upstream/inoue0426-awesome-computational-biology/catalogue/README.md

@@ -2,9 +2,9 @@
 title: "Awesome Computational Biology [![Awesome](https://awesome.re/badge.svg)](https://awesome.re)"
 task: ""
 lineage_type: import
-upstream_source: https://github.com/inoue0426/awesome-computational-biology/blob/7a064bf0/README.md
+upstream_source: https://github.com/inoue0426/awesome-computational-biology/blob/92dbe563/README.md
-upstream_sha: 7a064bf0
+upstream_sha: 92dbe563
-imported_at: 2026-08-08
+imported_at: 2026-08-14
 prompt_class: catalogue
 upstream_changes: accepted
 author: upstream
@@ -159,6 +159,7 @@ Browse and search the resources via the [GitHub Pages UI](https://inoue0426.gith
 - [GenBank](https://www.ncbi.nlm.nih.gov/genbank/) — NCBI's database of genetic sequences.
 - [UCSC Genome Browser](https://genome.ucsc.edu/) — UCSC's genome browser.
 - [cBioPortal](https://www.cbioportal.org/) — Cancer genomics database; aggregating many patient datasets.
+- [OncoKB](https://www.oncokb.org/) — Precision oncology knowledge base of cancer genes, variants, and therapeutic implications.
 - [10x Genomics Dataset](https://www.10xgenomics.com/resources/datasets) — Collection of single-cell datasets.
 - [The Genotype-Tissue Expression (GTEx)](https://gtexportal.org/home/) — Human gene expression and regulation resource.
 - [Dependency Map (DepMap)](https://depmap.org/portal/) — CRISPR-Cas9 screens in cancer cell lines.

upstream/inoue0426-awesome-computational-biology/catalogue/cspell.json

@@ -2,9 +2,9 @@
 title: "Cspell"
 task: ""
 lineage_type: import
-upstream_source: https://github.com/inoue0426/awesome-computational-biology/blob/7a064bf0/cspell.json
+upstream_source: https://github.com/inoue0426/awesome-computational-biology/blob/92dbe563/cspell.json
-upstream_sha: 7a064bf0
+upstream_sha: 92dbe563
-imported_at: 2026-08-08
+imported_at: 2026-08-14
 prompt_class: unknown
 upstream_changes: accepted
 author: upstream
@@ -59,6 +59,7 @@ validated: false
     "eukaryotic",
     "metabolites",
     "OMIM",
+    "OncoKB",
     "Mendelian",
     "DisGeNET",
     "GWAS",

upstream/inoue0426-awesome-computational-biology/catalogue/data/enrichment.cancer-databases-v1.yml

@@ -0,0 +1,96 @@
+---
+title: "Provenance-backed cancer and pharmacogenomics database enrichment batch."
+task: ""
+lineage_type: import
+upstream_source: https://github.com/inoue0426/awesome-computational-biology/blob/92dbe563/data/enrichment.cancer-databases-v1.yml
+upstream_sha: 92dbe563
+imported_at: 2026-08-14
+prompt_class: catalogue
+upstream_changes: accepted
+author: upstream
+validated: false
+---
+
+# Provenance-backed cancer and pharmacogenomics database enrichment batch.
+resources:
+  cancer_cell_line_encyclopedia:
+    entities: [cell, gene, disease, drug]
+    modalities: [genomics, transcriptomics]
+    documentation: https://sites.broadinstitute.org/ccle/
+    last_checked: 2026-08-08
+    metadata_sources:
+      - https://sites.broadinstitute.org/ccle/
+
+  catalogue_of_somatic_mutations_in_cancer_cosmic:
+    entities: [disease, gene, variant]
+    modalities: [genomics]
+    documentation: https://cancer.sanger.ac.uk/cosmic
+    last_checked: 2026-08-08
+    metadata_sources:
+      - https://cancer.sanger.ac.uk/cosmic
+
+  cbioportal:
+    entities: [disease, gene, variant]
+    modalities: [genomics, clinical]
+    github: https://github.com/cBioPortal/cbioportal
+    documentation: https://www.cbioportal.org/
+    last_checked: 2026-08-08
+    metadata_sources:
+      - https://www.cbioportal.org/
+      - https://github.com/cBioPortal/cbioportal
+
+  dependency_map_depmap:
+    entities: [cell, gene, disease, drug]
+    modalities: [genomics]
+    documentation: https://depmap.org/portal/
+    last_checked: 2026-08-08
+    metadata_sources:
+      - https://depmap.org/portal/
+
+  dgidb:
+    entities: [drug, gene]
+    modalities: [knowledge-graph]
+    documentation: https://www.dgidb.org/
+    last_checked: 2026-08-08
+    metadata_sources:
+      - https://www.dgidb.org/
+
+  drug_mechanism_database_drugmechdb:
+    entities: [drug, disease, gene, pathway]
+    modalities: [knowledge-graph]
+    github: https://github.com/SuLab/DrugMechDB
+    last_checked: 2026-08-08
+    metadata_sources:
+      - https://github.com/SuLab/DrugMechDB
+
+  drug_repurposing_hub:
+    entities: [drug, protein, disease]
+    modalities: [chemical-structure]
+    documentation: https://repo-hub.broadinstitute.org/repurposing
+    last_checked: 2026-08-08
+    metadata_sources:
+      - https://repo-hub.broadinstitute.org/repurposing
+
+  drugcentral:
+    entities: [drug, protein, disease]
+    modalities: [chemical-structure]
+    documentation: https://drugcentral.org/
+    last_checked: 2026-08-08
+    metadata_sources:
+      - https://drugcentral.org/
+
+  drugtargetcommons:
+    entities: [drug, protein]
+    modalities: [chemical-structure]
+    documentation: https://drugtargetcommons.fimm.fi/
+    last_checked: 2026-08-08
+    metadata_sources:
+      - https://drugtargetcommons.fimm.fi/
+
+  comparative_toxicogenomics_database:
+    entities: [compound, gene, disease]
+    modalities: [knowledge-graph]
+    documentation: https://ctdbase.org/
+    last_checked: 2026-08-08
+    metadata_sources:
+      - https://ctdbase.org/

upstream/inoue0426-awesome-computational-biology/catalogue/data/enrichment.core-databases-v1.yml

