diff --git a/upstream/inoue0426-awesome-computational-biology/catalogue/README.md b/upstream/inoue0426-awesome-computational-biology/catalogue/README.md index 77368fd..48d863c 100644 --- a/upstream/inoue0426-awesome-computational-biology/catalogue/README.md +++ b/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_sha: 7a064bf0 -imported_at: 2026-08-08 +upstream_source: https://github.com/inoue0426/awesome-computational-biology/blob/92dbe563/README.md +upstream_sha: 92dbe563 +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. diff --git a/upstream/inoue0426-awesome-computational-biology/catalogue/cspell.json b/upstream/inoue0426-awesome-computational-biology/catalogue/cspell.json index 407c31a..1890af9 100644 --- a/upstream/inoue0426-awesome-computational-biology/catalogue/cspell.json +++ b/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_sha: 7a064bf0 -imported_at: 2026-08-08 +upstream_source: https://github.com/inoue0426/awesome-computational-biology/blob/92dbe563/cspell.json +upstream_sha: 92dbe563 +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", diff --git a/upstream/inoue0426-awesome-computational-biology/catalogue/data/enrichment.cancer-databases-v1.yml b/upstream/inoue0426-awesome-computational-biology/catalogue/data/enrichment.cancer-databases-v1.yml new file mode 100644 index 0000000..13d9527 --- /dev/null +++ b/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/ diff --git a/upstream/inoue0426-awesome-computational-biology/catalogue/data/enrichment.core-databases-v1.yml b/upstream/inoue0426-awesome-computational-biology/catalogue/data/enrichment.core-databases-v1.yml new file mode 100644 index 0000000..97456e4 --- /dev/null +++ b/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/ diff --git a/upstream/inoue0426-awesome-computational-biology/catalogue/data/enrichment.toolkit-v1.yml b/upstream/inoue0426-awesome-computational-biology/catalogue/data/enrichment.toolkit-v1.yml new file mode 100644 index 0000000..e06ed5f --- /dev/null +++ b/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/ diff --git a/upstream/inoue0426-awesome-computational-biology/catalogue/data/resources.json b/upstream/inoue0426-awesome-computational-biology/catalogue/data/resources.json index 3a7a355..b04fc4a 100644 --- a/upstream/inoue0426-awesome-computational-biology/catalogue/data/resources.json +++ b/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_sha: 7a064bf0 -imported_at: 2026-08-08 +upstream_source: https://github.com/inoue0426/awesome-computational-biology/blob/92dbe563/data/resources.json +upstream_sha: 92dbe563 +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", - "Small Molecule" + "chemical-structure", + "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", - "Small Molecule" + "genomics", + "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", - "Small Molecule" + "knowledge-graph" ], "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", - "Small Molecule" + "knowledge-graph" ], "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", diff --git a/upstream/inoue0426-awesome-computational-biology/catalogue/data/resources.yml b/upstream/inoue0426-awesome-computational-biology/catalogue/data/resources.yml index 98e1aac..5c29340 100644 --- a/upstream/inoue0426-awesome-computational-biology/catalogue/data/resources.yml +++ b/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_sha: 7a064bf0 -imported_at: 2026-08-08 +upstream_source: https://github.com/inoue0426/awesome-computational-biology/blob/92dbe563/data/resources.yml +upstream_sha: 92dbe563 +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 diff --git a/upstream/inoue0426-awesome-computational-biology/catalogue/docs/data/resources.json b/upstream/inoue0426-awesome-computational-biology/catalogue/docs/data/resources.json index adc957c..e45e7a1 100644 --- a/upstream/inoue0426-awesome-computational-biology/catalogue/docs/data/resources.json +++ b/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_sha: 7a064bf0 -imported_at: 2026-08-08 +upstream_source: https://github.com/inoue0426/awesome-computational-biology/blob/92dbe563/docs/data/resources.json +upstream_sha: 92dbe563 +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", - "Small Molecule" + "chemical-structure", + "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", - "Small Molecule" + "genomics", + "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", - "Small Molecule" + "knowledge-graph" ], "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", - "Small Molecule" + "knowledge-graph" ], "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",