diff --git a/upstream/inoue0426-awesome-computational-biology/catalogue/.github/workflows/ai4bio-schema-check.yml b/upstream/inoue0426-awesome-computational-biology/catalogue/.github/workflows/ai4bio-schema-check.yml new file mode 100644 index 0000000..a53e3f9 --- /dev/null +++ b/upstream/inoue0426-awesome-computational-biology/catalogue/.github/workflows/ai4bio-schema-check.yml @@ -0,0 +1,61 @@ +--- +title: "Ai4Bio Schema Check" +task: "" +lineage_type: import +upstream_source: https://github.com/inoue0426/awesome-computational-biology/blob/7a064bf0/.github/workflows/ai4bio-schema-check.yml +upstream_sha: 7a064bf0 +imported_at: 2026-08-08 +prompt_class: unknown +upstream_changes: accepted +author: upstream +validated: false +--- + +name: AI4Bio Schema Check + +on: + pull_request: + paths: + - data/resources.yml + - data/enrichment.yml + - 'data/enrichment.*.yml' + - data/vocabulary.yml + - docs/data/resource.schema.json + - scripts/enrichment_fragments.py + - scripts/validate_resources.py + - scripts/build_resources_v2.py + push: + branches: [main] + paths: + - data/resources.yml + - data/enrichment.yml + - 'data/enrichment.*.yml' + - data/vocabulary.yml + - docs/data/resource.schema.json + - scripts/enrichment_fragments.py + - scripts/validate_resources.py + - scripts/build_resources_v2.py + +permissions: + contents: read + +jobs: + validate: + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v4 + - uses: astral-sh/setup-uv@v3 + - name: Validate schema and enrichment + run: uv run --with pyyaml python scripts/validate_resources.py + - name: Build enriched artifacts + run: uv run --with pyyaml python scripts/build_resources_v2.py + - name: Verify enriched artifacts are committed + run: | + if git diff --quiet; then + echo "AI4Bio artifacts are in sync." + exit 0 + fi + echo "Generated AI4Bio artifacts are out of date. Run:" + echo " uv run --with pyyaml python scripts/build_resources_v2.py" + git status --short + exit 1 diff --git a/upstream/inoue0426-awesome-computational-biology/catalogue/.github/workflows/landscape-ui-check.yml b/upstream/inoue0426-awesome-computational-biology/catalogue/.github/workflows/landscape-ui-check.yml new file mode 100644 index 0000000..0d8bead --- /dev/null +++ b/upstream/inoue0426-awesome-computational-biology/catalogue/.github/workflows/landscape-ui-check.yml @@ -0,0 +1,43 @@ +--- +title: "Landscape Ui Check" +task: "" +lineage_type: import +upstream_source: https://github.com/inoue0426/awesome-computational-biology/blob/7a064bf0/.github/workflows/landscape-ui-check.yml +upstream_sha: 7a064bf0 +imported_at: 2026-08-08 +prompt_class: unknown +upstream_changes: accepted +author: upstream +validated: false +--- + +name: Landscape UI Check + +on: + pull_request: + paths: + - docs/landscape.html + - docs/landscape.css + - docs/landscape.js + - .github/workflows/landscape-ui-check.yml + push: + branches: [main] + paths: + - docs/landscape.html + - docs/landscape.css + - docs/landscape.js + - .github/workflows/landscape-ui-check.yml + +permissions: + contents: read + +jobs: + ui-check: + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v4 + - uses: actions/setup-node@v4 + with: + node-version: 'lts/*' + - name: Check landscape JavaScript syntax + run: node --check docs/landscape.js diff --git a/upstream/inoue0426-awesome-computational-biology/catalogue/.github/workflows/sync_resources.yml b/upstream/inoue0426-awesome-computational-biology/catalogue/.github/workflows/sync_resources.yml index 5a871be..2831b9d 100644 --- a/upstream/inoue0426-awesome-computational-biology/catalogue/.github/workflows/sync_resources.yml +++ b/upstream/inoue0426-awesome-computational-biology/catalogue/.github/workflows/sync_resources.yml @@ -2,9 +2,9 @@ title: "Sync Resources" task: "" lineage_type: import -upstream_source: https://github.com/inoue0426/awesome-computational-biology/blob/12d87583/.github/workflows/sync_resources.yml -upstream_sha: 12d87583 -imported_at: 2026-06-26 +upstream_source: https://github.com/inoue0426/awesome-computational-biology/blob/7a064bf0/.github/workflows/sync_resources.yml +upstream_sha: 7a064bf0 +imported_at: 2026-08-08 prompt_class: unknown upstream_changes: accepted author: upstream @@ -20,6 +20,8 @@ on: paths: - README.md - data/resources.yml + - data/enrichment.yml + - 'data/enrichment.*.yml' - scripts/*.py - scripts/**/*.py @@ -55,7 +57,10 @@ jobs: - name: Sync From README if: contains(steps.changes.outputs.changed, 'README.md') - run: uv run python scripts/sync_resources_from_readme.py + run: uv run --with pyyaml python scripts/sync_resources_from_readme.py + + - name: Validate Resource Schema + run: uv run --with pyyaml python scripts/validate_resources.py - name: Build Artifacts run: uv run --with pyyaml python scripts/build_resources.py diff --git a/upstream/inoue0426-awesome-computational-biology/catalogue/README.md b/upstream/inoue0426-awesome-computational-biology/catalogue/README.md index cc9edd8..77368fd 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/478be843/README.md -upstream_sha: 478be843 -imported_at: 2026-07-17 +upstream_source: https://github.com/inoue0426/awesome-computational-biology/blob/7a064bf0/README.md +upstream_sha: 7a064bf0 +imported_at: 2026-08-08 prompt_class: catalogue upstream_changes: accepted author: upstream @@ -70,6 +70,7 @@ Browse and search the resources via the [GitHub Pages UI](https://inoue0426.gith - [Machine Learning Tasks and Models](#machine-learning-tasks-and-models) - [Drug Discovery](#drug-discovery) - [Drug Response Prediction](#drug-response-prediction) + - [Drug Perturbation](#drug-perturbation) - [Drug Repurposing](#drug-repurposing) - [Drug Target Interaction](#drug-target-interaction) - [Compound-Protein Interaction](#compound-protein-interaction) @@ -340,10 +341,15 @@ Browse and search the resources via the [GitHub Pages UI](https://inoue0426.gith - [RECOVER](https://github.com/RECOVERcoalition/Recover) — Machine learning framework for predicting synergistic drug combination responses across cell lines. - [TGSA](https://github.com/violet-sto/TGSA) — Tumor gene set and attention-based model leveraging biological pathway knowledge for drug response prediction. - [HiDRA](https://github.com/bsml320/HiDRA) — Hierarchical network model incorporating gene and pathway-level information for cancer drug response prediction. -- [PRNet](https://github.com/Perturbation-Response-Prediction/PRnet) — Deep generative model for predicting transcriptional responses to novel chemical perturbations for drug discovery. +- [DRUML](https://github.com/CutillasLab/DRUMLR) — Ensemble machine learning framework combining standard ML with deep learning to systematically rank anti-cancer drugs from proteomics and RNA-seq data. + +#### Drug Perturbation + +- [CellOT](https://github.com/bunnech/cellot) — Neural optimal transport framework for predicting single-cell responses to drug and genetic perturbations. +- [CMonge](https://github.com/AI4SCR/conditional-monge-gap) — Conditional optimal transport model for generalizable single-cell perturbation response prediction across drugs and doses. - [chemCPA](https://github.com/theislab/chemCPA) — Compositional perturbation autoencoder for predicting single-cell transcriptional responses to unseen drug perturbations and dose combinations. - [cycleCDR](https://github.com/hliulab/cycleCDR) — Interpretable cycle-consistency framework for modeling cellular responses to drug perturbations. -- [DRUML](https://github.com/CutillasLab/DRUMLR) — Ensemble machine learning framework combining standard ML with deep learning to systematically rank anti-cancer drugs from proteomics and RNA-seq data. +- [PRNet](https://github.com/Perturbation-Response-Prediction/PRnet) — Deep generative model for predicting transcriptional responses to novel chemical perturbations for drug discovery. #### Drug Repurposing diff --git a/upstream/inoue0426-awesome-computational-biology/catalogue/cspell.json b/upstream/inoue0426-awesome-computational-biology/catalogue/cspell.json index 99485cf..407c31a 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/12d87583/cspell.json -upstream_sha: 12d87583 -imported_at: 2026-06-26 +upstream_source: https://github.com/inoue0426/awesome-computational-biology/blob/7a064bf0/cspell.json +upstream_sha: 7a064bf0 +imported_at: 2026-08-08 prompt_class: unknown upstream_changes: accepted author: upstream @@ -157,7 +157,21 @@ validated: false "Pacc", "multiomics", "Pathomic", - "PLIP" + "PLIP", + "Omni", + "Bento", + "FFPE", + "Xenium", + "Zyme", + "Neur", + "Imageomics", + "AESTETIK", + "CellOT", + "CMonge", + "bowang", + "ctheodoris", + "OpenAI", + "GPT" ], "ignorePaths": [ "node_modules/**" diff --git a/upstream/inoue0426-awesome-computational-biology/catalogue/data/enrichment.benchmark-v2.yml b/upstream/inoue0426-awesome-computational-biology/catalogue/data/enrichment.benchmark-v2.yml new file mode 100644 index 0000000..1a3bd3d --- /dev/null +++ b/upstream/inoue0426-awesome-computational-biology/catalogue/data/enrichment.benchmark-v2.yml @@ -0,0 +1,56 @@ +--- +title: "Provenance-backed single-cell and biomedical benchmark enrichment batch." +task: "" +lineage_type: import +upstream_source: https://github.com/inoue0426/awesome-computational-biology/blob/7a064bf0/data/enrichment.benchmark-v2.yml +upstream_sha: 7a064bf0 +imported_at: 2026-08-08 +prompt_class: catalogue +upstream_changes: accepted +author: upstream +validated: false +--- + +# Provenance-backed single-cell and biomedical benchmark enrichment batch. +resources: + scmulan: + entities: [cell, gene] + methods: [language-model, transformer] + modalities: [epigenomics, multi-omics, proteomics, single-cell-rna-seq, transcriptomics] + tasks: [foundation-model-pretraining, representation-learning] + github: https://github.com/SuperBianC/scMulan + last_checked: 2026-08-08 + metadata_sources: + - https://github.com/SuperBianC/scMulan + + proteingym: + entities: [protein] + modalities: [protein-sequence] + tasks: [regression] + github: https://github.com/OATML-Markslab/ProteinGym + last_checked: 2026-08-08 + metadata_sources: + - https://github.com/OATML-Markslab/ProteinGym + + lincs_l1000: + entities: [cell, compound, gene] + modalities: [transcriptomics] + tasks: [perturbation-prediction] + last_checked: 2026-08-08 + metadata_sources: + - https://lincsproject.org/LINCS/tools/workflows/find-the-best-place-to-obtain-the-lincs-l1000-data + + prism: + entities: [cell, drug] + tasks: [drug-response-prediction] + last_checked: 2026-08-08 + metadata_sources: + - https://depmap.org/portal/prism/ + + pharmgkb: + entities: [drug, gene, phenotype, variant] + modalities: [clinical, genomics] + tasks: [drug-response-prediction] + last_checked: 2026-08-08 + metadata_sources: + - https://www.pharmgkb.org/ diff --git a/upstream/inoue0426-awesome-computational-biology/catalogue/data/enrichment.database-api-v1.yml b/upstream/inoue0426-awesome-computational-biology/catalogue/data/enrichment.database-api-v1.yml new file mode 100644 index 0000000..66f82ef --- /dev/null +++ b/upstream/inoue0426-awesome-computational-biology/catalogue/data/enrichment.database-api-v1.yml @@ -0,0 +1,91 @@ +--- +title: "Provenance-backed database and API enrichment batch." +task: "" +lineage_type: import +upstream_source: https://github.com/inoue0426/awesome-computational-biology/blob/7a064bf0/data/enrichment.database-api-v1.yml +upstream_sha: 7a064bf0 +imported_at: 2026-08-08 +prompt_class: catalogue +upstream_changes: accepted +author: upstream +validated: false +--- + +# Provenance-backed database and API enrichment batch. +resources: + chembl_web_services: + entities: [molecule, protein] + modalities: [chemical-structure] + documentation: https://www.ebi.ac.uk/chembl/api/data/docs + last_checked: 2026-08-08 + metadata_sources: + - https://www.ebi.ac.uk/chembl/api/data/docs + + clinicaltrials_gov_api: + entities: [disease, drug] + modalities: [clinical] + documentation: https://clinicaltrials.gov/data-api/api + last_checked: 2026-08-08 + metadata_sources: + - https://clinicaltrials.gov/data-api/api + + ensembl_rest_api: + entities: [gene, genome, transcript, variant] + modalities: [genomics] + documentation: https://rest.ensembl.org/ + last_checked: 2026-08-08 + metadata_sources: + - https://rest.ensembl.org/ + + kegg_rest_api: + entities: [compound, gene, pathway] + documentation: https://www.kegg.jp/kegg/rest/keggapi.html + last_checked: 2026-08-08 + metadata_sources: + - https://www.kegg.jp/kegg/rest/keggapi.html + + ncbi_e_utilities: + entities: [gene, genome, protein, transcript, variant] + modalities: [genomics, transcriptomics] + documentation: https://www.ncbi.nlm.nih.gov/books/NBK25501/ + last_checked: 2026-08-08 + metadata_sources: + - https://www.ncbi.nlm.nih.gov/books/NBK25501/ + + open_targets_platform_api: + entities: [disease, drug, gene, variant] + modalities: [genomics, knowledge-graph] + documentation: https://platform.opentargets.org/api + last_checked: 2026-08-08 + metadata_sources: + - https://platform.opentargets.org/api + + pubmed_e_utilities_esearch_efetch: + documentation: https://www.ncbi.nlm.nih.gov/books/NBK25501/ + last_checked: 2026-08-08 + metadata_sources: + - https://www.ncbi.nlm.nih.gov/books/NBK25501/ + + uniprot_rest_api: + entities: [protein] + modalities: [protein-sequence, proteomics] + documentation: https://www.uniprot.org/help/api + last_checked: 2026-08-08 + metadata_sources: + - https://www.uniprot.org/help/api + + drugbank: + entities: [disease, drug, protein] + modalities: [chemical-structure] + last_checked: 2026-08-08 + metadata_sources: + - https://go.drugbank.com/ + + string: + entities: [protein] + modalities: [knowledge-graph, proteomics] + documentation: https://string-db.org/help/api/ + last_checked: 2026-08-08 + metadata_sources: + - https://string-db.org/ + - https://string-db.org/help/api/ diff --git a/upstream/inoue0426-awesome-computational-biology/catalogue/data/enrichment.foundation-models-v2.yml b/upstream/inoue0426-awesome-computational-biology/catalogue/data/enrichment.foundation-models-v2.yml new file mode 100644 index 0000000..bd28efd --- /dev/null +++ b/upstream/inoue0426-awesome-computational-biology/catalogue/data/enrichment.foundation-models-v2.yml @@ -0,0 +1,73 @@ +--- +title: "Provenance-backed foundation model enrichment batch 2." +task: "" +lineage_type: import +upstream_source: https://github.com/inoue0426/awesome-computational-biology/blob/7a064bf0/data/enrichment.foundation-models-v2.yml +upstream_sha: 7a064bf0 +imported_at: 2026-08-08 +prompt_class: catalogue +upstream_changes: accepted +author: upstream +validated: false +--- + +# Provenance-backed foundation model enrichment batch 2. +resources: + nicheformer: + entities: [cell, gene, tissue] + methods: [self-supervised-learning, transformer] + modalities: [single-cell-rna-seq, spatial-transcriptomics, transcriptomics] + tasks: [foundation-model-pretraining, representation-learning] + year: 2024 + github: https://github.com/theislab/nicheformer + paper: https://doi.org/10.1101/2024.04.15.589472 + last_checked: 2026-08-08 + metadata_sources: + - https://github.com/theislab/nicheformer + - https://doi.org/10.1101/2024.04.15.589472 + + genept: + entities: [cell, gene] + methods: [language-model] + modalities: [single-cell-rna-seq, transcriptomics] + tasks: [batch-correction, classification, representation-learning] + year: 2023 + github: https://github.com/yiqunchen/GenePT + paper: https://www.biorxiv.org/content/10.1101/2023.10.16.562533v2 + last_checked: 2026-08-08 + metadata_sources: + - https://github.com/yiqunchen/GenePT + - https://www.biorxiv.org/content/10.1101/2023.10.16.562533v2 + + scgpt_spatial: + entities: [cell, gene, tissue] + methods: [generative-model, self-supervised-learning, transformer] + modalities: [multi-omics, single-cell-rna-seq, spatial-transcriptomics] + tasks: [foundation-model-pretraining, imputation, representation-learning] + year: 2025 + github: https://github.com/bowang-lab/scGPT-spatial + paper: https://www.biorxiv.org/content/10.1101/2025.02.05.636714v1 + last_checked: 2026-08-08 + metadata_sources: + - https://github.com/bowang-lab/scGPT-spatial + - https://www.biorxiv.org/content/10.1101/2025.02.05.636714v1 + + scprint: + entities: [cell, gene] + methods: [self-supervised-learning, transformer] + modalities: [single-cell-rna-seq, transcriptomics] + tasks: + - batch-correction + - cell-type-annotation + - foundation-model-pretraining + - gene-regulatory-network-inference + - imputation + - representation-learning + year: 2025 + github: https://github.com/cantinilab/scPRINT + documentation: https://www.jkobject.com/scPRINT/ + paper: https://www.nature.com/articles/s41467-025-58699-1 + last_checked: 2026-08-08 + metadata_sources: + - https://github.com/cantinilab/scPRINT + - https://www.nature.com/articles/s41467-025-58699-1 diff --git a/upstream/inoue0426-awesome-computational-biology/catalogue/data/enrichment.molecular-v2.yml b/upstream/inoue0426-awesome-computational-biology/catalogue/data/enrichment.molecular-v2.yml new file mode 100644 index 0000000..12f2538 --- /dev/null +++ b/upstream/inoue0426-awesome-computational-biology/catalogue/data/enrichment.molecular-v2.yml @@ -0,0 +1,62 @@ +--- +title: "Provenance-backed molecular model and benchmark enrichment batch." +task: "" +lineage_type: import +upstream_source: https://github.com/inoue0426/awesome-computational-biology/blob/7a064bf0/data/enrichment.molecular-v2.yml +upstream_sha: 7a064bf0 +imported_at: 2026-08-08 +prompt_class: catalogue +upstream_changes: accepted +author: upstream +validated: false +--- + +# Provenance-backed molecular model and benchmark enrichment batch. +resources: + chemberta_2: + entities: [molecule] + methods: [language-model, self-supervised-learning, transformer] + modalities: [chemical-structure] + tasks: [representation-learning] + github: https://github.com/seyonechithrananda/bert-loves-chemistry + last_checked: 2026-08-08 + metadata_sources: + - https://github.com/seyonechithrananda/bert-loves-chemistry + + molformer: + entities: [molecule] + methods: [language-model, self-supervised-learning, transformer] + modalities: [chemical-structure] + tasks: [representation-learning] + github: https://github.com/IBM/molformer + last_checked: 2026-08-08 + metadata_sources: + - https://github.com/IBM/molformer + + grover: + entities: [molecule] + methods: [graph-neural-network, self-supervised-learning, transformer] + modalities: [chemical-structure] + tasks: [representation-learning] + github: https://github.com/tencent-ailab/grover + last_checked: 2026-08-08 + metadata_sources: + - https://github.com/tencent-ailab/grover + + moleculenet: + entities: [molecule] + modalities: [chemical-structure] + tasks: [classification, regression] + github: https://github.com/deepchem/moleculenet + last_checked: 2026-08-08 + metadata_sources: + - https://github.com/deepchem/moleculenet + + guacamol: + entities: [molecule] + modalities: [chemical-structure] + tasks: [molecular-generation] + github: https://github.com/BenevolentAI/guacamol + last_checked: 2026-08-08 + metadata_sources: + - https://github.com/BenevolentAI/guacamol diff --git a/upstream/inoue0426-awesome-computational-biology/catalogue/data/enrichment.pharmacogenomics-v1.yml b/upstream/inoue0426-awesome-computational-biology/catalogue/data/enrichment.pharmacogenomics-v1.yml new file mode 100644 index 0000000..a9fdacb --- /dev/null +++ b/upstream/inoue0426-awesome-computational-biology/catalogue/data/enrichment.pharmacogenomics-v1.yml @@ -0,0 +1,92 @@ +--- +title: "Provenance-backed drug-response and pharmacogenomics enrichment batch." +task: "" +lineage_type: import +upstream_source: https://github.com/inoue0426/awesome-computational-biology/blob/7a064bf0/data/enrichment.pharmacogenomics-v1.yml +upstream_sha: 7a064bf0 +imported_at: 2026-08-08 +prompt_class: catalogue +upstream_changes: accepted +author: upstream +validated: false +--- + +# Provenance-backed drug-response and pharmacogenomics enrichment batch. +resources: + beat_aml: + entities: [cell, disease, drug, gene] + modalities: [genomics] + tasks: [drug-response-prediction] + last_checked: 2026-08-08 + metadata_sources: + - https://biodev.github.io/BeatAML2/ + + cancer_therapeutics_response_portal_ctrp: + entities: [cell, drug] + tasks: [drug-response-prediction] + last_checked: 2026-08-08 + metadata_sources: + - https://portals.broadinstitute.org/ctrp/ + + bindingdb_curated_sets: + entities: [molecule, protein] + modalities: [chemical-structure] + tasks: [drug-target-interaction] + last_checked: 2026-08-08 + metadata_sources: + - https://www.bindingdb.org/ + + bace: + entities: [molecule, protein] + modalities: [chemical-structure] + tasks: [classification, regression] + last_checked: 2026-08-08 + metadata_sources: + - https://www.kaggle.com/datasets/gokturkkoch/bace + + clintox: + entities: [drug] + modalities: [clinical] + tasks: [classification] + last_checked: 2026-08-08 + metadata_sources: + - https://tdcommons.ai/single_pred_tasks/tox/#clintox + + sider_side_effect_resource: + entities: [drug, phenotype] + modalities: [clinical] + last_checked: 2026-08-08 + metadata_sources: + - http://sideeffects.embl.de/ + + pk_db: + entities: [drug] + modalities: [clinical] + last_checked: 2026-08-08 + metadata_sources: + - https://pk-db.com/ + + scperturb: + entities: [cell, drug, gene] + modalities: [single-cell-rna-seq] + tasks: [perturbation-prediction] + github: https://github.com/sanderlab/scPerturb + last_checked: 2026-08-08 + metadata_sources: + - https://github.com/sanderlab/scPerturb + + genomics_of_drug_sensitivity_in_cancer_gdsc: + entities: [cell, drug, gene] + modalities: [genomics] + tasks: [drug-response-prediction] + last_checked: 2026-08-08 + metadata_sources: + - https://www.cancerrxgene.org/ + + cellminer_cross_database_cellminercdb: + entities: [cell, drug, gene] + modalities: [genomics] + tasks: [drug-response-prediction] + last_checked: 2026-08-08 + metadata_sources: + - https://discover.nci.nih.gov/cellminercdb/ diff --git a/upstream/inoue0426-awesome-computational-biology/catalogue/data/enrichment.protein-drug-v1.yml b/upstream/inoue0426-awesome-computational-biology/catalogue/data/enrichment.protein-drug-v1.yml new file mode 100644 index 0000000..d1e715c --- /dev/null +++ b/upstream/inoue0426-awesome-computational-biology/catalogue/data/enrichment.protein-drug-v1.yml @@ -0,0 +1,62 @@ +--- +title: "Provenance-backed protein and drug-discovery enrichment batch." +task: "" +lineage_type: import +upstream_source: https://github.com/inoue0426/awesome-computational-biology/blob/7a064bf0/data/enrichment.protein-drug-v1.yml +upstream_sha: 7a064bf0 +imported_at: 2026-08-08 +prompt_class: catalogue +upstream_changes: accepted +author: upstream +validated: false +--- + +# Provenance-backed protein and drug-discovery enrichment batch. +resources: + esmfold: + entities: [protein] + methods: [language-model, transformer] + modalities: [molecular-structure, protein-sequence] + tasks: [representation-learning, structure-prediction] + year: 2023 + github: https://github.com/facebookresearch/esm + last_checked: 2026-08-08 + metadata_sources: + - https://github.com/facebookresearch/esm + + proteinmpnn: + entities: [protein] + methods: [graph-neural-network, message-passing-neural-network] + modalities: [molecular-structure, protein-sequence] + tasks: [protein-sequence-design] + year: 2022 + github: https://github.com/dauparas/ProteinMPNN + last_checked: 2026-08-08 + metadata_sources: + - https://github.com/dauparas/ProteinMPNN + + diffdock: + entities: [molecule, protein] + methods: [diffusion, geometric-deep-learning] + modalities: [molecular-structure] + tasks: [docking] + year: 2023 + github: https://github.com/gcorso/DiffDock + paper: https://openreview.net/forum?id=kKF8_K-mBbS + last_checked: 2026-08-08 + metadata_sources: + - https://github.com/gcorso/DiffDock + - https://openreview.net/forum?id=kKF8_K-mBbS + + uni_mol: + entities: [molecule, protein] + methods: [self-supervised-learning, transformer] + modalities: [chemical-structure, molecular-structure] + tasks: [docking, representation-learning] + year: 2023 + github: https://github.com/deepmodeling/Uni-Mol + paper: https://openreview.net/forum?id=6K2RM6wVqKu + last_checked: 2026-08-08 + metadata_sources: + - https://github.com/deepmodeling/Uni-Mol + - https://openreview.net/forum?id=6K2RM6wVqKu diff --git a/upstream/inoue0426-awesome-computational-biology/catalogue/data/enrichment.protein-v2.yml b/upstream/inoue0426-awesome-computational-biology/catalogue/data/enrichment.protein-v2.yml new file mode 100644 index 0000000..ad2fdd2 --- /dev/null +++ b/upstream/inoue0426-awesome-computational-biology/catalogue/data/enrichment.protein-v2.yml @@ -0,0 +1,64 @@ +--- +title: "Provenance-backed protein model enrichment batch." +task: "" +lineage_type: import +upstream_source: https://github.com/inoue0426/awesome-computational-biology/blob/7a064bf0/data/enrichment.protein-v2.yml +upstream_sha: 7a064bf0 +imported_at: 2026-08-08 +prompt_class: catalogue +upstream_changes: accepted +author: upstream +validated: false +--- + +# Provenance-backed protein model enrichment batch. +resources: + esm3: + entities: [protein] + methods: [generative-model, language-model, transformer] + modalities: [molecular-structure, protein-sequence] + tasks: [protein-sequence-design, representation-learning] + github: https://github.com/evolutionaryscale/esm + last_checked: 2026-08-08 + metadata_sources: + - https://github.com/evolutionaryscale/esm + + evolutionary_scale_modeling_esm: + entities: [protein] + methods: [language-model, self-supervised-learning, transformer] + modalities: [protein-sequence] + tasks: [representation-learning] + github: https://github.com/facebookresearch/esm + last_checked: 2026-08-08 + metadata_sources: + - https://github.com/facebookresearch/esm + + prottrans: + entities: [protein] + methods: [language-model, self-supervised-learning, transformer] + modalities: [protein-sequence] + tasks: [representation-learning] + github: https://github.com/agemagician/ProtTrans + last_checked: 2026-08-08 + metadata_sources: + - https://github.com/agemagician/ProtTrans + + progen2: + entities: [protein] + methods: [generative-model, language-model, transformer] + modalities: [protein-sequence] + tasks: [protein-sequence-design, representation-learning] + github: https://github.com/salesforce/progen + last_checked: 2026-08-08 + metadata_sources: + - https://github.com/salesforce/progen + + alphafold3: + entities: [molecule, protein, protein-complex] + methods: [diffusion] + modalities: [molecular-structure, protein-sequence] + tasks: [structure-prediction] + github: https://github.com/google-deepmind/alphafold3 + last_checked: 2026-08-08 + metadata_sources: + - https://github.com/google-deepmind/alphafold3 diff --git a/upstream/inoue0426-awesome-computational-biology/catalogue/data/enrichment.spatial-imaging-v1.yml b/upstream/inoue0426-awesome-computational-biology/catalogue/data/enrichment.spatial-imaging-v1.yml new file mode 100644 index 0000000..f565129 --- /dev/null +++ b/upstream/inoue0426-awesome-computational-biology/catalogue/data/enrichment.spatial-imaging-v1.yml @@ -0,0 +1,110 @@ +--- +title: "Provenance-backed spatial transcriptomics and imaging enrichment batch." +task: "" +lineage_type: import +upstream_source: https://github.com/inoue0426/awesome-computational-biology/blob/7a064bf0/data/enrichment.spatial-imaging-v1.yml +upstream_sha: 7a064bf0 +imported_at: 2026-08-08 +prompt_class: catalogue +upstream_changes: accepted +author: upstream +validated: false +--- + +# Provenance-backed spatial transcriptomics and imaging enrichment batch. +resources: + aestetik: + entities: [cell, gene, tissue] + methods: [autoencoder] + modalities: [histopathology, spatial-transcriptomics] + tasks: [representation-learning] + github: https://github.com/ratschlab/aestetik + last_checked: 2026-08-08 + metadata_sources: + - https://github.com/ratschlab/aestetik + + conch: + entities: [tissue] + methods: [contrastive-learning, transformer] + modalities: [histopathology, imaging] + tasks: [foundation-model-pretraining, representation-learning] + github: https://github.com/mahmoodlab/CONCH + last_checked: 2026-08-08 + metadata_sources: + - https://github.com/mahmoodlab/CONCH + + deepspot: + entities: [gene, tissue] + modalities: [histopathology, spatial-transcriptomics] + tasks: [regression] + github: https://github.com/ratschlab/DeepSpot + last_checked: 2026-08-08 + metadata_sources: + - https://github.com/ratschlab/DeepSpot + + deepspot_m: + entities: [gene, tissue] + modalities: [histopathology, spatial-transcriptomics, transcriptomics] + tasks: [foundation-model-pretraining, regression] + github: https://github.com/ratschlab/DeepSpotM + last_checked: 2026-08-08 + metadata_sources: + - https://github.com/ratschlab/DeepSpotM + + deepspot2cell: + entities: [cell, gene, tissue] + modalities: [histopathology, spatial-transcriptomics] + tasks: [regression] + github: https://github.com/ratschlab/DeepSpot2Cell + last_checked: 2026-08-08 + metadata_sources: + - https://github.com/ratschlab/DeepSpot2Cell + + gigapath: + entities: [tissue] + methods: [self-supervised-learning, transformer] + modalities: [histopathology, imaging] + tasks: [foundation-model-pretraining, representation-learning] + github: https://github.com/prov-gigapath/prov-gigapath + last_checked: 2026-08-08 + metadata_sources: + - https://github.com/prov-gigapath/prov-gigapath + + phikon: + entities: [tissue] + methods: [self-supervised-learning, transformer] + modalities: [histopathology, imaging] + tasks: [foundation-model-pretraining, representation-learning] + documentation: https://huggingface.co/owkin/phikon + last_checked: 2026-08-08 + metadata_sources: + - https://huggingface.co/owkin/phikon + + plip: + entities: [tissue] + methods: [contrastive-learning] + modalities: [histopathology, imaging] + tasks: [classification, representation-learning] + github: https://github.com/PathologyFoundation/plip + last_checked: 2026-08-08 + metadata_sources: + - https://github.com/PathologyFoundation/plip + + uni: + entities: [tissue] + methods: [self-supervised-learning, transformer] + modalities: [histopathology, imaging] + tasks: [foundation-model-pretraining, representation-learning] + github: https://github.com/mahmoodlab/UNI + last_checked: 2026-08-08 + metadata_sources: + - https://github.com/mahmoodlab/UNI + + hest_xenium_virtual_spatial_transcriptomics: + entities: [cell, gene, tissue] + modalities: [histopathology, spatial-transcriptomics, transcriptomics] + tasks: [regression] + documentation: https://huggingface.co/datasets/ratschlab/HEST_Xenium_virtual_spatial_transcriptomics + last_checked: 2026-08-08 + metadata_sources: + - https://huggingface.co/datasets/ratschlab/HEST_Xenium_virtual_spatial_transcriptomics diff --git a/upstream/inoue0426-awesome-computational-biology/catalogue/data/enrichment.yml b/upstream/inoue0426-awesome-computational-biology/catalogue/data/enrichment.yml new file mode 100644 index 0000000..643e903 --- /dev/null +++ b/upstream/inoue0426-awesome-computational-biology/catalogue/data/enrichment.yml @@ -0,0 +1,128 @@ +--- +title: "AI4Bio landscape enrichment overlay" +task: "" +lineage_type: import +upstream_source: https://github.com/inoue0426/awesome-computational-biology/blob/7a064bf0/data/enrichment.yml +upstream_sha: 7a064bf0 +imported_at: 2026-08-08 +prompt_class: catalogue +upstream_changes: accepted +author: upstream +validated: false +--- + +# AI4Bio landscape enrichment overlay +# +# README.md remains the canonical source for resource membership and basic fields. +# Add richer, independently curated metadata here, keyed by the stable resource id. +# scripts/build_resources.py merges these fields into generated JSON/CSV artifacts. +# +# Enrichment values should be source-verifiable. Controlled vocabulary fields are +# validated against data/vocabulary.yml. + +resources: + scgpt: + entities: [cell, gene] + methods: [generative-model, self-supervised-learning, transformer] + modalities: [multi-omics, single-cell-rna-seq, transcriptomics] + tasks: + - cell-type-annotation + - foundation-model-pretraining + - gene-regulatory-network-inference + - perturbation-prediction + - representation-learning + year: 2024 + github: https://github.com/bowang-lab/scGPT + documentation: https://scgpt.readthedocs.io/en/latest/ + paper: https://www.nature.com/articles/s41592-024-02201-0 + last_checked: 2026-08-08 + metadata_sources: + - https://github.com/bowang-lab/scGPT + - https://www.nature.com/articles/s41592-024-02201-0 + + geneformer: + entities: [cell, gene] + methods: [self-supervised-learning, transformer] + modalities: [single-cell-rna-seq, transcriptomics] + tasks: + - classification + - foundation-model-pretraining + - perturbation-prediction + - representation-learning + year: 2023 + documentation: https://geneformer.readthedocs.io/ + paper: https://www.nature.com/articles/s41586-023-06139-9 + last_checked: 2026-08-08 + metadata_sources: + - https://huggingface.co/ctheodoris/Geneformer + - https://www.nature.com/articles/s41586-023-06139-9 + + scfoundation: + entities: [cell, gene] + methods: [self-supervised-learning, transformer] + modalities: [single-cell-rna-seq, transcriptomics] + tasks: + - cell-type-annotation + - drug-response-prediction + - foundation-model-pretraining + - perturbation-prediction + - representation-learning + year: 2024 + github: https://github.com/biomap-research/scFoundation + paper: https://www.nature.com/articles/s41592-024-02305-7 + last_checked: 2026-08-08 + metadata_sources: + - https://github.com/biomap-research/scFoundation + - https://www.nature.com/articles/s41592-024-02305-7 + + genecompass: + entities: [cell, gene] + methods: [self-supervised-learning, transformer] + modalities: [single-cell-rna-seq, transcriptomics] + tasks: [foundation-model-pretraining, representation-learning] + year: 2024 + github: https://github.com/xCompass-AI/GeneCompass + paper: https://www.nature.com/articles/s41422-024-01034-y + last_checked: 2026-08-08 + metadata_sources: + - https://github.com/xCompass-AI/GeneCompass + - https://www.nature.com/articles/s41422-024-01034-y + + uce: + entities: [cell] + methods: [self-supervised-learning] + modalities: [single-cell-rna-seq, transcriptomics] + tasks: [foundation-model-pretraining, representation-learning] + year: 2026 + github: https://github.com/snap-stanford/UCE + paper: https://www.nature.com/articles/s41586-026-10689-z + last_checked: 2026-08-08 + metadata_sources: + - https://github.com/snap-stanford/UCE + - https://www.nature.com/articles/s41586-026-10689-z + + cellplm: + entities: [cell, gene] + methods: [self-supervised-learning, transformer] + modalities: [single-cell-rna-seq, transcriptomics] + tasks: [foundation-model-pretraining, representation-learning] + year: 2023 + github: https://github.com/OmicsML/CellPLM + paper: https://www.biorxiv.org/content/10.1101/2023.10.03.560734v1 + last_checked: 2026-08-08 + metadata_sources: + - https://github.com/OmicsML/CellPLM + - https://www.biorxiv.org/content/10.1101/2023.10.03.560734v1 + + scbert: + entities: [cell, gene] + methods: [language-model, self-supervised-learning, transformer] + modalities: [single-cell-rna-seq, transcriptomics] + tasks: [cell-type-annotation, classification, foundation-model-pretraining] + year: 2022 + github: https://github.com/TencentAILabHealthcare/scBERT + paper: https://www.nature.com/articles/s42256-022-00534-z + last_checked: 2026-08-08 + metadata_sources: + - https://github.com/TencentAILabHealthcare/scBERT + - https://www.nature.com/articles/s42256-022-00534-z diff --git a/upstream/inoue0426-awesome-computational-biology/catalogue/data/resources.json b/upstream/inoue0426-awesome-computational-biology/catalogue/data/resources.json index 5130edb..3a7a355 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/478be843/data/resources.json -upstream_sha: 478be843 -imported_at: 2026-07-17 +upstream_source: https://github.com/inoue0426/awesome-computational-biology/blob/7a064bf0/data/resources.json +upstream_sha: 7a064bf0 +imported_at: 2026-08-08 prompt_class: catalogue upstream_changes: accepted author: upstream @@ -22,9 +22,20 @@ validated: false "api" ], "tasks": [], - "modalities": [], + "modalities": [ + "chemical-structure" + ], "organism": [], - "api": true + "api": true, + "entities": [ + "molecule", + "protein" + ], + "documentation": "https://www.ebi.ac.uk/chembl/api/data/docs", + "last_checked": "2026-08-08", + "metadata_sources": [ + "https://www.ebi.ac.uk/chembl/api/data/docs" + ] }, { "id": "clinicaltrials_gov_api", @@ -36,9 +47,20 @@ validated: false "api" ], "tasks": [], - "modalities": [], + "modalities": [ + "clinical" + ], "organism": [], - "api": true + "api": true, + "entities": [ + "disease", + "drug" + ], + "documentation": "https://clinicaltrials.gov/data-api/api", + "last_checked": "2026-08-08", + "metadata_sources": [ + "https://clinicaltrials.gov/data-api/api" + ] }, { "id": "ensembl_rest_api", @@ -50,9 +72,22 @@ validated: false "api" ], "tasks": [], - "modalities": [], + "modalities": [ + "genomics" + ], "organism": [], - "api": true + "api": true, + "entities": [ + "gene", + "genome", + "transcript", + "variant" + ], + "documentation": "https://rest.ensembl.org/", + "last_checked": "2026-08-08", + "metadata_sources": [ + "https://rest.ensembl.org/" + ] }, { "id": "kegg_rest_api", @@ -66,7 +101,17 @@ validated: false "tasks": [], "modalities": [], "organism": [], - "api": true + "api": true, + "entities": [ + "compound", + "gene", + "pathway" + ], + "documentation": "https://www.kegg.jp/kegg/rest/keggapi.html", + "last_checked": "2026-08-08", + "metadata_sources": [ + "https://www.kegg.jp/kegg/rest/keggapi.html" + ] }, { "id": "ncbi_e_utilities", @@ -78,9 +123,24 @@ validated: false "api" ], "tasks": [], - "modalities": [], + "modalities": [ + "genomics", + "transcriptomics" + ], "organism": [], - "api": true + "api": true, + "entities": [ + "gene", + "genome", + "protein", + "transcript", + "variant" + ], + "documentation": "https://www.ncbi.nlm.nih.gov/books/NBK25501/", + "last_checked": "2026-08-08", + "metadata_sources": [ + "https://www.ncbi.nlm.nih.gov/books/NBK25501/" + ] }, { "id": "open_targets_platform_api", @@ -92,9 +152,23 @@ validated: false "api" ], "tasks": [], - "modalities": [], + "modalities": [ + "genomics", + "knowledge-graph" + ], "organism": [], - "api": true + "api": true, + "entities": [ + "disease", + "drug", + "gene", + "variant" + ], + "documentation": "https://platform.opentargets.org/api", + "last_checked": "2026-08-08", + "metadata_sources": [ + "https://platform.opentargets.org/api" + ] }, { "id": "pubmed_e_utilities_esearch_efetch", @@ -108,7 +182,12 @@ validated: false "tasks": [], "modalities": [], "organism": [], - "api": true + "api": true, + "documentation": "https://www.ncbi.nlm.nih.gov/books/NBK25501/", + "last_checked": "2026-08-08", + "metadata_sources": [ + "https://www.ncbi.nlm.nih.gov/books/NBK25501/" + ] }, { "id": "uniprot_rest_api", @@ -120,9 +199,20 @@ validated: false "api" ], "tasks": [], - "modalities": [], + "modalities": [ + "protein-sequence", + "proteomics" + ], "organism": [], - "api": true + "api": true, + "entities": [ + "protein" + ], + "documentation": "https://www.uniprot.org/help/api", + "last_checked": "2026-08-08", + "metadata_sources": [ + "https://www.uniprot.org/help/api" + ] }, { "id": "1000_genomes_project", @@ -147,10 +237,23 @@ validated: false "tags": [ "benchmarks-and-datasets" ], - "tasks": [], - "modalities": [], + "tasks": [ + "classification", + "regression" + ], + "modalities": [ + "chemical-structure" + ], "organism": [], - "api": false + "api": false, + "entities": [ + "molecule", + "protein" + ], + "last_checked": "2026-08-08", + "metadata_sources": [ + "https://www.kaggle.com/datasets/gokturkkoch/bace" + ] }, { "id": "beat_aml", @@ -161,10 +264,24 @@ validated: false "tags": [ "benchmarks-and-datasets" ], - "tasks": [], - "modalities": [], + "tasks": [ + "drug-response-prediction" + ], + "modalities": [ + "genomics" + ], "organism": [], - "api": false + "api": false, + "entities": [ + "cell", + "disease", + "drug", + "gene" + ], + "last_checked": "2026-08-08", + "metadata_sources": [ + "https://biodev.github.io/BeatAML2/" + ] }, { "id": "bento", @@ -189,10 +306,22 @@ validated: false "tags": [ "benchmarks-and-datasets" ], - "tasks": [], - "modalities": [], + "tasks": [ + "drug-target-interaction" + ], + "modalities": [ + "chemical-structure" + ], "organism": [], - "api": false + "api": false, + "entities": [ + "molecule", + "protein" + ], + "last_checked": "2026-08-08", + "metadata_sources": [ + "https://www.bindingdb.org/" + ] }, { "id": "cancer_therapeutics_response_portal_ctrp", @@ -203,10 +332,20 @@ validated: false "tags": [ "benchmarks-and-datasets" ], - "tasks": [], + "tasks": [ + "drug-response-prediction" + ], "modalities": [], "organism": [], - "api": false + "api": false, + "entities": [ + "cell", + "drug" + ], + "last_checked": "2026-08-08", + "metadata_sources": [ + "https://portals.broadinstitute.org/ctrp/" + ] }, { "id": "clintox", @@ -217,10 +356,21 @@ validated: false "tags": [ "benchmarks-and-datasets" ], - "tasks": [], - "modalities": [], + "tasks": [ + "classification" + ], + "modalities": [ + "clinical" + ], "organism": [], - "api": false + "api": false, + "entities": [ + "drug" + ], + "last_checked": "2026-08-08", + "metadata_sources": [ + "https://tdcommons.ai/single_pred_tasks/tox/#clintox" + ] }, { "id": "cptac_clinical_proteomic_tumor_analysis_consortium", @@ -287,10 +437,22 @@ validated: false "tags": [ "benchmarks-and-datasets" ], - "tasks": [], - "modalities": [], + "tasks": [ + "molecular-generation" + ], + "modalities": [ + "chemical-structure" + ], "organism": [], - "api": false + "api": false, + "entities": [ + "molecule" + ], + "github": "https://github.com/BenevolentAI/guacamol", + "last_checked": "2026-08-08", + "metadata_sources": [ + "https://github.com/BenevolentAI/guacamol" + ] }, { "id": "hest_xenium_virtual_spatial_transcriptomics", @@ -301,10 +463,26 @@ validated: false "tags": [ "benchmarks-and-datasets" ], - "tasks": [], - "modalities": [], + "tasks": [ + "regression" + ], + "modalities": [ + "histopathology", + "spatial-transcriptomics", + "transcriptomics" + ], "organism": [], - "api": false + "api": false, + "entities": [ + "cell", + "gene", + "tissue" + ], + "documentation": "https://huggingface.co/datasets/ratschlab/HEST_Xenium_virtual_spatial_transcriptomics", + "last_checked": "2026-08-08", + "metadata_sources": [ + "https://huggingface.co/datasets/ratschlab/HEST_Xenium_virtual_spatial_transcriptomics" + ] }, { "id": "jump_cell_painting_datasets", @@ -329,10 +507,23 @@ validated: false "tags": [ "benchmarks-and-datasets" ], - "tasks": [], - "modalities": [], + "tasks": [ + "perturbation-prediction" + ], + "modalities": [ + "transcriptomics" + ], "organism": [], - "api": false + "api": false, + "entities": [ + "cell", + "compound", + "gene" + ], + "last_checked": "2026-08-08", + "metadata_sources": [ + "https://lincsproject.org/LINCS/tools/workflows/find-the-best-place-to-obtain-the-lincs-l1000-data" + ] }, { "id": "moleculenet", @@ -343,10 +534,23 @@ validated: false "tags": [ "benchmarks-and-datasets" ], - "tasks": [], - "modalities": [], + "tasks": [ + "classification", + "regression" + ], + "modalities": [ + "chemical-structure" + ], "organism": [], - "api": false + "api": false, + "entities": [ + "molecule" + ], + "github": "https://github.com/deepchem/moleculenet", + "last_checked": "2026-08-08", + "metadata_sources": [ + "https://github.com/deepchem/moleculenet" + ] }, { "id": "moses", @@ -399,10 +603,25 @@ validated: false "tags": [ "benchmarks-and-datasets" ], - "tasks": [], - "modalities": [], + "tasks": [ + "drug-response-prediction" + ], + "modalities": [ + "clinical", + "genomics" + ], "organism": [], - "api": false + "api": false, + "entities": [ + "drug", + "gene", + "phenotype", + "variant" + ], + "last_checked": "2026-08-08", + "metadata_sources": [ + "https://www.pharmgkb.org/" + ] }, { "id": "pk_db", @@ -414,9 +633,18 @@ validated: false "benchmarks-and-datasets" ], "tasks": [], - "modalities": [], + "modalities": [ + "clinical" + ], "organism": [], - "api": false + "api": false, + "entities": [ + "drug" + ], + "last_checked": "2026-08-08", + "metadata_sources": [ + "https://pk-db.com/" + ] }, { "id": "prism", @@ -427,10 +655,20 @@ validated: false "tags": [ "benchmarks-and-datasets" ], - "tasks": [], + "tasks": [ + "drug-response-prediction" + ], "modalities": [], "organism": [], - "api": false + "api": false, + "entities": [ + "cell", + "drug" + ], + "last_checked": "2026-08-08", + "metadata_sources": [ + "https://depmap.org/portal/prism/" + ] }, { "id": "proteingym", @@ -441,10 +679,22 @@ validated: false "tags": [ "benchmarks-and-datasets" ], - "tasks": [], - "modalities": [], + "tasks": [ + "regression" + ], + "modalities": [ + "protein-sequence" + ], "organism": [], - "api": false + "api": false, + "entities": [ + "protein" + ], + "github": "https://github.com/OATML-Markslab/ProteinGym", + "last_checked": "2026-08-08", + "metadata_sources": [ + "https://github.com/OATML-Markslab/ProteinGym" + ] }, { "id": "qm9", @@ -483,10 +733,24 @@ validated: false "tags": [ "benchmarks-and-datasets" ], - "tasks": [], - "modalities": [], + "tasks": [ + "perturbation-prediction" + ], + "modalities": [ + "single-cell-rna-seq" + ], "organism": [], - "api": false + "api": false, + "entities": [ + "cell", + "drug", + "gene" + ], + "github": "https://github.com/sanderlab/scPerturb", + "last_checked": "2026-08-08", + "metadata_sources": [ + "https://github.com/sanderlab/scPerturb" + ] }, { "id": "sider_side_effect_resource", @@ -498,9 +762,19 @@ validated: false "benchmarks-and-datasets" ], "tasks": [], - "modalities": [], + "modalities": [ + "clinical" + ], "organism": [], - "api": false + "api": false, + "entities": [ + "drug", + "phenotype" + ], + "last_checked": "2026-08-08", + "metadata_sources": [ + "http://sideeffects.embl.de/" + ] }, { "id": "tabula_muris", @@ -773,13 +1047,23 @@ validated: false "drug-cell-line-response", "interaction" ], - "tasks": [], + "tasks": [ + "drug-response-prediction" + ], "modalities": [ - "Gene Expression", - "Small Molecule" + "genomics" ], "organism": [], - "api": false + "api": false, + "entities": [ + "cell", + "drug", + "gene" + ], + "last_checked": "2026-08-08", + "metadata_sources": [ + "https://discover.nci.nih.gov/cellminercdb/" + ] }, { "id": "chebi", @@ -1040,10 +1324,19 @@ validated: false ], "tasks": [], "modalities": [ - "Disease" + "chemical-structure" ], "organism": [], - "api": false + "api": false, + "entities": [ + "disease", + "drug", + "protein" + ], + "last_checked": "2026-08-08", + "metadata_sources": [ + "https://go.drugbank.com/" + ] }, { "id": "drugcentral", @@ -1184,13 +1477,23 @@ validated: false "drug-cell-line-response", "interaction" ], - "tasks": [], + "tasks": [ + "drug-response-prediction" + ], "modalities": [ - "Gene Expression", - "Small Molecule" + "genomics" ], "organism": [], - "api": false + "api": false, + "entities": [ + "cell", + "drug", + "gene" + ], + "last_checked": "2026-08-08", + "metadata_sources": [ + "https://www.cancerrxgene.org/" + ] }, { "id": "gnomad", @@ -1957,10 +2260,20 @@ validated: false ], "tasks": [], "modalities": [ - "Protein" + "knowledge-graph", + "proteomics" ], "organism": [], - "api": false + "api": false, + "entities": [ + "protein" + ], + "documentation": "https://string-db.org/help/api/", + "last_checked": "2026-08-08", + "metadata_sources": [ + "https://string-db.org/", + "https://string-db.org/help/api/" + ] }, { "id": "the_genotype_tissue_expression_gtex", @@ -2135,14 +2448,27 @@ validated: false "spatial-foundation-models" ], "tasks": [ - "Foundation Model" + "representation-learning" ], "modalities": [ - "Single Cell", - "Spatial Transcriptomics" + "histopathology", + "spatial-transcriptomics" ], "organism": [], - "api": false + "api": false, + "entities": [ + "cell", + "gene", + "tissue" + ], + "methods": [ + "autoencoder" + ], + "github": "https://github.com/ratschlab/aestetik", + "last_checked": "2026-08-08", + "metadata_sources": [ + "https://github.com/ratschlab/aestetik" + ] }, { "id": "ai4chem_chemllm_7b_chat", @@ -2174,14 +2500,27 @@ validated: false "protein-structure-prediction-and-design" ], "tasks": [ - "Foundation Model", - "Protein Structure Prediction" + "structure-prediction" ], "modalities": [ - "Protein" + "molecular-structure", + "protein-sequence" ], "organism": [], - "api": false + "api": false, + "entities": [ + "molecule", + "protein", + "protein-complex" + ], + "methods": [ + "diffusion" + ], + "github": "https://github.com/google-deepmind/alphafold3", + "last_checked": "2026-08-08", + "metadata_sources": [ + "https://github.com/google-deepmind/alphafold3" + ] }, { "id": "ankh", @@ -2417,6 +2756,26 @@ validated: false "organism": [], "api": false }, + { + "id": "cellot", + "name": "CellOT", + "type": "model", + "url": "https://github.com/bunnech/cellot", + "description": "Neural optimal transport framework for predicting single-cell responses to drug and genetic perturbations.", + "tags": [ + "drug-discovery", + "drug-perturbation" + ], + "tasks": [ + "Drug Discovery", + "Drug Perturbation" + ], + "modalities": [ + "Small Molecule" + ], + "organism": [], + "api": false + }, { "id": "cellplm", "name": "CellPLM", @@ -2429,14 +2788,31 @@ validated: false "transcriptomics-foundation-models" ], "tasks": [ - "Foundation Model" + "foundation-model-pretraining", + "representation-learning" ], "modalities": [ - "Single Cell", - "Transcriptomics" + "single-cell-rna-seq", + "transcriptomics" ], "organism": [], - "api": false + "api": false, + "entities": [ + "cell", + "gene" + ], + "methods": [ + "self-supervised-learning", + "transformer" + ], + "year": 2023, + "github": "https://github.com/OmicsML/CellPLM", + "paper": "https://www.biorxiv.org/content/10.1101/2023.10.03.560734v1", + "last_checked": "2026-08-08", + "metadata_sources": [ + "https://github.com/OmicsML/CellPLM", + "https://www.biorxiv.org/content/10.1101/2023.10.03.560734v1" + ] }, { "id": "chai_1", @@ -2489,13 +2865,26 @@ validated: false "foundation-models" ], "tasks": [ - "Foundation Model" + "representation-learning" ], "modalities": [ - "Small Molecule" + "chemical-structure" ], "organism": [], - "api": false + "api": false, + "entities": [ + "molecule" + ], + "methods": [ + "language-model", + "self-supervised-learning", + "transformer" + ], + "github": "https://github.com/seyonechithrananda/bert-loves-chemistry", + "last_checked": "2026-08-08", + "metadata_sources": [ + "https://github.com/seyonechithrananda/bert-loves-chemistry" + ] }, { "id": "chemcpa", @@ -2505,11 +2894,11 @@ validated: false "description": "Compositional perturbation autoencoder for predicting single-cell transcriptional responses to unseen drug perturbations and dose combinations.", "tags": [ "drug-discovery", - "drug-response-prediction" + "drug-perturbation" ], "tasks": [ "Drug Discovery", - "Drug Response Prediction" + "Drug Perturbation" ], "modalities": [ "Small Molecule" @@ -2554,6 +2943,26 @@ validated: false "organism": [], "api": false }, + { + "id": "cmonge", + "name": "CMonge", + "type": "model", + "url": "https://github.com/AI4SCR/conditional-monge-gap", + "description": "Conditional optimal transport model for generalizable single-cell perturbation response prediction across drugs and doses.", + "tags": [ + "drug-discovery", + "drug-perturbation" + ], + "tasks": [ + "Drug Discovery", + "Drug Perturbation" + ], + "modalities": [ + "Small Molecule" + ], + "organism": [], + "api": false + }, { "id": "concerto", "name": "Concerto", @@ -2587,14 +2996,27 @@ validated: false "spatial-foundation-models" ], "tasks": [ - "Foundation Model" + "foundation-model-pretraining", + "representation-learning" ], "modalities": [ - "Single Cell", - "Spatial Transcriptomics" + "histopathology", + "imaging" ], "organism": [], - "api": false + "api": false, + "entities": [ + "tissue" + ], + "methods": [ + "contrastive-learning", + "transformer" + ], + "github": "https://github.com/mahmoodlab/CONCH", + "last_checked": "2026-08-08", + "metadata_sources": [ + "https://github.com/mahmoodlab/CONCH" + ] }, { "id": "cyclecdr", @@ -2604,11 +3026,11 @@ validated: false "description": "Interpretable cycle-consistency framework for modeling cellular responses to drug perturbations.", "tags": [ "drug-discovery", - "drug-response-prediction" + "drug-perturbation" ], "tasks": [ "Drug Discovery", - "Drug Response Prediction" + "Drug Perturbation" ], "modalities": [ "Small Molecule" @@ -2728,14 +3150,23 @@ validated: false "spatial-foundation-models" ], "tasks": [ - "Foundation Model" + "regression" ], "modalities": [ - "Single Cell", - "Spatial Transcriptomics" + "histopathology", + "spatial-transcriptomics" ], "organism": [], - "api": false + "api": false, + "entities": [ + "gene", + "tissue" + ], + "github": "https://github.com/ratschlab/DeepSpot", + "last_checked": "2026-08-08", + "metadata_sources": [ + "https://github.com/ratschlab/DeepSpot" + ] }, { "id": "deepspot_m", @@ -2749,14 +3180,25 @@ validated: false "spatial-foundation-models" ], "tasks": [ - "Foundation Model" + "foundation-model-pretraining", + "regression" ], "modalities": [ - "Single Cell", - "Spatial Transcriptomics" + "histopathology", + "spatial-transcriptomics", + "transcriptomics" ], "organism": [], - "api": false + "api": false, + "entities": [ + "gene", + "tissue" + ], + "github": "https://github.com/ratschlab/DeepSpotM", + "last_checked": "2026-08-08", + "metadata_sources": [ + "https://github.com/ratschlab/DeepSpotM" + ] }, { "id": "deepspot2cell", @@ -2770,14 +3212,24 @@ validated: false "spatial-foundation-models" ], "tasks": [ - "Foundation Model" + "regression" ], "modalities": [ - "Single Cell", - "Spatial Transcriptomics" + "histopathology", + "spatial-transcriptomics" ], "organism": [], - "api": false + "api": false, + "entities": [ + "cell", + "gene", + "tissue" + ], + "github": "https://github.com/ratschlab/DeepSpot2Cell", + "last_checked": "2026-08-08", + "metadata_sources": [ + "https://github.com/ratschlab/DeepSpot2Cell" + ] }, { "id": "dgdrp", @@ -2810,14 +3262,29 @@ validated: false "molecular-generation" ], "tasks": [ - "Drug Discovery", - "Molecular Generation" + "docking" ], "modalities": [ - "Small Molecule" + "molecular-structure" ], "organism": [], - "api": false + "api": false, + "entities": [ + "molecule", + "protein" + ], + "methods": [ + "diffusion", + "geometric-deep-learning" + ], + "year": 2023, + "github": "https://github.com/gcorso/DiffDock", + "paper": "https://openreview.net/forum?id=kKF8_K-mBbS", + "last_checked": "2026-08-08", + "metadata_sources": [ + "https://github.com/gcorso/DiffDock", + "https://openreview.net/forum?id=kKF8_K-mBbS" + ] }, { "id": "diffsbdd", @@ -2990,14 +3457,28 @@ validated: false "protein-structure-prediction-and-design" ], "tasks": [ - "Foundation Model", - "Protein Structure Prediction" + "protein-sequence-design", + "representation-learning" ], "modalities": [ - "Protein" + "molecular-structure", + "protein-sequence" ], "organism": [], - "api": false + "api": false, + "entities": [ + "protein" + ], + "methods": [ + "generative-model", + "language-model", + "transformer" + ], + "github": "https://github.com/evolutionaryscale/esm", + "last_checked": "2026-08-08", + "metadata_sources": [ + "https://github.com/evolutionaryscale/esm" + ] }, { "id": "esmfold", @@ -3011,14 +3492,28 @@ validated: false "protein-structure-prediction-and-design" ], "tasks": [ - "Foundation Model", - "Protein Structure Prediction" + "representation-learning", + "structure-prediction" ], "modalities": [ - "Protein" + "molecular-structure", + "protein-sequence" ], "organism": [], - "api": false + "api": false, + "entities": [ + "protein" + ], + "methods": [ + "language-model", + "transformer" + ], + "year": 2023, + "github": "https://github.com/facebookresearch/esm", + "last_checked": "2026-08-08", + "metadata_sources": [ + "https://github.com/facebookresearch/esm" + ] }, { "id": "evo", @@ -3072,13 +3567,26 @@ validated: false "protein-foundation-models" ], "tasks": [ - "Foundation Model" + "representation-learning" ], "modalities": [ - "Protein" + "protein-sequence" ], "organism": [], - "api": false + "api": false, + "entities": [ + "protein" + ], + "methods": [ + "language-model", + "self-supervised-learning", + "transformer" + ], + "github": "https://github.com/facebookresearch/esm", + "last_checked": "2026-08-08", + "metadata_sources": [ + "https://github.com/facebookresearch/esm" + ] }, { "id": "gears", @@ -3113,14 +3621,31 @@ validated: false "single-cell-foundation-models" ], "tasks": [ - "Foundation Model" + "foundation-model-pretraining", + "representation-learning" ], "modalities": [ - "Multi-Omics", - "Single Cell" + "single-cell-rna-seq", + "transcriptomics" ], "organism": [], - "api": false + "api": false, + "entities": [ + "cell", + "gene" + ], + "methods": [ + "self-supervised-learning", + "transformer" + ], + "year": 2024, + "github": "https://github.com/xCompass-AI/GeneCompass", + "paper": "https://www.nature.com/articles/s41422-024-01034-y", + "last_checked": "2026-08-08", + "metadata_sources": [ + "https://github.com/xCompass-AI/GeneCompass", + "https://www.nature.com/articles/s41422-024-01034-y" + ] }, { "id": "geneformer", @@ -3134,14 +3659,33 @@ validated: false "transcriptomics-foundation-models" ], "tasks": [ - "Foundation Model" + "classification", + "foundation-model-pretraining", + "perturbation-prediction", + "representation-learning" ], "modalities": [ - "Single Cell", - "Transcriptomics" + "single-cell-rna-seq", + "transcriptomics" ], "organism": [], - "api": false + "api": false, + "entities": [ + "cell", + "gene" + ], + "methods": [ + "self-supervised-learning", + "transformer" + ], + "year": 2023, + "documentation": "https://geneformer.readthedocs.io/", + "paper": "https://www.nature.com/articles/s41586-023-06139-9", + "last_checked": "2026-08-08", + "metadata_sources": [ + "https://huggingface.co/ctheodoris/Geneformer", + "https://www.nature.com/articles/s41586-023-06139-9" + ] }, { "id": "genegpt", @@ -3171,13 +3715,31 @@ validated: false "llm-for-biology" ], "tasks": [ - "Language Modeling" + "batch-correction", + "classification", + "representation-learning" ], "modalities": [ - "Text" + "single-cell-rna-seq", + "transcriptomics" ], "organism": [], - "api": false + "api": false, + "entities": [ + "cell", + "gene" + ], + "methods": [ + "language-model" + ], + "year": 2023, + "github": "https://github.com/yiqunchen/GenePT", + "paper": "https://www.biorxiv.org/content/10.1101/2023.10.16.562533v2", + "last_checked": "2026-08-08", + "metadata_sources": [ + "https://github.com/yiqunchen/GenePT", + "https://www.biorxiv.org/content/10.1101/2023.10.16.562533v2" + ] }, { "id": "gigapath", @@ -3191,14 +3753,27 @@ validated: false "spatial-foundation-models" ], "tasks": [ - "Foundation Model" + "foundation-model-pretraining", + "representation-learning" ], "modalities": [ - "Single Cell", - "Spatial Transcriptomics" + "histopathology", + "imaging" ], "organism": [], - "api": false + "api": false, + "entities": [ + "tissue" + ], + "methods": [ + "self-supervised-learning", + "transformer" + ], + "github": "https://github.com/prov-gigapath/prov-gigapath", + "last_checked": "2026-08-08", + "metadata_sources": [ + "https://github.com/prov-gigapath/prov-gigapath" + ] }, { "id": "glue", @@ -3273,13 +3848,26 @@ validated: false "foundation-models" ], "tasks": [ - "Foundation Model" + "representation-learning" ], "modalities": [ - "Small Molecule" + "chemical-structure" ], "organism": [], - "api": false + "api": false, + "entities": [ + "molecule" + ], + "methods": [ + "graph-neural-network", + "self-supervised-learning", + "transformer" + ], + "github": "https://github.com/tencent-ailab/grover", + "last_checked": "2026-08-08", + "metadata_sources": [ + "https://github.com/tencent-ailab/grover" + ] }, { "id": "hidra", @@ -3537,13 +4125,26 @@ validated: false "foundation-models" ], "tasks": [ - "Foundation Model" + "representation-learning" ], "modalities": [ - "Small Molecule" + "chemical-structure" ], "organism": [], - "api": false + "api": false, + "entities": [ + "molecule" + ], + "methods": [ + "language-model", + "self-supervised-learning", + "transformer" + ], + "github": "https://github.com/IBM/molformer", + "last_checked": "2026-08-08", + "metadata_sources": [ + "https://github.com/IBM/molformer" + ] }, { "id": "molgpt", @@ -3698,14 +4299,33 @@ validated: false "spatial-foundation-models" ], "tasks": [ - "Foundation Model" + "foundation-model-pretraining", + "representation-learning" ], "modalities": [ - "Single Cell", - "Spatial Transcriptomics" + "single-cell-rna-seq", + "spatial-transcriptomics", + "transcriptomics" ], "organism": [], - "api": false + "api": false, + "entities": [ + "cell", + "gene", + "tissue" + ], + "methods": [ + "self-supervised-learning", + "transformer" + ], + "year": 2024, + "github": "https://github.com/theislab/nicheformer", + "paper": "https://doi.org/10.1101/2024.04.15.589472", + "last_checked": "2026-08-08", + "metadata_sources": [ + "https://github.com/theislab/nicheformer", + "https://doi.org/10.1101/2024.04.15.589472" + ] }, { "id": "nucleotide_transformer", @@ -3819,14 +4439,27 @@ validated: false "spatial-foundation-models" ], "tasks": [ - "Foundation Model" + "foundation-model-pretraining", + "representation-learning" ], "modalities": [ - "Single Cell", - "Spatial Transcriptomics" + "histopathology", + "imaging" ], "organism": [], - "api": false + "api": false, + "entities": [ + "tissue" + ], + "methods": [ + "self-supervised-learning", + "transformer" + ], + "documentation": "https://huggingface.co/owkin/phikon", + "last_checked": "2026-08-08", + "metadata_sources": [ + "https://huggingface.co/owkin/phikon" + ] }, { "id": "plip", @@ -3839,13 +4472,26 @@ validated: false "multi-modal-foundation-models" ], "tasks": [ - "Foundation Model" + "classification", + "representation-learning" ], "modalities": [ - "Multi-Modal" + "histopathology", + "imaging" ], "organism": [], - "api": false + "api": false, + "entities": [ + "tissue" + ], + "methods": [ + "contrastive-learning" + ], + "github": "https://github.com/PathologyFoundation/plip", + "last_checked": "2026-08-08", + "metadata_sources": [ + "https://github.com/PathologyFoundation/plip" + ] }, { "id": "porpoise", @@ -3874,11 +4520,11 @@ validated: false "description": "Deep generative model for predicting transcriptional responses to novel chemical perturbations for drug discovery.", "tags": [ "drug-discovery", - "drug-response-prediction" + "drug-perturbation" ], "tasks": [ "Drug Discovery", - "Drug Response Prediction" + "Drug Perturbation" ], "modalities": [ "Small Molecule" @@ -3898,13 +4544,27 @@ validated: false "protein-foundation-models" ], "tasks": [ - "Foundation Model" + "protein-sequence-design", + "representation-learning" ], "modalities": [ - "Protein" + "protein-sequence" ], "organism": [], - "api": false + "api": false, + "entities": [ + "protein" + ], + "methods": [ + "generative-model", + "language-model", + "transformer" + ], + "github": "https://github.com/salesforce/progen", + "last_checked": "2026-08-08", + "metadata_sources": [ + "https://github.com/salesforce/progen" + ] }, { "id": "proteinmpnn", @@ -3918,14 +4578,27 @@ validated: false "protein-structure-prediction-and-design" ], "tasks": [ - "Foundation Model", - "Protein Structure Prediction" + "protein-sequence-design" ], "modalities": [ - "Protein" + "molecular-structure", + "protein-sequence" ], "organism": [], - "api": false + "api": false, + "entities": [ + "protein" + ], + "methods": [ + "graph-neural-network", + "message-passing-neural-network" + ], + "year": 2022, + "github": "https://github.com/dauparas/ProteinMPNN", + "last_checked": "2026-08-08", + "metadata_sources": [ + "https://github.com/dauparas/ProteinMPNN" + ] }, { "id": "prottrans", @@ -3939,13 +4612,26 @@ validated: false "protein-foundation-models" ], "tasks": [ - "Foundation Model" + "representation-learning" ], "modalities": [ - "Protein" + "protein-sequence" ], "organism": [], - "api": false + "api": false, + "entities": [ + "protein" + ], + "methods": [ + "language-model", + "self-supervised-learning", + "transformer" + ], + "github": "https://github.com/agemagician/ProtTrans", + "last_checked": "2026-08-08", + "metadata_sources": [ + "https://github.com/agemagician/ProtTrans" + ] }, { "id": "recover", @@ -4124,14 +4810,33 @@ validated: false "transcriptomics-foundation-models" ], "tasks": [ - "Foundation Model" + "cell-type-annotation", + "classification", + "foundation-model-pretraining" ], "modalities": [ - "Single Cell", - "Transcriptomics" + "single-cell-rna-seq", + "transcriptomics" ], "organism": [], - "api": false + "api": false, + "entities": [ + "cell", + "gene" + ], + "methods": [ + "language-model", + "self-supervised-learning", + "transformer" + ], + "year": 2022, + "github": "https://github.com/TencentAILabHealthcare/scBERT", + "paper": "https://www.nature.com/articles/s42256-022-00534-z", + "last_checked": "2026-08-08", + "metadata_sources": [ + "https://github.com/TencentAILabHealthcare/scBERT", + "https://www.nature.com/articles/s42256-022-00534-z" + ] }, { "id": "scbutterfly", @@ -4166,14 +4871,34 @@ validated: false "transcriptomics-foundation-models" ], "tasks": [ - "Foundation Model" + "cell-type-annotation", + "drug-response-prediction", + "foundation-model-pretraining", + "perturbation-prediction", + "representation-learning" ], "modalities": [ - "Single Cell", - "Transcriptomics" + "single-cell-rna-seq", + "transcriptomics" ], "organism": [], - "api": false + "api": false, + "entities": [ + "cell", + "gene" + ], + "methods": [ + "self-supervised-learning", + "transformer" + ], + "year": 2024, + "github": "https://github.com/biomap-research/scFoundation", + "paper": "https://www.nature.com/articles/s41592-024-02305-7", + "last_checked": "2026-08-08", + "metadata_sources": [ + "https://github.com/biomap-research/scFoundation", + "https://www.nature.com/articles/s41592-024-02305-7" + ] }, { "id": "scgpt", @@ -4187,14 +4912,37 @@ validated: false "transcriptomics-foundation-models" ], "tasks": [ - "Foundation Model" + "cell-type-annotation", + "foundation-model-pretraining", + "gene-regulatory-network-inference", + "perturbation-prediction", + "representation-learning" ], "modalities": [ - "Single Cell", - "Transcriptomics" + "multi-omics", + "single-cell-rna-seq", + "transcriptomics" ], "organism": [], - "api": false + "api": false, + "entities": [ + "cell", + "gene" + ], + "methods": [ + "generative-model", + "self-supervised-learning", + "transformer" + ], + "year": 2024, + "github": "https://github.com/bowang-lab/scGPT", + "documentation": "https://scgpt.readthedocs.io/en/latest/", + "paper": "https://www.nature.com/articles/s41592-024-02201-0", + "last_checked": "2026-08-08", + "metadata_sources": [ + "https://github.com/bowang-lab/scGPT", + "https://www.nature.com/articles/s41592-024-02201-0" + ] }, { "id": "scgpt_spatial", @@ -4208,14 +4956,35 @@ validated: false "spatial-foundation-models" ], "tasks": [ - "Foundation Model" + "foundation-model-pretraining", + "imputation", + "representation-learning" ], "modalities": [ - "Single Cell", - "Spatial Transcriptomics" + "multi-omics", + "single-cell-rna-seq", + "spatial-transcriptomics" ], "organism": [], - "api": false + "api": false, + "entities": [ + "cell", + "gene", + "tissue" + ], + "methods": [ + "generative-model", + "self-supervised-learning", + "transformer" + ], + "year": 2025, + "github": "https://github.com/bowang-lab/scGPT-spatial", + "paper": "https://www.biorxiv.org/content/10.1101/2025.02.05.636714v1", + "last_checked": "2026-08-08", + "metadata_sources": [ + "https://github.com/bowang-lab/scGPT-spatial", + "https://www.biorxiv.org/content/10.1101/2025.02.05.636714v1" + ] }, { "id": "scmulan", @@ -4229,14 +4998,31 @@ validated: false "single-cell-foundation-models" ], "tasks": [ - "Foundation Model" + "foundation-model-pretraining", + "representation-learning" ], "modalities": [ - "Multi-Omics", - "Single Cell" + "epigenomics", + "multi-omics", + "proteomics", + "single-cell-rna-seq", + "transcriptomics" ], "organism": [], - "api": false + "api": false, + "entities": [ + "cell", + "gene" + ], + "methods": [ + "language-model", + "transformer" + ], + "github": "https://github.com/SuperBianC/scMulan", + "last_checked": "2026-08-08", + "metadata_sources": [ + "https://github.com/SuperBianC/scMulan" + ] }, { "id": "scpair", @@ -4269,13 +5055,36 @@ validated: false "llm-for-biology" ], "tasks": [ - "Language Modeling" + "batch-correction", + "cell-type-annotation", + "foundation-model-pretraining", + "gene-regulatory-network-inference", + "imputation", + "representation-learning" ], "modalities": [ - "Text" + "single-cell-rna-seq", + "transcriptomics" ], "organism": [], - "api": false + "api": false, + "entities": [ + "cell", + "gene" + ], + "methods": [ + "self-supervised-learning", + "transformer" + ], + "year": 2025, + "github": "https://github.com/cantinilab/scPRINT", + "documentation": "https://www.jkobject.com/scPRINT/", + "paper": "https://www.nature.com/articles/s41467-025-58699-1", + "last_checked": "2026-08-08", + "metadata_sources": [ + "https://github.com/cantinilab/scPRINT", + "https://www.nature.com/articles/s41467-025-58699-1" + ] }, { "id": "sei", @@ -4471,14 +5280,29 @@ validated: false "transcriptomics-foundation-models" ], "tasks": [ - "Foundation Model" + "foundation-model-pretraining", + "representation-learning" ], "modalities": [ - "Single Cell", - "Transcriptomics" + "single-cell-rna-seq", + "transcriptomics" ], "organism": [], - "api": false + "api": false, + "entities": [ + "cell" + ], + "methods": [ + "self-supervised-learning" + ], + "year": 2026, + "github": "https://github.com/snap-stanford/UCE", + "paper": "https://www.nature.com/articles/s41586-026-10689-z", + "last_checked": "2026-08-08", + "metadata_sources": [ + "https://github.com/snap-stanford/UCE", + "https://www.nature.com/articles/s41586-026-10689-z" + ] }, { "id": "uni", @@ -4492,14 +5316,27 @@ validated: false "spatial-foundation-models" ], "tasks": [ - "Foundation Model" + "foundation-model-pretraining", + "representation-learning" ], "modalities": [ - "Single Cell", - "Spatial Transcriptomics" + "histopathology", + "imaging" ], "organism": [], - "api": false + "api": false, + "entities": [ + "tissue" + ], + "methods": [ + "self-supervised-learning", + "transformer" + ], + "github": "https://github.com/mahmoodlab/UNI", + "last_checked": "2026-08-08", + "metadata_sources": [ + "https://github.com/mahmoodlab/UNI" + ] }, { "id": "uni_mol", @@ -4513,13 +5350,31 @@ validated: false "foundation-models" ], "tasks": [ - "Foundation Model" + "docking", + "representation-learning" ], "modalities": [ - "Small Molecule" + "chemical-structure", + "molecular-structure" ], "organism": [], - "api": false + "api": false, + "entities": [ + "molecule", + "protein" + ], + "methods": [ + "self-supervised-learning", + "transformer" + ], + "year": 2023, + "github": "https://github.com/deepmodeling/Uni-Mol", + "paper": "https://openreview.net/forum?id=6K2RM6wVqKu", + "last_checked": "2026-08-08", + "metadata_sources": [ + "https://github.com/deepmodeling/Uni-Mol", + "https://openreview.net/forum?id=6K2RM6wVqKu" + ] }, { "id": "unitednet", diff --git a/upstream/inoue0426-awesome-computational-biology/catalogue/data/resources.yml b/upstream/inoue0426-awesome-computational-biology/catalogue/data/resources.yml index 270b724..98e1aac 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/478be843/data/resources.yml -upstream_sha: 478be843 -imported_at: 2026-07-17 +upstream_source: https://github.com/inoue0426/awesome-computational-biology/blob/7a064bf0/data/resources.yml +upstream_sha: 7a064bf0 +imported_at: 2026-08-08 prompt_class: catalogue upstream_changes: accepted author: upstream @@ -1678,6 +1678,17 @@ resources: organism: [] api: false + - id: cellot + name: "CellOT" + type: model + url: https://github.com/bunnech/cellot + description: "Neural optimal transport framework for predicting single-cell responses to drug and genetic perturbations." + tags: [drug-discovery, drug-perturbation] + tasks: [Drug Discovery, Drug Perturbation] + modalities: [Small Molecule] + organism: [] + api: false + - id: cellplm name: "CellPLM" type: model @@ -1727,8 +1738,8 @@ resources: type: model url: https://github.com/theislab/chemCPA description: "Compositional perturbation autoencoder for predicting single-cell transcriptional responses to unseen drug perturbations and dose combinations." - tags: [drug-discovery, drug-response-prediction] - tasks: [Drug Discovery, Drug Response Prediction] + tags: [drug-discovery, drug-perturbation] + tasks: [Drug Discovery, Drug Perturbation] modalities: [Small Molecule] organism: [] api: false @@ -1755,6 +1766,17 @@ resources: organism: [] api: false + - id: cmonge + name: "CMonge" + type: model + url: https://github.com/AI4SCR/conditional-monge-gap + description: "Conditional optimal transport model for generalizable single-cell perturbation response prediction across drugs and doses." + tags: [drug-discovery, drug-perturbation] + tasks: [Drug Discovery, Drug Perturbation] + modalities: [Small Molecule] + organism: [] + api: false + - id: concerto name: "Concerto" type: model @@ -1782,8 +1804,8 @@ resources: type: model url: https://github.com/hliulab/cycleCDR description: "Interpretable cycle-consistency framework for modeling cellular responses to drug perturbations." - tags: [drug-discovery, drug-response-prediction] - tasks: [Drug Discovery, Drug Response Prediction] + tags: [drug-discovery, drug-perturbation] + tasks: [Drug Discovery, Drug Perturbation] modalities: [Small Molecule] organism: [] api: false @@ -2475,8 +2497,8 @@ resources: type: model url: https://github.com/Perturbation-Response-Prediction/PRnet description: "Deep generative model for predicting transcriptional responses to novel chemical perturbations for drug discovery." - tags: [drug-discovery, drug-response-prediction] - tasks: [Drug Discovery, Drug Response Prediction] + tags: [drug-discovery, drug-perturbation] + tasks: [Drug Discovery, Drug Perturbation] modalities: [Small Molecule] organism: [] api: false diff --git a/upstream/inoue0426-awesome-computational-biology/catalogue/data/vocabulary.yml b/upstream/inoue0426-awesome-computational-biology/catalogue/data/vocabulary.yml new file mode 100644 index 0000000..11e4abc --- /dev/null +++ b/upstream/inoue0426-awesome-computational-biology/catalogue/data/vocabulary.yml @@ -0,0 +1,105 @@ +--- +title: "Canonical vocabulary for new AI4Bio enrichment metadata." +task: "" +lineage_type: import +upstream_source: https://github.com/inoue0426/awesome-computational-biology/blob/7a064bf0/data/vocabulary.yml +upstream_sha: 7a064bf0 +imported_at: 2026-08-08 +prompt_class: unknown +upstream_changes: accepted +author: upstream +validated: false +--- + +# Canonical vocabulary for new AI4Bio enrichment metadata. +# +# These values are enforced only for fields explicitly added through +# data/enrichment.yml. README-derived legacy values remain backward compatible. +# Canonical terms use lowercase kebab-case. + +version: 1 + +controlled_fields: + entities: + - cell + - compound + - disease + - drug + - gene + - genome + - molecule + - organism + - pathway + - phenotype + - protein + - protein-complex + - regulatory-element + - tissue + - transcript + - variant + + methods: + - autoencoder + - contrastive-learning + - convolutional-neural-network + - diffusion + - generative-model + - geometric-deep-learning + - graph-neural-network + - knowledge-graph + - language-model + - message-passing-neural-network + - multi-agent-system + - optimal-transport + - recurrent-neural-network + - reinforcement-learning + - retrieval-augmented-generation + - self-supervised-learning + - state-space-model + - supervised-learning + - transformer + - unsupervised-learning + - variational-autoencoder + + modalities: + - cell-painting + - chemical-structure + - clinical + - dna-sequence + - electronic-health-record + - epigenomics + - genomics + - histopathology + - imaging + - knowledge-graph + - metabolomics + - molecular-structure + - multi-omics + - protein-sequence + - proteomics + - rna-sequence + - single-cell-rna-seq + - spatial-transcriptomics + - transcriptomics + + tasks: + - batch-correction + - cell-type-annotation + - classification + - dimensionality-reduction + - docking + - drug-response-prediction + - drug-target-interaction + - foundation-model-pretraining + - gene-regulatory-network-inference + - imputation + - link-prediction + - molecular-generation + - perturbation-prediction + - protein-function-prediction + - protein-sequence-design + - regression + - representation-learning + - structure-prediction + - trajectory-inference + - virtual-screening diff --git a/upstream/inoue0426-awesome-computational-biology/catalogue/docs/AI4BIO_LANDSCAPE.md b/upstream/inoue0426-awesome-computational-biology/catalogue/docs/AI4BIO_LANDSCAPE.md new file mode 100644 index 0000000..2857767 --- /dev/null +++ b/upstream/inoue0426-awesome-computational-biology/catalogue/docs/AI4BIO_LANDSCAPE.md @@ -0,0 +1,73 @@ +--- +title: "AI4Bio Landscape Database" +task: "" +lineage_type: import +upstream_source: https://github.com/inoue0426/awesome-computational-biology/blob/7a064bf0/docs/AI4BIO_LANDSCAPE.md +upstream_sha: 7a064bf0 +imported_at: 2026-08-08 +prompt_class: catalogue +upstream_changes: accepted +author: upstream +validated: false +--- + +# AI4Bio Landscape Database + +The landscape view treats the existing computational biology registry as a multidimensional database rather than a single hierarchical list. + +## Design goals + +- Keep the current curated resource records and generation pipeline intact. +- Expose orthogonal facets so one resource can be explored by resource type, biological/ML task, data modality, organism, and domain tag. +- Make the landscape useful without introducing a server or build-time dependency. +- Keep the data model extensible for richer AI4Bio metadata over time. + +## Current facet model + +The landscape UI derives the following dimensions from `docs/data/resources.json`: + +| Dimension | Source field | Example values | +|---|---|---| +| Resource type | `type` | `database`, `benchmark`, `model`, `toolkit`, `api` | +| Task | `tasks` | `drug-response-prediction`, `cell-type-annotation`, `molecular-generation` | +| Modality | `modalities` | `transcriptomics`, `spatial-transcriptomics`, `protein-sequence` | +| Organism | `organism` | `human`, `mouse`, `multi-species` | +| Domain/tag | `tags` | `drug-discovery`, `single-cell`, `foundation-model` | + +These are deliberately treated as separate axes. A model can therefore be, for example, a `model` that performs `perturbation-prediction` on `single-cell-rna-seq` data for `human` and carry tags such as `drug-discovery` and `foundation-model`. + +## Recommended schema evolution + +The current schema is compatible with a richer landscape database. New fields should be added incrementally and only when they can be curated consistently. + +Suggested fields: + +| Field | Type | Purpose | +|---|---|---| +| `entities` | array of strings | Biological entities such as `gene`, `protein`, `compound`, `cell`, `disease` | +| `methods` | array of strings | Method families such as `transformer`, `gnn`, `diffusion`, `optimal-transport` | +| `organizations` | array of strings | Primary organizations responsible for the resource | +| `year` | integer | Initial public release/publication year | +| `github` | string | Source repository when distinct from the canonical landing page | +| `documentation` | string | Documentation URL | +| `maintenance_status` | string | Curated status such as `active`, `maintenance`, `archived`, `unknown` | +| `last_checked` | string | Date the metadata/link was last manually or automatically checked | + +Avoid adding dynamic popularity metrics such as GitHub stars directly to canonical records unless a reproducible refresh pipeline is introduced. Such values become stale quickly and should be stored as generated metadata rather than curated facts. + +## Canonical-source policy + +At present, `README.md` is the canonical curated list, with generated YAML/JSON/CSV artifacts. The landscape page intentionally consumes `docs/data/resources.json` without changing that policy. + +A future migration may make `data/resources.yml` the canonical source once all README-only categorization semantics can be represented explicitly in structured fields. That migration should be a separate change because it changes contribution workflow and source-of-truth semantics. + +## Landscape page + +Open `docs/landscape.html` through GitHub Pages. It provides: + +- full-text search across names, descriptions, tasks, modalities, organisms, and tags; +- filters for type, task, modality, organism, and