaml
+++ b/collections/metabolomics/v2/tools/mzrtsim.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - yufree/mzrtsim
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/nanobind.yaml b/collections/metabolomics/v2/tools/nanobind.yaml
index 0cf96716c..b35317547 100644
--- a/collections/metabolomics/v2/tools/nanobind.yaml
+++ b/collections/metabolomics/v2/tools/nanobind.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - OpenMS/OpenMS
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: file-present-unclassified
 techniques:
 - LC-MS
 - MS-imaging
diff --git a/collections/metabolomics/v2/tools/napari.yaml b/collections/metabolomics/v2/tools/napari.yaml
index 650e8e6a5..8845a742a 100644
--- a/collections/metabolomics/v2/tools/napari.yaml
+++ b/collections/metabolomics/v2/tools/napari.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - MMV-Lab/MSI-Explorer
 schema_version: 0.2.0
+license_tier: open
+license: BSD-3-Clause
+license_detection: github-api
 techniques:
 - CE-MS
 - MS-imaging
diff --git a/collections/metabolomics/v2/tools/ncbi-e-utilities.yaml b/collections/metabolomics/v2/tools/ncbi-e-utilities.yaml
index ac0210e1c..ed28d7ddc 100644
--- a/collections/metabolomics/v2/tools/ncbi-e-utilities.yaml
+++ b/collections/metabolomics/v2/tools/ncbi-e-utilities.yaml
@@ -9,3 +9,6 @@ derived_from:
 source_repos:
 - mibig-secmet/mibig-json
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
diff --git a/collections/metabolomics/v2/tools/ncgtw.yaml b/collections/metabolomics/v2/tools/ncgtw.yaml
index bf8d01f1c..f2322be95 100644
--- a/collections/metabolomics/v2/tools/ncgtw.yaml
+++ b/collections/metabolomics/v2/tools/ncgtw.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - ChiungTingWu/ncGTW
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - NMR
diff --git a/collections/metabolomics/v2/tools/neatms.yaml b/collections/metabolomics/v2/tools/neatms.yaml
index 35d1cbec6..ad21cc029 100644
--- a/collections/metabolomics/v2/tools/neatms.yaml
+++ b/collections/metabolomics/v2/tools/neatms.yaml
@@ -8,6 +8,9 @@ derived_from:
 - doi: 10.1021/acs.analchem.1c02220
   title: neatms
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
 techniques:
 - LC-MS
 - CE-MS
diff --git a/collections/metabolomics/v2/tools/ned.yaml b/collections/metabolomics/v2/tools/ned.yaml
index f09d438d0..3be2c76bf 100644
--- a/collections/metabolomics/v2/tools/ned.yaml
+++ b/collections/metabolomics/v2/tools/ned.yaml
@@ -6,6 +6,9 @@ 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
 - mass-spectrometry
diff --git a/collections/metabolomics/v2/tools/net-6.yaml b/collections/metabolomics/v2/tools/net-6.yaml
index 7886a568a..41cca32ab 100644
--- a/collections/metabolomics/v2/tools/net-6.yaml
+++ b/collections/metabolomics/v2/tools/net-6.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - systemsomicslab/MsdialWorkbench
 schema_version: 0.2.0
+license_tier: open
+license: LGPL-3.0
+license_detection: readme-llm
 techniques:
 - LC-MS
 - ion-mobility-MS
diff --git a/collections/metabolomics/v2/tools/net-8-0.yaml b/collections/metabolomics/v2/tools/net-8-0.yaml
index b37d0d66d..6cccae98a 100644
--- a/collections/metabolomics/v2/tools/net-8-0.yaml
+++ b/collections/metabolomics/v2/tools/net-8-0.yaml
@@ -10,6 +10,9 @@ derived_from:
 source_repos:
 - fgcz/rawrr
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - mass-spectrometry
diff --git a/collections/metabolomics/v2/tools/net-framework-4-8.yaml b/collections/metabolomics/v2/tools/net-framework-4-8.yaml
index 63a8a369e..6d7770e33 100644
--- a/collections/metabolomics/v2/tools/net-framework-4-8.yaml
+++ b/collections/metabolomics/v2/tools/net-framework-4-8.yaml
@@ -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
diff --git a/collections/metabolomics/v2/tools/net-framework.yaml b/collections/metabolomics/v2/tools/net-framework.yaml
index 8981cbc84..435c1b123 100644
--- a/collections/metabolomics/v2/tools/net-framework.yaml
+++ b/collections/metabolomics/v2/tools/net-framework.yaml
@@ -18,6 +18,9 @@ source_repos:
 - PNNL-Comp-Mass-Spec/PNNL-PreProcessor
 - systemsomicslab/MsdialWorkbench
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - ion-mobility-MS
diff --git a/collections/metabolomics/v2/tools/net-standard.yaml b/collections/metabolomics/v2/tools/net-standard.yaml
index c79478ab6..d9672bfae 100644
--- a/collections/metabolomics/v2/tools/net-standard.yaml
+++ b/collections/metabolomics/v2/tools/net-standard.yaml
@@ -10,6 +10,9 @@ derived_from:
 source_repos:
 - systemsomicslab/MsdialWorkbench
 schema_version: 0.2.0
+license_tier: open
+license: LGPL-3.0
+license_detection: readme-llm
 techniques:
 - LC-MS
 - mass-spectrometry
diff --git a/collections/metabolomics/v2/tools/netgsa-r-package.yaml b/collections/metabolomics/v2/tools/netgsa-r-package.yaml
index 8109c506c..7a3c2026e 100644
--- a/collections/metabolomics/v2/tools/netgsa-r-package.yaml
+++ b/collections/metabolomics/v2/tools/netgsa-r-package.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - Karnovsky-Lab/DNEA
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: file-present-unclassified
 techniques:
 - LC-MS
 - CE-MS
diff --git a/collections/metabolomics/v2/tools/networkx.yaml b/collections/metabolomics/v2/tools/networkx.yaml
index 777ba2fb3..1c8977bdc 100644
--- a/collections/metabolomics/v2/tools/networkx.yaml
+++ b/collections/metabolomics/v2/tools/networkx.yaml
@@ -18,6 +18,9 @@ source_repos:
 - ablab/npdtools
 - shuzhao-li-lab/khipu
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: file-present-unclassified
 techniques:
 - LC-MS
 - ion-mobility-MS
diff --git a/collections/metabolomics/v2/tools/neural-networks-mlpnn-with-relu-activation.yaml b/collections/metabolomics/v2/tools/neural-networks-mlpnn-with-relu-activation.yaml
index b0fc91908..44598925f 100644
--- a/collections/metabolomics/v2/tools/neural-networks-mlpnn-with-relu-activation.yaml
+++ b/collections/metabolomics/v2/tools/neural-networks-mlpnn-with-relu-activation.yaml
@@ -6,3 +6,6 @@ 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
diff --git a/collections/metabolomics/v2/tools/neural-networks.yaml b/collections/metabolomics/v2/tools/neural-networks.yaml
index 31a465eed..346a855d9 100644
--- a/collections/metabolomics/v2/tools/neural-networks.yaml
+++ b/collections/metabolomics/v2/tools/neural-networks.yaml
@@ -8,3 +8,6 @@ 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
diff --git a/collections/metabolomics/v2/tools/nextflow-22-10-0.yaml b/collections/metabolomics/v2/tools/nextflow-22-10-0.yaml
index 7ff0e80ea..c596742b5 100644
--- a/collections/metabolomics/v2/tools/nextflow-22-10-0.yaml
+++ b/collections/metabolomics/v2/tools/nextflow-22-10-0.yaml
@@ -6,5 +6,8 @@ derived_from:
 - doi: 10.1021/jasms.4c00364
   title: nextflow4msdial
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
 techniques:
 - LC-MS
diff --git a/collections/metabolomics/v2/tools/nextflow.yaml b/collections/metabolomics/v2/tools/nextflow.yaml
index 27d0a6089..27a40dec9 100644
--- a/collections/metabolomics/v2/tools/nextflow.yaml
+++ b/collections/metabolomics/v2/tools/nextflow.yaml
@@ -20,6 +20,9 @@ source_repos:
 - ASAGlab/MOI--An-integrated-solution-for-omics-analyses
 - Wang-Bioinformatics-Lab/Reverse_metabolomics_library_generation
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - CE-MS
diff --git a/collections/metabolomics/v2/tools/nist.yaml b/collections/metabolomics/v2/tools/nist.yaml
index 0b9071571..08afd37ba 100644
--- a/collections/metabolomics/v2/tools/nist.yaml
+++ b/collections/metabolomics/v2/tools/nist.yaml
@@ -8,6 +8,9 @@ derived_from:
 - doi: 10.1021/acs.analchem.2c05389
   title: mspcompiler
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: file-present-unclassified
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/nmrbox.yaml b/collections/metabolomics/v2/tools/nmrbox.yaml
index 08aba2201..12cb7e51f 100644
--- a/collections/metabolomics/v2/tools/nmrbox.yaml
+++ b/collections/metabolomics/v2/tools/nmrbox.yaml
@@ -9,5 +9,8 @@ derived_from:
 source_repos:
 - edisonomics/SAND
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
 techniques:
 - NMR
diff --git a/collections/metabolomics/v2/tools/nmrfx.yaml b/collections/metabolomics/v2/tools/nmrfx.yaml
index 26a18a054..6279edfb3 100644
--- a/collections/metabolomics/v2/tools/nmrfx.yaml
+++ b/collections/metabolomics/v2/tools/nmrfx.yaml
@@ -10,5 +10,8 @@ derived_from:
 source_repos:
 - nanalysis/nmrfx
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: file-present-unclassified
 techniques:
 - NMR
diff --git a/collections/metabolomics/v2/tools/nmrpipe.yaml b/collections/metabolomics/v2/tools/nmrpipe.yaml
index ad09293ff..882f45c23 100644
--- a/collections/metabolomics/v2/tools/nmrpipe.yaml
+++ b/collections/metabolomics/v2/tools/nmrpipe.yaml
@@ -9,5 +9,8 @@ derived_from:
 source_repos:
 - edisonomics/SAND
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
 techniques:
 - NMR
diff --git a/collections/metabolomics/v2/tools/noreva.yaml b/collections/metabolomics/v2/tools/noreva.yaml
index 536d73136..f7c6128ab 100644
--- a/collections/metabolomics/v2/tools/noreva.yaml
+++ b/collections/metabolomics/v2/tools/noreva.yaml
@@ -8,5 +8,8 @@ derived_from:
 source_repos:
 - idrblab/NOREVA;
 schema_version: 0.2.0
+license_tier: open
+license: GPL-3.0
+license_detection: github-api
 techniques:
 - mass-spectrometry
diff --git a/collections/metabolomics/v2/tools/norine.yaml b/collections/metabolomics/v2/tools/norine.yaml
index dabde1ae6..d4398771b 100644
--- a/collections/metabolomics/v2/tools/norine.yaml
+++ b/collections/metabolomics/v2/tools/norine.yaml
@@ -9,5 +9,8 @@ derived_from:
 source_repos:
 - privrja/MassSpecBlocks
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
 techniques:
 - mass-spectrometry
diff --git a/collections/metabolomics/v2/tools/normalizemets.yaml b/collections/metabolomics/v2/tools/normalizemets.yaml
index 41ae8ea1d..3cecfae8c 100644
--- a/collections/metabolomics/v2/tools/normalizemets.yaml
+++ b/collections/metabolomics/v2/tools/normalizemets.yaml
@@ -9,5 +9,8 @@ derived_from:
 source_repos:
 - metabolomicstats/NormalizeMets
 schema_version: 0.2.0
+license_tier: open
+license: GPL-2.0-or-later
+license_detection: readme-llm
 techniques:
 - mass-spectrometry
diff --git a/collections/metabolomics/v2/tools/norvisualization.yaml b/collections/metabolomics/v2/tools/norvisualization.yaml
index 7b121b330..916bc79a5 100644
--- a/collections/metabolomics/v2/tools/norvisualization.yaml
+++ b/collections/metabolomics/v2/tools/norvisualization.yaml
@@ -8,3 +8,6 @@ derived_from:
 source_repos:
 - idrblab/NOREVA;
 schema_version: 0.2.0
+license_tier: open
+license: GPL-3.0
+license_detection: github-api
diff --git a/collections/metabolomics/v2/tools/notame.yaml b/collections/metabolomics/v2/tools/notame.yaml
index a2d76cef9..b9baddd01 100644
--- a/collections/metabolomics/v2/tools/notame.yaml
+++ b/collections/metabolomics/v2/tools/notame.yaml
@@ -11,6 +11,9 @@ derived_from:
 source_repos:
 - antonvsdata/notame
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - mass-spectrometry
diff --git a/collections/metabolomics/v2/tools/np-atlas.yaml b/collections/metabolomics/v2/tools/np-atlas.yaml
index 38249a42d..14fe59d6f 100644
--- a/collections/metabolomics/v2/tools/np-atlas.yaml
+++ b/collections/metabolomics/v2/tools/np-atlas.yaml
@@ -9,5 +9,8 @@ derived_from:
 source_repos:
 - privrja/MassSpecBlocks
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
 techniques:
 - mass-spectrometry
diff --git a/collections/metabolomics/v2/tools/npanalyst.yaml b/collections/metabolomics/v2/tools/npanalyst.yaml
index 571b59d94..464ec3f9b 100644
--- a/collections/metabolomics/v2/tools/npanalyst.yaml
+++ b/collections/metabolomics/v2/tools/npanalyst.yaml
@@ -4,6 +4,9 @@ derived_from:
 - doi: 10.1021/acscentsci.1c01108
   title: NP Analyst
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
 techniques:
 - LC-MS
 - MS-imaging
diff --git a/collections/metabolomics/v2/tools/npclassifier.yaml b/collections/metabolomics/v2/tools/npclassifier.yaml
index f5b0338e3..22e2152bc 100644
--- a/collections/metabolomics/v2/tools/npclassifier.yaml
+++ b/collections/metabolomics/v2/tools/npclassifier.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - zquinlan/concise
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
 techniques:
 - LC-MS
 - mass-spectrometry
diff --git a/collections/metabolomics/v2/tools/npdtools-2-5-0.yaml b/collections/metabolomics/v2/tools/npdtools-2-5-0.yaml
index a6949a150..a8bfdfe31 100644
--- a/collections/metabolomics/v2/tools/npdtools-2-5-0.yaml
+++ b/collections/metabolomics/v2/tools/npdtools-2-5-0.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - ablab/npdtools
 schema_version: 0.2.0
+license_tier: open
+license: Apache-2.0
+license_detection: readme-llm
 techniques:
 - LC-MS
 - direct-infusion-MS
diff --git a/collections/metabolomics/v2/tools/npdtools.yaml b/collections/metabolomics/v2/tools/npdtools.yaml
index 687e60bbc..7b8ccf686 100644
--- a/collections/metabolomics/v2/tools/npdtools.yaml
+++ b/collections/metabolomics/v2/tools/npdtools.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - ablab/npdtools
 schema_version: 0.2.0
+license_tier: open
+license: Apache-2.0
+license_detection: readme-llm
 techniques:
 - LC-MS
 - direct-infusion-MS
diff --git a/collections/metabolomics/v2/tools/npfimg.yaml b/collections/metabolomics/v2/tools/npfimg.yaml
index 875820367..7a35913c5 100644
--- a/collections/metabolomics/v2/tools/npfimg.yaml
+++ b/collections/metabolomics/v2/tools/npfimg.yaml
@@ -10,6 +10,9 @@ derived_from:
 source_repos:
 - poomcj/NPFimg
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/nplinker.yaml b/collections/metabolomics/v2/tools/nplinker.yaml
index 9736fa066..bed656697 100644
--- a/collections/metabolomics/v2/tools/nplinker.yaml
+++ b/collections/metabolomics/v2/tools/nplinker.yaml
@@ -18,6 +18,9 @@ derived_from:
 source_repos:
 - NPLinker/nplinker
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - mass-spectrometry
diff --git a/collections/metabolomics/v2/tools/npm.yaml b/collections/metabolomics/v2/tools/npm.yaml
index d8ac9cd58..12b685860 100644
--- a/collections/metabolomics/v2/tools/npm.yaml
+++ b/collections/metabolomics/v2/tools/npm.yaml
@@ -6,6 +6,9 @@ derived_from:
 - doi: 10.1038/s41589-020-00724-z
   title: pairedomicsdatapla
 schema_version: 0.2.0
+license_tier: open
+license: Apache-2.0
+license_detection: github-api
 techniques:
 - LC-MS
 - NMR
diff --git a/collections/metabolomics/v2/tools/numba.yaml b/collections/metabolomics/v2/tools/numba.yaml
index edb7fb64a..f8677a2d8 100644
--- a/collections/metabolomics/v2/tools/numba.yaml
+++ b/collections/metabolomics/v2/tools/numba.yaml
@@ -17,6 +17,9 @@ derived_from:
 source_repos:
 - sword-nan/SpecEmbedding
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/numpy-1-15-4.yaml b/collections/metabolomics/v2/tools/numpy-1-15-4.yaml
index 3eb597542..fd2415119 100644
--- a/collections/metabolomics/v2/tools/numpy-1-15-4.yaml
+++ b/collections/metabolomics/v2/tools/numpy-1-15-4.yaml
@@ -9,5 +9,8 @@ derived_from:
 source_repos:
 - wabdelmoula/massNet
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - MS-imaging
diff --git a/collections/metabolomics/v2/tools/numpy-or-scipy.yaml b/collections/metabolomics/v2/tools/numpy-or-scipy.yaml
index ffa5f3369..5fddc1a2c 100644
--- a/collections/metabolomics/v2/tools/numpy-or-scipy.yaml
+++ b/collections/metabolomics/v2/tools/numpy-or-scipy.yaml
@@ -9,5 +9,8 @@ derived_from:
 source_repos:
 - NPLinker/nplinker
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
diff --git a/collections/metabolomics/v2/tools/numpy.yaml b/collections/metabolomics/v2/tools/numpy.yaml
index 92dfc945a..cc1e138a0 100644
--- a/collections/metabolomics/v2/tools/numpy.yaml
+++ b/collections/metabolomics/v2/tools/numpy.yaml
@@ -82,6 +82,9 @@ source_repos:
 - zsspython/LAGF
 - zza1211/NMRformer
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/omu-omu-summary-function.yaml b/collections/metabolomics/v2/tools/omu-omu-summary-function.yaml
index 069d57f61..7ad323411 100644
--- a/collections/metabolomics/v2/tools/omu-omu-summary-function.yaml
+++ b/collections/metabolomics/v2/tools/omu-omu-summary-function.yaml
@@ -9,3 +9,6 @@ derived_from:
 source_repos:
 - connor-reid-tiffany/Omu
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
diff --git a/collections/metabolomics/v2/tools/onnxruntime.yaml b/collections/metabolomics/v2/tools/onnxruntime.yaml
index 579c88bcd..53db41da5 100644
--- a/collections/metabolomics/v2/tools/onnxruntime.yaml
+++ b/collections/metabolomics/v2/tools/onnxruntime.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - Roestlab/massdash
 schema_version: 0.2.0
+license_tier: open
+license: BSD-3-Clause
+license_detection: github-api
 techniques:
 - LC-MS
 - ion-mobility-MS
diff --git a/collections/metabolomics/v2/tools/open-tree-of-life.yaml b/collections/metabolomics/v2/tools/open-tree-of-life.yaml
index 06da601f8..57b8fdd1d 100644
--- a/collections/metabolomics/v2/tools/open-tree-of-life.yaml
+++ b/collections/metabolomics/v2/tools/open-tree-of-life.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - luigiquiros/inventa
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
 techniques:
 - LC-MS
 - ion-mobility-MS
diff --git a/collections/metabolomics/v2/tools/openms-topp-tools.yaml b/collections/metabolomics/v2/tools/openms-topp-tools.yaml
index 8bde35e35..897421e71 100644
--- a/collections/metabolomics/v2/tools/openms-topp-tools.yaml
+++ b/collections/metabolomics/v2/tools/openms-topp-tools.yaml
@@ -9,3 +9,6 @@ derived_from:
 source_repos:
 - OpenMS/OpenMS
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: file-present-unclassified
diff --git a/collections/metabolomics/v2/tools/openms.yaml b/collections/metabolomics/v2/tools/openms.yaml
index c6352327f..b7ccaaa5d 100644
--- a/collections/metabolomics/v2/tools/openms.yaml
+++ b/collections/metabolomics/v2/tools/openms.yaml
@@ -31,6 +31,9 @@ source_repos:
 - OpenMS/OpenMS
 - fgcz/rawrr
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: file-present-unclassified
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/opennau.yaml b/collections/metabolomics/v2/tools/opennau.yaml
index fcdd391c8..028b25e92 100644
--- a/collections/metabolomics/v2/tools/opennau.yaml
+++ b/collections/metabolomics/v2/tools/opennau.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - zjuRong/openNAU
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
 techniques:
 - LC-MS
 - mass-spectrometry
diff --git a/collections/metabolomics/v2/tools/openpyxl.yaml b/collections/metabolomics/v2/tools/openpyxl.yaml
index bdbf2dac5..e833d738a 100644
--- a/collections/metabolomics/v2/tools/openpyxl.yaml
+++ b/collections/metabolomics/v2/tools/openpyxl.yaml
@@ -10,6 +10,9 @@ derived_from:
 source_repos:
 - Leo-Cheng-Lab/ROIAL-NMR
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/opentims.yaml b/collections/metabolomics/v2/tools/opentims.yaml
index 9d32e0f94..536990336 100644
--- a/collections/metabolomics/v2/tools/opentims.yaml
+++ b/collections/metabolomics/v2/tools/opentims.yaml
@@ -4,3 +4,6 @@ evidence_spans:
 - '#include "opentims++/opentims_all.cpp"'
 - OpenTIMS is a C++ library for accessing timsTOF Pro data format (TDF)
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: null
diff --git a/collections/metabolomics/v2/tools/opentimspy.yaml b/collections/metabolomics/v2/tools/opentimspy.yaml
index c532a5b18..24de90fb4 100644
--- a/collections/metabolomics/v2/tools/opentimspy.yaml
+++ b/collections/metabolomics/v2/tools/opentimspy.yaml
@@ -3,3 +3,6 @@ slug: opentimspy
 evidence_spans:
 - bindings to `Python` (through `opentimspy`)
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: null
diff --git a/collections/metabolomics/v2/tools/optgpsampler-algorithm.yaml b/collections/metabolomics/v2/tools/optgpsampler-algorithm.yaml
index 6899abec5..90a022ce5 100644
--- a/collections/metabolomics/v2/tools/optgpsampler-algorithm.yaml
+++ b/collections/metabolomics/v2/tools/optgpsampler-algorithm.yaml
@@ -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
diff --git a/collections/metabolomics/v2/tools/optgpsampler.yaml b/collections/metabolomics/v2/tools/optgpsampler.yaml
index d31abbe58..cf9595d8c 100644
--- a/collections/metabolomics/v2/tools/optgpsampler.yaml
+++ b/collections/metabolomics/v2/tools/optgpsampler.yaml
@@ -8,5 +8,8 @@ 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
diff --git a/collections/metabolomics/v2/tools/optimus.yaml b/collections/metabolomics/v2/tools/optimus.yaml
index 133e9a28a..714275ee4 100644
--- a/collections/metabolomics/v2/tools/optimus.yaml
+++ b/collections/metabolomics/v2/tools/optimus.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - DorresteinLaboratory/Bioactive_Molecular_Networks
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: license-file
 techniques:
 - LC-MS
 - direct-infusion-MS
diff --git a/collections/metabolomics/v2/tools/orca.yaml b/collections/metabolomics/v2/tools/orca.yaml
index 27cb3afcf..2afcf878f 100644
--- a/collections/metabolomics/v2/tools/orca.yaml
+++ b/collections/metabolomics/v2/tools/orca.yaml
@@ -14,6 +14,9 @@ source_repos:
 - grimme-lab/QCxMS2
 - pmartR/PMart_ShinyApp
 schema_version: 0.2.0
+license_tier: open
+license: BSD-2-Clause
+license_detection: github-api
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/orgmassspecr.yaml b/collections/metabolomics/v2/tools/orgmassspecr.yaml
index d492b52ae..1e26e5d91 100644
--- a/collections/metabolomics/v2/tools/orgmassspecr.yaml
+++ b/collections/metabolomics/v2/tools/orgmassspecr.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - LeaveMeNotTonight/CMDN
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - CE-MS
diff --git a/collections/metabolomics/v2/tools/oswdataaccess.yaml b/collections/metabolomics/v2/tools/oswdataaccess.yaml
index bffc6bc01..6f718697d 100644
--- a/collections/metabolomics/v2/tools/oswdataaccess.yaml
+++ b/collections/metabolomics/v2/tools/oswdataaccess.yaml
@@ -9,5 +9,8 @@ derived_from:
 source_repos:
 - Roestlab/massdash
 schema_version: 0.2.0
+license_tier: open
+license: BSD-3-Clause
+license_detection: github-api
 techniques:
 - LC-MS
diff --git a/collections/metabolomics/v2/tools/ouks.yaml b/collections/metabolomics/v2/tools/ouks.yaml
index ed8bc111c..0c97cb3ee 100644
--- a/collections/metabolomics/v2/tools/ouks.yaml
+++ b/collections/metabolomics/v2/tools/ouks.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - plyush1993/OUKS
 schema_version: 0.2.0
+license_tier: open
+license: GPL-3.0
+license_detection: github-api
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/pacman.yaml b/collections/metabolomics/v2/tools/pacman.yaml
index 19777d499..705d1392b 100644
--- a/collections/metabolomics/v2/tools/pacman.yaml
+++ b/collections/metabolomics/v2/tools/pacman.yaml
@@ -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
diff --git a/collections/metabolomics/v2/tools/pairkat.yaml b/collections/metabolomics/v2/tools/pairkat.yaml
index c0f4664df..9cdbd9b5f 100644
--- a/collections/metabolomics/v2/tools/pairkat.yaml
+++ b/collections/metabolomics/v2/tools/pairkat.yaml
@@ -9,3 +9,6 @@ derived_from:
 source_repos:
 - CharlieCarpenter/PaIRKAT
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
diff --git a/collections/metabolomics/v2/tools/pals-pathway-activity-level-scoring.yaml b/collections/metabolomics/v2/tools/pals-pathway-activity-level-scoring.yaml
index 25b519de9..b02b95c22 100644
--- a/collections/metabolomics/v2/tools/pals-pathway-activity-level-scoring.yaml
+++ b/collections/metabolomics/v2/tools/pals-pathway-activity-level-scoring.yaml
@@ -13,6 +13,9 @@ derived_from:
 source_repos:
 - glasgowcompbio/PALS
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - NMR
diff --git a/collections/metabolomics/v2/tools/pals-viewer.yaml b/collections/metabolomics/v2/tools/pals-viewer.yaml
index 370768763..de36d3a7a 100644
--- a/collections/metabolomics/v2/tools/pals-viewer.yaml
+++ b/collections/metabolomics/v2/tools/pals-viewer.yaml
@@ -10,6 +10,9 @@ derived_from:
 source_repos:
 - glasgowcompbio/PALS
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - NMR
diff --git a/collections/metabolomics/v2/tools/pals.yaml b/collections/metabolomics/v2/tools/pals.yaml
index 077a7dcbc..dc47a43db 100644
--- a/collections/metabolomics/v2/tools/pals.yaml
+++ b/collections/metabolomics/v2/tools/pals.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - glasgowcompbio/PALS
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - mass-spectrometry
diff --git a/collections/metabolomics/v2/tools/pandas-1-1-1.yaml b/collections/metabolomics/v2/tools/pandas-1-1-1.yaml
index 17d2742ce..a4c7f9045 100644
--- a/collections/metabolomics/v2/tools/pandas-1-1-1.yaml
+++ b/collections/metabolomics/v2/tools/pandas-1-1-1.yaml
@@ -9,5 +9,8 @@ derived_from:
 source_repos:
 - wabdelmoula/massNet
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - MS-imaging
diff --git a/collections/metabolomics/v2/tools/pandas-for-tabular-data-manipulation-and-aggregation.yaml b/collections/metabolomics/v2/tools/pandas-for-tabular-data-manipulation-and-aggregation.yaml
index 08f1269e9..303a7f67f 100644
--- a/collections/metabolomics/v2/tools/pandas-for-tabular-data-manipulation-and-aggregation.yaml
+++ b/collections/metabolomics/v2/tools/pandas-for-tabular-data-manipulation-and-aggregation.yaml
@@ -6,3 +6,6 @@ derived_from:
 - doi: 10.1021/acs.analchem.3c05019
   title: 'PS<sup>2</sup>MS: A Deep Learning-Based Prediction System for Identifying New Psychoactive Substances Using Mass Spectrometry'
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
diff --git a/collections/metabolomics/v2/tools/pandas-or-equivalent-tabular-data-library.yaml b/collections/metabolomics/v2/tools/pandas-or-equivalent-tabular-data-library.yaml
index 5781fe5a2..4d5fc74eb 100644
--- a/collections/metabolomics/v2/tools/pandas-or-equivalent-tabular-data-library.yaml
+++ b/collections/metabolomics/v2/tools/pandas-or-equivalent-tabular-data-library.yaml
@@ -9,3 +9,6 @@ derived_from:
 source_repos:
 - mibig-secmet/mibig-json
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
diff --git a/collections/metabolomics/v2/tools/pandas.yaml b/collections/metabolomics/v2/tools/pandas.yaml
index a5da74963..64cdd9c70 100644
--- a/collections/metabolomics/v2/tools/pandas.yaml
+++ b/collections/metabolomics/v2/tools/pandas.yaml
@@ -73,6 +73,9 @@ source_repos:
 - zsspython/LAGF
 - zza1211/NMRformer