@@ -0,0 +1,94 @@
+---
+title: "Provenance-backed core biological database enrichment batch."
+task: ""
+lineage_type: import
+upstream_source: https://github.com/inoue0426/awesome-computational-biology/blob/92dbe563/data/enrichment.core-databases-v1.yml
+upstream_sha: 92dbe563
+imported_at: 2026-08-14
+prompt_class: catalogue
+upstream_changes: accepted
+author: upstream
+validated: false
+---
+
+# Provenance-backed core biological database enrichment batch.
+resources:
+  10x_genomics_dataset:
+    entities: [cell, gene]
+    modalities: [single-cell-rna-seq, genomics]
+    documentation: https://www.10xgenomics.com/resources/datasets
+    last_checked: 2026-08-08
+    metadata_sources:
+      - https://www.10xgenomics.com/resources/datasets
+
+  alphafold_protein_structure_database:
+    entities: [protein]
+    modalities: [molecular-structure, protein-sequence]
+    documentation: https://alphafold.ebi.ac.uk/api-docs
+    last_checked: 2026-08-08
+    metadata_sources:
+      - https://alphafold.ebi.ac.uk/
+      - https://alphafold.ebi.ac.uk/api-docs
+
+  bindingdb:
+    entities: [molecule, protein]
+    modalities: [chemical-structure, molecular-structure]
+    documentation: https://www.bindingdb.org/rwd/bind/index.jsp
+    last_checked: 2026-08-08
+    metadata_sources:
+      - https://www.bindingdb.org/rwd/bind/index.jsp
+
+  biocyc:
+    entities: [gene, pathway, organism]
+    modalities: [genomics]
+    documentation: https://biocyc.org/
+    last_checked: 2026-08-08
+    metadata_sources:
+      - https://biocyc.org/
+
+  biogrid:
+    entities: [gene, protein]
+    documentation: https://thebiogrid.org/
+    last_checked: 2026-08-08
+    metadata_sources:
+      - https://thebiogrid.org/
+
+  cath_database:
+    entities: [protein]
+    modalities: [molecular-structure, protein-sequence]
+    documentation: https://www.cathdb.info/
+    last_checked: 2026-08-08
+    metadata_sources:
+      - https://www.cathdb.info/
+
+  chembl:
+    entities: [compound, molecule, protein]
+    modalities: [chemical-structure]
+    documentation: https://www.ebi.ac.uk/chembl/
+    last_checked: 2026-08-08
+    metadata_sources:
+      - https://www.ebi.ac.uk/chembl/
+
+  clinicaltrials_gov:
+    entities: [disease, drug]
+    modalities: [clinical]
+    documentation: https://clinicaltrials.gov/
+    last_checked: 2026-08-08
+    metadata_sources:
+      - https://clinicaltrials.gov/
+
+  cz_cellxgene:
+    entities: [cell, gene, tissue]
+    modalities: [single-cell-rna-seq, transcriptomics]
+    documentation: https://cellxgene.cziscience.com/
+    last_checked: 2026-08-08
+    metadata_sources:
+      - https://cellxgene.cziscience.com/
+
+  uniprot:
+    entities: [protein]
+    modalities: [protein-sequence]
+    documentation: https://www.uniprot.org/
+    last_checked: 2026-08-08
+    metadata_sources:
+      - https://www.uniprot.org/

upstream/inoue0426-awesome-computational-biology/catalogue/data/enrichment.toolkit-v1.yml

@@ -0,0 +1,113 @@
+---
+title: "Provenance-backed toolkit enrichment batch."
+task: ""
+lineage_type: import
+upstream_source: https://github.com/inoue0426/awesome-computational-biology/blob/92dbe563/data/enrichment.toolkit-v1.yml
+upstream_sha: 92dbe563
+imported_at: 2026-08-14
+prompt_class: catalogue
+upstream_changes: accepted
+author: upstream
+validated: false
+---
+
+# Provenance-backed toolkit enrichment batch.
+resources:
+  scanpy:
+    entities: [cell, gene]
+    modalities: [single-cell-rna-seq]
+    github: https://github.com/scverse/scanpy
+    documentation: https://scanpy.readthedocs.io/en/stable/
+    last_checked: 2026-08-08
+    metadata_sources:
+      - https://github.com/scverse/scanpy
+      - https://scanpy.readthedocs.io/en/stable/
+
+  seurat:
+    entities: [cell, gene]
+    modalities: [single-cell-rna-seq]
+    github: https://github.com/satijalab/seurat
+    documentation: https://satijalab.org/seurat/
+    last_checked: 2026-08-08
+    metadata_sources:
+      - https://github.com/satijalab/seurat
+      - https://satijalab.org/seurat/
+
+  scvi_tools:
+    entities: [cell, gene]
+    modalities: [single-cell-rna-seq, multi-omics]
+    github: https://github.com/scverse/scvi-tools
+    documentation: https://docs.scvi-tools.org/
+    last_checked: 2026-08-08
+    metadata_sources:
+      - https://github.com/scverse/scvi-tools
+      - https://docs.scvi-tools.org/
+
+  squidpy:
+    entities: [cell, tissue]
+    modalities: [spatial-transcriptomics]
+    github: https://github.com/scverse/squidpy
+    documentation: https://squidpy.readthedocs.io/
+    last_checked: 2026-08-08
+    metadata_sources:
+      - https://github.com/scverse/squidpy
+      - https://squidpy.readthedocs.io/
+
+  deepchem:
+    entities: [molecule, protein]
+    modalities: [chemical-structure, molecular-structure]
+    github: https://github.com/deepchem/deepchem
+    documentation: https://deepchem.readthedocs.io/
+    last_checked: 2026-08-08
+    metadata_sources:
+      - https://github.com/deepchem/deepchem
+      - https://deepchem.readthedocs.io/
+
+  rdkit:
+    entities: [molecule]
+    modalities: [chemical-structure]
+    github: https://github.com/rdkit/rdkit
+    documentation: https://www.rdkit.org/docs/
+    last_checked: 2026-08-08
+    metadata_sources:
+      - https://github.com/rdkit/rdkit
+      - https://www.rdkit.org/docs/
+
+  biopython:
+    entities: [gene, protein]
+    modalities: [dna-sequence, protein-sequence]
+    github: https://github.com/biopython/biopython
+    documentation: https://biopython.org/wiki/Documentation
+    last_checked: 2026-08-08
+    metadata_sources:
+      - https://github.com/biopython/biopython
+      - https://biopython.org/
+
+  cellchat:
+    entities: [cell, gene]
+    modalities: [single-cell-rna-seq]
+    github: https://github.com/sqjin/CellChat
+    last_checked: 2026-08-08
+    metadata_sources:
+      - https://github.com/sqjin/CellChat
+
+  celltypist:
+    entities: [cell, gene]
+    modalities: [single-cell-rna-seq]
+    tasks: [cell-type-annotation]
+    github: https://github.com/Teichlab/celltypist
+    documentation: https://celltypist.readthedocs.io/
+    last_checked: 2026-08-08
+    metadata_sources:
+      - https://github.com/Teichlab/celltypist
+      - https://celltypist.readthedocs.io/
+
+  cellcharter:
+    entities: [cell, tissue]
+    modalities: [spatial-transcriptomics]
+    github: https://github.com/CSOgroup/cellcharter
+    documentation: https://cellcharter.readthedocs.io/
+    last_checked: 2026-08-08
+    metadata_sources:
+      - https://github.com/CSOgroup/cellcharter
+      - https://cellcharter.readthedocs.io/