tag; +- summary counts for resources and major dimensions; +- frequency bars recalculated for the current filtered result set; +- direct resource and paper links; +- client-side rendering with no additional dependencies. diff --git a/upstream/inoue0426-awesome-computational-biology/catalogue/docs/FOUNDATION_MODEL_ENRICHMENT.md b/upstream/inoue0426-awesome-computational-biology/catalogue/docs/FOUNDATION_MODEL_ENRICHMENT.md new file mode 100644 index 0000000..c2293a8 --- /dev/null +++ b/upstream/inoue0426-awesome-computational-biology/catalogue/docs/FOUNDATION_MODEL_ENRICHMENT.md @@ -0,0 +1,72 @@ +--- +title: "Foundation Model Enrichment" +task: "" +lineage_type: import +upstream_source: https://github.com/inoue0426/awesome-computational-biology/blob/7a064bf0/docs/FOUNDATION_MODEL_ENRICHMENT.md +upstream_sha: 7a064bf0 +imported_at: 2026-08-08 +prompt_class: catalogue +upstream_changes: accepted +author: upstream +validated: false +--- + +# Foundation Model Enrichment + +This document tracks the first curated metadata-enrichment pass for AI4Bio foundation models. + +## Scope + +The initial pass focuses on representative single-cell and transcriptomics foundation models already present in the resource registry, beginning with: + +- scGPT +- Geneformer + +The scope may be expanded incrementally once the curation rules below are validated in practice. + +## Curation rules + +Metadata must be supported by at least one primary or official source: + +- official project repository or model card; +- official documentation; +- primary peer-reviewed publication or preprint. + +Unknown or ambiguous metadata is omitted rather than inferred. + +For each resource, curate fields where evidence is available: + +- `entities` +- `methods` +- `organizations` +- `year` +- `github` +- `documentation` +- `maintenance_status` +- `last_checked` +- `metadata_sources` + +`maintenance_status` should only be marked `active` when there is direct evidence of ongoing maintenance, such as a recent official release or repository activity. Otherwise use `unknown` or omit the field. + +## Initial evidence targets + +### scGPT + +Primary evidence should include the official `bowang-lab/scGPT` repository and the Nature Methods publication. + +### Geneformer + +Primary evidence should include the official `ctheodoris/Geneformer` model repository/model card and the primary Nature publication. + +## Completion criteria + +A resource is considered enriched when: + +1. all added metadata is supported by `metadata_sources`; +2. no unsupported organization, method, year, or maintenance claim is introduced; +3. generated JSON/CSV artifacts are regenerated and committed; +4. schema validation and resource-consistency CI checks pass. + +## Provenance + +This enrichment pass is being prepared with assistance from OpenAI GPT-5.6 Sol. Final metadata is intended to remain source-verifiable and reviewable through the recorded provenance URLs. diff --git a/upstream/inoue0426-awesome-computational-biology/catalogue/docs/data/README.md b/upstream/inoue0426-awesome-computational-biology/catalogue/docs/data/README.md new file mode 100644 index 0000000..ebdaa65 --- /dev/null +++ b/upstream/inoue0426-awesome-computational-biology/catalogue/docs/data/README.md @@ -0,0 +1,21 @@ +--- +title: "AI4Bio data files" +task: "" +lineage_type: import +upstream_source: https://github.com/inoue0426/awesome-computational-biology/blob/7a064bf0/docs/data/README.md +upstream_sha: 7a064bf0 +imported_at: 2026-08-08 +prompt_class: catalogue +upstream_changes: accepted +author: upstream +validated: false +--- + +# AI4Bio data files + +- `resources.json`: generated merged resource registry consumed by GitHub Pages. +- `resource.schema.json`: JSON Schema 2020-12 contract for one resource object. +- `SCHEMA.md`: original schema notes. +- `SCHEMA_V2.md`: richer AI4Bio landscape schema and enrichment workflow. + +The enriched build path is `scripts/build_resources_v2.py`, which combines `data/resources.yml` with `data/enrichment.yml` and runs `scripts/validate_resources.py` before writing artifacts. diff --git a/upstream/inoue0426-awesome-computational-biology/catalogue/docs/data/SCHEMA_V2.md b/upstream/inoue0426-awesome-computational-biology/catalogue/docs/data/SCHEMA_V2.md new file mode 100644 index 0000000..87bdf07 --- /dev/null +++ b/upstream/inoue0426-awesome-computational-biology/catalogue/docs/data/SCHEMA_V2.md @@ -0,0 +1,132 @@ +--- +title: "AI4Bio Resource Schema v2" +task: "" +lineage_type: import +upstream_source: https://github.com/inoue0426/awesome-computational-biology/blob/7a064bf0/docs/data/SCHEMA_V2.md +upstream_sha: 7a064bf0 +imported_at: 2026-08-08 +prompt_class: catalogue +upstream_changes: accepted +author: upstream +validated: false +--- + +# AI4Bio Resource Schema v2 + +This document defines the richer landscape metadata layered on top of the curated Awesome Computational Biology list. + +## Source model + +The repository intentionally separates **membership/basic metadata** from **landscape enrichment**: + +1. `README.md` is the canonical curated resource list. +2. `scripts/sync_resources_from_readme.py` derives `data/resources.yml` from README headings and bullets. +3. `data/enrichment.yml` stores richer metadata keyed by stable resource `id`. +4. `data/vocabulary.yml` defines canonical terms for controlled enrichment dimensions. +5. `scripts/build_resources.py` merges base records and enrichment, validates them, and writes `data/resources.json`, `data/resources.csv`, and `docs/data/resources.json`. + +This separation prevents hand-curated AI4Bio metadata from being erased by README synchronization. + +## Core identity fields + +These fields are required and may not be overridden by `data/enrichment.yml`: + +| Field | Type | Meaning | +|---|---|---| +| `id` | string | Stable lowercase `snake_case` identifier | +| `name` | string | Official display name | +| `type` | enum | `api`, `benchmark`, `database`, `model`, `resource`, or `toolkit` | +| `url` | URL | Canonical landing page | +| `description` | string | Short factual description | + +## Landscape dimensions + +| Field | Type | Meaning | +|---|---|---| +| `tasks` | string[] | Biological or ML tasks performed | +| `modalities` | string[] | Input/output data modalities | +| `organism` | string[] | Covered organisms or species groups | +| `entities` | string[] | Biological entities: gene, protein, compound, cell, disease, etc. | +| `methods` | string[] | Method families: transformer, GNN, diffusion, optimal transport, etc. | +| `tags` | string[] | Broad domain and curation labels | +| `organizations` | string[] | Organizations maintaining or primarily responsible for the resource | + +These dimensions are deliberately orthogonal. Do not encode a task as a modality or a biological entity as a resource type. + +## Controlled vocabulary + +New values added through `data/enrichment.yml` for `entities`, `methods`, `modalities`, and `tasks` must use canonical terms from `data/vocabulary.yml`. + +Canonical terms use lowercase kebab-case, for example: + +```yaml +entities: [cell, gene] +methods: [transformer, self-supervised-learning] +modalities: [single-cell-rna-seq, transcriptomics] +tasks: [foundation-model-pretraining, cell-type-annotation] +``` + +This rule is intentionally applied only to enrichment metadata. Existing README-derived values remain valid for backward compatibility and can be migrated separately without blocking routine resource updates. + +When a required concept is missing, add a reusable canonical term to `data/vocabulary.yml` instead of inventing a one-off spelling in an enrichment record. `tags`, `organism`, and `organizations` remain free-form because their vocabularies are broader or context dependent. + +## Provenance and lifecycle fields + +| Field | Type | Meaning | +|---|---|---| +| `year` | integer | Initial public release or primary publication year | +| `github` | URL | Source repository when available | +| `documentation` | URL | Documentation landing page | +| `paper` | URL | Primary publication or preprint | +| `license` | string | SPDX identifier preferred | +| `api` | boolean | Programmatic API availability | +| `access` | enum | `open`, `registration`, `restricted`, `commercial`, `unknown` | +| `maintenance_status` | enum | `active`, `maintenance`, `archived`, `unknown` | +| `updated` | date | Last-known upstream update date | +| `last_checked` | date | Date this repository verified the metadata | +| `metadata_sources` | URL[] | Sources supporting enriched metadata | + +`last_checked` is a curation timestamp, not an upstream release date. `updated` should only be populated when an upstream update date is known. + +## Enrichment rules + +`data/enrichment.yml` is a mapping keyed by resource id: + +```yaml +resources: + example_resource: + entities: [gene, disease] + methods: [transformer] + organizations: [Example Lab] + year: 2025 + github: https://github.com/example/project + documentation: https://example.org/docs + maintenance_status: active + access: open + last_checked: 2026-08-08 + metadata_sources: + - https://example.org/about +``` + +Enrichment cannot override `id`, `name`, `type`, `url`, or `description`. A referenced id must already exist in `data/resources.yml`. + +## Validation contract + +`python scripts/validate_resources.py` checks: + +- required fields and field types; +- stable id format and id uniqueness; +- allowed enum values; +- HTTP(S) URL shape; +- ISO `YYYY-MM-DD` dates; +- list uniqueness and non-empty values; +- enrichment references and forbidden identity overrides; +- controlled enrichment terms against `data/vocabulary.yml`; +- vocabulary uniqueness and lowercase kebab-case normalization; +- unknown field names. + +The machine-readable resource counterpart is `docs/data/resource.schema.json` (JSON Schema 2020-12). Controlled vocabulary enforcement is performed at the enrichment layer because legacy README-derived values intentionally remain backward compatible. + +## Curation guidance + +Prefer verified metadata over exhaustive metadata. Unknown fields should be omitted rather than guessed. For facts likely to change, include `last_checked` and at least one `metadata_sources` URL. Dynamic popularity metrics such as GitHub stars should remain generated telemetry rather than canonical curated fields. diff --git a/upstream/inoue0426-awesome-computational-biology/catalogue/docs/data/resource.schema.json b/upstream/inoue0426-awesome-computational-biology/catalogue/docs/data/resource.schema.json new file mode 100644 index 0000000..314ff34 --- /dev/null +++ b/upstream/inoue0426-awesome-computational-biology/catalogue/docs/data/resource.schema.json @@ -0,0 +1,53 @@ +--- +title: "Resource.Schema" +task: "" +lineage_type: import +upstream_source: https://github.com/inoue0426/awesome-computational-biology/blob/7a064bf0/docs/data/resource.schema.json +upstream_sha: 7a064bf0 +imported_at: 2026-08-08 +prompt_class: catalogue +upstream_changes: accepted +author: upstream +validated: false +--- + +{ + "$schema": "https://json-schema.org/draft/2020-12/schema", + "$id": "https://inoue0426.github.io/awesome-computational-biology/data/resource.schema.json", + "title": "AI4Bio Resource", + "type": "object", + "required": ["id", "name", "type", "url", "description"], + "additionalProperties": false, + "properties": { + "id": {"type": "string", "pattern": "^[a-z0-9]+(?:_[a-z0-9]+)*$"}, + "name": {"type": "string", "minLength": 1}, + "type": {"enum": ["api", "benchmark", "database", "model", "resource", "toolkit"]}, + "url": {"type": "string", "format": "uri", "pattern": "^https?://"}, + "description": {"type": "string", "minLength": 1}, + "tags": {"$ref": "#/$defs/stringArray"}, + "tasks": {"$ref": "#/$defs/stringArray"}, + "modalities": {"$ref": "#/$defs/stringArray"}, + "organism": {"$ref": "#/$defs/stringArray"}, + "entities": {"$ref": "#/$defs/stringArray"}, + "methods": {"$ref": "#/$defs/stringArray"}, + "organizations": {"$ref": "#/$defs/stringArray"}, + "metadata_sources": {"type": "array", "items": {"type": "string", "format": "uri", "pattern": "^https?://"}, "uniqueItems": true}, + "license": {"type": "string"}, + "api": {"type": "boolean"}, + "paper": {"type": "string", "format": "uri", "pattern": "^https?://"}, + "github": {"type": "string", "format": "uri", "pattern": "^https://github\\.com/"}, + "documentation": {"type": "string", "format": "uri", "pattern": "^https?://"}, + "year": {"type": "integer", "minimum": 1900, "maximum": 2100}, + "maintenance_status": {"enum": ["active", "maintenance", "archived", "unknown"]}, + "access": {"enum": ["open", "registration", "restricted", "commercial", "unknown"]}, + "updated": {"type": "string", "format": "date"}, + "last_checked": {"type": "string", "format": "date"} + }, + "$defs": { + "stringArray": { + "type": "array", + "items": {"type": "string", "minLength": 1}, + "uniqueItems": true + } + } +} 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 f001590..adc957c 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/478be843/docs/data/resources.json -upstream_sha: 478be843 -imported_at: 2026-07-17 +upstream_source: https://github.com/inoue0426/awesome-computational-biology/blob/7a064bf0/docs/data/resources.json +upstream_sha: 7a064bf0 +imported_at: 2026-08-08 prompt_class: catalogue upstream_changes: accepted author: upstream @@ -22,9 +22,20 @@ validated: false "api" ], "tasks": [], - "modalities": [], + "modalities": [ + "chemical-structure" + ], "organism": [], - "api": true + "api": true, + "entities": [ + "molecule", + "protein" + ], + "documentation": "https://www.ebi.ac.uk/chembl/api/data/docs", + "last_checked": "2026-08-08", + "metadata_sources": [ + "https://www.ebi.ac.uk/chembl/api/data/docs" + ] }, { "id": "clinicaltrials_gov_api", @@ -36,9 +47,20 @@ validated: false "api" ], "tasks": [], - "modalities": [], + "modalities": [ + "clinical" + ], "organism": [], - "api": true + "api": true, + "entities": [ + "disease", + "drug" + ], + "documentation": "https://clinicaltrials.gov/data-api/api", + "last_checked": "2026-08-08", + "metadata_sources": [ + "https://clinicaltrials.gov/data-api/api" + ] }, { "id": "ensembl_rest_api", @@ -50,9 +72,22 @@ validated: false "api" ], "tasks": [], - "modalities": [], + "modalities": [ + "genomics" + ], "organism": [], - "api": true + "api": true, + "entities": [ + "gene", + "genome", + "transcript", + "variant" + ], + "documentation": "https://rest.ensembl.org/", + "last_checked": "2026-08-08", + "metadata_sources": [ + "https://rest.ensembl.org/" + ] }, { "id": "kegg_rest_api", @@ -66,7 +101,17 @@ validated: false "tasks": [], "modalities": [], "organism": [], - "api": true + "api": true, + "entities": [ + "compound", + "gene", + "pathway" + ], + "documentation": "https://www.kegg.jp/kegg/rest/keggapi.html", + "last_checked": "2026-08-08", + "metadata_sources": [ + "https://www.kegg.jp/kegg/rest/keggapi.html" + ] }, { "id": "ncbi_e_utilities", @@ -78,9 +123,24 @@ validated: false "api" ], "tasks": [], - "modalities": [], + "modalities": [ + "genomics", + "transcriptomics" + ], "organism": [], - "api": true + "api": true, + "entities": [ + "gene", + "genome", + "protein", + "transcript", + "variant" + ], + "documentation": "https://www.ncbi.nlm.nih.gov/books/NBK25501/", + "last_checked": "2026-08-08", + "metadata_sources": [ + "https://www.ncbi.nlm.nih.gov/books/NBK25501/" + ] }, { "id": "open_targets_platform_api", @@ -92,9 +152,23 @@ validated: false "api" ], "tasks": [], - "modalities": [], + "modalities": [ + "genomics", + "knowledge-graph" + ], "organism": [], - "api": true + "api": true, + "entities": [ + "disease", + "drug", + "gene", + "variant" + ], + "documentation": "https://platform.opentargets.org/api", + "last_checked": "2026-08-08", + "metadata_sources": [ + "https://platform.opentargets.org/api" + ] }, { "id": "pubmed_e_utilities_esearch_efetch", @@ -108,7 +182,12 @@ validated: false "tasks": [], "modalities": [], "organism": [], - "api": true + "api": true, + "documentation": "https://www.ncbi.nlm.nih.gov/books/NBK25501/", + "last_checked": "2026-08-08", + "metadata_sources": [ + "https://www.ncbi.nlm.nih.gov/books/NBK25501/" + ] }, { "id": "uniprot_rest_api", @@ -120,9 +199,20 @@ validated: false "api" ], "tasks": [], - "modalities": [], + "modalities": [ + "protein-sequence", + "proteomics" + ], "organism": [], - "api": true + "api": true, + "entities": [ + "protein" + ], + "documentation": "https://www.uniprot.org/help/api", + "last_checked": "2026-08-08", + "metadata_sources": [ + "https://www.uniprot.org/help/api" + ] }, { "id": "1000_genomes_project", @@ -147,10 +237,23 @@ validated: false "tags": [ "benchmarks-and-datasets" ], - "tasks": [], - "modalities": [], + "tasks": [ + "classification", + "regression" + ], + "modalities": [ + "chemical-structure" + ], "organism": [], - "api": false + "api": false, + "entities": [ + "molecule", + "protein" + ], + "last_checked": "2026-08-08", + "metadata_sources": [ + "https://www.kaggle.com/datasets/gokturkkoch/bace" + ] }, { "id": "beat_aml", @@ -161,10 +264,24 @@ validated: false "tags": [ "benchmarks-and-datasets" ], - "tasks": [], - "modalities": [], + "tasks": [ + "drug-response-prediction" + ], + "modalities": [ + "genomics" + ], "organism": [], - "api": false + "api": false, + "entities": [ + "cell", + "disease", + "drug", + "gene" + ], + "last_checked": "2026-08-08", + "metadata_sources": [ + "https://biodev.github.io/BeatAML2/" + ] }, { "id": "bento", @@ -189,10 +306,22 @@ validated: false "tags": [ "benchmarks-and-datasets" ], - "tasks": [], - "modalities": [], + "tasks": [ + "drug-target-interaction" + ], + "modalities": [ + "chemical-structure" + ], "organism": [], - "api": false + "api": false, + "entities": [ + "molecule", + "protein" + ], + "last_checked": "2026-08-08", + "metadata_sources": [ + "https://www.bindingdb.org/" + ] }, { "id": "cancer_therapeutics_response_portal_ctrp", @@ -203,10 +332,20 @@ validated: false "tags": [ "benchmarks-and-datasets" ], - "tasks": [], + "tasks": [ + "drug-response-prediction" + ], "modalities": [], "organism": [], - "api": false + "api": false, + "entities": [ + "cell", + "drug" + ], + "last_checked": "2026-08-08", + "metadata_sources": [ + "https://portals.broadinstitute.org/ctrp/" + ] }, { "id": "clintox", @@ -217,10 +356,21 @@ validated: false "tags": [ "benchmarks-and-datasets" ], - "tasks": [], - "modalities": [], + "tasks": [ + "classification" + ], + "modalities": [ + "clinical" + ], "organism": [], - "api": false + "api": false, + "entities": [ + "drug" + ], + "last_checked": "2026-08-08", + "metadata_sources": [ + "https://tdcommons.ai/single_pred_tasks/tox/#clintox" + ] }, { "id": "cptac_clinical_proteomic_tumor_analysis_consortium", @@ -287,10 +437,22 @@ validated: false "tags": [ "benchmarks-and-datasets" ], - "tasks": [], - "modalities": [], + "tasks": [ + "molecular-generation" + ], + "modalities": [ + "chemical-structure" + ], "organism": [], - "api": false + "api": false, + "entities": [ + "molecule" + ], + "github": "https://github.com/BenevolentAI/guacamol", + "last_checked": "2026-08-08", + "metadata_sources": [ + "https://github.com/BenevolentAI/guacamol" + ] }, { "id": "hest_xenium_virtual_spatial_transcriptomics", @@ -301,10 +463,26 @@ validated: false "tags": [ "benchmarks-and-datasets" ], - "tasks": [], - "modalities": [], + "tasks": [ + "regression" + ], + "modalities": [ + "histopathology", + "spatial-transcriptomics", + "transcriptomics" + ], "organism": [], - "api": false + "api": false, + "entities": [ + "cell", + "gene", + "tissue" + ], + "documentation": "https://huggingface.co/datasets/ratschlab/HEST_Xenium_virtual_spatial_transcriptomics", + "last_checked": "2026-08-08", + "metadata_sources": [ + "https://huggingface.co/datasets/ratschlab/HEST_Xenium_virtual_spatial_transcriptomics" + ] }, { "id": "jump_cell_painting_datasets", @@ -329,10 +507,23 @@ validated: false "tags": [ "benchmarks-and-datasets" ], - "tasks": [], - "modalities": [], + "tasks": [ + "perturbation-prediction" + ], + "modalities": [ + "transcriptomics" + ], "organism": [], - "api": false + "api": false, + "entities": [ + "cell", + "compound", + "gene" + ], + "last_checked": "2026-08-08", + "metadata_sources": [ + "https://lincsproject.org/LINCS/tools/workflows/find-the-best-place-to-obtain-the-lincs-l1000-data" + ] }, { "id": "moleculenet", @@ -343,10 +534,23 @@ validated: false "tags": [ "benchmarks-and-datasets" ], - "tasks": [], - "modalities": [], + "tasks": [ + "classification", + "regression" + ], + "modalities": [ + "chemical-structure" + ], "organism": [], - "api": false + "api": false, + "entities": [ + "molecule" + ], + "github": "https://github.com/deepchem/moleculenet", + "last_checked": "2026-08-08", + "metadata_sources": [ + "https://github.com/deepchem/moleculenet" + ] }, { "id": "moses", @@ -399,10 +603,25 @@ validated: false "tags": [ "benchmarks-and-datasets" ], - "tasks": [], - "modalities": [], + "tasks": [ + "drug-response-prediction" + ], + "modalities": [ + "clinical", + "genomics" + ], "organism": [], - "api": false + "api": false, + "entities": [ + "drug", + "gene", + "phenotype", + "variant" + ], + "last_checked": "2026-08-08", + "metadata_sources": [ + "https://www.pharmgkb.org/" + ] }, { "id": "pk_db", @@ -414,9 +633,18 @@ validated: false "benchmarks-and-datasets" ], "tasks": [], - "modalities": [], + "modalities": [ + "clinical" + ], "organism": [], - "api": false + "api": false, + "entities": [ + "drug" + ], + "last_checked": "2026-08-08", + "metadata_sources": [ + "https://pk-db.com/" + ] }, { "id": "prism", @@ -427,10 +655,20 @@ validated: false "tags": [ "benchmarks-and-datasets" ], - "tasks": [], + "tasks": [ + "drug-response-prediction" + ], "modalities": [], "organism": [], - "api": false + "api": false, + "entities": [ + "cell", + "drug" + ], + "last_checked": "2026-08-08", + "metadata_sources": [ + "https://depmap.org/portal/prism/" + ] }, { "id": "proteingym", @@ -441,10 +679,22 @@ validated: false "tags": [ "benchmarks-and-datasets" ], - "tasks": [], - "modalities": [], + "tasks": [ + "regression" + ], + "modalities": [ + "protein-sequence" + ], "organism": [], - "api": false + "api": false, + "entities": [ + "protein" + ], + "github": "https://github.com/OATML-Markslab/ProteinGym", + "last_checked": "2026-08-08", + "metadata_sources": [ + "https://github.com/OATML-Markslab/ProteinGym" + ] }, { "id": "qm9", @@ -483,10 +733,24 @@ validated: false "tags": [ "benchmarks-and-datasets" ], - "tasks": [], - "modalities": [], + "tasks": [ + "perturbation-prediction" + ], + "modalities": [ + "single-cell-rna-seq" + ], "organism": [], - "api": false + "api": false, + "entities": [ + "cell", + "drug", + "gene" + ], + "github": "https://github.com/sanderlab/scPerturb", + "last_checked": "2026-08-08", + "metadata_sources": [ + "https://github.com/sanderlab/scPerturb" + ] }, { "id": "sider_side_effect_resource", @@ -498,9 +762,19 @@ validated: false "benchmarks-and-datasets" ], "tasks": [], - "modalities": [], + "modalities": [ + "clinical" + ], "organism": [], - "api": false + "api": false, + "entities": [ + "drug", + "phenotype" + ], + "last_checked": "2026-08-08", + "metadata_sources": [ + "http://sideeffects.embl.de/" + ] }, { "id": "tabula_muris", @@ -773,13 +1047,23 @@ validated: false "drug-cell-line-response", "interaction" ], - "tasks": [], + "tasks": [ + "drug-response-prediction" + ], "modalities": [ - "Gene Expression", - "Small Molecule" + "genomics" ], "organism": [], - "api": false + "api": false, + "entities": [ + "cell", + "drug", + "gene" + ], + "last_checked": "2026-08-08", + "metadata_sources": [ + "https://discover.nci.nih.gov/cellminercdb/" + ] }, { "id": "chebi", @@ -1040,10 +1324,19 @@ validated: false ], "tasks": [], "modalities": [ - "Disease" + "chemical-structure" ], "organism": [], - "api": false + "api": false, + "entities": [ + "disease", + "drug", + "protein" + ], + "last_checked": "2026-08-08", + "metadata_sources": [ + "https://go.drugbank.com/" + ] }, { "id": "drugcentral", @@ -1184,13 +1477,23 @@ validated: false "drug-cell-line-response", "interaction" ], - "tasks": [], + "tasks": [ + "drug-response-prediction" + ], "modalities": [ - "Gene Expression", - "Small Molecule" + "genomics" ], "organism": [], - "api": false + "api": false, + "entities": [ + "cell", + "drug", + "gene" + ], + "last_checked": "2026-08-08", + "metadata_sources": [ + "https://www.cancerrxgene.org/" + ] }, { "id": "gnomad", @@ -1957,10 +2260,20 @@ validated: false ], "tasks": [], "modalities": [ - "Protein" + "knowledge-graph", + "proteomics" ], "organism": [], - "api": false + "api": false, + "entities": [ + "protein" + ], + "documentation": "https://string-db.org/help/api/", + "last_checked": "2026-08-08", + "metadata_sources": [ + "https://string-db.org/", + "https://string-db.org/help/api/" + ] }, { "id": "the_genotype_tissue_expression_gtex", @@ -2135,14 +2448,27 @@ validated: false "spatial-foundation-models" ], "tasks": [ - "Foundation Model" + "representation-learning" ], "modalities": [ - "Single Cell", - "Spatial Transcriptomics" + "histopathology", + "spatial-transcriptomics" ], "organism": [], - "api": false + "api": false, + "entities": [ + "cell", + "gene", + "tissue" + ], + "methods": [ + "autoencoder" + ], + "github": "https://github.com/ratschlab/aestetik", + "last_checked": "2026-08-08", + "metadata_sources": [ + "https://github.com/ratschlab/aestetik" + ] }, { "id": "ai4chem_chemllm_7b_chat", @@ -2174,14 +2500,27 @@ validated: false "protein-structure-prediction-and-design" ], "tasks": [ - "Foundation Model", - "Protein Structure Prediction" + "structure-prediction" ], "modalities": [ - "Protein" + "molecular-structure", + "protein-sequence" ], "organism": [], - "api": false + "api": false, + "entities": [ + "molecule", + "protein", + "protein-complex" + ], + "methods": [ + "diffusion" + ], + "github": "https://github.com/google-deepmind/alphafold3", + "last_checked": "2026-08-08", + "metadata_sources": [ + "https://github.com/google-deepmind/alphafold3" + ] }, { "id": "ankh", @@ -2417,6 +2756,26 @@ validated: false "organism": [], "api": false }, + { + "id": "cellot", + "name": "CellOT", + "type": "model", + "url": "https://github.com/bunnech/cellot", + "description": "Neural optimal transport framework for predicting single-cell responses to drug and genetic perturbations.", + "tags": [ + "drug-discovery", + "drug-perturbation" + ], + "tasks": [ + "Drug Discovery", + "Drug Perturbation" + ], + "modalities": [ + "Small Molecule" + ], + "organism": [], + "api": false + }, { "id": "cellplm", "name": "CellPLM", @@ -2429,14 +2788,31 @@ validated: false "transcriptomics-foundation-models" ], "tasks": [ - "Foundation Model" + "foundation-model-pretraining", + "representation-learning" ], "modalities": [ - "Single Cell", - "Transcriptomics" + "single-cell-rna-seq", + "transcriptomics" ], "organism": [], - "api": false + "api": false, + "entities": [ + "cell", + "gene" + ], + "methods": [ + "self-supervised-learning", + "transformer" + ], + "year": 2023, + "github": "https://github.com/OmicsML/CellPLM", + "paper": "https://www.biorxiv.org/content/10.1101/2023.10.03.560734v1", + "last_checked": "2026-08-08", + "metadata_sources": [ + "https://github.com/OmicsML/CellPLM", + "https://www.biorxiv.org/content/10.1101/2023.10.03.560734v1" + ] }, { "id": "chai_1", @@ -2489,13 +2865,26 @@ validated: false "foundation-models" ], "tasks": [ - "Foundation Model" + "representation-learning" ], "modalities": [ - "Small Molecule" + "chemical-structure" ], "organism": [], - "api": false + "api": false, + "entities": [ + "molecule" + ], + "methods": [ + "language-model", + "self-supervised-learning", + "transformer" + ], + "github": "https://github.com/seyonechithrananda/bert-loves-chemistry", + "last_checked": "2026-08-08", + "metadata_sources": [ + "https://github.com/seyonechithrananda/bert-loves-chemistry" + ] }, { "id": "chemcpa", @@ -2505,11 +2894,11 @@ validated: false "description": "Compositional perturbation autoencoder for predicting single-cell transcriptional responses to unseen drug perturbations and dose combinations.", "tags": [ "drug-discovery", - "drug-response-prediction" + "drug-perturbation" ], "tasks": [ "Drug Discovery", - "Drug Response Prediction" + "Drug Perturbation" ], "modalities": [ "Small Molecule" @@ -2554,6 +2943,26 @@ validated: false "organism": [], "api": false }, + { + "id": "cmonge", + "name": "CMonge", + "type": "model", + "url": "https://github.com/AI4SCR/conditional-monge-gap", + "description": "Conditional optimal transport model for generalizable single-cell perturbation response prediction across drugs and doses.", + "tags": [ + "drug-discovery", + "drug-perturbation" + ], + "tasks": [ + "Drug Discovery", + "Drug Perturbation" + ], + "modalities": [ + "Small Molecule" + ], + "organism": [], + "api": false + }, { "id": "concerto", "name": "Concerto", @@ -2587,14 +2996,27 @@ validated: false "spatial-foundation-models" ], "tasks": [ - "Foundation Model" + "foundation-model-pretraining", + "representation-learning" ], "modalities": [ - "Single Cell", - "Spatial Transcriptomics" + "histopathology", + "imaging" ], "organism": [], - "api": false + "api": false, + "entities": [ + "tissue" + ], + "methods": [ + "contrastive-learning", + "transformer" + ], + "github": "https://github.com/mahmoodlab/CONCH", + "last_checked": "2026-08-08", + "metadata_sources": [ + "https://github.com/mahmoodlab/CONCH" + ] }, { "id": "cyclecdr", @@ -2604,11 +3026,11 @@ validated: false "description": "Interpretable cycle-consistency framework for modeling cellular responses to drug perturbations.", "tags": [ "drug-discovery", - "drug-response-prediction" + "drug-perturbation" ], "tasks": [ "Drug Discovery", - "Drug Response Prediction" + "Drug Perturbation" ], "modalities": [ "Small Molecule" @@ -2728,14 +3150,23 @@ validated: false "spatial-foundation-models" ], "tasks": [ - "Foundation Model" + "regression" ], "modalities": [ - "Single Cell", - "Spatial Transcriptomics" + "histopathology", + "spatial-transcriptomics" ], "organism": [], - "api": false + "api": false, + "entities": [ + "gene", + "tissue" + ], + "github": "https://github.com/ratschlab/DeepSpot", + "last_checked": "2026-08-08", + "metadata_sources": [ + "https://github.com/ratschlab/DeepSpot" + ] }, { "id": "deepspot_m", @@ -2749,14 +3180,25 @@ validated: false "spatial-foundation-models" ], "tasks": [ - "Foundation Model" + "foundation-model-pretraining", + "regression" ], "modalities": [ - "Single Cell", - "Spatial Transcriptomics" + "histopathology", + "spatial-transcriptomics", + "transcriptomics" ], "organism": [], - "api": false + "api": false, + "entities": [ + "gene", + "tissue" + ], + "github": "https://github.com/ratschlab/DeepSpotM", + "last_checked": "2026-08-08", + "metadata_sources": [ + "https://github.com/ratschlab/DeepSpotM" + ] }, { "id": "deepspot2cell", @@ -2770,14 +3212,24 @@ validated: false "spatial-foundation-models" ], "tasks": [ - "Foundation Model" + "regression" ], "modalities": [ - "Single Cell", - "Spatial Transcriptomics" + "histopathology", + "spatial-transcriptomics" ], "organism": [], - "api": false + "api": false, + "entities": [ + "cell", + "gene", + "tissue" + ], + "github": "https://github.com/ratschlab/DeepSpot2Cell", + "last_checked": "2026-08-08", + "metadata_sources": [ + "https://github.com/ratschlab/DeepSpot2Cell" + ] }, { "id": "dgdrp", @@ -2810,14 +3262,29 @@ validated: false "molecular-generation" ], "tasks": [ - "Drug Discovery", - "Molecular Generation" + "docking" ], "modalities": [ - "Small Molecule" + "molecular-structure" ], "organism": [], - "api": false + "api": false, + "entities": [ + "molecule", + "protein" + ], + "methods": [ + "diffusion", + "geometric-deep-learning" + ], + "year": 2023, + "github": "https://github.com/gcorso/DiffDock", + "paper": "https://openreview.net/forum?id=kKF8_K-mBbS", + "last_checked": "2026-08-08", + "metadata_sources": [ + "https://github.com/gcorso/DiffDock", + "https://openreview.net/forum?id=kKF8_K-mBbS" + ] }, { "id": "diffsbdd", @@ -2990,14 +3457,28 @@ validated: false "protein-structure-prediction-and-design" ], "tasks": [ - "Foundation Model", - "Protein Structure Prediction" + "protein-sequence-design", + "representation-learning" ], "modalities": [ - "Protein" + "molecular-structure", + "protein-sequence" ], "organism": [], - "api": false + "api": false, + "entities": [ + "protein" + ], + "methods": [ + "generative-model", + "language-model", + "transformer" + ], + "github": "https://github.com/evolutionaryscale/esm", + "last_checked": "2026-08-08", + "metadata_sources": [ + "https://github.com/evolutionaryscale/esm" + ] }, { "id": "esmfold", @@ -3011,14 +3492,28 @@ validated: false "protein-structure-prediction-and-design" ], "tasks": [ - "Foundation Model", - "Protein Structure Prediction" + "representation-learning", + "structure-prediction" ], "modalities": [ - "Protein" + "molecular-structure", + "protein-sequence" ], "organism": [], - "api": false + "api": false, + "entities": [ + "protein" + ], + "methods": [ + "language-model", + "transformer" + ], + "year": 2023, + "github": "https://github.com/facebookresearch/esm", + "last_checked": "2026-08-08", + "metadata_sources": [ + "https://github.com/facebookresearch/esm" + ] }, { "id": "evo", @@ -3072,13 +3567,26 @@ validated: false "protein-foundation-models" ], "tasks": [ - "Foundation Model" + "representation-learning" ], "modalities": [ - "Protein" + "protein-sequence" ], "organism": [], - "api": false + "api": false, + "entities": [ + "protein" + ], + "methods": [ + "language-model", + "self-supervised-learning", + "transformer" + ], + "github": "https://github.com/facebookresearch/esm", + "last_checked": "2026-08-08", + "metadata_sources": [ + "https://github.com/facebookresearch/esm" + ] }, { "id": "gears", @@ -3113,14 +3621,31 @@ validated: false "single-cell-foundation-models" ], "tasks": [ - "Foundation Model" + "foundation-model-pretraining", + "representation-learning" ], "modalities": [ - "Multi-Omics", - "Single Cell" + "single-cell-rna-seq", + "transcriptomics" ], "organism": [], - "api": false + "api": false, + "entities": [ + "cell", + "gene" + ], + "methods": [ + "self-supervised-learning", + "transformer" + ], + "year": 2024, + "github": "https://github.com/xCompass-AI/GeneCompass", + "paper": "https://www.nature.com/articles/s41422-024-01034-y", + "last_checked": "2026-08-08", + "metadata_sources": [ + "https://github.com/xCompass-AI/GeneCompass", + "https://www.nature.com/articles/s41422-024-01034-y" + ] }, { "id": "geneformer", @@ -3134,14 +3659,33 @@ validated: false "transcriptomics-foundation-models" ], "tasks": [ - "Foundation Model" + "classification", + "foundation-model-pretraining", + "perturbation-prediction", + "representation-learning" ], "modalities": [ - "Single Cell", - "Transcriptomics" + "single-cell-rna-seq", + "transcriptomics" ], "organism": [], - "api": false + "api": false, + "entities": [ + "cell", + "gene" + ], + "methods": [ + "self-supervised-learning", + "transformer" + ], + "year": 2023, + "documentation": "https://geneformer.readthedocs.io/", + "paper": "https://www.nature.com/articles/s41586-023-06139-9", + "last_checked": "2026-08-08", + "metadata_sources": [ + "https://huggingface.co/ctheodoris/Geneformer", + "https://www.nature.com/articles/s41586-023-06139-9" + ] }, { "id": "genegpt", @@ -3171,13 +3715,31 @@ validated: false "llm-for-biology" ], "tasks": [ - "Language Modeling" + "batch-correction", + "classification", + "representation-learning" ], "modalities": [ - "Text" + "single-cell-rna-seq", + "transcriptomics" ], "organism": [], - "api": false + "api": false, + "entities": [ + "cell", + "gene" + ], + "methods": [ + "language-model" + ], + "year": 2023, + "github": "https://github.com/yiqunchen/GenePT", + "paper": "https://www.biorxiv.org/content/10.1101/2023.10.16.562533v2", + "last_checked": "2026-08-08", + "metadata_sources": [ + "https://github.com/yiqunchen/GenePT", + "https://www.biorxiv.org/content/10.1101/2023.10.16.562533v2" + ] }, { "id": "gigapath", @@ -3191,14 +3753,27 @@ validated: false "spatial-foundation-models" ], "tasks": [ - "Foundation Model" + "foundation-model-pretraining", + "representation-learning" ], "modalities": [ - "Single Cell", - "Spatial Transcriptomics" + "histopathology", + "imaging" ], "organism": [], - "api": false + "api": false, + "entities": [ + "tissue" + ], + "methods": [ + "self-supervised-learning", + "transformer" + ], + "github": "https://github.com/prov-gigapath/prov-gigapath", + "last_checked": "2026-08-08", + "metadata_sources": [ + "https://github.com/prov-gigapath/prov-gigapath" + ] }, { "id": "glue", @@ -3273,13 +3848,26 @@ validated: false "foundation-models" ], "tasks": [ - "Foundation Model" + "representation-learning" ], "modalities": [ - "Small Molecule" + "chemical-structure" ], "organism": [], - "api": false + "api": false, + "entities": [ + "molecule" + ], + "methods": [ + "graph-neural-network", + "self-supervised-learning", + "transformer" + ], + "github": "https://github.com/tencent-ailab/grover", + "last_checked": "2026-08-08", + "metadata_sources": [ + "https://github.com/tencent-ailab/grover" + ] }, { "id": "hidra", @@ -3537,13 +4125,26 @@ validated: false "foundation-models" ], "tasks": [ - "Foundation Model" + "representation-learning" ], "modalities": [ - "Small Molecule" + "chemical-structure" ], "organism": [], - "api": false + "api": false, + "entities": [ + "molecule" + ], + "methods": [ + "language-model", + "self-supervised-learning", + "transformer" + ], + "github": "https://github.com/IBM/molformer", + "last_checked": "2026-08-08", + "metadata_sources": [ + "https://github.com/IBM/molformer" + ] }, { "id": "molgpt", @@ -3698,14 +4299,33 @@ validated: false "spatial-foundation-models" ], "tasks": [ - "Foundation Model" + "foundation-model-pretraining", + "representation-learning" ], "modalities": [ - "Single Cell", - "Spatial Transcriptomics" + "single-cell-rna-seq", + "spatial-transcriptomics", + "transcriptomics" ], "organism": [], - "api": false + "api": false, + "entities": [ + "cell", + "gene", + "tissue" + ], + "methods": [ + "self-supervised-learning", + "transformer" + ], + "year": 2024, + "github": "https://github.com/theislab/nicheformer", + "paper": "https://doi.org/10.1101/2024.04.15.589472", + "last_checked": "2026-08-08", + "metadata_sources": [ + "https://github.com/theislab/nicheformer", + "https://doi.org/10.1101/2024.04.15.589472" + ] }, { "id": "nucleotide_transformer", @@ -3819,14 +4439,27 @@ validated: false "spatial-foundation-models" ], "tasks": [ - "Foundation Model" + "foundation-model-pretraining", + "representation-learning" ], "modalities": [ - "Single Cell", - "Spatial Transcriptomics" + "histopathology", + "imaging" ], "organism": [], - "api": false + "api": false, + "entities": [ + "tissue" + ], + "methods": [ + "self-supervised-learning", + "transformer" + ], + "documentation": "https://huggingface.co/owkin/phikon", + "last_checked": "2026-08-08", + "metadata_sources": [ + "https://huggingface.co/owkin/phikon" + ] }, { "id": "plip", @@ -3839,13 +4472,26 @@ validated: false "multi-modal-foundation-models" ], "tasks": [ - "Foundation Model" + "classification", + "representation-learning" ], "modalities": [ - "Multi-Modal" + "histopathology", + "imaging" ], "organism": [], - "api": false + "api": false, + "entities": [ + "tissue" + ], + "methods": [ + "contrastive-learning" + ], + "github": "https://github.com/PathologyFoundation/plip", + "last_checked": "2026-08-08", + "metadata_sources": [ + "https://github.com/PathologyFoundation/plip" + ] }, { "id": "porpoise", @@ -3874,11 +4520,11 @@ validated: false "description": "Deep generative model for predicting transcriptional responses to novel chemical perturbations for drug discovery.", "tags": [ "drug-discovery", - "drug-response-prediction" + "drug-perturbation" ], "tasks": [ "Drug Discovery", - "Drug Response Prediction" + "Drug Perturbation" ], "modalities": [ "Small Molecule" @@ -3898,13 +4544,27 @@ validated: false "protein-foundation-models" ], "tasks": [ - "Foundation Model" + "protein-sequence-design", + "representation-learning" ], "modalities": [ - "Protein" + "protein-sequence" ], "organism": [], - "api": false + "api": false, + "entities": [ + "protein" + ], + "methods": [ + "generative-model", + "language-model", + "transformer" + ], + "github": "https://github.com/salesforce/progen", + "last_checked": "2026-08-08", + "metadata_sources": [ + "https://github.com/salesforce/progen" + ] }, { "id": "proteinmpnn", @@ -3918,14 +4578,27 @@ validated: false "protein-structure-prediction-and-design" ], "tasks": [ - "Foundation Model", - "Protein Structure Prediction" + "protein-sequence-design" ], "modalities": [ - "Protein" + "molecular-structure", + "protein-sequence" ], "organism": [], - "api": false + "api": false, + "entities": [ + "protein" + ], + "methods": [ + "graph-neural-network", + "message-passing-neural-network" + ], + "year": 2022, + "github": "https://github.com/dauparas/ProteinMPNN", + "last_checked": "2026-08-08", + "metadata_sources": [ + "https://github.com/dauparas/ProteinMPNN" + ] }, { "id": "prottrans", @@ -3939,13 +4612,26 @@ validated: false "protein-foundation-models" ], "tasks": [ - "Foundation Model" + "representation-learning" ], "modalities": [ - "Protein" + "protein-sequence" ], "organism": [], - "api": false + "api": false, + "entities": [ + "protein" + ], + "methods": [ + "language-model", + "self-supervised-learning", + "transformer" + ], + "github": "https://github.com/agemagician/ProtTrans", + "last_checked": "2026-08-08", + "metadata_sources": [ + "https://github.com/agemagician/ProtTrans" + ] }, { "id": "recover", @@ -4124,14 +4810,33 @@ validated: false "transcriptomics-foundation-models" ], "tasks": [ - "Foundation Model" + "cell-type-annotation", + "classification", + "foundation-model-pretraining" ], "modalities": [ - "Single Cell", - "Transcriptomics" + "single-cell-rna-seq", + "transcriptomics" ], "organism": [], - "api": false + "api": false, + "entities": [ + "cell", + "gene" + ], + "methods": [ + "language-model", + "self-supervised-learning", + "transformer" + ], + "year": 2022, + "github": "https://github.com/TencentAILabHealthcare/scBERT", + "paper": "https://www.nature.com/articles/s42256-022-00534-z", + "last_checked": "2026-08-08", + "metadata_sources": [ + "https://github.com/TencentAILabHealthcare/scBERT", + "https://www.nature.com/articles/s42256-022-00534-z" + ] }, { "id": "scbutterfly", @@ -4166,14 +4871,34 @@ validated: false "transcriptomics-foundation-models" ], "tasks": [ - "Foundation Model" + "cell-type-annotation", + "drug-response-prediction", + "foundation-model-pretraining", + "perturbation-prediction", + "representation-learning" ], "modalities": [ - "Single Cell", - "Transcriptomics" + "single-cell-rna-seq", + "transcriptomics" ], "organism": [], - "api": false + "api": false, + "entities": [ + "cell", + "gene" + ], + "methods": [ + "self-supervised-learning", + "transformer" + ], + "year": 2024, + "github": "https://github.com/biomap-research/scFoundation", + "paper": "https://www.nature.com/articles/s41592-024-02305-7", + "last_checked": "2026-08-08", + "metadata_sources": [ + "https://github.com/biomap-research/scFoundation", + "https://www.nature.com/articles/s41592-024-02305-7" + ] }, { "id": "scgpt", @@ -4187,14 +4912,37 @@ validated: false "transcriptomics-foundation-models" ], "tasks": [ - "Foundation Model" + "cell-type-annotation", + "foundation-model-pretraining", + "gene-regulatory-network-inference", + "perturbation-prediction", + "representation-learning" ], "modalities": [ - "Single Cell", - "Transcriptomics" + "multi-omics", + "single-cell-rna-seq", + "transcriptomics" ], "organism": [], - "api": false + "api": false, + "entities": [ + "cell", + "gene" + ], + "methods": [ + "generative-model", + "self-supervised-learning", + "transformer" + ], + "year": 2024, + "github": "https://github.com/bowang-lab/scGPT", + "documentation": "https://scgpt.readthedocs.io/en/latest/", + "paper": "https://www.nature.com/articles/s41592-024-02201-0", + "last_checked": "2026-08-08", + "metadata_sources": [ + "https://github.com/bowang-lab/scGPT", + "https://www.nature.com/articles/s41592-024-02201-0" + ] }, { "id": "scgpt_spatial", @@ -4208,14 +4956,35 @@ validated: false "spatial-foundation-models" ], "tasks": [ - "Foundation Model" + "foundation-model-pretraining", + "imputation", + "representation-learning" ], "modalities": [ - "Single Cell", - "Spatial Transcriptomics" + "multi-omics", + "single-cell-rna-seq", + "spatial-transcriptomics" ], "organism": [], - "api": false + "api": false, + "entities": [ + "cell", + "gene", + "tissue" + ], + "methods": [ + "generative-model", + "self-supervised-learning", + "transformer" + ], + "year": 2025, + "github": "https://github.com/bowang-lab/scGPT-spatial", + "paper": "https://www.biorxiv.org/content/10.1101/2025.02.05.636714v1", + "last_checked": "2026-08-08", + "metadata_sources": [ + "https://github.com/bowang-lab/scGPT-spatial", + "https://www.biorxiv.org/content/10.1101/2025.02.05.636714v1" + ] }, { "id": "scmulan", @@ -4229,14 +4998,31 @@ validated: false "single-cell-foundation-models" ], "tasks": [ - "Foundation Model" + "foundation-model-pretraining", + "representation-learning" ], "modalities": [ - "Multi-Omics", - "Single Cell" + "epigenomics", + "multi-omics", + "proteomics", + "single-cell-rna-seq", + "transcriptomics" ], "organism": [], - "api": false + "api": false, + "entities": [ + "cell", + "gene" + ], + "methods": [ + "language-model", + "transformer" + ], + "github": "https://github.com/SuperBianC/scMulan", + "last_checked": "2026-08-08", + "metadata_sources": [ + "https://github.com/SuperBianC/scMulan" + ] }, { "id": "scpair", @@ -4269,13 +5055,36 @@ validated: false "llm-for-biology" ], "tasks": [ - "Language Modeling" + "batch-correction", + "cell-type-annotation", + "foundation-model-pretraining", + "gene-regulatory-network-inference", + "imputation", + "representation-learning" ], "modalities": [ - "Text" + "single-cell-rna-seq", + "transcriptomics" ], "organism": [], - "api": false + "api": false, + "entities": [ + "cell", + "gene" + ], + "methods": [ + "self-supervised-learning", + "transformer" + ], + "year": 2025, + "github": "https://github.com/cantinilab/scPRINT", + "documentation": "https://www.jkobject.com/scPRINT/", + "paper": "https://www.nature.com/articles/s41467-025-58699-1", + "last_checked": "2026-08-08", + "metadata_sources": [ + "https://github.com/cantinilab/scPRINT", + "https://www.nature.com/articles/s41467-025-58699-1" + ] }, { "id": "sei", @@ -4471,14 +5280,29 @@ validated: false "transcriptomics-foundation-models" ], "tasks": [ - "Foundation Model" + "foundation-model-pretraining", + "representation-learning" ], "modalities": [ - "Single Cell", - "Transcriptomics" + "single-cell-rna-seq", + "transcriptomics" ], "organism": [], - "api": false + "api": false, + "entities": [ + "cell" + ], + "methods": [ + "self-supervised-learning" + ], + "year": 2026, + "github": "https://github.com/snap-stanford/UCE", + "paper": "https://www.nature.com/articles/s41586-026-10689-z", + "last_checked": "2026-08-08", + "metadata_sources": [ + "https://github.com/snap-stanford/UCE", + "https://www.nature.com/articles/s41586-026-10689-z" + ] }, { "id": "uni", @@ -4492,14 +5316,27 @@ validated: false "spatial-foundation-models" ], "tasks": [ - "Foundation Model" + "foundation-model-pretraining", + "representation-learning" ], "modalities": [ - "Single Cell", - "Spatial Transcriptomics" + "histopathology", + "imaging" ], "organism": [], - "api": false + "api": false, + "entities": [ + "tissue" + ], + "methods": [ + "self-supervised-learning", + "transformer" + ], + "github": "https://github.com/mahmoodlab/UNI", + "last_checked": "2026-08-08", + "metadata_sources": [ + "https://github.com/mahmoodlab/UNI" + ] }, { "id": "uni_mol", @@ -4513,13 +5350,31 @@ validated: false "foundation-models" ], "tasks": [ - "Foundation Model" + "docking", + "representation-learning" ], "modalities": [ - "Small Molecule" + "chemical-structure", + "molecular-structure" ], "organism": [], - "api": false + "api": false, + "entities": [ + "molecule", + "protein" + ], + "methods": [ + "self-supervised-learning", + "transformer" + ], + "year": 2023, + "github": "https://github.com/deepmodeling/Uni-Mol", + "paper": "https://openreview.net/forum?id=6K2RM6wVqKu", + "last_checked": "2026-08-08", + "metadata_sources": [ + "https://github.com/deepmodeling/Uni-Mol", + "https://openreview.net/forum?id=6K2RM6wVqKu" + ] }, { "id": "unitednet",