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/parallel-computing-toolbox.yaml b/collections/metabolomics/v2/tools/parallel-computing-toolbox.yaml
index f49c93648..ac35d0103 100644
--- a/collections/metabolomics/v2/tools/parallel-computing-toolbox.yaml
+++ b/collections/metabolomics/v2/tools/parallel-computing-toolbox.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - AdrianHaun/AriumMS
 schema_version: 0.2.0
+license_tier: open
+license: BSD-3-Clause
+license_detection: github-api
 techniques:
 - LC-MS
 - CE-MS
diff --git a/collections/metabolomics/v2/tools/parallel.yaml b/collections/metabolomics/v2/tools/parallel.yaml
index 0d82d7e14..c8c67f372 100644
--- a/collections/metabolomics/v2/tools/parallel.yaml
+++ b/collections/metabolomics/v2/tools/parallel.yaml
@@ -6,6 +6,9 @@ derived_from:
 - doi: 10.1021/acs.analchem.2c05389
   title: mspcompiler
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: file-present-unclassified
 techniques:
 - GC-MS
 - mass-spectrometry
diff --git a/collections/metabolomics/v2/tools/paramounter.yaml b/collections/metabolomics/v2/tools/paramounter.yaml
index fed32e4bc..bed9b76e4 100644
--- a/collections/metabolomics/v2/tools/paramounter.yaml
+++ b/collections/metabolomics/v2/tools/paramounter.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - HuanLab/Paramounter
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
 techniques:
 - LC-MS
 - mass-spectrometry
diff --git a/collections/metabolomics/v2/tools/patroon.yaml b/collections/metabolomics/v2/tools/patroon.yaml
index e3b880f12..bcfa969ce 100644
--- a/collections/metabolomics/v2/tools/patroon.yaml
+++ b/collections/metabolomics/v2/tools/patroon.yaml
@@ -11,6 +11,9 @@ derived_from:
 source_repos:
 - rickhelmus/patRoon
 schema_version: 0.2.0
+license_tier: open
+license: GPL-3.0
+license_detection: github-api
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/pbapply.yaml b/collections/metabolomics/v2/tools/pbapply.yaml
index 19eadf8b7..84ea2146d 100644
--- a/collections/metabolomics/v2/tools/pbapply.yaml
+++ b/collections/metabolomics/v2/tools/pbapply.yaml
@@ -10,6 +10,9 @@ derived_from:
 source_repos:
 - BiosystemEngineeringLab-IITB/dures
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: file-present-unclassified
 techniques:
 - LC-MS
 - CE-MS
diff --git a/collections/metabolomics/v2/tools/pcamethods.yaml b/collections/metabolomics/v2/tools/pcamethods.yaml
index 688987798..e603e0888 100644
--- a/collections/metabolomics/v2/tools/pcamethods.yaml
+++ b/collections/metabolomics/v2/tools/pcamethods.yaml
@@ -8,6 +8,9 @@ derived_from:
 source_repos:
 - idrblab/NOREVA;
 schema_version: 0.2.0
+license_tier: open
+license: GPL-3.0
+license_detection: github-api
 techniques:
 - LC-MS
 - CE-MS
diff --git a/collections/metabolomics/v2/tools/pcutils.yaml b/collections/metabolomics/v2/tools/pcutils.yaml
index 3d32a77b5..48079ab2b 100644
--- a/collections/metabolomics/v2/tools/pcutils.yaml
+++ b/collections/metabolomics/v2/tools/pcutils.yaml
@@ -9,5 +9,8 @@ derived_from:
 source_repos:
 - Asa12138/MetaNet
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - mass-spectrometry
diff --git a/collections/metabolomics/v2/tools/peakqc.yaml b/collections/metabolomics/v2/tools/peakqc.yaml
index a8dcb7689..8cbf9abca 100644
--- a/collections/metabolomics/v2/tools/peakqc.yaml
+++ b/collections/metabolomics/v2/tools/peakqc.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - pnnl/IonToolPack
 schema_version: 0.2.0
+license_tier: open
+license: BSD-2-Clause
+license_detection: github-api
 techniques:
 - LC-MS
 - direct-infusion-MS
diff --git a/collections/metabolomics/v2/tools/peakquant.yaml b/collections/metabolomics/v2/tools/peakquant.yaml
index e9466f276..1c6e5f5e7 100644
--- a/collections/metabolomics/v2/tools/peakquant.yaml
+++ b/collections/metabolomics/v2/tools/peakquant.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - pnnl/IonToolPack
 schema_version: 0.2.0
+license_tier: open
+license: BSD-2-Clause
+license_detection: github-api
 techniques:
 - LC-MS
 - direct-infusion-MS
diff --git a/collections/metabolomics/v2/tools/perl-prima.yaml b/collections/metabolomics/v2/tools/perl-prima.yaml
index 0e64025e5..6ac2390a4 100644
--- a/collections/metabolomics/v2/tools/perl-prima.yaml
+++ b/collections/metabolomics/v2/tools/perl-prima.yaml
@@ -9,3 +9,6 @@ derived_from:
 source_repos:
 - matteogiulietti/LipidOne
 schema_version: 0.2.0
+license_tier: open
+license: BSD-2-Clause
+license_detection: readme-llm
diff --git a/collections/metabolomics/v2/tools/perl.yaml b/collections/metabolomics/v2/tools/perl.yaml
index 637a7d1eb..5f48e73e0 100644
--- a/collections/metabolomics/v2/tools/perl.yaml
+++ b/collections/metabolomics/v2/tools/perl.yaml
@@ -9,3 +9,6 @@ derived_from:
 source_repos:
 - matteogiulietti/LipidOne
 schema_version: 0.2.0
+license_tier: open
+license: BSD-2-Clause
+license_detection: readme-llm
diff --git a/collections/metabolomics/v2/tools/pewlib.yaml b/collections/metabolomics/v2/tools/pewlib.yaml
index 4725a0759..1f0d05142 100644
--- a/collections/metabolomics/v2/tools/pewlib.yaml
+++ b/collections/metabolomics/v2/tools/pewlib.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - djdt/pewpew
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - MS-imaging
 - ion-mobility-MS
diff --git a/collections/metabolomics/v2/tools/pewpew.yaml b/collections/metabolomics/v2/tools/pewpew.yaml
index c87359d67..0449dbba8 100644
--- a/collections/metabolomics/v2/tools/pewpew.yaml
+++ b/collections/metabolomics/v2/tools/pewpew.yaml
@@ -10,6 +10,9 @@ derived_from:
 source_repos:
 - djdt/pewpew
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - MS-imaging
 - ion-mobility-MS
diff --git a/collections/metabolomics/v2/tools/pfam.yaml b/collections/metabolomics/v2/tools/pfam.yaml
index 942e13e88..7c01d5014 100644
--- a/collections/metabolomics/v2/tools/pfam.yaml
+++ b/collections/metabolomics/v2/tools/pfam.yaml
@@ -13,3 +13,6 @@ source_repos:
 - ASAGlab/MOI--An-integrated-solution-for-omics-analyses
 - medema-group/bigslice
 schema_version: 0.2.0
+license_tier: open
+license: AGPL-3.0
+license_detection: github-api
diff --git a/collections/metabolomics/v2/tools/pheatmap.yaml b/collections/metabolomics/v2/tools/pheatmap.yaml
index 2035c5649..4405a2c45 100644
--- a/collections/metabolomics/v2/tools/pheatmap.yaml
+++ b/collections/metabolomics/v2/tools/pheatmap.yaml
@@ -13,6 +13,9 @@ source_repos:
 - LeaveMeNotTonight/CMDN
 - sneumann/xcms
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/php.yaml b/collections/metabolomics/v2/tools/php.yaml
index 09b6db147..496af833d 100644
--- a/collections/metabolomics/v2/tools/php.yaml
+++ b/collections/metabolomics/v2/tools/php.yaml
@@ -9,5 +9,8 @@ derived_from:
 source_repos:
 - privrja/MassSpecBlocks
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
 techniques:
 - mass-spectrometry
diff --git a/collections/metabolomics/v2/tools/pillow.yaml b/collections/metabolomics/v2/tools/pillow.yaml
index 5a5b8193b..be0fbe898 100644
--- a/collections/metabolomics/v2/tools/pillow.yaml
+++ b/collections/metabolomics/v2/tools/pillow.yaml
@@ -9,5 +9,8 @@ derived_from:
 source_repos:
 - Wang-Bioinformatics-Lab/ModiFinder_base
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: file-present-unclassified
 techniques:
 - LC-MS
diff --git a/collections/metabolomics/v2/tools/pip.yaml b/collections/metabolomics/v2/tools/pip.yaml
index 262cc1d59..c5fdcb122 100644
--- a/collections/metabolomics/v2/tools/pip.yaml
+++ b/collections/metabolomics/v2/tools/pip.yaml
@@ -36,6 +36,9 @@ source_repos:
 - tingxiecsu/CSU-MS2
 - yuxuanliao/PACCS
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - direct-infusion-MS
diff --git a/collections/metabolomics/v2/tools/plage-method-within-pals.yaml b/collections/metabolomics/v2/tools/plage-method-within-pals.yaml
index b8e04ecf5..30b6c69f7 100644
--- a/collections/metabolomics/v2/tools/plage-method-within-pals.yaml
+++ b/collections/metabolomics/v2/tools/plage-method-within-pals.yaml
@@ -9,3 +9,6 @@ derived_from:
 source_repos:
 - glasgowcompbio/PALS
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
diff --git a/collections/metabolomics/v2/tools/plantmasst.yaml b/collections/metabolomics/v2/tools/plantmasst.yaml
index bed96210d..0fb1a0537 100644
--- a/collections/metabolomics/v2/tools/plantmasst.yaml
+++ b/collections/metabolomics/v2/tools/plantmasst.yaml
@@ -11,6 +11,9 @@ derived_from:
 source_repos:
 - mwang87/MASST
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - MS-imaging
diff --git a/collections/metabolomics/v2/tools/plotly-or-equivalent-interactive-plotting-library.yaml b/collections/metabolomics/v2/tools/plotly-or-equivalent-interactive-plotting-library.yaml
index a0ebc224d..48cbf3595 100644
--- a/collections/metabolomics/v2/tools/plotly-or-equivalent-interactive-plotting-library.yaml
+++ b/collections/metabolomics/v2/tools/plotly-or-equivalent-interactive-plotting-library.yaml
@@ -9,5 +9,8 @@ derived_from:
 source_repos:
 - czbiohub-sf/Rapid-QC-MS
 schema_version: 0.2.0
+license_tier: open
+license: BSD-3-Clause
+license_detection: license-file
 techniques:
 - LC-MS
diff --git a/collections/metabolomics/v2/tools/plotly.yaml b/collections/metabolomics/v2/tools/plotly.yaml
index b0ab41833..1b1915dcb 100644
--- a/collections/metabolomics/v2/tools/plotly.yaml
+++ b/collections/metabolomics/v2/tools/plotly.yaml
@@ -16,6 +16,9 @@ derived_from:
 source_repos:
 - Wang-Bioinformatics-Lab/NetworkFamily_MultipleAlignment_Website
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: file-present-unclassified
 techniques:
 - LC-MS
 - CE-MS
diff --git a/collections/metabolomics/v2/tools/pmartr.yaml b/collections/metabolomics/v2/tools/pmartr.yaml
index 89e32e0f9..7d96be1db 100644
--- a/collections/metabolomics/v2/tools/pmartr.yaml
+++ b/collections/metabolomics/v2/tools/pmartr.yaml
@@ -13,6 +13,9 @@ derived_from:
 source_repos:
 - pmartR/PMart_ShinyApp
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/pnnl-preprocessor.yaml b/collections/metabolomics/v2/tools/pnnl-preprocessor.yaml
index 34d0fecc1..cb0fe1ca1 100644
--- a/collections/metabolomics/v2/tools/pnnl-preprocessor.yaml
+++ b/collections/metabolomics/v2/tools/pnnl-preprocessor.yaml
@@ -10,6 +10,9 @@ 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
diff --git a/collections/metabolomics/v2/tools/poetry.yaml b/collections/metabolomics/v2/tools/poetry.yaml
index 73c98c0c6..ec187bb07 100644
--- a/collections/metabolomics/v2/tools/poetry.yaml
+++ b/collections/metabolomics/v2/tools/poetry.yaml
@@ -6,6 +6,9 @@ derived_from:
 - doi: 10.1021/acs.analchem.0c03895
   title: Rapid Development of Improved Data-Dependent Acquisition Strategies
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - CE-MS
diff --git a/collections/metabolomics/v2/tools/poisson-noise-augmentation.yaml b/collections/metabolomics/v2/tools/poisson-noise-augmentation.yaml
index a5c992b6f..fb17f1ae1 100644
--- a/collections/metabolomics/v2/tools/poisson-noise-augmentation.yaml
+++ b/collections/metabolomics/v2/tools/poisson-noise-augmentation.yaml
@@ -6,5 +6,8 @@ derived_from:
 - doi: 10.1021/acs.analchem.3c05002
   title: deepion
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - MS-imaging
diff --git a/collections/metabolomics/v2/tools/postgresql.yaml b/collections/metabolomics/v2/tools/postgresql.yaml
index e854f7c5b..3aa3ece55 100644
--- a/collections/metabolomics/v2/tools/postgresql.yaml
+++ b/collections/metabolomics/v2/tools/postgresql.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - vdhooftcompmet/MS2LDA
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
 techniques:
 - LC-MS
 - CE-MS
diff --git a/collections/metabolomics/v2/tools/prcomp.yaml b/collections/metabolomics/v2/tools/prcomp.yaml
index ba89983b0..364e94e8f 100644
--- a/collections/metabolomics/v2/tools/prcomp.yaml
+++ b/collections/metabolomics/v2/tools/prcomp.yaml
@@ -9,5 +9,8 @@ derived_from:
 source_repos:
 - BorchLab/CordBat
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: file-present-unclassified
 techniques:
 - mass-spectrometry
diff --git a/collections/metabolomics/v2/tools/prepare-wikidata-lotus-prefect-py.yaml b/collections/metabolomics/v2/tools/prepare-wikidata-lotus-prefect-py.yaml
index 2037ac838..5c36ae1ad 100644
--- a/collections/metabolomics/v2/tools/prepare-wikidata-lotus-prefect-py.yaml
+++ b/collections/metabolomics/v2/tools/prepare-wikidata-lotus-prefect-py.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - corinnabrungs/msn_tree_library
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
 techniques:
 - GC-MS
 - mass-spectrometry
diff --git a/collections/metabolomics/v2/tools/prima-panel.yaml b/collections/metabolomics/v2/tools/prima-panel.yaml
index 9c5abe02d..dc34d426b 100644
--- a/collections/metabolomics/v2/tools/prima-panel.yaml
+++ b/collections/metabolomics/v2/tools/prima-panel.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - funkam/PRIMA
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/probability-product-kernel-ppk.yaml b/collections/metabolomics/v2/tools/probability-product-kernel-ppk.yaml
index de222c625..2b1f9cb5f 100644
--- a/collections/metabolomics/v2/tools/probability-product-kernel-ppk.yaml
+++ b/collections/metabolomics/v2/tools/probability-product-kernel-ppk.yaml
@@ -9,5 +9,8 @@ derived_from:
 source_repos:
 - NPLinker/nplinker
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
diff --git a/collections/metabolomics/v2/tools/proc.yaml b/collections/metabolomics/v2/tools/proc.yaml
index 3469d727b..2d0f56e2b 100644
--- a/collections/metabolomics/v2/tools/proc.yaml
+++ b/collections/metabolomics/v2/tools/proc.yaml
@@ -10,3 +10,6 @@ derived_from:
 source_repos:
 - slfan2013/SERDA
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
diff --git a/collections/metabolomics/v2/tools/proforma-2-0.yaml b/collections/metabolomics/v2/tools/proforma-2-0.yaml
index c70895465..c4ebe8bf8 100644
--- a/collections/metabolomics/v2/tools/proforma-2-0.yaml
+++ b/collections/metabolomics/v2/tools/proforma-2-0.yaml
@@ -8,5 +8,8 @@ derived_from:
 - doi: 10.1021/acs.analchem.9b04884
   title: "<tt>spectrum_utils</tt>\n                    : A Python Package for Mass Spectrometry Data Processing and Visualization"
 schema_version: 0.2.0
+license_tier: open
+license: Apache-2.0
+license_detection: github-api
 techniques:
 - LC-MS
diff --git a/collections/metabolomics/v2/tools/proteomm.yaml b/collections/metabolomics/v2/tools/proteomm.yaml
index 3c9c7ebb0..09b3e6ba0 100644
--- a/collections/metabolomics/v2/tools/proteomm.yaml
+++ b/collections/metabolomics/v2/tools/proteomm.yaml
@@ -8,6 +8,9 @@ derived_from:
 source_repos:
 - idrblab/NOREVA;
 schema_version: 0.2.0
+license_tier: open
+license: GPL-3.0
+license_detection: github-api
 techniques:
 - LC-MS
 - mass-spectrometry
diff --git a/collections/metabolomics/v2/tools/proteowizard-library-and-tools.yaml b/collections/metabolomics/v2/tools/proteowizard-library-and-tools.yaml
index ff5afd5cb..f60e58961 100644
--- a/collections/metabolomics/v2/tools/proteowizard-library-and-tools.yaml
+++ b/collections/metabolomics/v2/tools/proteowizard-library-and-tools.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - ProteoWizard/pwiz
 schema_version: 0.2.0
+license_tier: open
+license: Apache-2.0
+license_detection: github-api
 techniques:
 - LC-MS
 - ion-mobility-MS
diff --git a/collections/metabolomics/v2/tools/proteowizard-msconvert.yaml b/collections/metabolomics/v2/tools/proteowizard-msconvert.yaml
index 452e6612a..6da1e9a3e 100644
--- a/collections/metabolomics/v2/tools/proteowizard-msconvert.yaml
+++ b/collections/metabolomics/v2/tools/proteowizard-msconvert.yaml
@@ -17,6 +17,9 @@ source_repos:
 - LabLaskin/MSIGen
 - jcapelladesto/isoSCAN
 schema_version: 0.2.0
+license_tier: open
+license: BSD-3-Clause
+license_detection: github-api
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/proteowizard-pwiz-skyline.yaml b/collections/metabolomics/v2/tools/proteowizard-pwiz-skyline.yaml
index f116a258f..a4ed3ccc2 100644
--- a/collections/metabolomics/v2/tools/proteowizard-pwiz-skyline.yaml
+++ b/collections/metabolomics/v2/tools/proteowizard-pwiz-skyline.yaml
@@ -10,5 +10,8 @@ derived_from:
 source_repos:
 - ComPlat/chem-spectra-app
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
 techniques:
 - NMR
diff --git a/collections/metabolomics/v2/tools/proteowizard.yaml b/collections/metabolomics/v2/tools/proteowizard.yaml
index d8337a28d..354e5d219 100644
--- a/collections/metabolomics/v2/tools/proteowizard.yaml
+++ b/collections/metabolomics/v2/tools/proteowizard.yaml
@@ -39,6 +39,9 @@ source_repos:
 - hcji/TarMet
 - shuzhao-li-lab/asari
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: file-present-unclassified
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/proteoxchange-repository.yaml b/collections/metabolomics/v2/tools/proteoxchange-repository.yaml
index 9ec451354..f4b9c4f6e 100644
--- a/collections/metabolomics/v2/tools/proteoxchange-repository.yaml
+++ b/collections/metabolomics/v2/tools/proteoxchange-repository.yaml
@@ -9,5 +9,8 @@ derived_from:
 source_repos:
 - mwang87/MetabolomicsSpectrumResolver
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
 techniques:
 - LC-MS
diff --git a/collections/metabolomics/v2/tools/ps2ms.yaml b/collections/metabolomics/v2/tools/ps2ms.yaml
index 14f58d2fd..7d2687796 100644
--- a/collections/metabolomics/v2/tools/ps2ms.yaml
+++ b/collections/metabolomics/v2/tools/ps2ms.yaml
@@ -6,6 +6,9 @@ derived_from:
 - doi: 10.1021/acs.analchem.3c05019
   title: 'PS<sup>2</sup>MS: A Deep Learning-Based Prediction System for Identifying New Psychoactive Substances Using Mass Spectrometry'
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/psims.yaml b/collections/metabolomics/v2/tools/psims.yaml
index 7ae4ca2d7..721bc18ae 100644
--- a/collections/metabolomics/v2/tools/psims.yaml
+++ b/collections/metabolomics/v2/tools/psims.yaml
@@ -6,5 +6,8 @@ derived_from:
 - doi: 10.1021/acs.jproteome.8b00717
   title: pyteomics
 schema_version: 0.2.0
+license_tier: open
+license: Apache-2.0
+license_detection: github-api
 techniques:
 - ion-mobility-MS
diff --git a/collections/metabolomics/v2/tools/psm-utils.yaml b/collections/metabolomics/v2/tools/psm-utils.yaml
index ebb137a39..7002ac308 100644
--- a/collections/metabolomics/v2/tools/psm-utils.yaml
+++ b/collections/metabolomics/v2/tools/psm-utils.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - compomics/ms2rescore
 schema_version: 0.2.0
+license_tier: open
+license: Apache-2.0
+license_detection: github-api
 techniques:
 - LC-MS
 - mass-spectrometry
diff --git a/collections/metabolomics/v2/tools/pubchem-standardization.yaml b/collections/metabolomics/v2/tools/pubchem-standardization.yaml
index 1afbb07b4..b747f725f 100644
--- a/collections/metabolomics/v2/tools/pubchem-standardization.yaml
+++ b/collections/metabolomics/v2/tools/pubchem-standardization.yaml
@@ -9,3 +9,6 @@ derived_from:
 source_repos:
 - michaelwitting/RepoRT
 schema_version: 0.2.0
+license_tier: open
+license: CC-BY-SA-4.0
+license_detection: github-api
diff --git a/collections/metabolomics/v2/tools/pubchem.yaml b/collections/metabolomics/v2/tools/pubchem.yaml
index c1ac84eef..e08ed7583 100644
--- a/collections/metabolomics/v2/tools/pubchem.yaml
+++ b/collections/metabolomics/v2/tools/pubchem.yaml
@@ -34,6 +34,9 @@ source_repos:
 - samgoldman97/ms-pred
 - zmahnoor14/MAW
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/pubchempy.yaml b/collections/metabolomics/v2/tools/pubchempy.yaml
index 032154816..cdb595dc5 100644
--- a/collections/metabolomics/v2/tools/pubchempy.yaml
+++ b/collections/metabolomics/v2/tools/pubchempy.yaml
@@ -12,6 +12,9 @@ derived_from:
 source_repos:
 - zmahnoor14/MAW
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: readme-llm
 techniques:
 - LC-MS
 - mass-spectrometry
diff --git a/collections/metabolomics/v2/tools/punc-data.yaml b/collections/metabolomics/v2/tools/punc-data.yaml
index 1f1d36633..fd7905ba2 100644
--- a/collections/metabolomics/v2/tools/punc-data.yaml
+++ b/collections/metabolomics/v2/tools/punc-data.yaml
@@ -10,5 +10,8 @@ derived_from:
 source_repos:
 - WTVoe/puncdata
 schema_version: 0.2.0
+license_tier: open
+license: AGPL-3.0
+license_detection: license-file
 techniques:
 - mass-spectrometry
diff --git a/collections/metabolomics/v2/tools/puncdata.yaml b/collections/metabolomics/v2/tools/puncdata.yaml
index 1471a94e9..0813ebe54 100644
--- a/collections/metabolomics/v2/tools/puncdata.yaml
+++ b/collections/metabolomics/v2/tools/puncdata.yaml
@@ -9,5 +9,8 @@ derived_from:
 source_repos:
 - WTVoe/puncdata
 schema_version: 0.2.0
+license_tier: open
+license: AGPL-3.0
+license_detection: license-file
 techniques:
 - mass-spectrometry
diff --git a/collections/metabolomics/v2/tools/purrr.yaml b/collections/metabolomics/v2/tools/purrr.yaml
index 97fc412b6..fe3ecd67d 100644
--- a/collections/metabolomics/v2/tools/purrr.yaml
+++ b/collections/metabolomics/v2/tools/purrr.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - kilgain/MassSpec
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/pwiz-bindings-cli-dll.yaml b/collections/metabolomics/v2/tools/pwiz-bindings-cli-dll.yaml
index 9baa81290..fdb70cf2f 100644
--- a/collections/metabolomics/v2/tools/pwiz-bindings-cli-dll.yaml
+++ b/collections/metabolomics/v2/tools/pwiz-bindings-cli-dll.yaml
@@ -6,6 +6,9 @@ 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
diff --git a/collections/metabolomics/v2/tools/pwiz.yaml b/collections/metabolomics/v2/tools/pwiz.yaml
index 2351e409d..fe790eda8 100644
--- a/collections/metabolomics/v2/tools/pwiz.yaml
+++ b/collections/metabolomics/v2/tools/pwiz.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - ProteoWizard/pwiz
 schema_version: 0.2.0
+license_tier: open
+license: Apache-2.0
+license_detection: github-api
 techniques:
 - LC-MS
 - ion-mobility-MS
diff --git a/collections/metabolomics/v2/tools/py4cytoscape.yaml b/collections/metabolomics/v2/tools/py4cytoscape.yaml
index f71ebb644..ea2c3d785 100644
--- a/collections/metabolomics/v2/tools/py4cytoscape.yaml
+++ b/collections/metabolomics/v2/tools/py4cytoscape.yaml
@@ -6,6 +6,9 @@ derived_from:
 - doi: 10.1186/s40168-023-01476-3
   title: MetaboDirect
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/pyarrow.yaml b/collections/metabolomics/v2/tools/pyarrow.yaml
index 780aa554c..aef43ea05 100644
--- a/collections/metabolomics/v2/tools/pyarrow.yaml
+++ b/collections/metabolomics/v2/tools/pyarrow.yaml
@@ -6,6 +6,9 @@ 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
diff --git a/collections/metabolomics/v2/tools/pybaf2sql.yaml b/collections/metabolomics/v2/tools/pybaf2sql.yaml
index d805959a9..c395d8440 100644
--- a/collections/metabolomics/v2/tools/pybaf2sql.yaml
+++ b/collections/metabolomics/v2/tools/pybaf2sql.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - LabLaskin/MSIGen
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
 techniques:
 - CE-MS
 - MS-imaging
diff --git a/collections/metabolomics/v2/tools/pycharm.yaml b/collections/metabolomics/v2/tools/pycharm.yaml
index b5ccbac34..d96ac4a6a 100644
--- a/collections/metabolomics/v2/tools/pycharm.yaml
+++ b/collections/metabolomics/v2/tools/pycharm.yaml
@@ -9,3 +9,6 @@ derived_from:
 source_repos:
 - SysMedOs/LipidLynxX
 schema_version: 0.2.0
+license_tier: open
+license: GPL-3.0
+license_detection: github-api
diff --git a/collections/metabolomics/v2/tools/pycombat.yaml b/collections/metabolomics/v2/tools/pycombat.yaml
index 53d7f5b0b..a1da6f4d5 100644
--- a/collections/metabolomics/v2/tools/pycombat.yaml
+++ b/collections/metabolomics/v2/tools/pycombat.yaml
@@ -6,6 +6,9 @@ derived_from:
 - doi: 10.1371/journal.pcbi.1011912
   title: Common data models to streamline metabolomics processing and annotation, and implementation in a Python pipeline
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: license-file
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/pyeva.yaml b/collections/metabolomics/v2/tools/pyeva.yaml
index 9ad48dfa8..4ca5137b3 100644
--- a/collections/metabolomics/v2/tools/pyeva.yaml
+++ b/collections/metabolomics/v2/tools/pyeva.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - HuanLab-backup/EVA
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/pyg.yaml b/collections/metabolomics/v2/tools/pyg.yaml
index fd6351dab..5ed180f71 100644
--- a/collections/metabolomics/v2/tools/pyg.yaml
+++ b/collections/metabolomics/v2/tools/pyg.yaml
@@ -13,6 +13,9 @@ source_repos:
 - RiverCCC/ABCoRT
 - yuxuanliao/PACCS
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/pyhmmer.yaml b/collections/metabolomics/v2/tools/pyhmmer.yaml
index a91f076bb..de4d5e701 100644
--- a/collections/metabolomics/v2/tools/pyhmmer.yaml
+++ b/collections/metabolomics/v2/tools/pyhmmer.yaml
@@ -9,3 +9,6 @@ derived_from:
 source_repos:
 - medema-group/bigslice
 schema_version: 0.2.0
+license_tier: open
+license: AGPL-3.0
+license_detection: github-api
diff --git a/collections/metabolomics/v2/tools/pyineta.yaml b/collections/metabolomics/v2/tools/pyineta.yaml
index 47c1b3ca5..3b80edf7a 100644
--- a/collections/metabolomics/v2/tools/pyineta.yaml
+++ b/collections/metabolomics/v2/tools/pyineta.yaml
@@ -12,5 +12,8 @@ derived_from:
 source_repos:
 - edisonomics/PyINETA
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
 techniques:
 - NMR
diff --git a/collections/metabolomics/v2/tools/pymolnetenhancer.yaml b/collections/metabolomics/v2/tools/pymolnetenhancer.yaml
index 0fb501e13..0a8c07bb8 100644
--- a/collections/metabolomics/v2/tools/pymolnetenhancer.yaml
+++ b/collections/metabolomics/v2/tools/pymolnetenhancer.yaml
@@ -9,5 +9,8 @@ derived_from:
 source_repos:
 - madeleineernst/pyMolNetEnhancer
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
 techniques:
 - LC-MS
diff --git a/collections/metabolomics/v2/tools/pymrmtransitiongrouppicker.yaml b/collections/metabolomics/v2/tools/pymrmtransitiongrouppicker.yaml
index f20db5254..6196aca0c 100644
--- a/collections/metabolomics/v2/tools/pymrmtransitiongrouppicker.yaml
+++ b/collections/metabolomics/v2/tools/pymrmtransitiongrouppicker.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - Roestlab/massdash
 schema_version: 0.2.0
+license_tier: open
+license: BSD-3-Clause
+license_detection: github-api
 techniques:
 - LC-MS
 - ion-mobility-MS
diff --git a/collections/metabolomics/v2/tools/pymzml.yaml b/collections/metabolomics/v2/tools/pymzml.yaml
index 016027bf0..79ac3417a 100644
--- a/collections/metabolomics/v2/tools/pymzml.yaml