upstream/inoue0426-awesome-computational-biology/catalogue/data/resources.json

@@ -2,9 +2,9 @@
 title: "Resources"
 task: ""
 lineage_type: import
-upstream_source: https://github.com/inoue0426/awesome-computational-biology/blob/7a064bf0/data/resources.json
+upstream_source: https://github.com/inoue0426/awesome-computational-biology/blob/92dbe563/data/resources.json
-upstream_sha: 7a064bf0
+upstream_sha: 92dbe563
-imported_at: 2026-08-08
+imported_at: 2026-08-14
 prompt_class: catalogue
 upstream_changes: accepted
 author: upstream
@@ -899,10 +899,20 @@ validated: false
     ],
     "tasks": [],
     "modalities": [
-      "Genomics"
+      "single-cell-rna-seq",
+      "genomics"
     ],
     "organism": [],
-    "api": false
+    "api": false,
+    "entities": [
+      "cell",
+      "gene"
+    ],
+    "documentation": "https://www.10xgenomics.com/resources/datasets",
+    "last_checked": "2026-08-08",
+    "metadata_sources": [
+      "https://www.10xgenomics.com/resources/datasets"
+    ]
   },
   {
     "id": "alphafold_protein_structure_database",
@@ -915,10 +925,20 @@ validated: false
     ],
     "tasks": [],
     "modalities": [
-      "Protein"
+      "molecular-structure",
+      "protein-sequence"
     ],
     "organism": [],
-    "api": false
+    "api": false,
+    "entities": [
+      "protein"
+    ],
+    "documentation": "https://alphafold.ebi.ac.uk/api-docs",
+    "last_checked": "2026-08-08",
+    "metadata_sources": [
+      "https://alphafold.ebi.ac.uk/",
+      "https://alphafold.ebi.ac.uk/api-docs"
+    ]
   },
   {
     "id": "bindingdb",
@@ -932,11 +952,20 @@ validated: false
     ],
     "tasks": [],
     "modalities": [
-      "Protein",
+      "chemical-structure",
-      "Small Molecule"
+      "molecular-structure"
     ],
     "organism": [],
-    "api": false
+    "api": false,
+    "entities": [
+      "molecule",
+      "protein"
+    ],
+    "documentation": "https://www.bindingdb.org/rwd/bind/index.jsp",
+    "last_checked": "2026-08-08",
+    "metadata_sources": [
+      "https://www.bindingdb.org/rwd/bind/index.jsp"
+    ]
   },
   {
     "id": "biocyc",
@@ -949,10 +978,20 @@ validated: false
     ],
     "tasks": [],
     "modalities": [
-      "Pathway"
+      "genomics"
     ],
     "organism": [],
-    "api": false
+    "api": false,
+    "entities": [
+      "gene",
+      "pathway",
+      "organism"
+    ],
+    "documentation": "https://biocyc.org/",
+    "last_checked": "2026-08-08",
+    "metadata_sources": [
+      "https://biocyc.org/"
+    ]
   },
   {
     "id": "biogrid",
@@ -969,7 +1008,16 @@ validated: false
       "Protein"
     ],
     "organism": [],
-    "api": false
+    "api": false,
+    "entities": [
+      "gene",
+      "protein"
+    ],
+    "documentation": "https://thebiogrid.org/",
+    "last_checked": "2026-08-08",
+    "metadata_sources": [
+      "https://thebiogrid.org/"
+    ]
   },
   {
     "id": "cancer_cell_line_encyclopedia",
@@ -983,11 +1031,22 @@ validated: false
     ],
     "tasks": [],
     "modalities": [
-      "Gene Expression",
+      "genomics",
-      "Small Molecule"
+      "transcriptomics"
     ],
     "organism": [],
-    "api": false
+    "api": false,
+    "entities": [
+      "cell",
+      "gene",
+      "disease",
+      "drug"
+    ],
+    "documentation": "https://sites.broadinstitute.org/ccle/",
+    "last_checked": "2026-08-08",
+    "metadata_sources": [
+      "https://sites.broadinstitute.org/ccle/"
+    ]
   },
   {
     "id": "catalogue_of_somatic_mutations_in_cancer_cosmic",
@@ -1000,10 +1059,20 @@ validated: false
     ],
     "tasks": [],
     "modalities": [
-      "Genomics"
+      "genomics"
     ],
     "organism": [],
-    "api": false
+    "api": false,
+    "entities": [
+      "disease",
+      "gene",
+      "variant"
+    ],
+    "documentation": "https://cancer.sanger.ac.uk/cosmic",
+    "last_checked": "2026-08-08",
+    "metadata_sources": [
+      "https://cancer.sanger.ac.uk/cosmic"
+    ]
   },
   {
     "id": "cath_database",
@@ -1016,10 +1085,19 @@ validated: false
     ],
     "tasks": [],
     "modalities": [
-      "Protein"
+      "molecular-structure",
+      "protein-sequence"
     ],
     "organism": [],
-    "api": false
+    "api": false,
+    "entities": [
+      "protein"
+    ],
+    "documentation": "https://www.cathdb.info/",
+    "last_checked": "2026-08-08",
+    "metadata_sources": [
+      "https://www.cathdb.info/"
+    ]
   },
   {
     "id": "cbioportal",
@@ -1032,10 +1110,23 @@ validated: false
     ],
     "tasks": [],
     "modalities": [
-      "Genomics"
+      "genomics",
+      "clinical"
     ],
     "organism": [],
-    "api": false
+    "api": false,
+    "entities": [
+      "disease",
+      "gene",
+      "variant"
+    ],
+    "github": "https://github.com/cBioPortal/cbioportal",
+    "documentation": "https://www.cbioportal.org/",
+    "last_checked": "2026-08-08",
+    "metadata_sources": [
+      "https://www.cbioportal.org/",
+      "https://github.com/cBioPortal/cbioportal"
+    ]
   },
   {
     "id": "cellminer_cross_database_cellminercdb",
@@ -1092,10 +1183,20 @@ validated: false
     ],
     "tasks": [],
     "modalities": [
-      "Small Molecule"
+      "chemical-structure"
     ],
     "organism": [],
-    "api": false
+    "api": false,
+    "entities": [
+      "compound",
+      "molecule",
+      "protein"
+    ],
+    "documentation": "https://www.ebi.ac.uk/chembl/",
+    "last_checked": "2026-08-08",
+    "metadata_sources": [
+      "https://www.ebi.ac.uk/chembl/"
+    ]
   },
   {
     "id": "chemspider",
@@ -1124,10 +1225,19 @@ validated: false