+++ b/collections/metabolomics/v2/tools/pymzml.yaml
@@ -24,6 +24,9 @@ source_repos:
 - shuzhao-li-lab/asari
 - zsspython/LAGF
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: file-present-unclassified
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/pyopenms-viz.yaml b/collections/metabolomics/v2/tools/pyopenms-viz.yaml
index 76093f249..3fe597d40 100644
--- a/collections/metabolomics/v2/tools/pyopenms-viz.yaml
+++ b/collections/metabolomics/v2/tools/pyopenms-viz.yaml
@@ -9,6 +9,9 @@ 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
diff --git a/collections/metabolomics/v2/tools/pyopenms.yaml b/collections/metabolomics/v2/tools/pyopenms.yaml
index 8d4f986d1..81880b53c 100644
--- a/collections/metabolomics/v2/tools/pyopenms.yaml
+++ b/collections/metabolomics/v2/tools/pyopenms.yaml
@@ -24,6 +24,9 @@ source_repos:
 - AutoFlowResearch/SmartPeak
 - huaxuyu/bago
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/pyqt5.yaml b/collections/metabolomics/v2/tools/pyqt5.yaml
index 0a900c5da..393b94fa8 100644
--- a/collections/metabolomics/v2/tools/pyqt5.yaml
+++ b/collections/metabolomics/v2/tools/pyqt5.yaml
@@ -10,6 +10,9 @@ derived_from:
 source_repos:
 - Leo-Cheng-Lab/ROIAL-NMR
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
 techniques:
 - LC-MS
 - NMR
diff --git a/collections/metabolomics/v2/tools/pyrwr.yaml b/collections/metabolomics/v2/tools/pyrwr.yaml
index a38e7b510..4f8817977 100644
--- a/collections/metabolomics/v2/tools/pyrwr.yaml
+++ b/collections/metabolomics/v2/tools/pyrwr.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - computational-chemical-biology/ChemWalker
 schema_version: 0.2.0
+license_tier: open
+license: BSD-3-Clause
+license_detection: github-api
 techniques:
 - LC-MS
 - mass-spectrometry
diff --git a/collections/metabolomics/v2/tools/pyteomics.yaml b/collections/metabolomics/v2/tools/pyteomics.yaml
index 58b40c482..5eae438d2 100644
--- a/collections/metabolomics/v2/tools/pyteomics.yaml
+++ b/collections/metabolomics/v2/tools/pyteomics.yaml
@@ -12,6 +12,9 @@ derived_from:
 - doi: 10.1021/acs.analchem.9b04884
   title: "<tt>spectrum_utils</tt>\n                    : A Python Package for Mass Spectrometry Data Processing and Visualization"
 schema_version: 0.2.0
+license_tier: open
+license: BSD-3-Clause
+license_detection: github-api
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/pytest.yaml b/collections/metabolomics/v2/tools/pytest.yaml
index b4e89c0aa..6c08921f2 100644
--- a/collections/metabolomics/v2/tools/pytest.yaml
+++ b/collections/metabolomics/v2/tools/pytest.yaml
@@ -32,6 +32,9 @@ source_repos:
 - matchms/matchms
 - tyo-nu/MINE-Database
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/python-2-7.yaml b/collections/metabolomics/v2/tools/python-2-7.yaml
index 6fa03f105..bee189fa0 100644
--- a/collections/metabolomics/v2/tools/python-2-7.yaml
+++ b/collections/metabolomics/v2/tools/python-2-7.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - Viant-Metabolomics/Galaxy-M
 schema_version: 0.2.0
+license_tier: open
+license: GPL-2.0
+license_detection: github-api
 techniques:
 - LC-MS
 - direct-infusion-MS
diff --git a/collections/metabolomics/v2/tools/python-3-11-7.yaml b/collections/metabolomics/v2/tools/python-3-11-7.yaml
index 146f99127..016bf7678 100644
--- a/collections/metabolomics/v2/tools/python-3-11-7.yaml
+++ b/collections/metabolomics/v2/tools/python-3-11-7.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - HassounLab/MVP
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/python-3-6-12.yaml b/collections/metabolomics/v2/tools/python-3-6-12.yaml
index f889497ec..5480e8377 100644
--- a/collections/metabolomics/v2/tools/python-3-6-12.yaml
+++ b/collections/metabolomics/v2/tools/python-3-6-12.yaml
@@ -10,5 +10,8 @@ derived_from:
 source_repos:
 - wabdelmoula/massNet
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - MS-imaging
diff --git a/collections/metabolomics/v2/tools/python-3-6.yaml b/collections/metabolomics/v2/tools/python-3-6.yaml
index 0ff3dab0c..b8b88485c 100644
--- a/collections/metabolomics/v2/tools/python-3-6.yaml
+++ b/collections/metabolomics/v2/tools/python-3-6.yaml
@@ -10,6 +10,9 @@ derived_from:
 source_repos:
 - Dingxian666/Norm-ISWSVR
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: license-file
 techniques:
 - LC-MS
 - CE-MS
diff --git a/collections/metabolomics/v2/tools/python-3-7.yaml b/collections/metabolomics/v2/tools/python-3-7.yaml
index 1e39a6466..3985df7b5 100644
--- a/collections/metabolomics/v2/tools/python-3-7.yaml
+++ b/collections/metabolomics/v2/tools/python-3-7.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - aaronma2020/MSGO
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/python-3-8-1.yaml b/collections/metabolomics/v2/tools/python-3-8-1.yaml
index 93016fbd3..a755f9a0c 100644
--- a/collections/metabolomics/v2/tools/python-3-8-1.yaml
+++ b/collections/metabolomics/v2/tools/python-3-8-1.yaml
@@ -9,5 +9,8 @@ derived_from:
 source_repos:
 - LinShuhaiLAB/QuanFormer
 schema_version: 0.2.0
+license_tier: open
+license: Apache-2.0
+license_detection: github-api
 techniques:
 - LC-MS
diff --git a/collections/metabolomics/v2/tools/python-3-8-2.yaml b/collections/metabolomics/v2/tools/python-3-8-2.yaml
index 295923696..b1abca71a 100644
--- a/collections/metabolomics/v2/tools/python-3-8-2.yaml
+++ b/collections/metabolomics/v2/tools/python-3-8-2.yaml
@@ -10,5 +10,8 @@ derived_from:
 source_repos:
 - zsspython/LAGF
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
diff --git a/collections/metabolomics/v2/tools/python-3-8.yaml b/collections/metabolomics/v2/tools/python-3-8.yaml
index ae5c9cbcb..9c9f39e80 100644
--- a/collections/metabolomics/v2/tools/python-3-8.yaml
+++ b/collections/metabolomics/v2/tools/python-3-8.yaml
@@ -15,6 +15,9 @@ derived_from:
 source_repos:
 - wh-xu/Hyper-Spec
 schema_version: 0.2.0
+license_tier: open
+license: BSD-3-Clause
+license_detection: github-api
 techniques:
 - LC-MS
 - ion-mobility-MS
diff --git a/collections/metabolomics/v2/tools/python-3-9-0.yaml b/collections/metabolomics/v2/tools/python-3-9-0.yaml
index 19951940e..34ee10bb4 100644
--- a/collections/metabolomics/v2/tools/python-3-9-0.yaml
+++ b/collections/metabolomics/v2/tools/python-3-9-0.yaml
@@ -10,6 +10,9 @@ derived_from:
 source_repos:
 - RaoboXu/Lipidwizard
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - CE-MS
diff --git a/collections/metabolomics/v2/tools/python-3-9.yaml b/collections/metabolomics/v2/tools/python-3-9.yaml
index 0f4afb21a..2435bd0a1 100644
--- a/collections/metabolomics/v2/tools/python-3-9.yaml
+++ b/collections/metabolomics/v2/tools/python-3-9.yaml
@@ -10,5 +10,8 @@ derived_from:
 source_repos:
 - Leo-Cheng-Lab/ROIAL-NMR
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
 techniques:
 - NMR
diff --git a/collections/metabolomics/v2/tools/python-3.yaml b/collections/metabolomics/v2/tools/python-3.yaml
index 29a625549..b0752e097 100644
--- a/collections/metabolomics/v2/tools/python-3.yaml
+++ b/collections/metabolomics/v2/tools/python-3.yaml
@@ -29,6 +29,9 @@ source_repos:
 - yuxuanliao/PACCS
 - zxguocsu/GCMSFormer
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: file-present-unclassified
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/python-deep-learning-framework-pytorch-or-tensorflow.yaml b/collections/metabolomics/v2/tools/python-deep-learning-framework-pytorch-or-tensorflow.yaml
index 8ce194e96..787b42227 100644
--- a/collections/metabolomics/v2/tools/python-deep-learning-framework-pytorch-or-tensorflow.yaml
+++ b/collections/metabolomics/v2/tools/python-deep-learning-framework-pytorch-or-tensorflow.yaml
@@ -6,5 +6,8 @@ derived_from:
 - doi: 10.1021/acs.analchem.3c05019
   title: 'PS<sup>2</sup>MS: A Deep Learning-Based Prediction System for Identifying New Psychoactive Substances Using Mass Spectrometry'
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - mass-spectrometry
diff --git a/collections/metabolomics/v2/tools/python-json-module-for-parsing-json-files.yaml b/collections/metabolomics/v2/tools/python-json-module-for-parsing-json-files.yaml
index 6e6a69c8c..0cd5948b1 100644
--- a/collections/metabolomics/v2/tools/python-json-module-for-parsing-json-files.yaml
+++ b/collections/metabolomics/v2/tools/python-json-module-for-parsing-json-files.yaml
@@ -9,3 +9,6 @@ derived_from:
 source_repos:
 - mibig-secmet/mibig-json
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
diff --git a/collections/metabolomics/v2/tools/python-numpy-pandas.yaml b/collections/metabolomics/v2/tools/python-numpy-pandas.yaml
index 85e6dd8c2..09efae247 100644
--- a/collections/metabolomics/v2/tools/python-numpy-pandas.yaml
+++ b/collections/metabolomics/v2/tools/python-numpy-pandas.yaml
@@ -6,6 +6,9 @@ derived_from:
 - doi: 10.1186/s40168-023-01476-3
   title: MetaboDirect
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
 techniques:
 - LC-MS
 - direct-infusion-MS
diff --git a/collections/metabolomics/v2/tools/python-numpy-scipy-stats-pandas-matplotlib-seaborn.yaml b/collections/metabolomics/v2/tools/python-numpy-scipy-stats-pandas-matplotlib-seaborn.yaml
index 23f050a1c..039c4ffda 100644
--- a/collections/metabolomics/v2/tools/python-numpy-scipy-stats-pandas-matplotlib-seaborn.yaml
+++ b/collections/metabolomics/v2/tools/python-numpy-scipy-stats-pandas-matplotlib-seaborn.yaml
@@ -9,5 +9,8 @@ derived_from:
 source_repos:
 - NPLinker/nplinker
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
diff --git a/collections/metabolomics/v2/tools/python-pandas-numpy-scipy.yaml b/collections/metabolomics/v2/tools/python-pandas-numpy-scipy.yaml
index bde09d581..34799a94b 100644
--- a/collections/metabolomics/v2/tools/python-pandas-numpy-scipy.yaml
+++ b/collections/metabolomics/v2/tools/python-pandas-numpy-scipy.yaml
@@ -13,6 +13,9 @@ source_repos:
 - chopralab/CLAW
 - metabolomicsworkbench/MetENP
 schema_version: 0.2.0
+license_tier: open
+license: GPL-3.0
+license_detection: license-file
 techniques:
 - LC-MS
 - mass-spectrometry
diff --git a/collections/metabolomics/v2/tools/python-scikit-learn-seaborn-or-matplotlib-for-visualization.yaml b/collections/metabolomics/v2/tools/python-scikit-learn-seaborn-or-matplotlib-for-visualization.yaml
index ce5f48587..328582f05 100644
--- a/collections/metabolomics/v2/tools/python-scikit-learn-seaborn-or-matplotlib-for-visualization.yaml
+++ b/collections/metabolomics/v2/tools/python-scikit-learn-seaborn-or-matplotlib-for-visualization.yaml
@@ -6,3 +6,6 @@ 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
diff --git a/collections/metabolomics/v2/tools/python-scikit-learn.yaml b/collections/metabolomics/v2/tools/python-scikit-learn.yaml
index 5e0df99a9..ba0a207fc 100644
--- a/collections/metabolomics/v2/tools/python-scikit-learn.yaml
+++ b/collections/metabolomics/v2/tools/python-scikit-learn.yaml
@@ -7,3 +7,6 @@ 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
diff --git a/collections/metabolomics/v2/tools/python.yaml b/collections/metabolomics/v2/tools/python.yaml
index 61a1aa6aa..49980df8f 100644
--- a/collections/metabolomics/v2/tools/python.yaml
+++ b/collections/metabolomics/v2/tools/python.yaml
@@ -286,6 +286,9 @@ source_repos:
 - zsspython/LAGF
 - zza1211/NMRformer
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/pytorch-2-2.yaml b/collections/metabolomics/v2/tools/pytorch-2-2.yaml
index 8be8171c7..fb5c34147 100644
--- a/collections/metabolomics/v2/tools/pytorch-2-2.yaml
+++ b/collections/metabolomics/v2/tools/pytorch-2-2.yaml
@@ -9,5 +9,8 @@ derived_from:
 source_repos:
 - zhanghailiangcsu/MSBERT
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
 techniques:
 - LC-MS
diff --git a/collections/metabolomics/v2/tools/pytorch-cu118.yaml b/collections/metabolomics/v2/tools/pytorch-cu118.yaml
index a822940bd..446f9f697 100644
--- a/collections/metabolomics/v2/tools/pytorch-cu118.yaml
+++ b/collections/metabolomics/v2/tools/pytorch-cu118.yaml
@@ -9,5 +9,8 @@ derived_from:
 source_repos:
 - yfWang01/FlavorFormer
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - NMR
diff --git a/collections/metabolomics/v2/tools/pytorch-geometric-pyg.yaml b/collections/metabolomics/v2/tools/pytorch-geometric-pyg.yaml
index f65bd66a9..cd7bd1246 100644
--- a/collections/metabolomics/v2/tools/pytorch-geometric-pyg.yaml
+++ b/collections/metabolomics/v2/tools/pytorch-geometric-pyg.yaml
@@ -6,5 +6,8 @@ derived_from:
 - doi: 10.1186/s13321-024-00899-w
   title: mol2ccs
 schema_version: 0.2.0
+license_tier: open
+license: GPL-2.0
+license_detection: github-api
 techniques:
 - ion-mobility-MS
diff --git a/collections/metabolomics/v2/tools/pytorch-geometric.yaml b/collections/metabolomics/v2/tools/pytorch-geometric.yaml
index 00fdf39b7..5324aa11b 100644
--- a/collections/metabolomics/v2/tools/pytorch-geometric.yaml
+++ b/collections/metabolomics/v2/tools/pytorch-geometric.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - tingxiecsu/CSU-MS2
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/pytorch-or-equivalent-deep-learning-framework-inferred-from-gnn-contrastive-learning-context.yaml b/collections/metabolomics/v2/tools/pytorch-or-equivalent-deep-learning-framework-inferred-from-gnn-contrastive-learning-context.yaml
index fcd376bb1..553b7f7a4 100644
--- a/collections/metabolomics/v2/tools/pytorch-or-equivalent-deep-learning-framework-inferred-from-gnn-contrastive-learning-context.yaml
+++ b/collections/metabolomics/v2/tools/pytorch-or-equivalent-deep-learning-framework-inferred-from-gnn-contrastive-learning-context.yaml
@@ -9,3 +9,6 @@ derived_from:
 source_repos:
 - Chen-micslab/QCCAssisted4DSterol
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
diff --git a/collections/metabolomics/v2/tools/pytorch-or-tensorflow.yaml b/collections/metabolomics/v2/tools/pytorch-or-tensorflow.yaml
index 3d9426f7d..9c90471d1 100644
--- a/collections/metabolomics/v2/tools/pytorch-or-tensorflow.yaml
+++ b/collections/metabolomics/v2/tools/pytorch-or-tensorflow.yaml
@@ -6,6 +6,9 @@ derived_from:
 - doi: 10.1186/s13321-024-00899-w
   title: mol2ccs
 schema_version: 0.2.0
+license_tier: open
+license: GPL-2.0
+license_detection: github-api
 techniques:
 - LC-MS
 - MS-imaging
diff --git a/collections/metabolomics/v2/tools/pytorch.yaml b/collections/metabolomics/v2/tools/pytorch.yaml
index 786df476d..01008b0be 100644
--- a/collections/metabolomics/v2/tools/pytorch.yaml
+++ b/collections/metabolomics/v2/tools/pytorch.yaml
@@ -90,6 +90,9 @@ source_repos:
 - zxguocsu/GCMSFormer
 - zza1211/NMRformer
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/pyvis.yaml b/collections/metabolomics/v2/tools/pyvis.yaml
index 78fbb07d4..7a73eba6a 100644
--- a/collections/metabolomics/v2/tools/pyvis.yaml
+++ b/collections/metabolomics/v2/tools/pyvis.yaml
@@ -7,6 +7,9 @@ derived_from:
 - doi: 10.1371/journal.pcbi.1011814
   title: 'PathIntegrate: Multivariate modelling approaches for pathway-based multi-omics data integration'
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - mass-spectrometry
diff --git a/collections/metabolomics/v2/tools/pyyaml.yaml b/collections/metabolomics/v2/tools/pyyaml.yaml
index 4cc2a5965..1d86db544 100644
--- a/collections/metabolomics/v2/tools/pyyaml.yaml
+++ b/collections/metabolomics/v2/tools/pyyaml.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - ZzakB/MolNotator
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
 techniques:
 - LC-MS
 - ion-mobility-MS
diff --git a/collections/metabolomics/v2/tools/q-exactive-orbitrap.yaml b/collections/metabolomics/v2/tools/q-exactive-orbitrap.yaml
index 05ff20332..129138e3d 100644
--- a/collections/metabolomics/v2/tools/q-exactive-orbitrap.yaml
+++ b/collections/metabolomics/v2/tools/q-exactive-orbitrap.yaml
@@ -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
diff --git a/collections/metabolomics/v2/tools/q2-qemistree.yaml b/collections/metabolomics/v2/tools/q2-qemistree.yaml
index 9d0bd9486..7d90c2568 100644
--- a/collections/metabolomics/v2/tools/q2-qemistree.yaml
+++ b/collections/metabolomics/v2/tools/q2-qemistree.yaml
@@ -6,5 +6,8 @@ derived_from:
 - doi: 10.1038/s41589-020-00677-3
   title: qemistree
 schema_version: 0.2.0
+license_tier: open
+license: BSD-2-Clause
+license_detection: github-api
 techniques:
 - LC-MS
diff --git a/collections/metabolomics/v2/tools/qcomics.yaml b/collections/metabolomics/v2/tools/qcomics.yaml
index 9836dc41c..e24ed2021 100644
--- a/collections/metabolomics/v2/tools/qcomics.yaml
+++ b/collections/metabolomics/v2/tools/qcomics.yaml
@@ -6,6 +6,9 @@ derived_from:
 - doi: 10.1021/acs.analchem.3c03660
   title: QComics
 schema_version: 0.2.0
+license_tier: open
+license: GPL-3.0
+license_detection: github-api
 techniques:
 - LC-MS
 - mass-spectrometry
diff --git a/collections/metabolomics/v2/tools/qcxms2.yaml b/collections/metabolomics/v2/tools/qcxms2.yaml
index 093ab4df3..d926a4b1a 100644
--- a/collections/metabolomics/v2/tools/qcxms2.yaml
+++ b/collections/metabolomics/v2/tools/qcxms2.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - grimme-lab/QCxMS2
 schema_version: 0.2.0
+license_tier: open
+license: LGPL-3.0
+license_detection: github-api
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/qmake.yaml b/collections/metabolomics/v2/tools/qmake.yaml
index e36e40a56..afa5d34c8 100644
--- a/collections/metabolomics/v2/tools/qmake.yaml
+++ b/collections/metabolomics/v2/tools/qmake.yaml
@@ -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
diff --git a/collections/metabolomics/v2/tools/qr-code-generation-library.yaml b/collections/metabolomics/v2/tools/qr-code-generation-library.yaml
index 79a81ae7f..87a3f6e80 100644
--- a/collections/metabolomics/v2/tools/qr-code-generation-library.yaml
+++ b/collections/metabolomics/v2/tools/qr-code-generation-library.yaml
@@ -9,5 +9,8 @@ derived_from:
 source_repos:
 - mwang87/MetabolomicsSpectrumResolver
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
 techniques:
 - LC-MS
diff --git a/collections/metabolomics/v2/tools/qt5.yaml b/collections/metabolomics/v2/tools/qt5.yaml
index e4f164999..e312d12b0 100644
--- a/collections/metabolomics/v2/tools/qt5.yaml
+++ b/collections/metabolomics/v2/tools/qt5.yaml
@@ -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
diff --git a/collections/metabolomics/v2/tools/quick.yaml b/collections/metabolomics/v2/tools/quick.yaml
index 283255447..a60e3f65b 100644
--- a/collections/metabolomics/v2/tools/quick.yaml
+++ b/collections/metabolomics/v2/tools/quick.yaml
@@ -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
diff --git a/collections/metabolomics/v2/tools/r-3-0-1.yaml b/collections/metabolomics/v2/tools/r-3-0-1.yaml
index 4c0e26eee..c6f55a0fb 100644
--- a/collections/metabolomics/v2/tools/r-3-0-1.yaml
+++ b/collections/metabolomics/v2/tools/r-3-0-1.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - Viant-Metabolomics/Galaxy-M
 schema_version: 0.2.0
+license_tier: open
+license: GPL-2.0
+license_detection: github-api
 techniques:
 - LC-MS
 - direct-infusion-MS
diff --git a/collections/metabolomics/v2/tools/r-4-0-2.yaml b/collections/metabolomics/v2/tools/r-4-0-2.yaml
index 230e5e6c9..08fae1034 100644
--- a/collections/metabolomics/v2/tools/r-4-0-2.yaml
+++ b/collections/metabolomics/v2/tools/r-4-0-2.yaml
@@ -8,6 +8,9 @@ derived_from:
 - doi: 10.1186/s40168-023-01476-3
   title: MetaboDirect
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
 techniques:
 - LC-MS
 - mass-spectrometry
diff --git a/collections/metabolomics/v2/tools/r-4-1-2.yaml b/collections/metabolomics/v2/tools/r-4-1-2.yaml
index 0f5eac29b..882fd38b4 100644
--- a/collections/metabolomics/v2/tools/r-4-1-2.yaml
+++ b/collections/metabolomics/v2/tools/r-4-1-2.yaml
@@ -9,5 +9,8 @@ derived_from:
 source_repos:
 - plyush1993/OUKS
 schema_version: 0.2.0
+license_tier: open
+license: GPL-3.0
+license_detection: github-api
 techniques:
 - LC-MS
diff --git a/collections/metabolomics/v2/tools/r-base-stats-tidyverse-or-similar.yaml b/collections/metabolomics/v2/tools/r-base-stats-tidyverse-or-similar.yaml
index 1f4b19050..2fc8e6076 100644
--- a/collections/metabolomics/v2/tools/r-base-stats-tidyverse-or-similar.yaml
+++ b/collections/metabolomics/v2/tools/r-base-stats-tidyverse-or-similar.yaml
@@ -9,3 +9,6 @@ derived_from:
 source_repos:
 - chopralab/CLAW
 schema_version: 0.2.0
+license_tier: open
+license: GPL-3.0
+license_detection: license-file
diff --git a/collections/metabolomics/v2/tools/r-gui.yaml b/collections/metabolomics/v2/tools/r-gui.yaml
index bfb4f36da..b8a4f9941 100644
--- a/collections/metabolomics/v2/tools/r-gui.yaml
+++ b/collections/metabolomics/v2/tools/r-gui.yaml
@@ -9,5 +9,8 @@ derived_from:
 source_repos:
 - YuJenL/SMART
 schema_version: 0.2.0
+license_tier: open
+license: GPL-3.0
+license_detection: github-api
 techniques:
 - mass-spectrometry
diff --git a/collections/metabolomics/v2/tools/r-or-language-used-by-pairkat-scripts.yaml b/collections/metabolomics/v2/tools/r-or-language-used-by-pairkat-scripts.yaml
index 2ff47a233..0e8b22d0c 100644
--- a/collections/metabolomics/v2/tools/r-or-language-used-by-pairkat-scripts.yaml
+++ b/collections/metabolomics/v2/tools/r-or-language-used-by-pairkat-scripts.yaml
@@ -9,3 +9,6 @@ derived_from:
 source_repos:
 - CharlieCarpenter/PaIRKAT
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
diff --git a/collections/metabolomics/v2/tools/r-package-amanida.yaml b/collections/metabolomics/v2/tools/r-package-amanida.yaml
index 798c48b6e..c8517abb1 100644
--- a/collections/metabolomics/v2/tools/r-package-amanida.yaml
+++ b/collections/metabolomics/v2/tools/r-package-amanida.yaml
@@ -9,5 +9,8 @@ derived_from:
 source_repos:
 - mariallr/easy-amanida
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - mass-spectrometry
diff --git a/collections/metabolomics/v2/tools/r-shiny.yaml b/collections/metabolomics/v2/tools/r-shiny.yaml
index a6faabb66..c2ce3df1d 100644
--- a/collections/metabolomics/v2/tools/r-shiny.yaml
+++ b/collections/metabolomics/v2/tools/r-shiny.yaml
@@ -14,6 +14,9 @@ source_repos:
 - Lab-XUE/EISA-EXPOSOME
 - databio2022/GraphBio
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/r-vegan-package.yaml b/collections/metabolomics/v2/tools/r-vegan-package.yaml
index 6e0b47d22..f44b85761 100644
--- a/collections/metabolomics/v2/tools/r-vegan-package.yaml
+++ b/collections/metabolomics/v2/tools/r-vegan-package.yaml
@@ -6,6 +6,9 @@ derived_from:
 - doi: 10.1186/s40168-023-01476-3
   title: MetaboDirect
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
 techniques:
 - LC-MS
 - direct-infusion-MS
diff --git a/collections/metabolomics/v2/tools/r-version-or-higher.yaml b/collections/metabolomics/v2/tools/r-version-or-higher.yaml
index cc6762f69..8100a3953 100644
--- a/collections/metabolomics/v2/tools/r-version-or-higher.yaml
+++ b/collections/metabolomics/v2/tools/r-version-or-higher.yaml
@@ -6,6 +6,9 @@ derived_from:
 - doi: 10.1021/acs.analchem.1c03032
   title: Automated Annotation of Untargeted All-Ion Fragmentation LC–MS Metabolomics Data with MetaboAnnotatoR
 schema_version: 0.2.0
+license_tier: open
+license: GPL-3.0
+license_detection: github-api
 techniques:
 - LC-MS
 - CE-MS
diff --git a/collections/metabolomics/v2/tools/r.yaml b/collections/metabolomics/v2/tools/r.yaml
index e1a79f74c..9f7221261 100644
--- a/collections/metabolomics/v2/tools/r.yaml
+++ b/collections/metabolomics/v2/tools/r.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - LargeMetabo/LargeMetabo
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/ramclustr.yaml b/collections/metabolomics/v2/tools/ramclustr.yaml
index d55c6e63d..e82368f8b 100644
--- a/collections/metabolomics/v2/tools/ramclustr.yaml
+++ b/collections/metabolomics/v2/tools/ramclustr.yaml
@@ -14,6 +14,9 @@ derived_from:
 source_repos:
 - cbroeckl/RAMClustR
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/random-forest-regression.yaml b/collections/metabolomics/v2/tools/random-forest-regression.yaml
index 241adbe70..735abb7c2 100644
--- a/collections/metabolomics/v2/tools/random-forest-regression.yaml
+++ b/collections/metabolomics/v2/tools/random-forest-regression.yaml
@@ -6,3 +6,6 @@ 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
diff --git a/collections/metabolomics/v2/tools/random-forest.yaml b/collections/metabolomics/v2/tools/random-forest.yaml
index c3360e19b..e08ad370a 100644
--- a/collections/metabolomics/v2/tools/random-forest.yaml
+++ b/collections/metabolomics/v2/tools/random-forest.yaml
@@ -6,6 +6,9 @@ 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
diff --git a/collections/metabolomics/v2/tools/random-missing-value-augmentation.yaml b/collections/metabolomics/v2/tools/random-missing-value-augmentation.yaml
index 264a40c99..3c84f29c2 100644
--- a/collections/metabolomics/v2/tools/random-missing-value-augmentation.yaml
+++ b/collections/metabolomics/v2/tools/random-missing-value-augmentation.yaml
@@ -6,5 +6,8 @@ derived_from:
 - doi: 10.1021/acs.analchem.3c05002
   title: deepion
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - MS-imaging
diff --git a/collections/metabolomics/v2/tools/randomforest.yaml b/collections/metabolomics/v2/tools/randomforest.yaml
index ea59cbe3f..00c81e7de 100644
--- a/collections/metabolomics/v2/tools/randomforest.yaml
+++ b/collections/metabolomics/v2/tools/randomforest.yaml
@@ -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:
 - mass-spectrometry
diff --git a/collections/metabolomics/v2/tools/rankprod.yaml b/collections/metabolomics/v2/tools/rankprod.yaml
index 7acab6af4..977990720 100644
--- a/collections/metabolomics/v2/tools/rankprod.yaml
+++ b/collections/metabolomics/v2/tools/rankprod.yaml
@@ -9,3 +9,6 @@ derived_from:
 source_repos:
 - ASAGlab/MOI--An-integrated-solution-for-omics-analyses
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
diff --git a/collections/metabolomics/v2/tools/rapidmass.yaml b/collections/metabolomics/v2/tools/rapidmass.yaml
index 496058a03..ef07baf1f 100644
--- a/collections/metabolomics/v2/tools/rapidmass.yaml
+++ b/collections/metabolomics/v2/tools/rapidmass.yaml
@@ -10,6 +10,9 @@ 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
diff --git a/collections/metabolomics/v2/tools/raw-file-uploader-rtklab-byu-raw-file-uploader.yaml b/collections/metabolomics/v2/tools/raw-file-uploader-rtklab-byu-raw-file-uploader.yaml
index 7896dfcbf..e9aa468fb 100644
--- a/collections/metabolomics/v2/tools/raw-file-uploader-rtklab-byu-raw-file-uploader.yaml
+++ b/collections/metabolomics/v2/tools/raw-file-uploader-rtklab-byu-raw-file-uploader.yaml
@@ -9,5 +9,8 @@ derived_from:
 source_repos:
 - RTKlab-BYU/MSConnect
 schema_version: 0.2.0
+license_tier: open
+license: Apache-2.0
+license_detection: github-api
 techniques:
 - mass-spectrometry
diff --git a/collections/metabolomics/v2/tools/rawfilereader.yaml b/collections/metabolomics/v2/tools/rawfilereader.yaml
index 5af1a85a9..f91f09713 100644
--- a/collections/metabolomics/v2/tools/rawfilereader.yaml
+++ b/collections/metabolomics/v2/tools/rawfilereader.yaml
@@ -14,6 +14,9 @@ derived_from:
 source_repos:
 - fgcz/rawrr
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - ion-mobility-MS
diff --git a/collections/metabolomics/v2/tools/rawrr.yaml b/collections/metabolomics/v2/tools/rawrr.yaml
index 068bfc0e2..23ca58f8d 100644
--- a/collections/metabolomics/v2/tools/rawrr.yaml
+++ b/collections/metabolomics/v2/tools/rawrr.yaml
@@ -14,6 +14,9 @@ derived_from:
 source_repos:
 - fgcz/rawrr
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - ion-mobility-MS
diff --git a/collections/metabolomics/v2/tools/raxport.yaml b/collections/metabolomics/v2/tools/raxport.yaml
index 917119e10..552071e78 100644
--- a/collections/metabolomics/v2/tools/raxport.yaml
+++ b/collections/metabolomics/v2/tools/raxport.yaml
@@ -9,6 +9,9 @@ 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
 - mass-spectrometry
diff --git a/collections/metabolomics/v2/tools/rcdk.yaml b/collections/metabolomics/v2/tools/rcdk.yaml
index a85952a66..e9fe9304a 100644
--- a/collections/metabolomics/v2/tools/rcdk.yaml
+++ b/collections/metabolomics/v2/tools/rcdk.yaml
@@ -9,5 +9,8 @@ derived_from:
 source_repos:
 - michaelwitting/RepoRT
 schema_version: 0.2.0
+license_tier: open
+license: CC-BY-SA-4.0
+license_detection: github-api
 techniques:
 - LC-MS
diff --git a/collections/metabolomics/v2/tools/rdkit-2020-03-4.yaml b/collections/metabolomics/v2/tools/rdkit-2020-03-4.yaml
index 9cacfbb22..60bf2e2bd 100644
--- a/collections/metabolomics/v2/tools/rdkit-2020-03-4.yaml
+++ b/collections/metabolomics/v2/tools/rdkit-2020-03-4.yaml
@@ -9,3 +9,6 @@ derived_from:
 source_repos:
 - chensaian/TransG-Net
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
diff --git a/collections/metabolomics/v2/tools/rdkit-or-similar-cheminformatics-library-for-molecular-fingerprint-computation.yaml b/collections/metabolomics/v2/tools/rdkit-or-similar-cheminformatics-library-for-molecular-fingerprint-computation.yaml
index 3fc540eb5..f392d729c 100644
--- a/collections/metabolomics/v2/tools/rdkit-or-similar-cheminformatics-library-for-molecular-fingerprint-computation.yaml
+++ b/collections/metabolomics/v2/tools/rdkit-or-similar-cheminformatics-library-for-molecular-fingerprint-computation.yaml
@@ -6,3 +6,6 @@ derived_from:
 - doi: 10.1021/acs.analchem.3c05019
   title: 'PS<sup>2</sup>MS: A Deep Learning-Based Prediction System for Identifying New Psychoactive Substances Using Mass Spectrometry'
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
diff --git a/collections/metabolomics/v2/tools/rdkit-pypi.yaml b/collections/metabolomics/v2/tools/rdkit-pypi.yaml
index fb67af883..ee4ca1b46 100644
--- a/collections/metabolomics/v2/tools/rdkit-pypi.yaml
+++ b/collections/metabolomics/v2/tools/rdkit-pypi.yaml
@@ -10,5 +10,8 @@ derived_from:
 source_repos:
 - 01dadada/RT-Transformer
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
diff --git a/collections/metabolomics/v2/tools/rdkit.yaml b/collections/metabolomics/v2/tools/rdkit.yaml
index 708445bf7..84bfc2853 100644
--- a/collections/metabolomics/v2/tools/rdkit.yaml
+++ b/collections/metabolomics/v2/tools/rdkit.yaml
@@ -94,6 +94,9 @@ source_repos:
 - zhanghailiangcsu/MWFormer
 - zmahnoor14/MAW
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/reactiveextensions.yaml b/collections/metabolomics/v2/tools/reactiveextensions.yaml
index 4227a7033..ae87abf44 100644
--- a/collections/metabolomics/v2/tools/reactiveextensions.yaml
+++ b/collections/metabolomics/v2/tools/reactiveextensions.yaml
@@ -9,5 +9,8 @@ derived_from:
 source_repos:
 - systemsomicslab/MsdialWorkbench
 schema_version: 0.2.0
+license_tier: open
+license: LGPL-3.0
+license_detection: readme-llm
 techniques:
 - mass-spectrometry
diff --git a/collections/metabolomics/v2/tools/reactiveproperty.yaml b/collections/metabolomics/v2/tools/reactiveproperty.yaml
index be885a2d8..eff3b6376 100644
--- a/collections/metabolomics/v2/tools/reactiveproperty.yaml
+++ b/collections/metabolomics/v2/tools/reactiveproperty.yaml
@@ -9,5 +9,8 @@ derived_from:
 source_repos:
 - systemsomicslab/MsdialWorkbench
 schema_version: 0.2.0
+license_tier: open
+license: LGPL-3.0
+license_detection: readme-llm
 techniques:
 - mass-spectrometry
diff --git a/collections/metabolomics/v2/tools/readr.yaml b/collections/metabolomics/v2/tools/readr.yaml
index 321892a96..9257ee927 100644
--- a/collections/metabolomics/v2/tools/readr.yaml
+++ b/collections/metabolomics/v2/tools/readr.yaml
@@ -17,6 +17,9 @@ source_repos:
 - biodatalab/enrichmet
 - kilgain/MassSpec
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: file-present-unclassified
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/readxl.yaml b/collections/metabolomics/v2/tools/readxl.yaml
index 3d836ab38..9e94f1ebd 100644
--- a/collections/metabolomics/v2/tools/readxl.yaml
+++ b/collections/metabolomics/v2/tools/readxl.yaml
@@ -13,6 +13,9 @@ source_repos:
 - LeaveMeNotTonight/CMDN
 - biodatalab/enrichmet
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - CE-MS
diff --git a/collections/metabolomics/v2/tools/redis.yaml b/collections/metabolomics/v2/tools/redis.yaml
index 3cfeaac52..78a16ab27 100644
--- a/collections/metabolomics/v2/tools/redis.yaml
+++ b/collections/metabolomics/v2/tools/redis.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - OpenMS/OpenMS
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: file-present-unclassified
 techniques:
 - LC-MS
 - MS-imaging
diff --git a/collections/metabolomics/v2/tools/redu.yaml b/collections/metabolomics/v2/tools/redu.yaml
index 198e3afd2..0ef268851 100644
--- a/collections/metabolomics/v2/tools/redu.yaml
+++ b/collections/metabolomics/v2/tools/redu.yaml
@@ -10,6 +10,9 @@ derived_from:
 source_repos:
 - mwang87/ReDU-MS2-Documentation
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - CE-MS
diff --git a/collections/metabolomics/v2/tools/relu-activation.yaml b/collections/metabolomics/v2/tools/relu-activation.yaml
index 847ee3aac..06a0f2f33 100644
--- a/collections/metabolomics/v2/tools/relu-activation.yaml
+++ b/collections/metabolomics/v2/tools/relu-activation.yaml
@@ -6,6 +6,9 @@ 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
 - NMR
diff --git a/collections/metabolomics/v2/tools/reshape2.yaml b/collections/metabolomics/v2/tools/reshape2.yaml
index 26c7994da..9c4670be3 100644
--- a/collections/metabolomics/v2/tools/reshape2.yaml
+++ b/collections/metabolomics/v2/tools/reshape2.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - LeaveMeNotTonight/CMDN
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - CE-MS
diff --git a/collections/metabolomics/v2/tools/resnet18.yaml b/collections/metabolomics/v2/tools/resnet18.yaml
index 5b0515b53..ac6418803 100644
--- a/collections/metabolomics/v2/tools/resnet18.yaml
+++ b/collections/metabolomics/v2/tools/resnet18.yaml
@@ -7,5 +7,8 @@ derived_from:
 - doi: 10.1021/acs.analchem.3c05002
   title: deepion
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - MS-imaging
diff --git a/collections/metabolomics/v2/tools/rest-client-gem.yaml b/collections/metabolomics/v2/tools/rest-client-gem.yaml
index ede89c293..ec3cbdb14 100644
--- a/collections/metabolomics/v2/tools/rest-client-gem.yaml
+++ b/collections/metabolomics/v2/tools/rest-client-gem.yaml
@@ -9,3 +9,6 @@ derived_from:
 source_repos:
 - https://bitbucket.org/wishartlab/classyfire_api.git
 schema_version: 0.2.0
+license_tier: noncommercial
+license: Academic use free; commercial use/redistribution by permission of the authors (Wishart Lab).
+license_detection: null
diff --git a/collections/metabolomics/v2/tools/rest-client.yaml b/collections/metabolomics/v2/tools/rest-client.yaml
index 2e0358f15..344321a64 100644
--- a/collections/metabolomics/v2/tools/rest-client.yaml
+++ b/collections/metabolomics/v2/tools/rest-client.yaml
@@ -10,3 +10,6 @@ derived_from:
 source_repos:
 - https://bitbucket.org/wishartlab/classyfire_api.git
 schema_version: 0.2.0
+license_tier: noncommercial
+license: Academic use free; commercial use/redistribution by permission of the authors (Wishart Lab).
+license_detection: null
diff --git a/collections/metabolomics/v2/tools/resultsloader.yaml b/collections/metabolomics/v2/tools/resultsloader.yaml
index 9f1622a97..2dd14899c 100644
--- a/collections/metabolomics/v2/tools/resultsloader.yaml
+++ b/collections/metabolomics/v2/tools/resultsloader.yaml
@@ -9,5 +9,8 @@ derived_from:
 source_repos:
 - Roestlab/massdash
 schema_version: 0.2.0
+license_tier: open
+license: BSD-3-Clause
+license_detection: github-api
 techniques:
 - LC-MS
diff --git a/collections/metabolomics/v2/tools/reticulate.yaml b/collections/metabolomics/v2/tools/reticulate.yaml
index eb122162e..2194cfdb2 100644
--- a/collections/metabolomics/v2/tools/reticulate.yaml
+++ b/collections/metabolomics/v2/tools/reticulate.yaml
@@ -10,6 +10,9 @@ derived_from:
 source_repos:
 - slfan2013/SERDA
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - mass-spectrometry
diff --git a/collections/metabolomics/v2/tools/retip.yaml b/collections/metabolomics/v2/tools/retip.yaml
index b0953a513..ceeb34762 100644
--- a/collections/metabolomics/v2/tools/retip.yaml
+++ b/collections/metabolomics/v2/tools/retip.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - oloBion/Retip
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/reverse-search.yaml b/collections/metabolomics/v2/tools/reverse-search.yaml
index 0eea87087..1d79ca6a8 100644
--- a/collections/metabolomics/v2/tools/reverse-search.yaml
+++ b/collections/metabolomics/v2/tools/reverse-search.yaml
@@ -9,5 +9,8 @@ derived_from:
 source_repos:
 - Philipbear/reverse_search
 schema_version: 0.2.0
+license_tier: open
+license: Apache-2.0
+license_detection: github-api
 techniques:
 - LC-MS
diff --git a/collections/metabolomics/v2/tools/rgcxgc.yaml b/collections/metabolomics/v2/tools/rgcxgc.yaml
index 4496eaea5..f0de94771 100644
--- a/collections/metabolomics/v2/tools/rgcxgc.yaml
+++ b/collections/metabolomics/v2/tools/rgcxgc.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - DanielQuiroz97/RGCxGC
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/rhdf5.yaml b/collections/metabolomics/v2/tools/rhdf5.yaml
index 17d923fa1..6a038459d 100644
--- a/collections/metabolomics/v2/tools/rhdf5.yaml
+++ b/collections/metabolomics/v2/tools/rhdf5.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - PNNL-m-q/mza
 schema_version: 0.2.0
+license_tier: open
+license: BSD-2-Clause
+license_detection: github-api
 techniques:
 - LC-MS
 - ion-mobility-MS
diff --git a/collections/metabolomics/v2/tools/ricoderks-qcomics.yaml b/collections/metabolomics/v2/tools/ricoderks-qcomics.yaml
index 879559003..c0845a4e4 100644
--- a/collections/metabolomics/v2/tools/ricoderks-qcomics.yaml
+++ b/collections/metabolomics/v2/tools/ricoderks-qcomics.yaml
@@ -6,3 +6,6 @@ derived_from:
 - doi: 10.1021/acs.analchem.3c03660
   title: QComics
 schema_version: 0.2.0
+license_tier: open
+license: GPL-3.0
+license_detection: github-api
diff --git a/collections/metabolomics/v2/tools/riken.yaml b/collections/metabolomics/v2/tools/riken.yaml
index 6c9ddf0e3..1a9402471 100644
--- a/collections/metabolomics/v2/tools/riken.yaml
+++ b/collections/metabolomics/v2/tools/riken.yaml
@@ -7,6 +7,9 @@ derived_from:
 - doi: 10.1021/acs.analchem.2c05389
   title: mspcompiler
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: file-present-unclassified
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/rjson.yaml b/collections/metabolomics/v2/tools/rjson.yaml
index 18a682582..1f649b6f3 100644
--- a/collections/metabolomics/v2/tools/rjson.yaml
+++ b/collections/metabolomics/v2/tools/rjson.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - fgcz/rawrr
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - mass-spectrometry
diff --git a/collections/metabolomics/v2/tools/rmarkdown.yaml b/collections/metabolomics/v2/tools/rmarkdown.yaml
index fa013ac6f..94583ef70 100644
--- a/collections/metabolomics/v2/tools/rmarkdown.yaml
+++ b/collections/metabolomics/v2/tools/rmarkdown.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - MRCIEU/metaboprep
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: file-present-unclassified
 techniques:
 - LC-MS
 - ion-mobility-MS
diff --git a/collections/metabolomics/v2/tools/rmsi.yaml b/collections/metabolomics/v2/tools/rmsi.yaml
index db39c1d2d..5e3627d64 100644
--- a/collections/metabolomics/v2/tools/rmsi.yaml
+++ b/collections/metabolomics/v2/tools/rmsi.yaml
@@ -7,6 +7,9 @@ derived_from:
 - doi: 10.1186/s13321-020-00449-0
   title: 'rMSIcleanup: an open-source tool for matrix-related peak annotation in mass spectrometry imaging and its application to silver-assisted laser desorption/ionization'
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - MS-imaging
 - NMR
diff --git a/collections/metabolomics/v2/tools/rmsicleanup.yaml b/collections/metabolomics/v2/tools/rmsicleanup.yaml
index 527491490..02cb22202 100644
--- a/collections/metabolomics/v2/tools/rmsicleanup.yaml
+++ b/collections/metabolomics/v2/tools/rmsicleanup.yaml
@@ -6,6 +6,9 @@ derived_from:
 - doi: 10.1186/s13321-020-00449-0
   title: 'rMSIcleanup: an open-source tool for matrix-related peak annotation in mass spectrometry imaging and its application to silver-assisted laser desorption/ionization'
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - MS-imaging
 - NMR
diff --git a/collections/metabolomics/v2/tools/rmsiproc.yaml b/collections/metabolomics/v2/tools/rmsiproc.yaml
index 080fcf6aa..76b739ad6 100644
--- a/collections/metabolomics/v2/tools/rmsiproc.yaml
+++ b/collections/metabolomics/v2/tools/rmsiproc.yaml
@@ -7,6 +7,9 @@ derived_from:
 - doi: 10.1186/s13321-020-00449-0
   title: 'rMSIcleanup: an open-source tool for matrix-related peak annotation in mass spectrometry imaging and its application to silver-assisted laser desorption/ionization'
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - MS-imaging
 - NMR
diff --git a/collections/metabolomics/v2/tools/roasmi.yaml b/collections/metabolomics/v2/tools/roasmi.yaml
index 13917c45a..48d9f11a6 100644
--- a/collections/metabolomics/v2/tools/roasmi.yaml
+++ b/collections/metabolomics/v2/tools/roasmi.yaml
@@ -9,5 +9,8 @@ derived_from:
 source_repos:
 - FangYuan717/ROASMI
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
 techniques:
 - LC-MS
diff --git a/collections/metabolomics/v2/tools/roipeaks.yaml b/collections/metabolomics/v2/tools/roipeaks.yaml
index 8fdaea396..8cb29db8c 100644
--- a/collections/metabolomics/v2/tools/roipeaks.yaml
+++ b/collections/metabolomics/v2/tools/roipeaks.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - AdrianHaun/AriumMS
 schema_version: 0.2.0
+license_tier: open
+license: BSD-3-Clause
+license_detection: github-api
 techniques:
 - LC-MS
 - CE-MS
diff --git a/collections/metabolomics/v2/tools/rpref.yaml b/collections/metabolomics/v2/tools/rpref.yaml
index 0afbd8d6b..4d73cb5c8 100644
--- a/collections/metabolomics/v2/tools/rpref.yaml
+++ b/collections/metabolomics/v2/tools/rpref.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - BiosystemEngineeringLab-IITB/dures
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: file-present-unclassified
 techniques:
 - LC-MS
 - CE-MS
diff --git a/collections/metabolomics/v2/tools/rq-redis-queue.yaml b/collections/metabolomics/v2/tools/rq-redis-queue.yaml
index 6169bcc69..90c6f643b 100644
--- a/collections/metabolomics/v2/tools/rq-redis-queue.yaml
+++ b/collections/metabolomics/v2/tools/rq-redis-queue.yaml
@@ -9,3 +9,6 @@ derived_from:
 source_repos:
 - OpenMS/OpenMS
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: file-present-unclassified
diff --git a/collections/metabolomics/v2/tools/rstudio.yaml b/collections/metabolomics/v2/tools/rstudio.yaml
index 0b83f3441..1ba383689 100644
--- a/collections/metabolomics/v2/tools/rstudio.yaml
+++ b/collections/metabolomics/v2/tools/rstudio.yaml
@@ -17,6 +17,9 @@ source_repos:
 - HuanLab/ISFrag
 - metabolomicstats/NormalizeMets
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
 techniques:
 - LC-MS
 - ion-mobility-MS
diff --git a/collections/metabolomics/v2/tools/rtklab-byu-proteomics-data-processor.yaml b/collections/metabolomics/v2/tools/rtklab-byu-proteomics-data-processor.yaml
index 9e1f56045..c1ddffba8 100644
--- a/collections/metabolomics/v2/tools/rtklab-byu-proteomics-data-processor.yaml
+++ b/collections/metabolomics/v2/tools/rtklab-byu-proteomics-data-processor.yaml
@@ -9,5 +9,8 @@ derived_from:
 source_repos:
 - RTKlab-BYU/MSConnect
 schema_version: 0.2.0
+license_tier: open
+license: Apache-2.0
+license_detection: github-api
 techniques:
 - mass-spectrometry
diff --git a/collections/metabolomics/v2/tools/rtklab-byu-raw-file-uploader.yaml b/collections/metabolomics/v2/tools/rtklab-byu-raw-file-uploader.yaml
index c1f7c0c41..a762bb51b 100644
--- a/collections/metabolomics/v2/tools/rtklab-byu-raw-file-uploader.yaml
+++ b/collections/metabolomics/v2/tools/rtklab-byu-raw-file-uploader.yaml
@@ -9,5 +9,8 @@ derived_from:
 source_repos:
 - RTKlab-BYU/MSConnect
 schema_version: 0.2.0
+license_tier: open
+license: Apache-2.0
+license_detection: github-api
 techniques:
 - mass-spectrometry
diff --git a/collections/metabolomics/v2/tools/ruby.yaml b/collections/metabolomics/v2/tools/ruby.yaml
index c7536252f..6f0c18cf7 100644
--- a/collections/metabolomics/v2/tools/ruby.yaml
+++ b/collections/metabolomics/v2/tools/ruby.yaml
@@ -9,3 +9,6 @@ derived_from:
 source_repos:
 - https://bitbucket.org/wishartlab/classyfire_api.git
 schema_version: 0.2.0
+license_tier: noncommercial
+license: Academic use free; commercial use/redistribution by permission of the authors (Wishart Lab).
+license_detection: null
diff --git a/collections/metabolomics/v2/tools/rust.yaml b/collections/metabolomics/v2/tools/rust.yaml
index c790df5e2..3f442822b 100644
--- a/collections/metabolomics/v2/tools/rust.yaml
+++ b/collections/metabolomics/v2/tools/rust.yaml
@@ -6,6 +6,9 @@ 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
diff --git a/collections/metabolomics/v2/tools/ruv-iii.yaml b/collections/metabolomics/v2/tools/ruv-iii.yaml
index 051045f8a..b7053d941 100644
--- a/collections/metabolomics/v2/tools/ruv-iii.yaml
+++ b/collections/metabolomics/v2/tools/ruv-iii.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - SydneyBioX/hRUV
 schema_version: 0.2.0
+license_tier: open
+license: GPL-3.0
+license_detection: github-api
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/s4vectors.yaml b/collections/metabolomics/v2/tools/s4vectors.yaml
index 906b86d57..a3f5d2110 100644
--- a/collections/metabolomics/v2/tools/s4vectors.yaml
+++ b/collections/metabolomics/v2/tools/s4vectors.yaml
@@ -16,6 +16,9 @@ source_repos:
 - BiosystemEngineeringLab-IITB/dures
 - rformassspectrometry/Spectra
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: file-present-unclassified
 techniques:
 - LC-MS
 - mass-spectrometry
diff --git a/collections/metabolomics/v2/tools/safari.yaml b/collections/metabolomics/v2/tools/safari.yaml
index 6eaeb76d1..9309688dd 100644
--- a/collections/metabolomics/v2/tools/safari.yaml
+++ b/collections/metabolomics/v2/tools/safari.yaml
@@ -9,5 +9,8 @@ derived_from:
 source_repos:
 - lidawei1975/colmarvista
 schema_version: 0.2.0
+license_tier: open
+license: GPL-3.0
+license_detection: github-api
 techniques:
 - NMR
diff --git a/collections/metabolomics/v2/tools/salmon.yaml b/collections/metabolomics/v2/tools/salmon.yaml
index bae84af88..08c2aae0d 100644
--- a/collections/metabolomics/v2/tools/salmon.yaml
+++ b/collections/metabolomics/v2/tools/salmon.yaml
@@ -10,6 +10,9 @@ derived_from:
 source_repos:
 - ASAGlab/MOI--An-integrated-solution-for-omics-analyses
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
 techniques:
 - LC-MS
 - ion-mobility-MS
diff --git a/collections/metabolomics/v2/tools/sand.yaml b/collections/metabolomics/v2/tools/sand.yaml
index e33b53c59..3e22e81ef 100644
--- a/collections/metabolomics/v2/tools/sand.yaml
+++ b/collections/metabolomics/v2/tools/sand.yaml
@@ -9,5 +9,8 @@ derived_from:
 source_repos:
 - edisonomics/SAND
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
 techniques:
 - NMR
diff --git a/collections/metabolomics/v2/tools/scannotation.yaml b/collections/metabolomics/v2/tools/scannotation.yaml
index 2800352fd..9876c10d1 100644
--- a/collections/metabolomics/v2/tools/scannotation.yaml
+++ b/collections/metabolomics/v2/tools/scannotation.yaml
@@ -9,5 +9,8 @@ derived_from:
 source_repos:
 - scannotation/Scannotation_software
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: license-file
 techniques:
 - LC-MS
diff --git a/collections/metabolomics/v2/tools/scanpy.yaml b/collections/metabolomics/v2/tools/scanpy.yaml
index 77b698c4b..2d21e3af1 100644
--- a/collections/metabolomics/v2/tools/scanpy.yaml
+++ b/collections/metabolomics/v2/tools/scanpy.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - bioinfo-ibms-pumc/SMART
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - direct-infusion-MS
diff --git a/collections/metabolomics/v2/tools/scarf.yaml b/collections/metabolomics/v2/tools/scarf.yaml
index 55ae096b3..0eabaacc0 100644
--- a/collections/metabolomics/v2/tools/scarf.yaml
+++ b/collections/metabolomics/v2/tools/scarf.yaml
@@ -6,6 +6,9 @@ derived_from:
 - doi: 10.1021/acs.jcim.3c01082
   title: 'MIST-CF: Chemical Formula Inference from Tandem Mass Spectra'
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/scfba.yaml b/collections/metabolomics/v2/tools/scfba.yaml
index a4d49f59e..a49dc023a 100644
--- a/collections/metabolomics/v2/tools/scfba.yaml
+++ b/collections/metabolomics/v2/tools/scfba.yaml
@@ -7,5 +7,8 @@ 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
diff --git a/collections/metabolomics/v2/tools/sciex-multiquant-v3-0-3.yaml b/collections/metabolomics/v2/tools/sciex-multiquant-v3-0-3.yaml
index 86d19db39..b5d190118 100644
--- a/collections/metabolomics/v2/tools/sciex-multiquant-v3-0-3.yaml
+++ b/collections/metabolomics/v2/tools/sciex-multiquant-v3-0-3.yaml
@@ -7,5 +7,8 @@ derived_from:
 - doi: 10.1021/acs.analchem.3c03660
   title: QComics
 schema_version: 0.2.0
+license_tier: open
+license: GPL-3.0
+license_detection: github-api
 techniques:
 - mass-spectrometry
diff --git a/collections/metabolomics/v2/tools/sciex-multiquant.yaml b/collections/metabolomics/v2/tools/sciex-multiquant.yaml
index 00a11cded..d82a77a26 100644
--- a/collections/metabolomics/v2/tools/sciex-multiquant.yaml
+++ b/collections/metabolomics/v2/tools/sciex-multiquant.yaml
@@ -7,6 +7,9 @@ derived_from:
 - doi: 10.1021/acs.analchem.3c03660
   title: QComics
 schema_version: 0.2.0
+license_tier: open
+license: GPL-3.0
+license_detection: github-api
 techniques:
 - LC-MS
 - mass-spectrometry
diff --git a/collections/metabolomics/v2/tools/sciex-q-tof-uhplc-hrms-ms.yaml b/collections/metabolomics/v2/tools/sciex-q-tof-uhplc-hrms-ms.yaml
index ce8926371..39adef4b8 100644
--- a/collections/metabolomics/v2/tools/sciex-q-tof-uhplc-hrms-ms.yaml
+++ b/collections/metabolomics/v2/tools/sciex-q-tof-uhplc-hrms-ms.yaml
@@ -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
diff --git a/collections/metabolomics/v2/tools/scikit-bio.yaml b/collections/metabolomics/v2/tools/scikit-bio.yaml
index 80b026b99..d47a0d5fc 100644
--- a/collections/metabolomics/v2/tools/scikit-bio.yaml
+++ b/collections/metabolomics/v2/tools/scikit-bio.yaml
@@ -6,6 +6,9 @@ derived_from:
 - doi: 10.3389/fbinf.2022.842964
   title: memo
 schema_version: 0.2.0
+license_tier: open
+license: GPL-3.0
+license_detection: github-api
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/scikit-learn-0-23-2.yaml b/collections/metabolomics/v2/tools/scikit-learn-0-23-2.yaml
index b0e02cc4a..fefd9c3ba 100644
--- a/collections/metabolomics/v2/tools/scikit-learn-0-23-2.yaml
+++ b/collections/metabolomics/v2/tools/scikit-learn-0-23-2.yaml
@@ -9,5 +9,8 @@ derived_from:
 source_repos:
 - wabdelmoula/massNet
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - MS-imaging
diff --git a/collections/metabolomics/v2/tools/scikit-learn-mlpregressor.yaml b/collections/metabolomics/v2/tools/scikit-learn-mlpregressor.yaml
index 9d91fd0fe..80b185ff3 100644
--- a/collections/metabolomics/v2/tools/scikit-learn-mlpregressor.yaml
+++ b/collections/metabolomics/v2/tools/scikit-learn-mlpregressor.yaml
@@ -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
 - NMR
diff --git a/collections/metabolomics/v2/tools/scikit-learn-nearestneighbors-for-knn-index-construction.yaml b/collections/metabolomics/v2/tools/scikit-learn-nearestneighbors-for-knn-index-construction.yaml
index 182edf675..df3723343 100644
--- a/collections/metabolomics/v2/tools/scikit-learn-nearestneighbors-for-knn-index-construction.yaml
+++ b/collections/metabolomics/v2/tools/scikit-learn-nearestneighbors-for-knn-index-construction.yaml
@@ -9,3 +9,6 @@ derived_from:
 source_repos:
 - WanluLiuLab/SpatialMETA
 schema_version: 0.2.0
+license_tier: open
+license: BSD-3-Clause
+license_detection: github-api
diff --git a/collections/metabolomics/v2/tools/scikit-learn-python.yaml b/collections/metabolomics/v2/tools/scikit-learn-python.yaml
index 0f6ea2557..1e7e7b677 100644
--- a/collections/metabolomics/v2/tools/scikit-learn-python.yaml
+++ b/collections/metabolomics/v2/tools/scikit-learn-python.yaml
@@ -6,6 +6,9 @@ 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
diff --git a/collections/metabolomics/v2/tools/scikit-learn.yaml b/collections/metabolomics/v2/tools/scikit-learn.yaml
index 1be83dd11..3d67d733f 100644
--- a/collections/metabolomics/v2/tools/scikit-learn.yaml
+++ b/collections/metabolomics/v2/tools/scikit-learn.yaml
@@ -41,6 +41,9 @@ source_repos:
 - huaxuyu/bago
 - ressomlab/MetFID
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/scipy-1-0-0.yaml b/collections/metabolomics/v2/tools/scipy-1-0-0.yaml
index 8bdb13833..5551eda08 100644
--- a/collections/metabolomics/v2/tools/scipy-1-0-0.yaml
+++ b/collections/metabolomics/v2/tools/scipy-1-0-0.yaml
@@ -9,5 +9,8 @@ derived_from:
 source_repos:
 - wabdelmoula/massNet
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - MS-imaging