     ],
     "tasks": [],
     "modalities": [
-      "Clinical"
+      "clinical"
     ],
     "organism": [],
-    "api": false
+    "api": false,
+    "entities": [
+      "disease",
+      "drug"
+    ],
+    "documentation": "https://clinicaltrials.gov/",
+    "last_checked": "2026-08-08",
+    "metadata_sources": [
+      "https://clinicaltrials.gov/"
+    ]
   },
   {
     "id": "comparative_toxicogenomics_database",
@@ -1141,11 +1251,20 @@ validated: false
     ],
     "tasks": [],
     "modalities": [
-      "Gene",
+      "knowledge-graph"
-      "Small Molecule"
     ],
     "organism": [],
-    "api": false
+    "api": false,
+    "entities": [
+      "compound",
+      "gene",
+      "disease"
+    ],
+    "documentation": "https://ctdbase.org/",
+    "last_checked": "2026-08-08",
+    "metadata_sources": [
+      "https://ctdbase.org/"
+    ]
   },
   {
     "id": "critical_assessment_of_structure_prediction_casp",
@@ -1174,10 +1293,21 @@ validated: false
     ],
     "tasks": [],
     "modalities": [
-      "Single Cell"
+      "single-cell-rna-seq",
+      "transcriptomics"
     ],
     "organism": [],
-    "api": false
+    "api": false,
+    "entities": [
+      "cell",
+      "gene",
+      "tissue"
+    ],
+    "documentation": "https://cellxgene.cziscience.com/",
+    "last_checked": "2026-08-08",
+    "metadata_sources": [
+      "https://cellxgene.cziscience.com/"
+    ]
   },
   {
     "id": "davis_kinase_inhibitors_db",
@@ -1208,10 +1338,21 @@ validated: false
     ],
     "tasks": [],
     "modalities": [
-      "Genomics"
+      "genomics"
     ],
     "organism": [],
-    "api": false
+    "api": false,
+    "entities": [
+      "cell",
+      "gene",
+      "disease",
+      "drug"
+    ],
+    "documentation": "https://depmap.org/portal/",
+    "last_checked": "2026-08-08",
+    "metadata_sources": [
+      "https://depmap.org/portal/"
+    ]
   },
   {
     "id": "dgidb",
@@ -1225,11 +1366,19 @@ validated: false
     ],
     "tasks": [],
     "modalities": [
-      "Gene",
+      "knowledge-graph"
-      "Small Molecule"
     ],
     "organism": [],
-    "api": false
+    "api": false,
+    "entities": [
+      "drug",
+      "gene"
+    ],
+    "documentation": "https://www.dgidb.org/",
+    "last_checked": "2026-08-08",
+    "metadata_sources": [
+      "https://www.dgidb.org/"
+    ]
   },
   {
     "id": "diseases",
@@ -1292,10 +1441,21 @@ validated: false
     ],
     "tasks": [],
     "modalities": [
-      "Knowledge Graph"
+      "knowledge-graph"
     ],
     "organism": [],
-    "api": false
+    "api": false,
+    "entities": [
+      "drug",
+      "disease",
+      "gene",
+      "pathway"
+    ],
+    "github": "https://github.com/SuLab/DrugMechDB",
+    "last_checked": "2026-08-08",
+    "metadata_sources": [
+      "https://github.com/SuLab/DrugMechDB"
+    ]
   },
   {
     "id": "drug_repurposing_hub",
@@ -1308,10 +1468,20 @@ validated: false
     ],
     "tasks": [],
     "modalities": [
-      "Small Molecule"
+      "chemical-structure"
     ],
     "organism": [],
-    "api": false
+    "api": false,
+    "entities": [
+      "drug",
+      "protein",
+      "disease"
+    ],
+    "documentation": "https://repo-hub.broadinstitute.org/repurposing",
+    "last_checked": "2026-08-08",
+    "metadata_sources": [
+      "https://repo-hub.broadinstitute.org/repurposing"
+    ]
   },
   {
     "id": "drugbank",
@@ -1349,10 +1519,20 @@ validated: false
     ],
     "tasks": [],
     "modalities": [
-      "Small Molecule"
+      "chemical-structure"
     ],
     "organism": [],
-    "api": false
+    "api": false,
+    "entities": [
+      "drug",
+      "protein",
+      "disease"
+    ],
+    "documentation": "https://drugcentral.org/",
+    "last_checked": "2026-08-08",
+    "metadata_sources": [
+      "https://drugcentral.org/"
+    ]
   },
   {
     "id": "drugtargetcommons",
@@ -1365,10 +1545,19 @@ validated: false
     ],
     "tasks": [],
     "modalities": [
-      "Small Molecule"
+      "chemical-structure"
     ],
     "organism": [],
-    "api": false
+    "api": false,
+    "entities": [
+      "drug",
+      "protein"
+    ],
+    "documentation": "https://drugtargetcommons.fimm.fi/",
+    "last_checked": "2026-08-08",
+    "metadata_sources": [
+      "https://drugtargetcommons.fimm.fi/"
+    ]
   },
   {
     "id": "encode",
@@ -1936,6 +2125,22 @@ validated: false
     "organism": [],
     "api": false
   },
+  {
+    "id": "oncokb",
+    "name": "OncoKB",
+    "type": "database",
+    "url": "https://www.oncokb.org/",
+    "description": "Precision oncology knowledge base of cancer genes, variants, and therapeutic implications.",
+    "tags": [
+      "genome"
+    ],
+    "tasks": [],
+    "modalities": [
+      "Genomics"
+    ],
+    "organism": [],
+    "api": false
+  },
   {
     "id": "open_targets_platform",
     "name": "Open Targets Platform",
@@ -2383,10 +2588,18 @@ validated: false
     ],
     "tasks": [],
     "modalities": [
-      "Protein"
+      "protein-sequence"
     ],
     "organism": [],
-    "api": false
+    "api": false,
+    "entities": [
+      "protein"
+    ],
+    "documentation": "https://www.uniprot.org/",
+    "last_checked": "2026-08-08",
+    "metadata_sources": [
+      "https://www.uniprot.org/"
+    ]
   },
   {
     "id": "uniref",
@@ -5444,9 +5657,23 @@ validated: false
     "tasks": [
       "Preprocessing"
     ],
-    "modalities": [],
+    "modalities": [
+      "dna-sequence",
+      "protein-sequence"
+    ],
     "organism": [],
-    "api": false
+    "api": false,
+    "entities": [
+      "gene",
+      "protein"
+    ],
+    "github": "https://github.com/biopython/biopython",
+    "documentation": "https://biopython.org/wiki/Documentation",
+    "last_checked": "2026-08-08",
+    "metadata_sources": [
+      "https://github.com/biopython/biopython",
+      "https://biopython.org/"
+    ]
   },
   {
     "id": "casper",
@@ -5476,9 +5703,22 @@ validated: false
     "tasks": [
       "Preprocessing"
     ],
-    "modalities": [],
+    "modalities": [
+      "spatial-transcriptomics"
+    ],
     "organism": [],
-    "api": false
+    "api": false,
+    "entities": [
+      "cell",
+      "tissue"
+    ],
+    "github": "https://github.com/CSOgroup/cellcharter",
+    "documentation": "https://cellcharter.readthedocs.io/",
+    "last_checked": "2026-08-08",
+    "metadata_sources": [
+      "https://github.com/CSOgroup/cellcharter",
+      "https://cellcharter.readthedocs.io/"
+    ]
   },
   {
     "id": "cellchat",
@@ -5492,9 +5732,20 @@ validated: false
     "tasks": [
       "Preprocessing"
     ],
-    "modalities": [],
+    "modalities": [
+      "single-cell-rna-seq"
+    ],
     "organism": [],
-    "api": false
+    "api": false,
+    "entities": [
+      "cell",
+      "gene"
+    ],
+    "github": "https://github.com/sqjin/CellChat",
+    "last_checked": "2026-08-08",
+    "metadata_sources": [
+      "https://github.com/sqjin/CellChat"
+    ]
   },
   {
     "id": "celltypist",
@@ -5506,11 +5757,24 @@ validated: false
       "preprocessing-tools"
     ],
     "tasks": [
-      "Preprocessing"
+      "cell-type-annotation"
+    ],
+    "modalities": [
+      "single-cell-rna-seq"
     ],
-    "modalities": [],
     "organism": [],
-    "api": false
+    "api": false,
+    "entities": [
+      "cell",
+      "gene"
+    ],
+    "github": "https://github.com/Teichlab/celltypist",
+    "documentation": "https://celltypist.readthedocs.io/",
+    "last_checked": "2026-08-08",
+    "metadata_sources": [
+      "https://github.com/Teichlab/celltypist",
+      "https://celltypist.readthedocs.io/"
+    ]
   },
   {
     "id": "chatspatial",
@@ -5572,9 +5836,23 @@ validated: false
     "tasks": [
       "Preprocessing"
     ],
-    "modalities": [],
+    "modalities": [
+      "chemical-structure",
+      "molecular-structure"
+    ],
     "organism": [],
-    "api": false
+    "api": false,
+    "entities": [
+      "molecule",
+      "protein"
+    ],
+    "github": "https://github.com/deepchem/deepchem",
+    "documentation": "https://deepchem.readthedocs.io/",
+    "last_checked": "2026-08-08",
+    "metadata_sources": [
+      "https://github.com/deepchem/deepchem",
+      "https://deepchem.readthedocs.io/"
+    ]
   },
   {
     "id": "deeptalk",
@@ -5796,9 +6074,21 @@ validated: false
     "tasks": [
       "Preprocessing"
     ],
-    "modalities": [],
+    "modalities": [
+      "chemical-structure"
+    ],
     "organism": [],
-    "api": false
+    "api": false,
+    "entities": [
+      "molecule"
+    ],
+    "github": "https://github.com/rdkit/rdkit",
+    "documentation": "https://www.rdkit.org/docs/",
+    "last_checked": "2026-08-08",
+    "metadata_sources": [
+      "https://github.com/rdkit/rdkit",
+      "https://www.rdkit.org/docs/"
+    ]
   },
   {
     "id": "scanpy",
@@ -5812,9 +6102,22 @@ validated: false
     "tasks": [
       "Preprocessing"
     ],
-    "modalities": [],
+    "modalities": [
+      "single-cell-rna-seq"
+    ],
     "organism": [],
-    "api": false
+    "api": false,
+    "entities": [
+      "cell",
+      "gene"
+    ],
+    "github": "https://github.com/scverse/scanpy",
+    "documentation": "https://scanpy.readthedocs.io/en/stable/",
+    "last_checked": "2026-08-08",
+    "metadata_sources": [
+      "https://github.com/scverse/scanpy",
+      "https://scanpy.readthedocs.io/en/stable/"
+    ]
   },
   {
     "id": "scenic",
@@ -5876,9 +6179,23 @@ validated: false
     "tasks": [
       "Preprocessing"
     ],
-    "modalities": [],
+    "modalities": [
+      "single-cell-rna-seq",
+      "multi-omics"
+    ],
     "organism": [],
-    "api": false
+    "api": false,
+    "entities": [
+      "cell",
+      "gene"
+    ],
+    "github": "https://github.com/scverse/scvi-tools",
+    "documentation": "https://docs.scvi-tools.org/",
+    "last_checked": "2026-08-08",
+    "metadata_sources": [
+      "https://github.com/scverse/scvi-tools",
+      "https://docs.scvi-tools.org/"
+    ]
   },
   {
     "id": "seqbench",
@@ -5908,9 +6225,22 @@ validated: false
     "tasks": [
       "Preprocessing"
     ],
-    "modalities": [],
+    "modalities": [
+      "single-cell-rna-seq"
+    ],
     "organism": [],
-    "api": false
+    "api": false,
+    "entities": [
+      "cell",
+      "gene"
+    ],
+    "github": "https://github.com/satijalab/seurat",
+    "documentation": "https://satijalab.org/seurat/",
+    "last_checked": "2026-08-08",
+    "metadata_sources": [
+      "https://github.com/satijalab/seurat",
+      "https://satijalab.org/seurat/"
+    ]
   },
   {
     "id": "squidpy",
@@ -5924,9 +6254,22 @@ validated: false
     "tasks": [
       "Preprocessing"
     ],
-    "modalities": [],
+    "modalities": [
+      "spatial-transcriptomics"
+    ],
     "organism": [],
-    "api": false
+    "api": false,
+    "entities": [
+      "cell",
+      "tissue"
+    ],
+    "github": "https://github.com/scverse/squidpy",
+    "documentation": "https://squidpy.readthedocs.io/",
+    "last_checked": "2026-08-08",
+    "metadata_sources": [
+      "https://github.com/scverse/squidpy",
+      "https://squidpy.readthedocs.io/"
+    ]
   },
   {
     "id": "stagate",