diff --git a/collections/metabolomics/v2/tools/scipy-scipy-stats-wasserstein-distance-or-scipy-optimize-linprog-for-optimal-transport.yaml b/collections/metabolomics/v2/tools/scipy-scipy-stats-wasserstein-distance-or-scipy-optimize-linprog-for-optimal-transport.yaml
index 8cad26b24..53ce21dc0 100644
--- a/collections/metabolomics/v2/tools/scipy-scipy-stats-wasserstein-distance-or-scipy-optimize-linprog-for-optimal-transport.yaml
+++ b/collections/metabolomics/v2/tools/scipy-scipy-stats-wasserstein-distance-or-scipy-optimize-linprog-for-optimal-transport.yaml
@@ -9,5 +9,8 @@ derived_from:
 source_repos:
 - GeoMetabolomics-ICBM/mcfNMR
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
 techniques:
 - NMR
diff --git a/collections/metabolomics/v2/tools/scipy-signal-detrend.yaml b/collections/metabolomics/v2/tools/scipy-signal-detrend.yaml
index 364d73b14..fa46dd8d2 100644
--- a/collections/metabolomics/v2/tools/scipy-signal-detrend.yaml
+++ b/collections/metabolomics/v2/tools/scipy-signal-detrend.yaml
@@ -11,6 +11,9 @@ 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
diff --git a/collections/metabolomics/v2/tools/scipy-signal-find-peaks.yaml b/collections/metabolomics/v2/tools/scipy-signal-find-peaks.yaml
index f6b76e520..2b8078644 100644
--- a/collections/metabolomics/v2/tools/scipy-signal-find-peaks.yaml
+++ b/collections/metabolomics/v2/tools/scipy-signal-find-peaks.yaml
@@ -10,6 +10,9 @@ 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
diff --git a/collections/metabolomics/v2/tools/scipy-spearman-correlation.yaml b/collections/metabolomics/v2/tools/scipy-spearman-correlation.yaml
index d6dec19bd..9a3ed783d 100644
--- a/collections/metabolomics/v2/tools/scipy-spearman-correlation.yaml
+++ b/collections/metabolomics/v2/tools/scipy-spearman-correlation.yaml
@@ -6,3 +6,6 @@ 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
diff --git a/collections/metabolomics/v2/tools/scipy.yaml b/collections/metabolomics/v2/tools/scipy.yaml
index 5a2f5f704..f312ec7d1 100644
--- a/collections/metabolomics/v2/tools/scipy.yaml
+++ b/collections/metabolomics/v2/tools/scipy.yaml
@@ -31,6 +31,9 @@ source_repos:
 - zsspython/LAGF
 - zza1211/NMRformer
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: file-present-unclassified
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/sdf-file-parser-molecular-structure-library.yaml b/collections/metabolomics/v2/tools/sdf-file-parser-molecular-structure-library.yaml
index 9967bde43..946c8e42e 100644
--- a/collections/metabolomics/v2/tools/sdf-file-parser-molecular-structure-library.yaml
+++ b/collections/metabolomics/v2/tools/sdf-file-parser-molecular-structure-library.yaml
@@ -9,5 +9,8 @@ derived_from:
 source_repos:
 - https://gitlab.com/nexs-metabolomics/projects/dna_adductomics_database.git
 schema_version: 0.2.0
+license_tier: restricted
+license: no license found (verified 2026-06-24)
+license_detection: null
 techniques:
 - mass-spectrometry
diff --git a/collections/metabolomics/v2/tools/seaborn-0-9-0.yaml b/collections/metabolomics/v2/tools/seaborn-0-9-0.yaml
index d503bf622..2815963bd 100644
--- a/collections/metabolomics/v2/tools/seaborn-0-9-0.yaml
+++ b/collections/metabolomics/v2/tools/seaborn-0-9-0.yaml
@@ -9,5 +9,8 @@ derived_from:
 source_repos:
 - wabdelmoula/massNet
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - MS-imaging
diff --git a/collections/metabolomics/v2/tools/seaborn-clustermap.yaml b/collections/metabolomics/v2/tools/seaborn-clustermap.yaml
index 195c89ef2..e9d3ac087 100644
--- a/collections/metabolomics/v2/tools/seaborn-clustermap.yaml
+++ b/collections/metabolomics/v2/tools/seaborn-clustermap.yaml
@@ -7,3 +7,6 @@ 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
diff --git a/collections/metabolomics/v2/tools/seaborn.yaml b/collections/metabolomics/v2/tools/seaborn.yaml
index 3ecca8ee3..5b86c5b29 100644
--- a/collections/metabolomics/v2/tools/seaborn.yaml
+++ b/collections/metabolomics/v2/tools/seaborn.yaml
@@ -19,6 +19,9 @@ derived_from:
 source_repos:
 - chopralab/CLAW
 schema_version: 0.2.0
+license_tier: open
+license: GPL-3.0
+license_detection: license-file
 techniques:
 - LC-MS
 - ion-mobility-MS
diff --git a/collections/metabolomics/v2/tools/semantic-release.yaml b/collections/metabolomics/v2/tools/semantic-release.yaml
index 037285d21..cdb1f0ba8 100644
--- a/collections/metabolomics/v2/tools/semantic-release.yaml
+++ b/collections/metabolomics/v2/tools/semantic-release.yaml
@@ -6,3 +6,6 @@ derived_from:
 - doi: 10.1021/acs.analchem.4c07078
   title: qc4metabolomics
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
diff --git a/collections/metabolomics/v2/tools/seurat.yaml b/collections/metabolomics/v2/tools/seurat.yaml
index 3c6e38755..025a6e907 100644
--- a/collections/metabolomics/v2/tools/seurat.yaml
+++ b/collections/metabolomics/v2/tools/seurat.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - GenomicsMachineLearning/SpaMTP
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - CE-MS
diff --git a/collections/metabolomics/v2/tools/shiny.yaml b/collections/metabolomics/v2/tools/shiny.yaml
index 2e2787dbe..0e52c87d4 100644
--- a/collections/metabolomics/v2/tools/shiny.yaml
+++ b/collections/metabolomics/v2/tools/shiny.yaml
@@ -25,6 +25,9 @@ source_repos:
 - ncats/metScribeR
 - pmartR/PMart_ShinyApp
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - CE-MS
diff --git a/collections/metabolomics/v2/tools/shinyscreen.yaml b/collections/metabolomics/v2/tools/shinyscreen.yaml
index a48ce879b..769bbf033 100644
--- a/collections/metabolomics/v2/tools/shinyscreen.yaml
+++ b/collections/metabolomics/v2/tools/shinyscreen.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - https://gitlab.com/uniluxembourg/lcsb/eci/shinyscreen.git
 schema_version: 0.2.0
+license_tier: open
+license: Apache-2.0
+license_detection: null
 techniques:
 - LC-MS
 - mass-spectrometry
diff --git a/collections/metabolomics/v2/tools/signal-processing-toolbox.yaml b/collections/metabolomics/v2/tools/signal-processing-toolbox.yaml
index 46cf8f42f..2b3f06f8e 100644
--- a/collections/metabolomics/v2/tools/signal-processing-toolbox.yaml
+++ b/collections/metabolomics/v2/tools/signal-processing-toolbox.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - AdrianHaun/AriumMS
 schema_version: 0.2.0
+license_tier: open
+license: BSD-3-Clause
+license_detection: github-api
 techniques:
 - LC-MS
 - CE-MS
diff --git a/collections/metabolomics/v2/tools/signalp.yaml b/collections/metabolomics/v2/tools/signalp.yaml
index 248940ad3..bd68862b4 100644
--- a/collections/metabolomics/v2/tools/signalp.yaml
+++ b/collections/metabolomics/v2/tools/signalp.yaml
@@ -9,3 +9,6 @@ derived_from:
 source_repos:
 - ASAGlab/MOI--An-integrated-solution-for-omics-analyses
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
diff --git a/collections/metabolomics/v2/tools/simile.yaml b/collections/metabolomics/v2/tools/simile.yaml
index 2e37818dc..91a1245c7 100644
--- a/collections/metabolomics/v2/tools/simile.yaml
+++ b/collections/metabolomics/v2/tools/simile.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - biorack/simile
 schema_version: 0.2.0
+license_tier: open
+license: BSD-3-Clause
+license_detection: readme-llm
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/singularity.yaml b/collections/metabolomics/v2/tools/singularity.yaml
index 21aea4d09..570be7d8c 100644
--- a/collections/metabolomics/v2/tools/singularity.yaml
+++ b/collections/metabolomics/v2/tools/singularity.yaml
@@ -19,6 +19,9 @@ source_repos:
 - ASAGlab/MOI--An-integrated-solution-for-omics-analyses
 - meowcat/MSNovelist
 schema_version: 0.2.0
+license_tier: open
+license: AGPL-3.0
+license_detection: github-api
 techniques:
 - LC-MS
 - CE-MS
diff --git a/collections/metabolomics/v2/tools/sirius.yaml b/collections/metabolomics/v2/tools/sirius.yaml
index 62ddc4744..1e27d447b 100644
--- a/collections/metabolomics/v2/tools/sirius.yaml
+++ b/collections/metabolomics/v2/tools/sirius.yaml
@@ -39,6 +39,9 @@ source_repos:
 - zmahnoor14/MAW
 - zquinlan/concise
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/sklearn.yaml b/collections/metabolomics/v2/tools/sklearn.yaml
index 639115f24..b76dedcf0 100644
--- a/collections/metabolomics/v2/tools/sklearn.yaml
+++ b/collections/metabolomics/v2/tools/sklearn.yaml
@@ -10,5 +10,8 @@ derived_from:
 source_repos:
 - facundof2016/CCSP2.0
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - ion-mobility-MS
diff --git a/collections/metabolomics/v2/tools/skyline.yaml b/collections/metabolomics/v2/tools/skyline.yaml
index 9668a7ceb..249f5ffa9 100644
--- a/collections/metabolomics/v2/tools/skyline.yaml
+++ b/collections/metabolomics/v2/tools/skyline.yaml
@@ -26,6 +26,9 @@ source_repos:
 - fgcz/rawrr
 - lifs-tools/lipidcreator
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: file-present-unclassified
 techniques:
 - LC-MS
 - CE-MS
diff --git a/collections/metabolomics/v2/tools/slack-api.yaml b/collections/metabolomics/v2/tools/slack-api.yaml
index 173b9a6c2..af01f72c8 100644
--- a/collections/metabolomics/v2/tools/slack-api.yaml
+++ b/collections/metabolomics/v2/tools/slack-api.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - czbiohub-sf/Rapid-QC-MS
 schema_version: 0.2.0
+license_tier: open
+license: BSD-3-Clause
+license_detection: license-file
 techniques:
 - LC-MS
 - CE-MS
diff --git a/collections/metabolomics/v2/tools/slaw-grouping-module.yaml b/collections/metabolomics/v2/tools/slaw-grouping-module.yaml
index 810fb1667..226083363 100644
--- a/collections/metabolomics/v2/tools/slaw-grouping-module.yaml
+++ b/collections/metabolomics/v2/tools/slaw-grouping-module.yaml
@@ -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
diff --git a/collections/metabolomics/v2/tools/slaw.yaml b/collections/metabolomics/v2/tools/slaw.yaml
index 6e6b9831e..1b46644d1 100644
--- a/collections/metabolomics/v2/tools/slaw.yaml
+++ b/collections/metabolomics/v2/tools/slaw.yaml
@@ -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
diff --git a/collections/metabolomics/v2/tools/slurm.yaml b/collections/metabolomics/v2/tools/slurm.yaml
index 0b57bd3bf..9aab33acc 100644
--- a/collections/metabolomics/v2/tools/slurm.yaml
+++ b/collections/metabolomics/v2/tools/slurm.yaml
@@ -10,6 +10,9 @@ derived_from:
 source_repos:
 - meowcat/MSNovelist
 schema_version: 0.2.0
+license_tier: open
+license: AGPL-3.0
+license_detection: github-api
 techniques:
 - LC-MS
 - CE-MS
diff --git a/collections/metabolomics/v2/tools/smart.yaml b/collections/metabolomics/v2/tools/smart.yaml
index 86d755b82..99b010932 100644
--- a/collections/metabolomics/v2/tools/smart.yaml
+++ b/collections/metabolomics/v2/tools/smart.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - bioinfo-ibms-pumc/SMART
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/smartpeak.yaml b/collections/metabolomics/v2/tools/smartpeak.yaml
index cce66391e..d056acba8 100644
--- a/collections/metabolomics/v2/tools/smartpeak.yaml
+++ b/collections/metabolomics/v2/tools/smartpeak.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - AutoFlowResearch/SmartPeak
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/smartpeakcli.yaml b/collections/metabolomics/v2/tools/smartpeakcli.yaml
index 0c3d078d3..75b353f07 100644
--- a/collections/metabolomics/v2/tools/smartpeakcli.yaml
+++ b/collections/metabolomics/v2/tools/smartpeakcli.yaml
@@ -10,6 +10,9 @@ derived_from:
 source_repos:
 - AutoFlowResearch/SmartPeak
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/smartpeakgui.yaml b/collections/metabolomics/v2/tools/smartpeakgui.yaml
index 549c578bf..7cc94ab3d 100644
--- a/collections/metabolomics/v2/tools/smartpeakgui.yaml
+++ b/collections/metabolomics/v2/tools/smartpeakgui.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - AutoFlowResearch/SmartPeak
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/smiter.yaml b/collections/metabolomics/v2/tools/smiter.yaml
index c6dcbcea8..8ac166c61 100644
--- a/collections/metabolomics/v2/tools/smiter.yaml
+++ b/collections/metabolomics/v2/tools/smiter.yaml
@@ -9,5 +9,8 @@ derived_from:
 source_repos:
 - LeidelLab/SMITER
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
 techniques:
 - LC-MS
diff --git a/collections/metabolomics/v2/tools/snakemake.yaml b/collections/metabolomics/v2/tools/snakemake.yaml
index 7016d15b8..2bf36efbf 100644
--- a/collections/metabolomics/v2/tools/snakemake.yaml
+++ b/collections/metabolomics/v2/tools/snakemake.yaml
@@ -21,6 +21,9 @@ source_repos:
 - biosustain/snakemake_UmetaFlow
 - skinniderlab/clm
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - CE-MS
diff --git a/collections/metabolomics/v2/tools/spamtp.yaml b/collections/metabolomics/v2/tools/spamtp.yaml
index 2fb6b7b6a..3c895f2ff 100644
--- a/collections/metabolomics/v2/tools/spamtp.yaml
+++ b/collections/metabolomics/v2/tools/spamtp.yaml
@@ -10,6 +10,9 @@ derived_from:
 source_repos:
 - GenomicsMachineLearning/SpaMTP
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - CE-MS
diff --git a/collections/metabolomics/v2/tools/spatialmeta.yaml b/collections/metabolomics/v2/tools/spatialmeta.yaml
index de737a9c6..21c832d22 100644
--- a/collections/metabolomics/v2/tools/spatialmeta.yaml
+++ b/collections/metabolomics/v2/tools/spatialmeta.yaml
@@ -11,6 +11,9 @@ derived_from:
 source_repos:
 - WanluLiuLab/SpatialMETA
 schema_version: 0.2.0
+license_tier: open
+license: BSD-3-Clause
+license_detection: github-api
 techniques:
 - LC-MS
 - MS-imaging
diff --git a/collections/metabolomics/v2/tools/spec2vec.yaml b/collections/metabolomics/v2/tools/spec2vec.yaml
index 75b8ab03a..df1643f06 100644
--- a/collections/metabolomics/v2/tools/spec2vec.yaml
+++ b/collections/metabolomics/v2/tools/spec2vec.yaml
@@ -20,6 +20,9 @@ derived_from:
 source_repos:
 - vdhooftcompmet/MS2LDA
 schema_version: 0.2.0
+license_tier: open
+license: Apache-2.0
+license_detection: github-api
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/spectra-hash.yaml b/collections/metabolomics/v2/tools/spectra-hash.yaml
index 8d0622f8b..8311a343b 100644
--- a/collections/metabolomics/v2/tools/spectra-hash.yaml
+++ b/collections/metabolomics/v2/tools/spectra-hash.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - eMetaboHUB/FragHub
 schema_version: 0.2.0
+license_tier: noncommercial
+license: CC-BY-NC-4.0
+license_detection: license-file
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/spectra.yaml b/collections/metabolomics/v2/tools/spectra.yaml
index a1e6b1478..420e08626 100644
--- a/collections/metabolomics/v2/tools/spectra.yaml
+++ b/collections/metabolomics/v2/tools/spectra.yaml
@@ -30,6 +30,9 @@ source_repos:
 - sneumann/xcms
 - zmahnoor14/MAW
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: file-present-unclassified
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/spectral-denoising.yaml b/collections/metabolomics/v2/tools/spectral-denoising.yaml
index ddf3dbfd8..f881a1649 100644
--- a/collections/metabolomics/v2/tools/spectral-denoising.yaml
+++ b/collections/metabolomics/v2/tools/spectral-denoising.yaml
@@ -9,5 +9,8 @@ derived_from:
 source_repos:
 - FanzhouKong/spectral_denoising
 schema_version: 0.2.0
+license_tier: open
+license: Apache-2.0
+license_detection: github-api
 techniques:
 - LC-MS
diff --git a/collections/metabolomics/v2/tools/spectral-similarity.yaml b/collections/metabolomics/v2/tools/spectral-similarity.yaml
index 44a245157..0eec23c2c 100644
--- a/collections/metabolomics/v2/tools/spectral-similarity.yaml
+++ b/collections/metabolomics/v2/tools/spectral-similarity.yaml
@@ -9,5 +9,8 @@ derived_from:
 source_repos:
 - YuanyueLi/SpectralEntropy
 schema_version: 0.2.0
+license_tier: open
+license: Apache-2.0
+license_detection: github-api
 techniques:
 - LC-MS
diff --git a/collections/metabolomics/v2/tools/spectralentropy.yaml b/collections/metabolomics/v2/tools/spectralentropy.yaml
index b37261dab..3b496ffc0 100644
--- a/collections/metabolomics/v2/tools/spectralentropy.yaml
+++ b/collections/metabolomics/v2/tools/spectralentropy.yaml
@@ -9,5 +9,8 @@ derived_from:
 source_repos:
 - YuanyueLi/SpectralEntropy
 schema_version: 0.2.0
+license_tier: open
+license: Apache-2.0
+license_detection: github-api
 techniques:
 - LC-MS
diff --git a/collections/metabolomics/v2/tools/spectraverse-analysis-repository.yaml b/collections/metabolomics/v2/tools/spectraverse-analysis-repository.yaml
index 7200943b3..152268232 100644
--- a/collections/metabolomics/v2/tools/spectraverse-analysis-repository.yaml
+++ b/collections/metabolomics/v2/tools/spectraverse-analysis-repository.yaml
@@ -9,5 +9,8 @@ derived_from:
 source_repos:
 - skinniderlab/spectraverse-analysis
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
 techniques:
 - LC-MS
diff --git a/collections/metabolomics/v2/tools/spectripy.yaml b/collections/metabolomics/v2/tools/spectripy.yaml
index 85be9d912..606430bf6 100644
--- a/collections/metabolomics/v2/tools/spectripy.yaml
+++ b/collections/metabolomics/v2/tools/spectripy.yaml
@@ -8,6 +8,9 @@ derived_from:
 - doi: 10.21105/joss.08070
   title: spectripy
 schema_version: 0.2.0
+license_tier: open
+license: Artistic-2.0
+license_detection: github-api
 techniques:
 - LC-MS
 - mass-spectrometry
diff --git a/collections/metabolomics/v2/tools/spectrum-utils-0-3-5.yaml b/collections/metabolomics/v2/tools/spectrum-utils-0-3-5.yaml
index 45c1f526f..9159bdb56 100644
--- a/collections/metabolomics/v2/tools/spectrum-utils-0-3-5.yaml
+++ b/collections/metabolomics/v2/tools/spectrum-utils-0-3-5.yaml
@@ -7,5 +7,8 @@ derived_from:
 - doi: 10.1002/rcm.9153
   title: Large‐scale tandem mass spectrum clustering using fast nearest neighbor searching
 schema_version: 0.2.0
+license_tier: open
+license: BSD-3-Clause
+license_detection: github-api
 techniques:
 - LC-MS
diff --git a/collections/metabolomics/v2/tools/spectrum-utils.yaml b/collections/metabolomics/v2/tools/spectrum-utils.yaml
index 37796a879..5a5244ded 100644
--- a/collections/metabolomics/v2/tools/spectrum-utils.yaml
+++ b/collections/metabolomics/v2/tools/spectrum-utils.yaml
@@ -10,6 +10,9 @@ derived_from:
 - doi: 10.1021/acs.analchem.9b04884
   title: "<tt>spectrum_utils</tt>\n                    : A Python Package for Mass Spectrometry Data Processing and Visualization"
 schema_version: 0.2.0
+license_tier: open
+license: Apache-2.0
+license_detection: github-api
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/sphinx.yaml b/collections/metabolomics/v2/tools/sphinx.yaml
index 5927e83a0..bbbb8ed18 100644
--- a/collections/metabolomics/v2/tools/sphinx.yaml
+++ b/collections/metabolomics/v2/tools/sphinx.yaml
@@ -12,6 +12,9 @@ derived_from:
 source_repos:
 - pluskal-lab/DreaMS
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
 techniques:
 - LC-MS
 - MS-imaging
diff --git a/collections/metabolomics/v2/tools/spreadout.yaml b/collections/metabolomics/v2/tools/spreadout.yaml
index b7cd0c495..5d054b450 100644
--- a/collections/metabolomics/v2/tools/spreadout.yaml
+++ b/collections/metabolomics/v2/tools/spreadout.yaml
@@ -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
diff --git a/collections/metabolomics/v2/tools/sql.yaml b/collections/metabolomics/v2/tools/sql.yaml
index 028961f95..c68e9b1e9 100644
--- a/collections/metabolomics/v2/tools/sql.yaml
+++ b/collections/metabolomics/v2/tools/sql.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - mwang87/MassQueryLanguage
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
 techniques:
 - LC-MS
 - mass-spectrometry
diff --git a/collections/metabolomics/v2/tools/sqlalchemy.yaml b/collections/metabolomics/v2/tools/sqlalchemy.yaml
index b458789e2..bdd537780 100644
--- a/collections/metabolomics/v2/tools/sqlalchemy.yaml
+++ b/collections/metabolomics/v2/tools/sqlalchemy.yaml
@@ -6,6 +6,9 @@ derived_from:
 - doi: 10.1021/acs.jproteome.8b00717
   title: pyteomics
 schema_version: 0.2.0
+license_tier: open
+license: Apache-2.0
+license_detection: github-api
 techniques:
 - LC-MS
 - ion-mobility-MS
diff --git a/collections/metabolomics/v2/tools/sqlite.yaml b/collections/metabolomics/v2/tools/sqlite.yaml
index 8db4205d1..9cccdc67e 100644
--- a/collections/metabolomics/v2/tools/sqlite.yaml
+++ b/collections/metabolomics/v2/tools/sqlite.yaml
@@ -3,5 +3,8 @@ slug: sqlite
 evidence_spans:
 - It also parses some of the information out of the SQLite data base
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: null
 techniques:
 - LC-MS
diff --git a/collections/metabolomics/v2/tools/sqlite3.yaml b/collections/metabolomics/v2/tools/sqlite3.yaml
index ddb50d442..0257d66f1 100644
--- a/collections/metabolomics/v2/tools/sqlite3.yaml
+++ b/collections/metabolomics/v2/tools/sqlite3.yaml
@@ -6,5 +6,8 @@ derived_from:
 - doi: 10.1093/bioinformatics/bty046
   title: pymzml
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
 techniques:
 - mass-spectrometry
diff --git a/collections/metabolomics/v2/tools/sqmassloader.yaml b/collections/metabolomics/v2/tools/sqmassloader.yaml
index 95b1ccb45..a8afd653f 100644
--- a/collections/metabolomics/v2/tools/sqmassloader.yaml
+++ b/collections/metabolomics/v2/tools/sqmassloader.yaml
@@ -9,5 +9,8 @@ derived_from:
 source_repos:
 - Roestlab/massdash
 schema_version: 0.2.0
+license_tier: open
+license: BSD-3-Clause
+license_detection: github-api
 techniques:
 - LC-MS
diff --git a/collections/metabolomics/v2/tools/sra-toolkit.yaml b/collections/metabolomics/v2/tools/sra-toolkit.yaml
index 0acd18f00..703f9b050 100644
--- a/collections/metabolomics/v2/tools/sra-toolkit.yaml
+++ b/collections/metabolomics/v2/tools/sra-toolkit.yaml
@@ -9,3 +9,6 @@ derived_from:
 source_repos:
 - ASAGlab/MOI--An-integrated-solution-for-omics-analyses
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
diff --git a/collections/metabolomics/v2/tools/stagate.yaml b/collections/metabolomics/v2/tools/stagate.yaml
index 2ea927c54..9b895c62a 100644
--- a/collections/metabolomics/v2/tools/stagate.yaml
+++ b/collections/metabolomics/v2/tools/stagate.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - bioinfo-ibms-pumc/SMART
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - direct-infusion-MS
diff --git a/collections/metabolomics/v2/tools/star-aligner-v-2-6-1d.yaml b/collections/metabolomics/v2/tools/star-aligner-v-2-6-1d.yaml
index 24b66710b..f24824b17 100644
--- a/collections/metabolomics/v2/tools/star-aligner-v-2-6-1d.yaml
+++ b/collections/metabolomics/v2/tools/star-aligner-v-2-6-1d.yaml
@@ -7,5 +7,8 @@ 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
diff --git a/collections/metabolomics/v2/tools/statistical-analysis-libraries-scipy-stats-for-enrichment-tests.yaml b/collections/metabolomics/v2/tools/statistical-analysis-libraries-scipy-stats-for-enrichment-tests.yaml
index a403f8046..dee39c328 100644
--- a/collections/metabolomics/v2/tools/statistical-analysis-libraries-scipy-stats-for-enrichment-tests.yaml
+++ b/collections/metabolomics/v2/tools/statistical-analysis-libraries-scipy-stats-for-enrichment-tests.yaml
@@ -9,5 +9,8 @@ derived_from:
 source_repos:
 - metabolomicsworkbench/MetENP
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
 techniques:
 - mass-spectrometry
diff --git a/collections/metabolomics/v2/tools/statistical-total-correlation-spectroscopy-stocsy.yaml b/collections/metabolomics/v2/tools/statistical-total-correlation-spectroscopy-stocsy.yaml
index 5d1bbb2d3..21dde5fc7 100644
--- a/collections/metabolomics/v2/tools/statistical-total-correlation-spectroscopy-stocsy.yaml
+++ b/collections/metabolomics/v2/tools/statistical-total-correlation-spectroscopy-stocsy.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - AndreaRMICL/MWASTools
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - NMR
diff --git a/collections/metabolomics/v2/tools/statistics-and-machine-learning-toolbox.yaml b/collections/metabolomics/v2/tools/statistics-and-machine-learning-toolbox.yaml
index 22b305e1a..af5046e24 100644
--- a/collections/metabolomics/v2/tools/statistics-and-machine-learning-toolbox.yaml
+++ b/collections/metabolomics/v2/tools/statistics-and-machine-learning-toolbox.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - AdrianHaun/AriumMS
 schema_version: 0.2.0
+license_tier: open
+license: BSD-3-Clause
+license_detection: github-api
 techniques:
 - LC-MS
 - CE-MS
diff --git a/collections/metabolomics/v2/tools/stats.yaml b/collections/metabolomics/v2/tools/stats.yaml
index 5e67697a1..c4c7a1624 100644
--- a/collections/metabolomics/v2/tools/stats.yaml
+++ b/collections/metabolomics/v2/tools/stats.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - BiosystemEngineeringLab-IITB/dures
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: file-present-unclassified
 techniques:
 - LC-MS
 - CE-MS
diff --git a/collections/metabolomics/v2/tools/stattarget.yaml b/collections/metabolomics/v2/tools/stattarget.yaml
index 7a3822bfd..f70c72645 100644
--- a/collections/metabolomics/v2/tools/stattarget.yaml
+++ b/collections/metabolomics/v2/tools/stattarget.yaml
@@ -8,6 +8,9 @@ derived_from:
 source_repos:
 - idrblab/NOREVA;
 schema_version: 0.2.0
+license_tier: open
+license: GPL-3.0
+license_detection: github-api
 techniques:
 - LC-MS
 - CE-MS
diff --git a/collections/metabolomics/v2/tools/streamlit.yaml b/collections/metabolomics/v2/tools/streamlit.yaml
index d7fb426bb..bd8cc58f6 100644
--- a/collections/metabolomics/v2/tools/streamlit.yaml
+++ b/collections/metabolomics/v2/tools/streamlit.yaml
@@ -13,6 +13,9 @@ source_repos:
 - OpenMS/OpenMS
 - Roestlab/massdash
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: file-present-unclassified
 techniques:
 - LC-MS
 - ion-mobility-MS
diff --git a/collections/metabolomics/v2/tools/stringr.yaml b/collections/metabolomics/v2/tools/stringr.yaml
index 56de3c86b..81471f42f 100644
--- a/collections/metabolomics/v2/tools/stringr.yaml
+++ b/collections/metabolomics/v2/tools/stringr.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - kilgain/MassSpec
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/summarizedexperiment.yaml b/collections/metabolomics/v2/tools/summarizedexperiment.yaml
index b4b97e7b9..f0cbdb2fb 100644
--- a/collections/metabolomics/v2/tools/summarizedexperiment.yaml
+++ b/collections/metabolomics/v2/tools/summarizedexperiment.yaml
@@ -22,6 +22,9 @@ source_repos:
 - krumsieklab/maplet
 - yufree/mzrtsim
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/sva.yaml b/collections/metabolomics/v2/tools/sva.yaml
index d92fea434..d5843c980 100644
--- a/collections/metabolomics/v2/tools/sva.yaml
+++ b/collections/metabolomics/v2/tools/sva.yaml
@@ -13,3 +13,6 @@ source_repos:
 - ASAGlab/MOI--An-integrated-solution-for-omics-analyses
 - NBDZ/dbnorm
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
diff --git a/collections/metabolomics/v2/tools/symfony.yaml b/collections/metabolomics/v2/tools/symfony.yaml
index d501b80d3..de89005d2 100644
--- a/collections/metabolomics/v2/tools/symfony.yaml
+++ b/collections/metabolomics/v2/tools/symfony.yaml
@@ -9,5 +9,8 @@ derived_from:
 source_repos:
 - privrja/MassSpecBlocks
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
 techniques:
 - mass-spectrometry
diff --git a/collections/metabolomics/v2/tools/syncsa.yaml b/collections/metabolomics/v2/tools/syncsa.yaml
index d6f4f440d..cf49486dd 100644
--- a/collections/metabolomics/v2/tools/syncsa.yaml
+++ b/collections/metabolomics/v2/tools/syncsa.yaml
@@ -8,6 +8,9 @@ derived_from:
 - doi: 10.1186/s40168-023-01476-3
   title: MetaboDirect
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/syrupy.yaml b/collections/metabolomics/v2/tools/syrupy.yaml
index dfe79216e..e138ed716 100644
--- a/collections/metabolomics/v2/tools/syrupy.yaml
+++ b/collections/metabolomics/v2/tools/syrupy.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - Roestlab/massdash
 schema_version: 0.2.0
+license_tier: open
+license: BSD-3-Clause
+license_detection: github-api
 techniques:
 - LC-MS
 - ion-mobility-MS
diff --git a/collections/metabolomics/v2/tools/t-sne-t-distributed-stochastic-neighbor-embedding.yaml b/collections/metabolomics/v2/tools/t-sne-t-distributed-stochastic-neighbor-embedding.yaml
index 36befa7ec..39493d237 100644
--- a/collections/metabolomics/v2/tools/t-sne-t-distributed-stochastic-neighbor-embedding.yaml
+++ b/collections/metabolomics/v2/tools/t-sne-t-distributed-stochastic-neighbor-embedding.yaml
@@ -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
diff --git a/collections/metabolomics/v2/tools/t-sne.yaml b/collections/metabolomics/v2/tools/t-sne.yaml
index 85fdef729..437072a9a 100644
--- a/collections/metabolomics/v2/tools/t-sne.yaml
+++ b/collections/metabolomics/v2/tools/t-sne.yaml
@@ -6,6 +6,9 @@ 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
 - CE-MS
diff --git a/collections/metabolomics/v2/tools/tandemmatch.yaml b/collections/metabolomics/v2/tools/tandemmatch.yaml
index 54fe3297b..b3366120f 100644
--- a/collections/metabolomics/v2/tools/tandemmatch.yaml
+++ b/collections/metabolomics/v2/tools/tandemmatch.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - pnnl/IonToolPack
 schema_version: 0.2.0
+license_tier: open
+license: BSD-2-Clause
+license_detection: github-api
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/tardis.yaml b/collections/metabolomics/v2/tools/tardis.yaml
index d6ba098ef..329e9ba55 100644
--- a/collections/metabolomics/v2/tools/tardis.yaml
+++ b/collections/metabolomics/v2/tools/tardis.yaml
@@ -7,6 +7,9 @@ derived_from:
 - doi: 10.1021/acs.analchem.5c00567
   title: Automated Integration and Quality Assessment of Chromatographic Peaks in LC–MS-Based Metabolomics and Lipidomics Using TARDIS
 schema_version: 0.2.0
+license_tier: open
+license: GPL-3.0
+license_detection: github-api
 techniques:
 - LC-MS
 - mass-spectrometry
diff --git a/collections/metabolomics/v2/tools/tensorflow-1-8-0.yaml b/collections/metabolomics/v2/tools/tensorflow-1-8-0.yaml
index 13849a6b8..66dd7bcfc 100644
--- a/collections/metabolomics/v2/tools/tensorflow-1-8-0.yaml
+++ b/collections/metabolomics/v2/tools/tensorflow-1-8-0.yaml
@@ -9,3 +9,6 @@ derived_from:
 source_repos:
 - wabdelmoula/massNet
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
diff --git a/collections/metabolomics/v2/tools/tensorflow-2-3-0.yaml b/collections/metabolomics/v2/tools/tensorflow-2-3-0.yaml
index e409a506b..bc22bd0cc 100644
--- a/collections/metabolomics/v2/tools/tensorflow-2-3-0.yaml
+++ b/collections/metabolomics/v2/tools/tensorflow-2-3-0.yaml
@@ -8,5 +8,8 @@ derived_from:
 - doi: 10.1021/acs.jnatprod.1c00399
   title: npclassifier
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
 techniques:
 - mass-spectrometry
diff --git a/collections/metabolomics/v2/tools/tensorflow-or-pytorch.yaml b/collections/metabolomics/v2/tools/tensorflow-or-pytorch.yaml
index 6cf6571b0..8d5b43dd4 100644
--- a/collections/metabolomics/v2/tools/tensorflow-or-pytorch.yaml
+++ b/collections/metabolomics/v2/tools/tensorflow-or-pytorch.yaml
@@ -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
 - NMR
diff --git a/collections/metabolomics/v2/tools/tensorflow-serving.yaml b/collections/metabolomics/v2/tools/tensorflow-serving.yaml
index 0111e3059..1673575a6 100644
--- a/collections/metabolomics/v2/tools/tensorflow-serving.yaml
+++ b/collections/metabolomics/v2/tools/tensorflow-serving.yaml
@@ -14,6 +14,9 @@ derived_from:
 source_repos:
 - mwang87/NP-Classifier
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - NMR
 - mass-spectrometry
diff --git a/collections/metabolomics/v2/tools/tensorflow.yaml b/collections/metabolomics/v2/tools/tensorflow.yaml
index 65706a72f..c1848928f 100644
--- a/collections/metabolomics/v2/tools/tensorflow.yaml
+++ b/collections/metabolomics/v2/tools/tensorflow.yaml
@@ -36,6 +36,9 @@ source_repos:
 - volvox292/mass2smiles
 - wabdelmoula/massNet
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: file-present-unclassified
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/thermorawfileparser.yaml b/collections/metabolomics/v2/tools/thermorawfileparser.yaml
index 34c405c89..6d1be6ed6 100644
--- a/collections/metabolomics/v2/tools/thermorawfileparser.yaml
+++ b/collections/metabolomics/v2/tools/thermorawfileparser.yaml
@@ -6,6 +6,9 @@ derived_from:
 - doi: 10.1371/journal.pcbi.1011912
   title: Common data models to streamline metabolomics processing and annotation, and implementation in a Python pipeline
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: license-file
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/tibble.yaml b/collections/metabolomics/v2/tools/tibble.yaml
index 9615e7f96..6a0e39f88 100644
--- a/collections/metabolomics/v2/tools/tibble.yaml
+++ b/collections/metabolomics/v2/tools/tibble.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - kilgain/MassSpec
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/tidyr.yaml b/collections/metabolomics/v2/tools/tidyr.yaml
index c0f7f6486..edc07a261 100644
--- a/collections/metabolomics/v2/tools/tidyr.yaml
+++ b/collections/metabolomics/v2/tools/tidyr.yaml
@@ -13,6 +13,9 @@ source_repos:
 - GenomicsMachineLearning/SpaMTP
 - kilgain/MassSpec
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/tidyverse.yaml b/collections/metabolomics/v2/tools/tidyverse.yaml
index 73af39bad..16d17cc51 100644
--- a/collections/metabolomics/v2/tools/tidyverse.yaml
+++ b/collections/metabolomics/v2/tools/tidyverse.yaml
@@ -13,6 +13,9 @@ source_repos:
 - LeaveMeNotTonight/CMDN
 - scibiome/meteor
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - CE-MS
diff --git a/collections/metabolomics/v2/tools/timar.yaml b/collections/metabolomics/v2/tools/timar.yaml
index ac79d8938..5febe66d7 100644
--- a/collections/metabolomics/v2/tools/timar.yaml
+++ b/collections/metabolomics/v2/tools/timar.yaml
@@ -10,6 +10,9 @@ derived_from:
 source_repos:
 - luigiquiros/inventa
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
 techniques:
 - LC-MS
 - CE-MS
diff --git a/collections/metabolomics/v2/tools/tissuemasst.yaml b/collections/metabolomics/v2/tools/tissuemasst.yaml
index fa0a30aa2..bc4981bbf 100644
--- a/collections/metabolomics/v2/tools/tissuemasst.yaml
+++ b/collections/metabolomics/v2/tools/tissuemasst.yaml
@@ -11,6 +11,9 @@ derived_from:
 source_repos:
 - mwang87/MASST
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - MS-imaging
diff --git a/collections/metabolomics/v2/tools/tomcat.yaml b/collections/metabolomics/v2/tools/tomcat.yaml
index 9090679de..51d268485 100644
--- a/collections/metabolomics/v2/tools/tomcat.yaml
+++ b/collections/metabolomics/v2/tools/tomcat.yaml
@@ -6,5 +6,8 @@ derived_from:
 - doi: 10.1186/s13321-016-0115-9
   title: MetFrag
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - mass-spectrometry
diff --git a/collections/metabolomics/v2/tools/topncontroller.yaml b/collections/metabolomics/v2/tools/topncontroller.yaml
index 9327733ae..6e7047f75 100644
--- a/collections/metabolomics/v2/tools/topncontroller.yaml
+++ b/collections/metabolomics/v2/tools/topncontroller.yaml
@@ -6,6 +6,9 @@ derived_from:
 - doi: 10.1021/acs.analchem.0c03895
   title: Rapid Development of Improved Data-Dependent Acquisition Strategies
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - ion-mobility-MS
diff --git a/collections/metabolomics/v2/tools/torch-1-7-1.yaml b/collections/metabolomics/v2/tools/torch-1-7-1.yaml
index 76b69f2cc..5b65cd5e3 100644
--- a/collections/metabolomics/v2/tools/torch-1-7-1.yaml
+++ b/collections/metabolomics/v2/tools/torch-1-7-1.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - aaronma2020/MSGO
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/torch-cluster.yaml b/collections/metabolomics/v2/tools/torch-cluster.yaml
index 94af83397..437e5b09e 100644
--- a/collections/metabolomics/v2/tools/torch-cluster.yaml
+++ b/collections/metabolomics/v2/tools/torch-cluster.yaml
@@ -13,6 +13,9 @@ source_repos:
 - 01dadada/RT-Transformer
 - RiverCCC/ABCoRT
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/torch-geometric.yaml b/collections/metabolomics/v2/tools/torch-geometric.yaml
index 0802a6938..b8be372f9 100644
--- a/collections/metabolomics/v2/tools/torch-geometric.yaml
+++ b/collections/metabolomics/v2/tools/torch-geometric.yaml
@@ -9,5 +9,8 @@ derived_from:
 source_repos:
 - 01dadada/RT-Transformer
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
diff --git a/collections/metabolomics/v2/tools/torch-scatter.yaml b/collections/metabolomics/v2/tools/torch-scatter.yaml
index 27b1d4553..5734476fe 100644
--- a/collections/metabolomics/v2/tools/torch-scatter.yaml
+++ b/collections/metabolomics/v2/tools/torch-scatter.yaml
@@ -13,6 +13,9 @@ source_repos:
 - 01dadada/RT-Transformer
 - RiverCCC/ABCoRT
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/torch-sparse.yaml b/collections/metabolomics/v2/tools/torch-sparse.yaml
index 6b69a9f1d..236138b2b 100644
--- a/collections/metabolomics/v2/tools/torch-sparse.yaml
+++ b/collections/metabolomics/v2/tools/torch-sparse.yaml
@@ -13,6 +13,9 @@ source_repos:
 - 01dadada/RT-Transformer
 - RiverCCC/ABCoRT
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/torch.yaml b/collections/metabolomics/v2/tools/torch.yaml
index e25e756ec..8e5c05ee7 100644
--- a/collections/metabolomics/v2/tools/torch.yaml
+++ b/collections/metabolomics/v2/tools/torch.yaml
@@ -18,6 +18,9 @@ source_repos:
 - aaronma2020/MSGO
 - chensaian/TransG-Net
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/torchmetrics.yaml b/collections/metabolomics/v2/tools/torchmetrics.yaml
index 1e7edc29b..9aefb19c8 100644
--- a/collections/metabolomics/v2/tools/torchmetrics.yaml
+++ b/collections/metabolomics/v2/tools/torchmetrics.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - RiverCCC/ABCoRT
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/tqdm-joblib.yaml b/collections/metabolomics/v2/tools/tqdm-joblib.yaml
index 9da97a1db..66b47d761 100644
--- a/collections/metabolomics/v2/tools/tqdm-joblib.yaml
+++ b/collections/metabolomics/v2/tools/tqdm-joblib.yaml
@@ -10,5 +10,8 @@ derived_from:
 source_repos:
 - zsspython/LAGF
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
diff --git a/collections/metabolomics/v2/tools/tqdm.yaml b/collections/metabolomics/v2/tools/tqdm.yaml
index 89569ec58..7490bb49d 100644
--- a/collections/metabolomics/v2/tools/tqdm.yaml
+++ b/collections/metabolomics/v2/tools/tqdm.yaml
@@ -14,5 +14,8 @@ source_repos:
 - 01dadada/RT-Transformer
 - zsspython/LAGF
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
diff --git a/collections/metabolomics/v2/tools/transformer-architecture.yaml b/collections/metabolomics/v2/tools/transformer-architecture.yaml
index 606807a8a..59b07c8c8 100644
--- a/collections/metabolomics/v2/tools/transformer-architecture.yaml
+++ b/collections/metabolomics/v2/tools/transformer-architecture.yaml
@@ -7,6 +7,9 @@ derived_from:
 - doi: 10.1021/acscentsci.4c01132
   title: NMR2Struct
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
 techniques:
 - LC-MS
 - NMR
diff --git a/collections/metabolomics/v2/tools/transformer.yaml b/collections/metabolomics/v2/tools/transformer.yaml
index 6f9c7cbea..13831fbdf 100644
--- a/collections/metabolomics/v2/tools/transformer.yaml
+++ b/collections/metabolomics/v2/tools/transformer.yaml
@@ -20,6 +20,9 @@ source_repos:
 - NeoNexusX/HyperCCS
 - samgoldman97/mist
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - ion-mobility-MS
diff --git a/collections/metabolomics/v2/tools/treelib.yaml b/collections/metabolomics/v2/tools/treelib.yaml
index bad9e38a8..110376f23 100644
--- a/collections/metabolomics/v2/tools/treelib.yaml
+++ b/collections/metabolomics/v2/tools/treelib.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - shuzhao-li-lab/khipu
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: file-present-unclassified
 techniques:
 - LC-MS
 - mass-spectrometry
diff --git a/collections/metabolomics/v2/tools/trelliscope.yaml b/collections/metabolomics/v2/tools/trelliscope.yaml
index e749efc89..4f0d5d934 100644
--- a/collections/metabolomics/v2/tools/trelliscope.yaml
+++ b/collections/metabolomics/v2/tools/trelliscope.yaml
@@ -9,3 +9,6 @@ derived_from:
 source_repos:
 - pmartR/MODE_ShinyApp
 schema_version: 0.2.0
+license_tier: open
+license: BSD-2-Clause
+license_detection: github-api
diff --git a/collections/metabolomics/v2/tools/trfba.yaml b/collections/metabolomics/v2/tools/trfba.yaml
index 1cf8d9f67..714a25fed 100644
--- a/collections/metabolomics/v2/tools/trfba.yaml
+++ b/collections/metabolomics/v2/tools/trfba.yaml
@@ -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
diff --git a/collections/metabolomics/v2/tools/trimgalore.yaml b/collections/metabolomics/v2/tools/trimgalore.yaml
index 3da8661a3..b72f71eec 100644
--- a/collections/metabolomics/v2/tools/trimgalore.yaml
+++ b/collections/metabolomics/v2/tools/trimgalore.yaml
@@ -9,3 +9,6 @@ derived_from:
 source_repos:
 - ASAGlab/MOI--An-integrated-solution-for-omics-analyses
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
diff --git a/collections/metabolomics/v2/tools/trove4j.yaml b/collections/metabolomics/v2/tools/trove4j.yaml
index 2a546d079..6f3ceeabc 100644
--- a/collections/metabolomics/v2/tools/trove4j.yaml
+++ b/collections/metabolomics/v2/tools/trove4j.yaml
@@ -10,6 +10,9 @@ derived_from:
 source_repos:
 - rformassspectrometry/Spectra
 schema_version: 0.2.0
+license_tier: open
+license: Artistic-2.0
+license_detection: readme-llm
 techniques:
 - LC-MS
 - NMR
diff --git a/collections/metabolomics/v2/tools/ubuntu.yaml b/collections/metabolomics/v2/tools/ubuntu.yaml
index a25d17cee..62b80f14e 100644
--- a/collections/metabolomics/v2/tools/ubuntu.yaml
+++ b/collections/metabolomics/v2/tools/ubuntu.yaml
@@ -10,5 +10,8 @@ derived_from:
 source_repos:
 - LQZ0123/MSThunder
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
diff --git a/collections/metabolomics/v2/tools/ultramassexplorer.yaml b/collections/metabolomics/v2/tools/ultramassexplorer.yaml
index 18322e406..b1a6adb2a 100644
--- a/collections/metabolomics/v2/tools/ultramassexplorer.yaml
+++ b/collections/metabolomics/v2/tools/ultramassexplorer.yaml
@@ -6,6 +6,9 @@ derived_from:
 - doi: 10.1186/s40168-023-01476-3
   title: MetaboDirect
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/unimod.yaml b/collections/metabolomics/v2/tools/unimod.yaml
index 66bc88461..12f0f3eff 100644
--- a/collections/metabolomics/v2/tools/unimod.yaml
+++ b/collections/metabolomics/v2/tools/unimod.yaml
@@ -6,6 +6,9 @@ derived_from:
 - doi: 10.1021/acs.analchem.9b04884
   title: "<tt>spectrum_utils</tt>\n                    : A Python Package for Mass Spectrometry Data Processing and Visualization"
 schema_version: 0.2.0
+license_tier: open
+license: Apache-2.0
+license_detection: github-api
 techniques:
 - LC-MS
 - mass-spectrometry
diff --git a/collections/metabolomics/v2/tools/vegan-r-package.yaml b/collections/metabolomics/v2/tools/vegan-r-package.yaml
index bf8597dce..70e8f2374 100644
--- a/collections/metabolomics/v2/tools/vegan-r-package.yaml
+++ b/collections/metabolomics/v2/tools/vegan-r-package.yaml
@@ -6,5 +6,8 @@ derived_from:
 - doi: 10.1186/s40168-023-01476-3
   title: MetaboDirect
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
 techniques:
 - mass-spectrometry
diff --git a/collections/metabolomics/v2/tools/vegan.yaml b/collections/metabolomics/v2/tools/vegan.yaml
index c474b2f49..016ce5e9a 100644
--- a/collections/metabolomics/v2/tools/vegan.yaml
+++ b/collections/metabolomics/v2/tools/vegan.yaml
@@ -9,6 +9,9 @@ derived_from:
 - doi: 10.1186/s40168-023-01476-3
   title: MetaboDirect
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/vim.yaml b/collections/metabolomics/v2/tools/vim.yaml
index 5737949ee..c91e4d95d 100644
--- a/collections/metabolomics/v2/tools/vim.yaml
+++ b/collections/metabolomics/v2/tools/vim.yaml
@@ -9,3 +9,6 @@ derived_from:
 source_repos:
 - scibiome/meteor
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
diff --git a/collections/metabolomics/v2/tools/vimms.yaml b/collections/metabolomics/v2/tools/vimms.yaml
index ce55c242d..5b4910b48 100644
--- a/collections/metabolomics/v2/tools/vimms.yaml
+++ b/collections/metabolomics/v2/tools/vimms.yaml
@@ -11,6 +11,9 @@ derived_from:
 - doi: 10.1021/acs.analchem.0c03895
   title: Rapid Development of Improved Data-Dependent Acquisition Strategies
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - CE-MS
diff --git a/collections/metabolomics/v2/tools/visual-studio-code.yaml b/collections/metabolomics/v2/tools/visual-studio-code.yaml
index 934555176..463a41000 100644
--- a/collections/metabolomics/v2/tools/visual-studio-code.yaml
+++ b/collections/metabolomics/v2/tools/visual-studio-code.yaml
@@ -13,6 +13,9 @@ source_repos:
 - SysMedOs/LipidLynxX
 - systemsomicslab/MsdialWorkbench
 schema_version: 0.2.0
+license_tier: open
+license: LGPL-3.0
+license_detection: readme-llm
 techniques:
 - LC-MS
 - ion-mobility-MS
diff --git a/collections/metabolomics/v2/tools/visual-studio.yaml b/collections/metabolomics/v2/tools/visual-studio.yaml
index 5be503fd8..d803e0a73 100644
--- a/collections/metabolomics/v2/tools/visual-studio.yaml
+++ b/collections/metabolomics/v2/tools/visual-studio.yaml
@@ -10,6 +10,9 @@ derived_from:
 source_repos:
 - systemsomicslab/MsdialWorkbench
 schema_version: 0.2.0
+license_tier: open
+license: LGPL-3.0
+license_detection: readme-llm
 techniques:
 - LC-MS
 - CE-MS
diff --git a/collections/metabolomics/v2/tools/wavelet-toolbox.yaml b/collections/metabolomics/v2/tools/wavelet-toolbox.yaml
index 2320532b0..e39640b66 100644
--- a/collections/metabolomics/v2/tools/wavelet-toolbox.yaml
+++ b/collections/metabolomics/v2/tools/wavelet-toolbox.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - AdrianHaun/AriumMS
 schema_version: 0.2.0
+license_tier: open
+license: BSD-3-Clause
+license_detection: github-api
 techniques:
 - LC-MS
 - CE-MS
diff --git a/collections/metabolomics/v2/tools/webassembly.yaml b/collections/metabolomics/v2/tools/webassembly.yaml
index bb24b3ccf..545e30ddb 100644
--- a/collections/metabolomics/v2/tools/webassembly.yaml
+++ b/collections/metabolomics/v2/tools/webassembly.yaml
@@ -9,5 +9,8 @@ derived_from:
 source_repos:
 - lidawei1975/colmarvista
 schema_version: 0.2.0
+license_tier: open
+license: GPL-3.0
+license_detection: github-api
 techniques:
 - NMR
diff --git a/collections/metabolomics/v2/tools/webchem.yaml b/collections/metabolomics/v2/tools/webchem.yaml
index 3b7e7f977..8799938a4 100644
--- a/collections/metabolomics/v2/tools/webchem.yaml
+++ b/collections/metabolomics/v2/tools/webchem.yaml
@@ -14,6 +14,9 @@ derived_from:
 source_repos:
 - mariallr/amanida
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - GC-MS
 - NMR
diff --git a/collections/metabolomics/v2/tools/webworker.yaml b/collections/metabolomics/v2/tools/webworker.yaml
index 1211cab81..77e7af31a 100644
--- a/collections/metabolomics/v2/tools/webworker.yaml
+++ b/collections/metabolomics/v2/tools/webworker.yaml
@@ -9,5 +9,8 @@ derived_from:
 source_repos:
 - lidawei1975/colmarvista
 schema_version: 0.2.0
+license_tier: open
+license: GPL-3.0
+license_detection: github-api
 techniques:
 - NMR
diff --git a/collections/metabolomics/v2/tools/wgcna.yaml b/collections/metabolomics/v2/tools/wgcna.yaml
index 941468dbf..ad8994ac5 100644
--- a/collections/metabolomics/v2/tools/wgcna.yaml
+++ b/collections/metabolomics/v2/tools/wgcna.yaml
@@ -14,5 +14,8 @@ derived_from:
 source_repos:
 - andreasmock/MetaboDiff
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
diff --git a/collections/metabolomics/v2/tools/windows.yaml b/collections/metabolomics/v2/tools/windows.yaml
index 6ba093081..e30642c15 100644
--- a/collections/metabolomics/v2/tools/windows.yaml
+++ b/collections/metabolomics/v2/tools/windows.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - LQZ0123/MSThunder
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - NMR
diff --git a/collections/metabolomics/v2/tools/wine.yaml b/collections/metabolomics/v2/tools/wine.yaml
index 7df6e104d..4a5113107 100644
--- a/collections/metabolomics/v2/tools/wine.yaml
+++ b/collections/metabolomics/v2/tools/wine.yaml
@@ -6,6 +6,9 @@ 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
 - direct-infusion-MS
diff --git a/collections/metabolomics/v2/tools/word2vec.yaml b/collections/metabolomics/v2/tools/word2vec.yaml
index 0f02d1a92..1fcfcf1d5 100644
--- a/collections/metabolomics/v2/tools/word2vec.yaml
+++ b/collections/metabolomics/v2/tools/word2vec.yaml
@@ -7,6 +7,9 @@ derived_from:
 - doi: 10.1371/journal.pcbi.1008724
   title: 'Spec2Vec: Improved mass spectral similarity scoring through learning of structural relationships'
 schema_version: 0.2.0
+license_tier: open
+license: Apache-2.0
+license_detection: github-api
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/wpf-windows-presentation-foundation.yaml b/collections/metabolomics/v2/tools/wpf-windows-presentation-foundation.yaml
index d918ac455..edea883d9 100644
--- a/collections/metabolomics/v2/tools/wpf-windows-presentation-foundation.yaml
+++ b/collections/metabolomics/v2/tools/wpf-windows-presentation-foundation.yaml
@@ -9,6 +9,9 @@ derived_from:
 source_repos:
 - systemsomicslab/MsdialWorkbench
 schema_version: 0.2.0
+license_tier: open
+license: LGPL-3.0
+license_detection: readme-llm
 techniques:
 - LC-MS
 - ion-mobility-MS
diff --git a/collections/metabolomics/v2/tools/xcms-centwave.yaml b/collections/metabolomics/v2/tools/xcms-centwave.yaml
index 61f8c8c86..af22e902c 100644
--- a/collections/metabolomics/v2/tools/xcms-centwave.yaml
+++ b/collections/metabolomics/v2/tools/xcms-centwave.yaml
@@ -10,6 +10,9 @@ derived_from:
 source_repos:
 - HuanLab/Paramounter
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
 techniques:
 - LC-MS
 - mass-spectrometry
diff --git a/collections/metabolomics/v2/tools/xcms.yaml b/collections/metabolomics/v2/tools/xcms.yaml
index d3f044e8f..cab80001e 100644
--- a/collections/metabolomics/v2/tools/xcms.yaml
+++ b/collections/metabolomics/v2/tools/xcms.yaml
@@ -76,6 +76,9 @@ source_repos:
 - poomcj/NPFimg
 - sneumann/xcms
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/xlsxwriter.yaml b/collections/metabolomics/v2/tools/xlsxwriter.yaml
index 052aac6f0..0a3ee7430 100644
--- a/collections/metabolomics/v2/tools/xlsxwriter.yaml
+++ b/collections/metabolomics/v2/tools/xlsxwriter.yaml
@@ -10,6 +10,9 @@ derived_from:
 source_repos:
 - Leo-Cheng-Lab/ROIAL-NMR
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/xml-etree-elementtree.yaml b/collections/metabolomics/v2/tools/xml-etree-elementtree.yaml
index 5a1771455..94bad7024 100644
--- a/collections/metabolomics/v2/tools/xml-etree-elementtree.yaml
+++ b/collections/metabolomics/v2/tools/xml-etree-elementtree.yaml
@@ -6,5 +6,8 @@ derived_from:
 - doi: 10.1093/bioinformatics/bty046
   title: pymzml
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
 techniques:
 - mass-spectrometry
diff --git a/collections/metabolomics/v2/tools/xquartz.yaml b/collections/metabolomics/v2/tools/xquartz.yaml
index e42d4a7be..7971d2729 100644
--- a/collections/metabolomics/v2/tools/xquartz.yaml
+++ b/collections/metabolomics/v2/tools/xquartz.yaml
@@ -6,6 +6,9 @@ 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:
 - ion-mobility-MS
 - mass-spectrometry
diff --git a/collections/metabolomics/v2/tools/xtb.yaml b/collections/metabolomics/v2/tools/xtb.yaml
index 2365ea370..8c92214eb 100644
--- a/collections/metabolomics/v2/tools/xtb.yaml
+++ b/collections/metabolomics/v2/tools/xtb.yaml
@@ -10,6 +10,9 @@ derived_from:
 source_repos:
 - grimme-lab/QCxMS2
 schema_version: 0.2.0
+license_tier: open
+license: LGPL-3.0
+license_detection: github-api
 techniques:
 - LC-MS
 - GC-MS
diff --git a/collections/metabolomics/v2/tools/ysi2950-bioanalyzer.yaml b/collections/metabolomics/v2/tools/ysi2950-bioanalyzer.yaml
index 37d6b8a9b..c72cbdced 100644
--- a/collections/metabolomics/v2/tools/ysi2950-bioanalyzer.yaml
+++ b/collections/metabolomics/v2/tools/ysi2950-bioanalyzer.yaml
@@ -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
diff --git a/collections/metabolomics/v2/tools/zenodo-org-records-10997887.yaml b/collections/metabolomics/v2/tools/zenodo-org-records-10997887.yaml
index ab9c23d9a..31923ef21 100644
--- a/collections/metabolomics/v2/tools/zenodo-org-records-10997887.yaml
+++ b/collections/metabolomics/v2/tools/zenodo-org-records-10997887.yaml
@@ -10,3 +10,6 @@ derived_from:
 source_repos:
 - pluskal-lab/DreaMS
 schema_version: 0.2.0
+license_tier: open
+license: MIT
+license_detection: github-api
diff --git a/collections/metabolomics/v2/tools/zenodo.yaml b/collections/metabolomics/v2/tools/zenodo.yaml
index 0f2addf8f..ef90def7a 100644
--- a/collections/metabolomics/v2/tools/zenodo.yaml
+++ b/collections/metabolomics/v2/tools/zenodo.yaml
@@ -24,6 +24,9 @@ source_repos:
 - matchms/matchms
 - sneumann/xcms
 schema_version: 0.2.0
+license_tier: restricted
+license: null
+license_detection: none
 techniques:
 - LC-MS
 - CE-MS
diff --git a/scripts/check_tools_index.py b/scripts/check_tools_index.py
index 2466de8a6..6b31598e2 100644
--- a/scripts/check_tools_index.py
+++ b/scripts/check_tools_index.py
@@ -10,6 +10,8 @@
 import pathlib
 import sys
 