upstream/inoue0426-awesome-computational-biology/catalogue/data/resources.yml

@@ -2,9 +2,9 @@
 title: "Awesome Computational Biology - machine-readable resource list"
 task: ""
 lineage_type: import
-upstream_source: https://github.com/inoue0426/awesome-computational-biology/blob/7a064bf0/data/resources.yml
+upstream_source: https://github.com/inoue0426/awesome-computational-biology/blob/92dbe563/data/resources.yml
-upstream_sha: 7a064bf0
+upstream_sha: 92dbe563
-imported_at: 2026-08-08
+imported_at: 2026-08-14
 prompt_class: catalogue
 upstream_changes: accepted
 author: upstream
@@ -1183,6 +1183,17 @@ resources:
     organism: []
     api: false
 
+  - id: oncokb
+    name: "OncoKB"
+    type: database
+    url: https://www.oncokb.org/
+    description: "Precision oncology knowledge base of cancer genes, variants, and therapeutic implications."
+    tags: [genome]
+    tasks: []
+    modalities: [Genomics]
+    organism: []
+    api: false
+
   - id: open_targets_platform
     name: "Open Targets Platform"
     type: database

upstream/inoue0426-awesome-computational-biology/catalogue/docs/data/resources.json

@@ -2,9 +2,9 @@
 title: "Resources"
 task: ""
 lineage_type: import
-upstream_source: https://github.com/inoue0426/awesome-computational-biology/blob/7a064bf0/docs/data/resources.json
+upstream_source: https://github.com/inoue0426/awesome-computational-biology/blob/92dbe563/docs/data/resources.json
-upstream_sha: 7a064bf0
+upstream_sha: 92dbe563
-imported_at: 2026-08-08
+imported_at: 2026-08-14
 prompt_class: catalogue
 upstream_changes: accepted
 author: upstream
@@ -899,10 +899,20 @@ validated: false
     ],
     "tasks": [],
     "modalities": [
-      "Genomics"
+      "single-cell-rna-seq",
+      "genomics"
     ],
     "organism": [],
-    "api": false
+    "api": false,
+    "entities": [
+      "cell",
+      "gene"
+    ],
+    "documentation": "https://www.10xgenomics.com/resources/datasets",
+    "last_checked": "2026-08-08",
+    "metadata_sources": [
+      "https://www.10xgenomics.com/resources/datasets"
+    ]
   },
   {
     "id": "alphafold_protein_structure_database",
@@ -915,10 +925,20 @@ validated: false
     ],
     "tasks": [],
     "modalities": [
-      "Protein"
+      "molecular-structure",
+      "protein-sequence"
     ],
     "organism": [],
-    "api": false
+    "api": false,
+    "entities": [
+      "protein"
+    ],
+    "documentation": "https://alphafold.ebi.ac.uk/api-docs",
+    "last_checked": "2026-08-08",
+    "metadata_sources": [
+      "https://alphafold.ebi.ac.uk/",
+      "https://alphafold.ebi.ac.uk/api-docs"
+    ]
   },
   {
     "id": "bindingdb",
@@ -932,11 +952,20 @@ validated: false
     ],
     "tasks": [],
     "modalities": [
-      "Protein",
+      "chemical-structure",
-      "Small Molecule"
+      "molecular-structure"
     ],
     "organism": [],
-    "api": false
+    "api": false,
+    "entities": [
+      "molecule",
+      "protein"
+    ],
+    "documentation": "https://www.bindingdb.org/rwd/bind/index.jsp",
+    "last_checked": "2026-08-08",
+    "metadata_sources": [
+      "https://www.bindingdb.org/rwd/bind/index.jsp"
+    ]
   },
   {
     "id": "biocyc",
@@ -949,10 +978,20 @@ validated: false
     ],
     "tasks": [],
     "modalities": [
-      "Pathway"
+      "genomics"
     ],
     "organism": [],
-    "api": false
+    "api": false,
+    "entities": [
+      "gene",
+      "pathway",
+      "organism"
+    ],
+    "documentation": "https://biocyc.org/",
+    "last_checked": "2026-08-08",
+    "metadata_sources": [
+      "https://biocyc.org/"
+    ]
   },
   {
     "id": "biogrid",
@@ -969,7 +1008,16 @@ validated: false
       "Protein"
     ],
     "organism": [],
-    "api": false
+    "api": false,
+    "entities": [
+      "gene",
+      "protein"
+    ],
+    "documentation": "https://thebiogrid.org/",
+    "last_checked": "2026-08-08",
+    "metadata_sources": [
+      "https://thebiogrid.org/"
+    ]
   },
   {
     "id": "cancer_cell_line_encyclopedia",
@@ -983,11 +1031,22 @@ validated: false
     ],
     "tasks": [],
     "modalities": [
-      "Gene Expression",
+      "genomics",
-      "Small Molecule"
+      "transcriptomics"
     ],
     "organism": [],
-    "api": false
+    "api": false,
+    "entities": [
+      "cell",
+      "gene",
+      "disease",
+      "drug"
+    ],
+    "documentation": "https://sites.broadinstitute.org/ccle/",
+    "last_checked": "2026-08-08",
+    "metadata_sources": [
+      "https://sites.broadinstitute.org/ccle/"
+    ]
   },
   {
     "id": "catalogue_of_somatic_mutations_in_cancer_cosmic",
@@ -1000,10 +1059,20 @@ validated: false
     ],
     "tasks": [],
     "modalities": [
-      "Genomics"
+      "genomics"
     ],
     "organism": [],
-    "api": false
+    "api": false,
+    "entities": [
+      "disease",
+      "gene",
+      "variant"
+    ],
+    "documentation": "https://cancer.sanger.ac.uk/cosmic",
+    "last_checked": "2026-08-08",
+    "metadata_sources": [
+      "https://cancer.sanger.ac.uk/cosmic"
+    ]
   },
   {
     "id": "cath_database",
@@ -1016,10 +1085,19 @@ validated: false
     ],
     "tasks": [],
     "modalities": [
-      "Protein"
+      "molecular-structure",
+      "protein-sequence"
     ],
     "organism": [],
-    "api": false
+    "api": false,
+    "entities": [
+      "protein"
+    ],
+    "documentation": "https://www.cathdb.info/",
+    "last_checked": "2026-08-08",
+    "metadata_sources": [
+      "https://www.cathdb.info/"
+    ]
   },
   {
     "id": "cbioportal",
@@ -1032,10 +1110,23 @@ validated: false
     ],
     "tasks": [],
     "modalities": [
-      "Genomics"
+      "genomics",
+      "clinical"
     ],
     "organism": [],
-    "api": false
+    "api": false,
+    "entities": [
+      "disease",
+      "gene",
+      "variant"
+    ],
+    "github": "https://github.com/cBioPortal/cbioportal",
+    "documentation": "https://www.cbioportal.org/",
+    "last_checked": "2026-08-08",