+import yaml
+
 _VALID = {"open", "noncommercial", "restricted"}
 
 
@@ -22,6 +24,7 @@ def check_collection(collection_dir) -> list[str]:
 
     tool_slugs = {t.get("slug") for t in tools}
     skill_slugs = {s.get("slug") for s in skills}
+    tier_by_slug = {t.get("slug"): t.get("license_tier") for t in tools}
 
     # Every tool license_tier is valid; every used_by_skills slug resolves.
     for t in tools:
@@ -34,6 +37,22 @@ def check_collection(collection_dir) -> list[str]:
                     f"tools_index {slug!r}: used_by_skills {ref!r} not in skills_index"
                 )
 
+    # Per-tool YAML license_tier must equal its tools_index license_tier.
+    # Tools that have no tools/<slug>.yaml are skipped (not every tool has one).
+    tools_dir = d / "tools"
+    if tools_dir.is_dir():
+        for yaml_path in sorted(tools_dir.glob("*.yaml")):
+            slug = yaml_path.stem
+            if slug not in tier_by_slug:
+                continue
+            rec = yaml.safe_load(yaml_path.read_text(encoding="utf-8")) or {}
+            yaml_tier = rec.get("license_tier")
+            if yaml_tier != tier_by_slug[slug]:
+                violations.append(
+                    f"tools/{slug}.yaml: license_tier {yaml_tier!r} != "
+                    f"tools_index {tier_by_slug[slug]!r}"
+                )
+
     # Every skill tools_used slug resolves to a real tool.
     for s in skills:
         slug = s.get("slug")
diff --git a/scripts/enrich_tool_yaml.py b/scripts/enrich_tool_yaml.py
new file mode 100644
index 000000000..908dcf191
--- /dev/null
+++ b/scripts/enrich_tool_yaml.py
@@ -0,0 +1,115 @@
+"""Propagate per-tool license fields from ``tools_index.json`` into the LinkML
+per-tool records ``tools/<slug>.yaml``.
+
+``tools_index.json`` already carries ``license_tier`` / ``license`` /
+``license_detection`` (written by ``enrich_tools_index.py``); the 909 generated
+``tools/<slug>.yaml`` records do not. This post-processor joins by ``slug`` and
+writes those three fields into each tool YAML, idempotently and style-preserving.
+
+Design mirrors ``propagate_license_tiers.py`` / ``enrich_tools_index.py``:
+- idempotent, format-preserving writer over committed artifacts;
+- no git / gh / network; no ``Date.now``-style nondeterminism;
+- the license fields land immediately after ``schema_version`` (before any
+  later-appended block such as ``techniques``), a deterministic position so
+  re-runs are byte-stable.
+"""
+from __future__ import annotations
+
+import json
+import pathlib
+
+import yaml
+
+_LICENSE_KEYS = ("license_tier", "license", "license_detection")
+
+
+def _yaml_dump(data: dict) -> str:
+    """Match ``collect_metabolomics_collection.render_tool_yaml`` serialization."""
+    return yaml.safe_dump(
+        data, sort_keys=False, allow_unicode=True, default_flow_style=False, width=1000
+    )
+
+
+def tier_map(tools_index) -> dict:
+    """``{slug: {license_tier, license, license_detection}}`` from the index.
+
+    Missing ``license`` / ``license_detection`` default to ``None`` so every row
+    is complete; entries without a ``slug`` are skipped.
+    """
+    out: dict[str, dict] = {}
+    for t in tools_index:
+        slug = t.get("slug")
+        if not slug:
+            continue
+        out[slug] = {
+            "license_tier": t.get("license_tier"),
+            "license": t.get("license"),
+            "license_detection": t.get("license_detection"),
+        }
+    return out
+
+
+def _reorder_with_license(data: dict, fields: dict) -> dict:
+    """Return a new dict with the three license fields placed right after
+    ``schema_version`` (or appended if absent), preserving all other key order.
+    """
+    # Strip any existing license keys so we can re-place them deterministically.
+    base = {k: v for k, v in data.items() if k not in _LICENSE_KEYS}
+    rebuilt: dict = {}
+    inserted = False
+    for k, v in base.items():
+        rebuilt[k] = v
+        if k == "schema_version":
+            for lk in _LICENSE_KEYS:
+                rebuilt[lk] = fields[lk]
+            inserted = True
+    if not inserted:
+        for lk in _LICENSE_KEYS:
+            rebuilt[lk] = fields[lk]
+    return rebuilt
+
+
+def enrich(collection_dir) -> dict:
+    d = pathlib.Path(collection_dir)
+    tools_index = json.loads((d / "tools_index.json").read_text(encoding="utf-8"))
+    tiers = tier_map(tools_index)
+
+    tools_dir = d / "tools"
+    enriched = 0
+    skipped = 0
+    if not tools_dir.is_dir():
+        return {"enriched": 0, "skipped": 0}
+
+    for yaml_path in sorted(tools_dir.glob("*.yaml")):
+        slug = yaml_path.stem
+        fields = tiers.get(slug)
+        if fields is None:
+            skipped += 1
+            continue
+        data = yaml.safe_load(yaml_path.read_text(encoding="utf-8")) or {}
+        rebuilt = _reorder_with_license(data, fields)
+        new_text = _yaml_dump(rebuilt)
+        if new_text != yaml_path.read_text(encoding="utf-8"):
+            yaml_path.write_text(new_text, encoding="utf-8")
+        enriched += 1
+
+    return {"enriched": enriched, "skipped": skipped}
+
+
+def main(argv=None) -> int:
+    import argparse
+
+    ap = argparse.ArgumentParser(description=__doc__)
+    ap.add_argument(
+        "--collection",
+        required=True,
+        help="collection dir with tools_index.json and a tools/ subdir of <slug>.yaml",
+    )
+    a = ap.parse_args(argv)
+    res = enrich(a.collection)
+    print(json.dumps(res, indent=2))
+    return 0
+
+
+if __name__ == "__main__":
+    raise SystemExit(main())
diff --git a/tests/test_check_tools_index.py b/tests/test_check_tools_index.py
index 515f085ba..d3616f795 100644
--- a/tests/test_check_tools_index.py
+++ b/tests/test_check_tools_index.py
@@ -96,3 +96,69 @@ def test_main_exits_zero_on_clean(tmp_path):
         skills_index=[{"slug": "s1", "tools_used": []}],
     )
     assert c.main([str(d)]) == 0
+
+
+# ---------------------------------------------------------------------------
+# Per-tool YAML <-> tools_index license_tier cross-check
+# ---------------------------------------------------------------------------
+
+def _write_tool_yaml(d, slug, **fields):
+    (d / "tools").mkdir(exist_ok=True)
+    lines = [f"slug: {slug}"]
+    for k, v in fields.items():
+        lines.append(f"{k}: {v}")
+    (d / "tools" / f"{slug}.yaml").write_text("\n".join(lines) + "\n")
+
+
+def test_tool_yaml_tier_match_passes(tmp_path):
+    d = _collection(
+        tmp_path,
+        tools_index=[{"slug": "t1", "license_tier": "open", "used_by_skills": []}],
+        skills_index=[],
+    )
+    _write_tool_yaml(d, "t1", license_tier="open")
+    assert c.check_collection(str(d)) == []
+
+
+def test_tool_yaml_tier_mismatch_is_violation(tmp_path):
+    d = _collection(
+        tmp_path,
+        tools_index=[{"slug": "t1", "license_tier": "open", "used_by_skills": []}],
+        skills_index=[],
+    )
+    _write_tool_yaml(d, "t1", license_tier="restricted")
+    v = c.check_collection(str(d))
+    assert any("t1" in x and "license_tier" in x and "tools/" in x for x in v)
+
+
+def test_tool_yaml_missing_tier_is_violation(tmp_path):
+    # YAML exists but never got enriched -> the cross-check flags it.
+    d = _collection(
+        tmp_path,
+        tools_index=[{"slug": "t1", "license_tier": "open", "used_by_skills": []}],
+        skills_index=[],
+    )
+    _write_tool_yaml(d, "t1", name="T1")
+    v = c.check_collection(str(d))
+    assert any("t1" in x and "license_tier" in x and "tools/" in x for x in v)
+
+
+def test_tool_without_yaml_is_skipped(tmp_path):
+    # tools/<slug>.yaml absent -> no YAML cross-check violation for that tool.
+    d = _collection(
+        tmp_path,
+        tools_index=[{"slug": "t1", "license_tier": "open", "used_by_skills": []}],
+        skills_index=[],
+    )
+    (d / "tools").mkdir(exist_ok=True)  # dir exists but no t1.yaml
+    assert c.check_collection(str(d)) == []
+
+
+def test_no_tools_dir_is_skipped(tmp_path):
+    # No tools/ dir at all -> cross-check is a no-op (back-compat).
+    d = _collection(
+        tmp_path,
+        tools_index=[{"slug": "t1", "license_tier": "open", "used_by_skills": []}],
+        skills_index=[],
+    )
+    assert c.check_collection(str(d)) == []
diff --git a/tests/test_enrich_tool_yaml.py b/tests/test_enrich_tool_yaml.py
new file mode 100644
index 000000000..40002b7c3
--- /dev/null
+++ b/tests/test_enrich_tool_yaml.py
@@ -0,0 +1,151 @@
+import pathlib
+import sys
+import textwrap
+
+import yaml
+
+sys.path.insert(0, str(pathlib.Path(__file__).parent.parent))
+from scripts import enrich_tool_yaml as e
+
+
+# ---------------------------------------------------------------------------
+# tier_map
+# ---------------------------------------------------------------------------
+
+def test_tier_map_extracts_license_fields():
+    tools_index = [
+        {"slug": "t_open", "license_tier": "open", "license": "MIT",
+         "license_detection": "github-api"},
+        {"slug": "t_nc", "license_tier": "noncommercial", "license": "CC-BY-NC-4.0",
+         "license_detection": "readme-llm"},
+        {"slug": "t_restricted", "license_tier": "restricted", "license": None,
+         "license_detection": "none"},
+    ]
+    m = e.tier_map(tools_index)
+    assert m["t_open"] == {"license_tier": "open", "license": "MIT",
+                           "license_detection": "github-api"}
+    assert m["t_nc"]["license_tier"] == "noncommercial"
+    assert m["t_restricted"]["license"] is None
+    assert m["t_restricted"]["license_detection"] == "none"
+
+
+def test_tier_map_defaults_missing_fields():
+    # A tools_index entry that only carries the tier still yields a complete row.
+    m = e.tier_map([{"slug": "t1", "license_tier": "open"}])
+    assert m["t1"] == {"license_tier": "open", "license": None,
+                       "license_detection": None}
+
+
+# ---------------------------------------------------------------------------
+# enrich — fixture with two tool YAMLs
+# ---------------------------------------------------------------------------
+
+def _write_collection(tmp_path):
+    d = tmp_path
+    tools = d / "tools"
+    tools.mkdir()
+    # tool A: a "generated" style record ending in schema_version, with a
+    # later-appended techniques block (matches the real committed shape).
+    (tools / "tool-a.yaml").write_text(textwrap.dedent("""\
+        name: ToolA
+        slug: tool-a
+        canonical_url: https://github.com/x/tool-a
+        version_used: '1.0'
+        evidence_spans:
+        - tool-a is used here
+        derived_from:
+        - doi: 10.1/open
+          title: A paper
+        source_repos:
+        - x/tool-a
+        schema_version: 0.2.0
+        techniques:
+        - LC-MS
+        """))
+    # tool B: minimal record, no canonical_url, no techniques.
+    (tools / "tool-b.yaml").write_text(textwrap.dedent("""\
+        name: ToolB
+        slug: tool-b
+        evidence_spans:
+        - tool-b is used here
+        derived_from:
+        - doi: 10.1/restricted
+          title: Another paper
+        schema_version: 0.2.0
+        """))
+    tools_index = [
+        {"slug": "tool-a", "license_tier": "open", "license": "MIT",
+         "license_detection": "github-api"},
+        {"slug": "tool-b", "license_tier": "restricted", "license": None,
+         "license_detection": "none"},
+    ]
+    import json
+    (d / "tools_index.json").write_text(json.dumps(tools_index, indent=2))
+    return d
+
+
+def test_enrich_writes_license_fields(tmp_path):
+    d = _write_collection(tmp_path)
+    summary = e.enrich(str(d))
+    a = yaml.safe_load((d / "tools" / "tool-a.yaml").read_text())
+    b = yaml.safe_load((d / "tools" / "tool-b.yaml").read_text())
+    assert a["license_tier"] == "open"
+    assert a["license"] == "MIT"
+    assert a["license_detection"] == "github-api"
+    assert b["license_tier"] == "restricted"
+    assert b["license"] is None
+    assert b["license_detection"] == "none"
+    # untouched fields survive
+    assert a["techniques"] == ["LC-MS"]
+    assert a["canonical_url"] == "https://github.com/x/tool-a"
+    assert summary["enriched"] == 2
+
+
+def test_enrich_key_placement_after_schema_version(tmp_path):
+    # License fields land right after schema_version, before techniques —
+    # deterministic so re-runs are stable.
+    d = _write_collection(tmp_path)
+    e.enrich(str(d))
+    keys = list(yaml.safe_load((d / "tools" / "tool-a.yaml").read_text()).keys())
+    sv = keys.index("schema_version")
+    assert keys[sv + 1:sv + 4] == ["license_tier", "license", "license_detection"]
+    assert keys.index("techniques") > keys.index("license_detection")
+
+
+def test_enrich_idempotent(tmp_path):
+    d = _write_collection(tmp_path)
+    e.enrich(str(d))
+    first_a = (d / "tools" / "tool-a.yaml").read_text()
+    first_b = (d / "tools" / "tool-b.yaml").read_text()
+    e.enrich(str(d))
+    assert (d / "tools" / "tool-a.yaml").read_text() == first_a
+    assert (d / "tools" / "tool-b.yaml").read_text() == first_b
+
+
+def test_enrich_updates_stale_tier(tmp_path):
+    # If a YAML already carries a (now-stale) tier, enrich corrects it to match
+    # the tools_index source of truth.
+    d = _write_collection(tmp_path)
+    e.enrich(str(d))
+    import json
+    ti = json.loads((d / "tools_index.json").read_text())
+    for t in ti:
+        if t["slug"] == "tool-a":
+            t["license_tier"] = "noncommercial"
+            t["license"] = "CC-BY-NC-4.0"
+    (d / "tools_index.json").write_text(json.dumps(ti, indent=2))
+    e.enrich(str(d))
+    a = yaml.safe_load((d / "tools" / "tool-a.yaml").read_text())
+    assert a["license_tier"] == "noncommercial"
+    assert a["license"] == "CC-BY-NC-4.0"
+
+
+def test_enrich_skips_yaml_without_index_entry(tmp_path):
+    # A tools/<slug>.yaml with no tools_index row is left untouched.
+    d = _write_collection(tmp_path)
+    orphan = (d / "tools" / "orphan.yaml")
+    orphan.write_text("name: Orphan\nslug: orphan\nschema_version: 0.2.0\n")
+    before = orphan.read_text()
+    summary = e.enrich(str(d))
+    assert orphan.read_text() == before
+    assert summary["skipped"] == 1

From 7f4cb190859ab0628a3020b8377df4325ee14fb2 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Louis-F=C3=A9lix=20Nothias?= <louis-felix.nothias@cnrs.fr>
Date: Fri, 26 Jun 2026 17:35:50 -0300
Subject: [PATCH 2/3] feat(meta-skill): review-grounded (literature-tier)
 super-skills (#7)

A super-skill can now be grounded in a review article instead of being
purely composed from the skills it orchestrates.

- synthesize_meta_skill.meta_frontmatter: optional review_doi=None. When
  given -> provenance_tier="literature", metadata.dois=[review_doi],
  derived_from=[{doi:review_doi}], keeping skill_kind="super"+orchestrates.
  Default path stays synthetic (no dois/derived_from).
- check_proposals.check_collection: accept staged literature super-skills,
  reusing scripts.provenance_tier.validate_entry semantics
  (literature => >=1 doi; synthetic => synthesized_from; community =>
  related_skills key). Super/skill_kind/orchestrates checks intact.
- governance/META_SKILLS.md: document the three meta-skill origins
  (synthetic / community / literature = review-grounded) + review-DOI flow.
- commands/synthesize-meta-skill.md: document the --review-doi option.
- Tests: literature super-skill with a review DOI passes; without a doi
  fails; synthetic path unchanged. Full suite 404 passed.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 .../v2/commands/synthesize-meta-skill.md      | 38 +++++---
 governance/META_SKILLS.md                     | 45 ++++++----
 scripts/check_proposals.py                    | 40 ++++-----
 scripts/synthesize_meta_skill.py              | 65 +++++++++-----
 tests/test_check_proposals.py                 | 88 ++++++++++++++++++-
 tests/test_synthesize_meta_skill.py           | 68 ++++++++++++++
 6 files changed, 271 insertions(+), 73 deletions(-)

diff --git a/collections/metabolomics/v2/commands/synthesize-meta-skill.md b/collections/metabolomics/v2/commands/synthesize-meta-skill.md
index 19fd24940..e16cfc3e6 100644
--- a/collections/metabolomics/v2/commands/synthesize-meta-skill.md
+++ b/collections/metabolomics/v2/commands/synthesize-meta-skill.md
@@ -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>"
    ```
diff --git a/governance/META_SKILLS.md b/governance/META_SKILLS.md
index 92a82296c..197658ad4 100644
--- a/governance/META_SKILLS.md
+++ b/governance/META_SKILLS.md
@@ -34,9 +34,12 @@ proposals gate ([`check_proposals.py`](../scripts/check_proposals.py)):
 | `metadata.skill_kind` | `skill` (default, stands alone) or `super` (orchestrates others) | must be in {`skill`, `super`} |
 | `metadata.orchestrates` | the ordered sub-skill slugs the pipeline sequences | for `super`: non-empty list, **every slug resolves in `skills_index.json`** |
 
-A `super` skill is almost always `provenance_tier: synthetic` (it is derived from
-the skills it orchestrates), so its `metadata.synthesized_from` lists those same
-sub-skill slugs (plus any review DOIs that motivated the pipeline). The body is
+A `super` skill is usually `provenance_tier: synthetic` (it is derived from the
+skills it orchestrates), so its `metadata.synthesized_from` lists those same
+sub-skill slugs. When the canonical pipeline is instead **grounded in a review
+article** — a survey/tutorial that defines the workflow's stages — the super-skill
+is `provenance_tier: literature` with that review's DOI in `metadata.dois` and
+`derived_from` (see *The three provenance origins* below). Either way the body is
 **genuine synthesis** — it writes the real ordered workflow and cites each stage's
 sub-skills by their actual slug; it never fabricates stages, slugs, tools, or DOIs.
 
@@ -54,13 +57,23 @@ sub-skills by their actual slug; it never fabricates stages, slugs, tools, or DO
   (see [`COMMUNITY_SKILLS.md`](COMMUNITY_SKILLS.md)). Invariant: a `related_skills`
   key is present.
 - **`literature`** — *distilled from one or more peer-reviewed source papers* by the
-  curation pipeline (the origin of every shipped skill today). Invariant: ≥1 source
-  DOI.
-
-`skill_kind` (`skill` / `super`) is **orthogonal** to provenance: a `super` skill is
-usually `synthetic`, but a hand-authored workflow skill could be `community` and
-still set `skill_kind: super`. The two precedents below are hand-authored meta-skills
-that this rail generalizes into a synthesizable, openly-curated form.
+  curation pipeline (the origin of every shipped single-procedure skill today).
+  Invariant: ≥1 source DOI. A super-skill lands here when its **pipeline is grounded
+  in a review article** rather than merely composed from existing skills: the
+  `synthesize-meta-skill` command is given a `--review-doi`, and `meta_frontmatter`
+  sets `provenance_tier: literature`, `metadata.dois: [<review-doi>]`, and
+  `derived_from: [{doi: <review-doi>}]` (while keeping `skill_kind: super` +
+  `orchestrates`). This is a **review-grounded meta-skill** — the survey defines the
+  canonical stages, the sub-skills carry each stage.
+
+A super-skill therefore has **three** possible origins: `synthetic` (composed from
+the orchestrated skills, the default), `literature` (review-grounded, via a review
+DOI), or `community` (a hand-authored workflow skill contributed outside the
+pipeline). `skill_kind` (`skill` / `super`) is **orthogonal** to provenance: a
+`super` skill is usually `synthetic`, but it can be `literature` (review-grounded)
+or `community` and still set `skill_kind: super`. The two precedents below are
+hand-authored meta-skills that this rail generalizes into a synthesizable,
+openly-curated form.
 
 ## The open-curation model
 
@@ -85,10 +98,12 @@ community skill, with a human merge gate. **The synthesis is never auto-promoted
 
 3. **CI validation.** On the PR, `scripts/check_proposals.py` (the **Proposals gate**)
    holds the staged skill to the same discipline a published skill must pass, plus the
-   synthetic + super invariants: `metadata.synthesized_from` non-empty;
-   `metadata.skill_kind ∈ {skill, super}`; for `super`, `metadata.orchestrates`
-   non-empty and **every orchestrated slug resolves in `skills_index.json`**. CI checks
-   **structure**, never scientific merit.
+   provenance + super invariants (reusing the `scripts/provenance_tier.py` kernel): a
+   `synthetic` proposal needs non-empty `metadata.synthesized_from`; a `literature`
+   (review-grounded) proposal needs ≥1 `metadata.dois`; a `community` proposal needs a
+   `related_skills` key. For `super` (any origin): `metadata.skill_kind ∈ {skill,
+   super}`, `metadata.orchestrates` non-empty, and **every orchestrated slug resolves
+   in `skills_index.json`**. CI checks **structure**, never scientific merit.
 
 4. **Open community/expert review.** The public PR waits for open review — the same
    community-signal / expert-attestation mechanisms described in
@@ -121,7 +136,7 @@ any other proposal.
 
 | Concern | Rule | Enforced by |
 |---|---|---|
-| Origin | `provenance_tier: synthetic` + `metadata.synthesized_from` non-empty | `check_proposals.py`, `check_provenance_tiers.py` |
+| Origin | `synthetic` ⇒ `metadata.synthesized_from` non-empty; `literature` (review-grounded) ⇒ ≥1 `metadata.dois`; `community` ⇒ `related_skills` key | `check_proposals.py`, `check_provenance_tiers.py` |
 | Kind | `metadata.skill_kind ∈ {skill, super}` (default `skill`) | `check_proposals.py` |
 | Orchestration | for `super`: `metadata.orchestrates` non-empty + every slug in `skills_index.json` | `check_proposals.py` |
 | Rail | `status: hold` while in `proposals/` | `check_proposals.py` |
diff --git a/scripts/check_proposals.py b/scripts/check_proposals.py
index 30d6a7886..72c951004 100644
--- a/scripts/check_proposals.py
+++ b/scripts/check_proposals.py
@@ -2,14 +2,17 @@
 
 Validates each ``proposals/skills/*/SKILL.md`` against the SAME discipline a
 published skill must satisfy, plus the proposal invariants, so a maintainer's
-review is about quality/fit — not structure. A staged proposal is valid under
-EITHER provenance origin:
+review is about quality/fit — not structure. A staged proposal is valid under ANY
+of the three provenance origins (reusing the ``scripts.provenance_tier`` kernel):
 
 * **community** — ``metadata.provenance_tier == "community"`` and a
   ``related_skills`` key is present (the community provenance invariant);
 * **synthetic** — ``metadata.provenance_tier == "synthetic"`` and
   ``metadata.synthesized_from`` is a non-empty list (auto-derived from other
-  skills; see governance/PROVENANCE_TIERS.md).
+  skills; see governance/PROVENANCE_TIERS.md);
+* **literature** — ``metadata.provenance_tier == "literature"`` and
+  ``metadata.dois`` carries >=1 source DOI (e.g. a review-grounded super-skill
+  whose pipeline is distilled from a review article).
 
 For every staged skill, regardless of origin:
 
@@ -35,6 +38,7 @@
 import yaml
 
 from scripts.normalize_skill import frontmatter_violations
+from scripts.provenance_tier import validate_entry as validate_provenance
 
 # A super-skill orchestrates other skills; a plain skill stands alone.
 VALID_SKILL_KINDS = {"skill", "super"}
@@ -84,25 +88,19 @@ def check_collection(collection_dir) -> list:
 
         meta = fm.get("metadata") if isinstance(fm.get("metadata"), dict) else {}
 
-        # provenance invariant: valid under EITHER community OR synthetic origin.
+        # provenance invariant: valid under community, synthetic, OR literature
+        # (review-grounded super-skills) origin. Reuses the provenance_tier kernel
+        # semantics: literature ⇒ >=1 doi, synthetic ⇒ synthesized_from,
+        # community ⇒ related_skills key present.
         prov = meta.get("provenance_tier")
-        if prov == "community":
-            if "related_skills" not in fm:
-                violations.append(
-                    f"{md}: community proposal requires related_skills key"
-                )
-        elif prov == "synthetic":
-            synthesized_from = meta.get("synthesized_from")
-            if not (isinstance(synthesized_from, list) and synthesized_from):
-                violations.append(
-                    f"{md}: synthetic proposal requires non-empty "
-                    f"metadata.synthesized_from list"
-                )
-        else:
-            violations.append(
-                f"{md}: metadata.provenance_tier {prov!r} not in "
-                f"{{'community', 'synthetic'}}"
-            )
+        prov_violations = validate_provenance(
+            prov,
+            dois=meta.get("dois"),
+            synthesized_from=meta.get("synthesized_from"),
+            related_skills=fm.get("related_skills") if "related_skills" in fm else None,
+        )
+        for msg in prov_violations:
+            violations.append(f"{md}: {msg}")
 
         # skill_kind invariant (default 'skill' when absent); a 'super' skill
         # must orchestrate a non-empty list of resolvable sub-skill slugs.
diff --git a/scripts/synthesize_meta_skill.py b/scripts/synthesize_meta_skill.py
index 04e4c00b9..909145bf2 100644
--- a/scripts/synthesize_meta_skill.py
+++ b/scripts/synthesize_meta_skill.py
@@ -1,4 +1,5 @@
-"""Synthesizer helper for auto-created **super-skills** (synthetic provenance).
+"""Synthesizer helper for auto-created **super-skills** (synthetic, or
+review-grounded **literature**, provenance).
 
 The deterministic half of the ``synthesize-meta-skill`` flow (the agentic
 ``commands/synthesize-meta-skill.md`` does the identify-the-pipeline + body
@@ -10,13 +11,15 @@
   (:func:`scripts.skill_match.match_skills`, injectable for tests) that gathers
   the candidate sub-skills clustered around a pipeline seed plus the tools they
   ground on (via :func:`scripts.skill_match.match_tools`).
-* :func:`meta_frontmatter` — assemble a schema-correct ``super``/``synthetic``
-  frontmatter, reusing :func:`scripts.normalize_skill.normalized_frontmatter`
-  (``provenance_tier="synthetic"``, ``status="hold"``) and adding
-  ``metadata.skill_kind="super"`` + ``metadata.orchestrates``. ``related_skills``
-  mirrors ``orchestrates`` so the result also satisfies the community
-  ``related_skills``-key expectation. Yields zero
-  :func:`scripts.normalize_skill.frontmatter_violations`.
+* :func:`meta_frontmatter` — assemble a schema-correct ``super`` frontmatter,
+  reusing :func:`scripts.normalize_skill.normalized_frontmatter`
+  (``status="hold"``) and adding ``metadata.skill_kind="super"`` +
+  ``metadata.orchestrates``. The default origin is ``synthetic`` (derived from the
+  orchestrated skills); passing a ``review_doi`` instead grounds the pipeline in a
+  *review article* → ``provenance_tier="literature"`` with ``metadata.dois`` +
+  ``derived_from`` carrying that DOI. ``related_skills`` mirrors ``orchestrates``
+  so the result also satisfies the community ``related_skills``-key expectation.
+  Yields zero :func:`scripts.normalize_skill.frontmatter_violations`.
 * :func:`stage_meta_skill` — stage the synthesized SKILL.md + a
   ``wave-meta-skills-<date>.yaml`` ledger, **reusing
   :mod:`scripts.propose_skill`'s** idempotent writers (DRY; same proposals rail).
@@ -90,37 +93,57 @@ def meta_frontmatter(
     synthesized_from,
     tools_used,
     license_tier: str = "open",
+    review_doi: str | None = None,
 ) -> dict:
-    """Assemble a schema-correct super-skill (synthetic) frontmatter.
+    """Assemble a schema-correct super-skill frontmatter (synthetic or literature).
 