+    "metadata_sources": [
+      "https://www.cbioportal.org/",
+      "https://github.com/cBioPortal/cbioportal"
+    ]
   },
   {
     "id": "cellminer_cross_database_cellminercdb",
@@ -1092,10 +1183,20 @@ validated: false
     ],
     "tasks": [],
     "modalities": [
-      "Small Molecule"
+      "chemical-structure"
     ],
     "organism": [],
-    "api": false
+    "api": false,
+    "entities": [
+      "compound",
+      "molecule",
+      "protein"
+    ],
+    "documentation": "https://www.ebi.ac.uk/chembl/",
+    "last_checked": "2026-08-08",
+    "metadata_sources": [
+      "https://www.ebi.ac.uk/chembl/"
+    ]
   },
   {
     "id": "chemspider",
@@ -1124,10 +1225,19 @@ validated: false
     ],
     "tasks": [],
     "modalities": [
-      "Clinical"
+      "clinical"
     ],
     "organism": [],
-    "api": false
+    "api": false,
+    "entities": [
+      "disease",
+      "drug"
+    ],
+    "documentation": "https://clinicaltrials.gov/",
+    "last_checked": "2026-08-08",
+    "metadata_sources": [
+      "https://clinicaltrials.gov/"
+    ]
   },
   {
     "id": "comparative_toxicogenomics_database",
@@ -1141,11 +1251,20 @@ validated: false
     ],
     "tasks": [],
     "modalities": [
-      "Gene",
+      "knowledge-graph"
-      "Small Molecule"
     ],
     "organism": [],
-    "api": false
+    "api": false,
+    "entities": [
+      "compound",
+      "gene",
+      "disease"
+    ],
+    "documentation": "https://ctdbase.org/",
+    "last_checked": "2026-08-08",
+    "metadata_sources": [
+      "https://ctdbase.org/"
+    ]
   },
   {
     "id": "critical_assessment_of_structure_prediction_casp",
@@ -1174,10 +1293,21 @@ validated: false
     ],
     "tasks": [],
     "modalities": [
-      "Single Cell"
+      "single-cell-rna-seq",
+      "transcriptomics"
     ],
     "organism": [],
-    "api": false
+    "api": false,
+    "entities": [
+      "cell",
+      "gene",
+      "tissue"
+    ],
+    "documentation": "https://cellxgene.cziscience.com/",
+    "last_checked": "2026-08-08",
+    "metadata_sources": [
+      "https://cellxgene.cziscience.com/"
+    ]
   },
   {
     "id": "davis_kinase_inhibitors_db",
@@ -1208,10 +1338,21 @@ validated: false
     ],
     "tasks": [],
     "modalities": [
-      "Genomics"
+      "genomics"
     ],
     "organism": [],
-    "api": false
+    "api": false,
+    "entities": [
+      "cell",
+      "gene",
+      "disease",
+      "drug"
+    ],
+    "documentation": "https://depmap.org/portal/",
+    "last_checked": "2026-08-08",
+    "metadata_sources": [
+      "https://depmap.org/portal/"
+    ]
   },
   {
     "id": "dgidb",
@@ -1225,11 +1366,19 @@ validated: false
     ],
     "tasks": [],
     "modalities": [
-      "Gene",
+      "knowledge-graph"
-      "Small Molecule"
     ],
     "organism": [],
-    "api": false
+    "api": false,
+    "entities": [
+      "drug",
+      "gene"
+    ],
+    "documentation": "https://www.dgidb.org/",
+    "last_checked": "2026-08-08",
+    "metadata_sources": [
+      "https://www.dgidb.org/"
+    ]
   },
   {
     "id": "diseases",
@@ -1292,10 +1441,21 @@ validated: false
     ],
     "tasks": [],
     "modalities": [
-      "Knowledge Graph"
+      "knowledge-graph"
     ],
     "organism": [],
-    "api": false
+    "api": false,
+    "entities": [
+      "drug",
+      "disease",
+      "gene",
+      "pathway"
+    ],
+    "github": "https://github.com/SuLab/DrugMechDB",
+    "last_checked": "2026-08-08",
+    "metadata_sources": [
+      "https://github.com/SuLab/DrugMechDB"
+    ]
   },
   {
     "id": "drug_repurposing_hub",
@@ -1308,10 +1468,20 @@ validated: false
     ],
     "tasks": [],
     "modalities": [
-      "Small Molecule"
+      "chemical-structure"
     ],
     "organism": [],
-    "api": false
+    "api": false,
+    "entities": [
+      "drug",
+      "protein",
+      "disease"
+    ],
+    "documentation": "https://repo-hub.broadinstitute.org/repurposing",
+    "last_checked": "2026-08-08",
+    "metadata_sources": [
+      "https://repo-hub.broadinstitute.org/repurposing"
+    ]
   },
   {
     "id": "drugbank",
@@ -1349,10 +1519,20 @@ validated: false
     ],
     "tasks": [],
     "modalities": [
-      "Small Molecule"
+      "chemical-structure"
     ],
     "organism": [],
-    "api": false
+    "api": false,
+    "entities": [
+      "drug",
+      "protein",
+      "disease"
+    ],
+    "documentation": "https://drugcentral.org/",
+    "last_checked": "2026-08-08",
+    "metadata_sources": [
+      "https://drugcentral.org/"
+    ]
   },
   {
     "id": "drugtargetcommons",
@@ -1365,10 +1545,19 @@ validated: false
     ],
     "tasks": [],
     "modalities": [
-      "Small Molecule"
+      "chemical-structure"
     ],
     "organism": [],
-    "api": false
+    "api": false,
+    "entities": [
+      "drug",
+      "protein"
+    ],
+    "documentation": "https://drugtargetcommons.fimm.fi/",
+    "last_checked": "2026-08-08",
+    "metadata_sources": [
+      "https://drugtargetcommons.fimm.fi/"
+    ]
   },
   {
     "id": "encode",
@@ -1936,6 +2125,22 @@ validated: false
     "organism": [],
     "api": false
   },
+  {
+    "id": "oncokb",
+    "name": "OncoKB",
+    "type": "database",
+    "url": "https://www.oncokb.org/",
+    "description": "Precision oncology knowledge base of cancer genes, variants, and therapeutic implications.",
+    "tags": [
+      "genome"
+    ],
+    "tasks": [],
+    "modalities": [
+      "Genomics"
+    ],
+    "organism": [],
+    "api": false
+  },
   {
     "id": "open_targets_platform",
     "name": "Open Targets Platform",
@@ -2383,10 +2588,18 @@ validated: false
     ],
     "tasks": [],
     "modalities": [
-      "Protein"
+      "protein-sequence"
     ],
     "organism": [],
-    "api": false
+    "api": false,
+    "entities": [
+      "protein"
+    ],
+    "documentation": "https://www.uniprot.org/",
+    "last_checked": "2026-08-08",
+    "metadata_sources": [