-    Reuses :func:`scripts.normalize_skill.normalized_frontmatter` with
-    ``provenance_tier="synthetic"`` and ``status="hold"`` (so the deterministic
-    EDAM/tool/tier assembly is shared with the community rail), then layers the
-    super-skill invariants the proposals gate checks:
+    Reuses :func:`scripts.normalize_skill.normalized_frontmatter` and
+    ``status="hold"`` (so the deterministic EDAM/tool/tier assembly is shared with
+    the community rail), then layers the super-skill invariants the proposals gate
+    checks:
 
     * ``metadata.skill_kind = "super"``,
     * ``metadata.orchestrates = orchestrates`` (the sub-skill slugs it sequences),
-    * ``metadata.synthesized_from = synthesized_from`` (the synthetic-provenance
-      invariant — non-empty list).
-
-    ``related_skills`` mirrors ``orchestrates`` so a synthetic super-skill also
-    satisfies any community ``related_skills``-key expectation. The result yields
-    zero :func:`scripts.normalize_skill.frontmatter_violations`. Inputs are not
-    mutated.
+    * ``metadata.synthesized_from = synthesized_from`` (the source skill slugs;
+      kept non-empty for the synthetic invariant and as provenance even for a
+      review-grounded super-skill).
+
+    Origin (``provenance_tier``):
+
+    * **default (synthetic)** — ``review_doi is None``: the super-skill is derived
+      from the skills it orchestrates (``provenance_tier="synthetic"``).
+    * **literature** — when a ``review_doi`` is given, the pipeline is grounded in a
+      *review article*: ``provenance_tier="literature"``, ``metadata.dois =
+      [review_doi]`` (the literature ⇒ ≥1 doi invariant), and
+      ``derived_from = [{"doi": review_doi}]``. The super orchestration
+      (``skill_kind``/``orchestrates``/``synthesized_from``) is preserved.
+
+    ``related_skills`` mirrors ``orchestrates`` so the super-skill also satisfies
+    any community ``related_skills``-key expectation. The result yields zero
+    :func:`scripts.normalize_skill.frontmatter_violations`. Inputs are not mutated.
     """
     raw = {"name": name, "description": description}
+    if review_doi:
+        provenance_tier = "literature"
+        derived_from = [{"doi": review_doi}]
+    else:
+        provenance_tier = "synthetic"
+        derived_from = None
     fm = normalized_frontmatter(
         raw,
         related_skills=list(orchestrates),
         tools_used=list(tools_used),
         license_tier=license_tier,
-        provenance_tier="synthetic",
+        provenance_tier=provenance_tier,
         status="hold",
+        derived_from=derived_from,
     )
     meta = fm["metadata"]
     meta["skill_kind"] = "super"
     meta["orchestrates"] = list(orchestrates)
     meta["synthesized_from"] = list(synthesized_from)
+    if review_doi:
+        meta["dois"] = [review_doi]
     return fm
 
 
diff --git a/tests/test_check_proposals.py b/tests/test_check_proposals.py
index 253ec0939..f691453d6 100644
--- a/tests/test_check_proposals.py
+++ b/tests/test_check_proposals.py
@@ -70,6 +70,48 @@ def _synthetic_fm(
     return fm
 
 
+def _literature_fm(
+    slug="my-review-meta-skill",
+    tools_used=None,
+    dois=("10.1021/acs.analchem.0c01234",),
+    synthesized_from=("lc-ms-feature-extraction", "spectral-similarity-scoring"),
+    skill_kind="super",
+    orchestrates=("lc-ms-feature-extraction", "spectral-similarity-scoring"),
+    **overrides,
+):
+    """A review-grounded (literature-provenance) staged super-skill frontmatter.
+
+    Literature proposals are valid via >=1 source ``metadata.dois`` (the review
+    DOI), while keeping the super orchestration invariants.
+    """
+    meta = {
+        "edam_operation": "http://edamontology.org/operation_3215",
+        "edam_topics": ["http://edamontology.org/topic_0091"],
+        "license_tier": "open",
+        "provenance_tier": "literature",
+        "tools_used": ["mzmine"] if tools_used is None else tools_used,
+    }
+    if dois is not None:
+        meta["dois"] = list(dois)
+    if synthesized_from is not None:
+        meta["synthesized_from"] = list(synthesized_from)
+    if skill_kind is not None:
+        meta["skill_kind"] = skill_kind
+    if orchestrates is not None:
+        meta["orchestrates"] = list(orchestrates)
+    fm = {
+        "name": slug,
+        "description": VALID_DESC,
+        "license": "CC-BY-4.0",
+        "metadata": meta,
+        "status": "hold",
+    }
+    if dois is not None:
+        fm["derived_from"] = [{"doi": d} for d in dois]
+    fm.update(overrides)
+    return fm
+
+
 def _write_skill(col, fm, body="# Skill\n\nbody\n"):
     slug = fm["name"]
     d = col / "proposals" / "skills" / slug
@@ -115,13 +157,13 @@ def test_clean_staged_skill_passes(tmp_path):
 
 # --- bad provenance tier -----------------------------------------------------
 
-def test_non_community_provenance_tier_fails(tmp_path):
+def test_unknown_provenance_tier_fails(tmp_path):
     col = _collection(tmp_path)
     fm = _good_fm()
-    fm["metadata"]["provenance_tier"] = "literature"
+    fm["metadata"]["provenance_tier"] = "made-up"
     _write_skill(col, fm)
     v = c.check_collection(str(col))
-    assert any("provenance_tier" in x and "community" in x for x in v)
+    assert any("provenance_tier" in x and "made-up" in x for x in v)
 
 
 # --- missing related_skills key ----------------------------------------------
@@ -269,6 +311,46 @@ def test_invalid_skill_kind_fails(tmp_path):
     assert any("skill_kind" in x for x in v)
 
 
+# --- literature provenance (review-grounded super-skills) --------------------
+
+def test_clean_literature_super_skill_passes(tmp_path):
+    # A review-grounded super-skill is valid via >=1 source DOI + a resolvable
+    # orchestrates list — no community related_skills key required.
+    col = _collection(tmp_path)
+    _write_skill(col, _literature_fm())
+    assert c.check_collection(str(col)) == []
+
+
+def test_literature_without_doi_fails(tmp_path):
+    col = _collection(tmp_path)
+    fm = _literature_fm(dois=None)
+    _write_skill(col, fm)
+    v = c.check_collection(str(col))
+    assert any("doi" in x.lower() for x in v)
+
+
+def test_literature_with_empty_dois_fails(tmp_path):
+    col = _collection(tmp_path)
+    fm = _literature_fm()
+    fm["metadata"]["dois"] = []
+    _write_skill(col, fm)
+    v = c.check_collection(str(col))
+    assert any("doi" in x.lower() for x in v)
+
+
+def test_literature_super_still_resolves_orchestrates(tmp_path):
+    # The super invariants apply regardless of provenance: a literature super
+    # with a dangling orchestrate slug must fail.
+    col = _collection(tmp_path)
+    fm = _literature_fm(
+        synthesized_from=("lc-ms-feature-extraction", "ghost-skill"),
+        orchestrates=("lc-ms-feature-extraction", "ghost-skill"),
+    )
+    _write_skill(col, fm)
+    v = c.check_collection(str(col))
+    assert any("ghost-skill" in x for x in v)
+
+
 def test_community_skill_with_super_kind_resolves_orchestrates(tmp_path):
     # skill_kind/orchestrates apply regardless of provenance; a community super
     # with a dangling orchestrate slug must fail.
diff --git a/tests/test_synthesize_meta_skill.py b/tests/test_synthesize_meta_skill.py
index 132dce917..83edbd2ac 100644
--- a/tests/test_synthesize_meta_skill.py
+++ b/tests/test_synthesize_meta_skill.py
@@ -188,6 +188,74 @@ def test_meta_frontmatter_does_not_mutate_inputs():
     assert tools == list(TOOLS)
 
 
+# --- meta_frontmatter: review-grounded (literature) super-skills -------------
+
+REVIEW_DOI = "10.1021/acs.analchem.0c01234"
+
+
+def test_meta_frontmatter_review_doi_sets_literature_tier():
+    # A review DOI flips the origin to literature: provenance_tier="literature",
+    # dois=[review_doi], derived_from=[{doi: review_doi}], keeping the super
+    # orchestration intact.
+    fm = s.meta_frontmatter(
+        name="molecular-networking",
+        description=VALID_DESC,
+        orchestrates=list(SUBSKILLS),
+        synthesized_from=list(SUBSKILLS),
+        tools_used=list(TOOLS),
+        review_doi=REVIEW_DOI,
+    )
+    meta = fm["metadata"]
+    assert meta["provenance_tier"] == "literature"
+    assert meta["dois"] == [REVIEW_DOI]
+    assert fm["derived_from"] == [{"doi": REVIEW_DOI}]
+    # super orchestration is preserved
+    assert meta["skill_kind"] == "super"
+    assert meta["orchestrates"] == list(SUBSKILLS)
+    assert meta["synthesized_from"] == list(SUBSKILLS)
+    assert fm["status"] == "hold"
+    assert frontmatter_violations(fm) == []
+
+
+def test_meta_frontmatter_default_path_stays_synthetic():
+    # Without a review DOI, the default path is unchanged: synthetic, no dois,
+    # no derived_from.
+    fm = s.meta_frontmatter(
+        name="molecular-networking",
+        description=VALID_DESC,
+        orchestrates=list(SUBSKILLS),
+        synthesized_from=list(SUBSKILLS),
+        tools_used=list(TOOLS),
+    )
+    meta = fm["metadata"]
+    assert meta["provenance_tier"] == "synthetic"
+    assert "dois" not in meta
+    assert "derived_from" not in fm
+
+
+def test_meta_frontmatter_review_doi_passes_check_collection(tmp_path):
+    # A staged review-grounded (literature) super-skill is accepted by the gate.
+    col = _collection(tmp_path)
+    fm = s.meta_frontmatter(
+        name="molecular-networking",
+        description=VALID_DESC,
+        orchestrates=list(SUBSKILLS),
+        synthesized_from=list(SUBSKILLS),
+        tools_used=list(TOOLS),
+        review_doi=REVIEW_DOI,
+    )
+    ledger_meta = {
+        "slug": "molecular-networking",
+        "synthesized_from": list(SUBSKILLS),
+        "orchestrates": list(SUBSKILLS),
+        "tools_used": list(TOOLS),
+        "license_tier": "open",
+        "date": "2026-06-26",
+    }
+    s.stage_meta_skill(str(col), fm, BODY, ledger_meta)
+    assert cp.check_collection(str(col)) == []
+
+
 # --- stage_meta_skill --------------------------------------------------------
 
 BODY = "# Molecular Networking\n\nOrdered orchestration body.\n"

From ee68c14c2059d697352ba4940b4cc0fe484db3b0 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Louis-F=C3=A9lix=20Nothias?= <louis-felix.nothias@cnrs.fr>
Date: Fri, 26 Jun 2026 17:52:42 -0300
Subject: [PATCH 3/3] =?UTF-8?q?fix(#4):=20drop=20vendored=20asb=5Fskill=5F?=
 =?UTF-8?q?bundle.yaml=20=E2=80=94=20schema=20belongs=20in=20the=20asb-sch?=
 =?UTF-8?q?ema=20package?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

The LinkML Tool-class slots (license_tier/license/license_detection) should be
added in the unpublished asb-schema sibling package, not vendored as a 639-line
copy here (divergence risk; the gate is warn-only + asb-schema not on PyPI, so
this preserves dev's behavior). The real deliverable — 909 enriched tools/*.yaml
+ the check_tools_index cross-check + enrich_tool_yaml — is retained.

FOLLOW-UP (asb-schema repo): add the 3 license slots to the Tool class so the
enriched tools/*.yaml validate once asb-schema is published.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 asb_skill_bundle.yaml | 639 ------------------------------------------
 1 file changed, 639 deletions(-)
 delete mode 100644 asb_skill_bundle.yaml

diff --git a/asb_skill_bundle.yaml b/asb_skill_bundle.yaml
deleted file mode 100644
index 85d1a7b17..000000000
--- a/asb_skill_bundle.yaml
+++ /dev/null
@@ -1,639 +0,0 @@
-id: https://w3id.org/holobiomicslab/asb-schema/skill-bundle/v0.2
-name: asb_skill_bundle_v0_2
-description: >-
-  LinkML schema for SciTask Skill Bundle v0.1 — a versioned, curated description of
-  one reusable computational skill identified across multiple papers. Each bundle
-  contains a human-readable skill description and 12 structured sidecars.
-
-license: CC-BY-4.0
-version: "0.2.0"
-
-prefixes:
-  linkml:   https://w3id.org/linkml/
-  asb:      https://w3id.org/holobiomicslab/asb-schema/
-  asbskill: https://w3id.org/holobiomicslab/asb-skill/
-  schema:   http://schema.org/
-  dcterms:  http://purl.org/dc/terms/
-  pplan:    http://purl.org/net/p-plan#
-  prov:     http://www.w3.org/ns/prov#
-  EDAM:     http://edamontology.org/
-  rocrate:  https://w3id.org/ro/crate#
-
-imports:
-  - linkml:types
-
-default_prefix: asb
-default_range: string
-
-# ---------------------------------------------------------------------------
-# Classes
-# ---------------------------------------------------------------------------
-
-classes:
-
-  ToolRecord:
-    description: >-
-      A tool referenced in a Skill Bundle's tools.json sidecar.
-    attributes:
-      tool_name:
-        description: Tool name (e.g. matchms, scikit-learn)
-        range: string
-        required: true
-        annotations:
-          importance: must_have
-        close_mappings:
-          - EDAM:operation_0004
-      canonical_url:
-        description: Canonical URL (GitHub, bio.tools, PyPI, etc.)
-        range: uri
-        annotations:
-          importance: should_have
-        close_mappings:
-          - schema:codeRepository
-      version:
-        description: Version string used or recommended
-        range: string
-        annotations:
-          importance: should_have
-        close_mappings:
-          - schema:softwareVersion
-      tool_description:
-        description: Short description of the tool
-        range: string
-        annotations:
-          importance: should_have
-        exact_mappings:
-          - schema:description
-      edam_topics:
-        description: EDAM topic IRIs for this tool
-        range: uri
-        multivalued: true
-        annotations:
-          importance: nice_to_have
-        exact_mappings:
-          - EDAM:topic_0003
-
-  PaperReference:
-    description: A reference to a source paper that contributed to this skill bundle.
-    attributes:
-      doi:
-        description: DOI of the paper
-        range: string
-        annotations:
-          importance: should_have
-        exact_mappings:
-          - schema:identifier
-      title:
-        description: Title of the paper
-        range: string
-        annotations:
-          importance: must_have
-        exact_mappings:
-          - schema:name
-      relevance:
-        description: Short note on the relevance of this paper to the skill
-        range: string
-        annotations:
-          importance: nice_to_have
-        close_mappings:
-          - schema:description
-      task_ids:
-        description: task_id values from this paper that surfaced this skill
-        range: string
-        multivalued: true
-        annotations:
-          importance: nice_to_have
-        close_mappings:
-          - dcterms:isPartOf
-
-  MergeAuditRecord:
-    description: >-
-      Per-merge audit record documenting alias deduplication decisions.
-      Surfaces the data ``corpus_artifacts._semantic_dedup`` already records
-      so dedup decisions are queryable and citable (IDEAS-E / spec §11).
-    attributes:
-      alias:
-        description: Original skill label before deduplication
-        range: string
-        required: true
-        annotations:
-          importance: must_have
-        close_mappings:
-          - schema:alternateName
-      target_slug:
-        description: Canonical slug this alias was merged into
-        range: string
-        required: true
-        annotations:
-          importance: must_have
-        exact_mappings:
-          - schema:identifier
-      jaccard_score:
-        description: Token-set Jaccard similarity score used for the merge decision
-        range: float
-        annotations:
-          importance: should_have
-        close_mappings:
-          - schema:value
-      embedding_cosine:
-        description: Cosine similarity of MiniLM embeddings (when semantic dedup ran)
-        range: float
-        annotations:
-          importance: should_have
-        close_mappings:
-          - schema:value
-      edam_match:
-        description: True when both records share an EDAM operation IRI
-        range: boolean
-        annotations:
-          importance: nice_to_have
-        close_mappings:
-          - schema:sameAs
-      llm_judge_verdict:
-        description: Free-form judgement string from an LLM dedup judge (if used)
-        range: string
-        annotations:
-          importance: nice_to_have
-        close_mappings:
-          - schema:description
-      method:
-        description: Deduplication method (e.g. token_set_jaccard, semantic_embed, llm_judge)
-        range: string
-        annotations:
-          importance: should_have
-        close_mappings:
-          - prov:wasGeneratedBy
-      decision:
-        description: Final merge decision
-        range: MergeDecisionEnum
-        required: true
-        annotations:
-          importance: must_have
-        close_mappings:
-          - prov:wasInfluencedBy
-      decided_at:
-        description: When the merge decision was recorded (ISO 8601)
-        range: datetime
-        annotations:
-          importance: should_have
-        close_mappings:
-          - prov:generatedAtTime
-      decided_by:
-        description: Agent or person that made the decision (e.g. "agent:dedup", "orcid:0000-...")
-        range: string
-        annotations:
-          importance: should_have
-        close_mappings:
-          - prov:wasAttributedTo
-
-  SkillBundle:
-    description: >-
-      A versioned, curated description of one reusable computational skill
-      identified across multiple papers. Contains a human-readable skill
-      description and 12 structured sidecars (papers, parameters, failure modes,
-      tools, environments, links, etc.).
-    tree_root: true
-    slots:
-      - slug
-      - skill_name
-      - skill_description
-      - when_to_use
-      - skill_tools
-      - edam_topics
-      - edam_operation
-      - scripts
-      - skill_kb_path
-      - bundle_dir
-      - bundle_version
-      - source_task_ids
-      - source_papers
-      - merged_aliases
-      - merged_alias_records
-
-  ASBSkill:
-    description: >-
-      Collection-time aggregated skill record — the deduplicated, paper-grounded
-      scientific competency surfaced by ``corpus_artifacts.collect_skills`` at
-      release time. Distinct from ``SkillBundle`` which is the per-capsule
-      artifact. Mirrors the Python dataclass at agentic_science_builder.schemas.ASBSkill
-      (renamed from SciSkill in Plan 2a / ASB-runtime).
-    slots:
-      - slug
-      - skill_name
-      - description
-      - when_to_use
-      - related_tools
-      - source_task_ids
-      - source_paper_doi
-      - source_paper_title
-      - source_papers
-      - merged_aliases
-      - merged_alias_records
-      - edam_operation
-      - edam_topics
-      - kb_path
-      - bundle_dir
-
-  ASBTool:
-    description: >-
-      Collection-time aggregated tool record — the deduplicated, paper-grounded
-      software-tool reference surfaced by ``corpus_artifacts.collect_tools``.
-      Mirrors the Python dataclass at agentic_science_builder.schemas.ASBTool
-      (renamed from SciTool in Plan 2a / ASB-runtime).
-    slots:
-      - slug
-      - tool_name
-      - canonical_url
-      - related_skills
-      - source_task_ids
-      - source_paper_doi
-      - source_paper_title
-      - evidence_spans
-      - version_used
-      - install
-      - resolution_attempts
-      - edam_operation
-      - edam_topics
-      - bio_tools_id
-      - license_tier
-      - license
-      - license_detection
-
-  ToolAffordance:
-    description: >-
-      W3C WoT ActionAffordance-aligned mixin (IDEAS-F / spec §15).
-      RESERVED for v1 — slot definitions exist but no ASB class consumes
-      them yet. When the ecosystem standardises on WoT for executable
-      tools, ASBTool (or an ExecutableTool subclass) will inherit from
-      this mixin without breaking existing instances.
-    mixin: true
-    slots:
-      - input_schema
-      - output_schema
-      - precondition
-      - effect
-      - side_effect_free
-
-# ---------------------------------------------------------------------------
-# Slots
-# ---------------------------------------------------------------------------
-
-slots:
-
-  slug:
-    description: >-
-      Lowercase, hyphen-separated unique identifier for this skill bundle
-      (e.g. spectral-similarity-scoring)
-    range: string
-    required: true
-    annotations:
-      importance: must_have
-    exact_mappings:
-      - schema:identifier
-
-  skill_name:
-    description: Human-readable canonical name of the skill
-    range: string
-    required: true
-    annotations:
-      importance: must_have
-    exact_mappings:
-      - schema:name
-
-  skill_description:
-    description: Full description of the skill's purpose and scope
-    range: string
-    annotations:
-      importance: must_have
-    exact_mappings:
-      - schema:description
-
-  when_to_use:
-    description: Guidance on when and how to apply this skill
-    range: string
-    annotations:
-      importance: should_have
-    close_mappings:
-      - pplan:Plan
-
-  skill_tools:
-    description: Tool records for tools associated with this skill
-    range: ToolRecord
-    multivalued: true
-    annotations:
-      importance: must_have
-    close_mappings:
-      - EDAM:operation_0004
-
-  edam_topics:
-    description: EDAM topic IRIs for this skill (e.g. http://edamontology.org/topic_3172)
-    range: uri
-    multivalued: true
-    annotations:
-      importance: should_have
-    exact_mappings:
-      - EDAM:topic_0003
-
-  edam_operation:
-    description: Primary EDAM operation IRI for this skill (e.g. http://edamontology.org/operation_3799)
-    range: uri
-    annotations:
-      importance: should_have
-    exact_mappings:
-      - EDAM:operation_0004
-
-  scripts:
-    description: >-
-      Paths to embedded script chunks from linked GitHub repositories
-      (line-range copies, not full clones)
-    range: string
-    multivalued: true
-    annotations:
-      importance: nice_to_have
-    exact_mappings:
-      - prov:atLocation
-
-  skill_kb_path:
-    description: Relative path to the skill's knowledge base entry file (e.g. docs/skill_name.md)
-    range: string
-    annotations:
-      importance: nice_to_have
-    exact_mappings:
-      - prov:atLocation
-
-  bundle_dir:
-    description: Absolute path to the offline skill knowledge base bundle directory
-    range: string
-    annotations:
-      importance: nice_to_have
-    exact_mappings:
-      - prov:atLocation
-
-  bundle_version:
-    description: Version of this skill bundle (e.g. 0.1.0)
-    range: string
-    required: true
-    annotations:
-      importance: must_have
-    close_mappings:
-      - schema:version
-
-  source_task_ids:
-    description: task_id values of the SciTask Cards from which this skill was extracted
-    range: string
-    multivalued: true
-    annotations:
-      importance: should_have
-    close_mappings:
-      - dcterms:isPartOf
-
-  source_papers:
-    description: Structured references to papers that contributed to this bundle
-    range: PaperReference
-    multivalued: true
-    annotations:
-      importance: should_have
-    close_mappings:
-      - dcterms:source
-
-  merged_aliases:
-    description: Original labels of skills merged into this canonical entry
-    range: string
-    multivalued: true
-    annotations:
-      importance: nice_to_have
-    close_mappings:
-      - schema:alternateName
-
-  merged_alias_records:
-    description: Per-merge audit records documenting alias deduplication decisions
-    range: MergeAuditRecord
-    multivalued: true
-    annotations:
-      importance: nice_to_have
-    close_mappings:
-      - prov:wasGeneratedBy
-
-  description:
-    description: >-
-      Retrieval-key description for an ASBSkill. Discipline-constrained
-      (IDEAS-D / spec §5): 50–300 chars, leads with "Use when …", no marketing
-      tokens. The CI gate in asb-skill-collections additionally enforces the
-      banned-token list at release time.
-    range: string
-    required: true
-    minimum_value: 50
-    maximum_value: 300
-    pattern: "^[Uu]se when .+"
-    annotations:
-      importance: must_have
-      banned_tokens:
-        - revolutionary
-        - cutting-edge
-        - best-in-class
-        - powerful
-        - amazing
-        - state-of-the-art
-        - groundbreaking
-    exact_mappings:
-      - schema:description
-
-  related_tools:
-    description: Canonical URLs / slugs of tools used by this skill
-    range: string
-    multivalued: true
-    annotations:
-      importance: should_have
-    close_mappings:
-      - EDAM:operation_0004
-
-  source_paper_doi:
-    description: Primary source paper DOI (flat field, complements source_papers[])
-    range: string
-    annotations:
-      importance: should_have
-    exact_mappings:
-      - schema:identifier
-
-  source_paper_title:
-    description: Primary source paper title (flat field, complements source_papers[])
-    range: string
-    annotations:
-      importance: nice_to_have
-    exact_mappings:
-      - schema:name
-
-  kb_path:
-    description: Relative path to the skill's knowledge-base entry file
-    range: string
-    annotations:
-      importance: nice_to_have
-    exact_mappings:
-      - prov:atLocation
-
-  tool_name:
-    description: Tool name (mirrors ToolRecord.tool_name; used by ASBTool)
-    range: string
-    required: true
-    annotations:
-      importance: must_have
-    close_mappings:
-      - schema:name
-
-  canonical_url:
-    description: Canonical URL for the tool (GitHub, bio.tools, PyPI, etc.)
-    range: uri
-    annotations:
-      importance: should_have
-    close_mappings:
-      - schema:codeRepository
-
-  related_skills:
-    description: Slugs of ASBSkill records that reference this tool
-    range: string
-    multivalued: true
-    annotations:
-      importance: should_have
-    close_mappings:
-      - dcterms:isPartOf
-
-  evidence_spans:
-    description: Verbatim quotes from source papers anchoring this tool reference
-    range: string
-    multivalued: true
-    annotations:
-      importance: should_have
-    close_mappings:
-      - prov:wasDerivedFrom
-
-  version_used:
-    description: Version string actually used in the source paper(s)
-    range: string
-    annotations:
-      importance: nice_to_have
-    close_mappings:
-      - schema:softwareVersion
-
-  install:
-    description: Install metadata dict (conda / pip / docker / etc.) produced by tool_resolver
-    range: string
-    annotations:
-      importance: nice_to_have
-    close_mappings:
-      - schema:installUrl
-
-  resolution_attempts:
-    description: Audit list of resolver attempts (each entry a dict; serialized as JSON)
-    range: string
-    multivalued: true
-    annotations:
-      importance: nice_to_have
-    close_mappings:
-      - prov:wasGeneratedBy
-
-  bio_tools_id:
-    description: >-
-      bio.tools identifier for this tool (IDEAS-G). Reserved slot for the
-      future bio.tools federation work; not populated in v1.
-    range: string
-    annotations:
-      importance: nice_to_have
-    close_mappings:
-      - schema:identifier
-
-  license_tier:
-    description: >-
-      Consumer-facing license tier for this tool, rolled up most-restrictively
-      across its source papers/repos (open / noncommercial / restricted). The
-      same value carried in tools_index.json; propagated into tools/<slug>.yaml
-      by scripts/enrich_tool_yaml.py.
-    range: LicenseTierEnum
-    annotations:
-      importance: should_have
-    close_mappings:
-      - schema:license
-
-  license:
-    description: >-
-      Detected SPDX-ish license identifier for the tool's primary repo
-      (e.g. MIT, GPL-2.0, CC-BY-NC-4.0); null when undetected.
-    range: string
-    annotations:
-      importance: nice_to_have
-    exact_mappings:
-      - schema:license
-
-  license_detection:
-    description: >-
-      How the license was detected (e.g. github-api, readme-llm, none) — audit
-      trail for the license_tier rollup.
-    range: string
-    annotations:
-      importance: nice_to_have
-    close_mappings:
-      - prov:wasGeneratedBy
-
-  input_schema:
-    description: JSON Schema describing the tool's input payload (WoT ActionAffordance.input)
-    range: string
-    annotations:
-      importance: nice_to_have
-    close_mappings:
-      - schema:potentialAction
-
-  output_schema:
-    description: JSON Schema describing the tool's output payload (WoT ActionAffordance.output)
-    range: string
-    annotations:
-      importance: nice_to_have
-    close_mappings:
-      - schema:potentialAction
-
-  precondition:
-    description: Free-form precondition (e.g. "requires CUDA 12.x") — WoT-style affordance hint
-    range: string
-    annotations:
-      importance: nice_to_have
-    close_mappings:
-      - prov:wasInfluencedBy
-
-  effect:
-    description: Free-form effect description for downstream agents
-    range: string
-    annotations:
-      importance: nice_to_have
-    close_mappings:
-      - prov:generated
-
-  side_effect_free:
-    description: True when invoking the tool has no observable side effects (pure function)
-    range: boolean
-    annotations:
-      importance: nice_to_have
-    close_mappings:
-      - schema:propertyID
-
-enums:
-  MergeDecisionEnum:
-    description: Possible outcomes recorded by a MergeAuditRecord
-    permissible_values:
-      auto_merge:
-        description: Auto-merged above the auto threshold
-      manual_merge:
-        description: Manually merged by a curator
-      kept_separate:
-        description: Reviewed and explicitly kept as distinct entries
-      needs_review:
-        description: Pending human review
-
-  LicenseTierEnum:
-    description: >-
-      Consumer-facing license tier, orthogonal to open-access status. Governs
-      acknowledgement / link-only handling for tools and skills.
-    permissible_values:
-      open:
-        description: Permissive / open license — freely reusable
-      noncommercial:
-        description: Noncommercial-only license (e.g. CC-BY-NC) — requires acknowledgement
-      restricted:
-        description: Restricted or undetected license — link-only, conservative default