+      "https://www.uniprot.org/"
+    ]
   },
   {
     "id": "uniref",
@@ -5444,9 +5657,23 @@ validated: false
     "tasks": [
       "Preprocessing"
     ],
-    "modalities": [],
+    "modalities": [
+      "dna-sequence",
+      "protein-sequence"
+    ],
     "organism": [],
-    "api": false
+    "api": false,
+    "entities": [
+      "gene",
+      "protein"
+    ],
+    "github": "https://github.com/biopython/biopython",
+    "documentation": "https://biopython.org/wiki/Documentation",
+    "last_checked": "2026-08-08",
+    "metadata_sources": [
+      "https://github.com/biopython/biopython",
+      "https://biopython.org/"
+    ]
   },
   {
     "id": "casper",
@@ -5476,9 +5703,22 @@ validated: false
     "tasks": [
       "Preprocessing"
     ],
-    "modalities": [],
+    "modalities": [
+      "spatial-transcriptomics"
+    ],
     "organism": [],
-    "api": false
+    "api": false,
+    "entities": [
+      "cell",
+      "tissue"
+    ],
+    "github": "https://github.com/CSOgroup/cellcharter",
+    "documentation": "https://cellcharter.readthedocs.io/",
+    "last_checked": "2026-08-08",
+    "metadata_sources": [
+      "https://github.com/CSOgroup/cellcharter",
+      "https://cellcharter.readthedocs.io/"
+    ]
   },
   {
     "id": "cellchat",
@@ -5492,9 +5732,20 @@ validated: false
     "tasks": [
       "Preprocessing"
     ],
-    "modalities": [],
+    "modalities": [
+      "single-cell-rna-seq"
+    ],
     "organism": [],
-    "api": false
+    "api": false,
+    "entities": [
+      "cell",
+      "gene"
+    ],
+    "github": "https://github.com/sqjin/CellChat",
+    "last_checked": "2026-08-08",
+    "metadata_sources": [
+      "https://github.com/sqjin/CellChat"
+    ]
   },
   {
     "id": "celltypist",
@@ -5506,11 +5757,24 @@ validated: false
       "preprocessing-tools"
     ],
     "tasks": [
-      "Preprocessing"
+      "cell-type-annotation"
+    ],
+    "modalities": [
+      "single-cell-rna-seq"
     ],
-    "modalities": [],
     "organism": [],
-    "api": false
+    "api": false,
+    "entities": [
+      "cell",
+      "gene"
+    ],
+    "github": "https://github.com/Teichlab/celltypist",
+    "documentation": "https://celltypist.readthedocs.io/",
+    "last_checked": "2026-08-08",
+    "metadata_sources": [
+      "https://github.com/Teichlab/celltypist",
+      "https://celltypist.readthedocs.io/"
+    ]
   },
   {
     "id": "chatspatial",
@@ -5572,9 +5836,23 @@ validated: false
     "tasks": [
       "Preprocessing"
     ],
-    "modalities": [],
+    "modalities": [
+      "chemical-structure",
+      "molecular-structure"
+    ],
     "organism": [],
-    "api": false
+    "api": false,
+    "entities": [
+      "molecule",
+      "protein"
+    ],
+    "github": "https://github.com/deepchem/deepchem",
+    "documentation": "https://deepchem.readthedocs.io/",
+    "last_checked": "2026-08-08",
+    "metadata_sources": [
+      "https://github.com/deepchem/deepchem",
+      "https://deepchem.readthedocs.io/"
+    ]
   },
   {
     "id": "deeptalk",
@@ -5796,9 +6074,21 @@ validated: false
     "tasks": [
       "Preprocessing"
     ],
-    "modalities": [],
+    "modalities": [
+      "chemical-structure"
+    ],
     "organism": [],
-    "api": false
+    "api": false,
+    "entities": [
+      "molecule"
+    ],
+    "github": "https://github.com/rdkit/rdkit",
+    "documentation": "https://www.rdkit.org/docs/",
+    "last_checked": "2026-08-08",
+    "metadata_sources": [
+      "https://github.com/rdkit/rdkit",
+      "https://www.rdkit.org/docs/"
+    ]
   },
   {
     "id": "scanpy",
@@ -5812,9 +6102,22 @@ validated: false
     "tasks": [
       "Preprocessing"
     ],
-    "modalities": [],
+    "modalities": [
+      "single-cell-rna-seq"
+    ],
     "organism": [],
-    "api": false
+    "api": false,
+    "entities": [
+      "cell",
+      "gene"
+    ],
+    "github": "https://github.com/scverse/scanpy",
+    "documentation": "https://scanpy.readthedocs.io/en/stable/",
+    "last_checked": "2026-08-08",
+    "metadata_sources": [
+      "https://github.com/scverse/scanpy",
+      "https://scanpy.readthedocs.io/en/stable/"
+    ]
   },
   {
     "id": "scenic",
@@ -5876,9 +6179,23 @@ validated: false
     "tasks": [
       "Preprocessing"
     ],
-    "modalities": [],
+    "modalities": [
+      "single-cell-rna-seq",
+      "multi-omics"
+    ],
     "organism": [],
-    "api": false
+    "api": false,
+    "entities": [
+      "cell",
+      "gene"
+    ],
+    "github": "https://github.com/scverse/scvi-tools",
+    "documentation": "https://docs.scvi-tools.org/",
+    "last_checked": "2026-08-08",
+    "metadata_sources": [
+      "https://github.com/scverse/scvi-tools",
+      "https://docs.scvi-tools.org/"
+    ]
   },
   {
     "id": "seqbench",
@@ -5908,9 +6225,22 @@ validated: false
     "tasks": [
       "Preprocessing"
     ],
-    "modalities": [],
+    "modalities": [
+      "single-cell-rna-seq"
+    ],
     "organism": [],
-    "api": false
+    "api": false,
+    "entities": [
+      "cell",
+      "gene"
+    ],
+    "github": "https://github.com/satijalab/seurat",
+    "documentation": "https://satijalab.org/seurat/",
+    "last_checked": "2026-08-08",
+    "metadata_sources": [
+      "https://github.com/satijalab/seurat",
+      "https://satijalab.org/seurat/"
+    ]
   },
   {
     "id": "squidpy",
@@ -5924,9 +6254,22 @@ validated: false
     "tasks": [
       "Preprocessing"
     ],
-    "modalities": [],
+    "modalities": [
+      "spatial-transcriptomics"
+    ],
     "organism": [],
-    "api": false
+    "api": false,
+    "entities": [
+      "cell",
+      "tissue"
+    ],
+    "github": "https://github.com/scverse/squidpy",
+    "documentation": "https://squidpy.readthedocs.io/",
+    "last_checked": "2026-08-08",
+    "metadata_sources": [
+      "https://github.com/scverse/squidpy",
+      "https://squidpy.readthedocs.io/"
+    ]
   },
   {
     "id": "stagate",