[upstream-sync] README.md from ai-boost/awesome-ai-for-science@06f0c449 [catalogue]

2026-08-27 04:57:41 +00:00
6 changed files with 164 additions and 909 deletions
@@ -2,9 +2,9 @@
 title: "Readme"
 task: ""
 lineage_type: import
-upstream_source: https://github.com/ai-boost/awesome-ai-for-science/blob/ec6f3650/README.md
-upstream_sha: ec6f3650
-imported_at: 2026-08-21
+upstream_source: https://github.com/ai-boost/awesome-ai-for-science/blob/06f0c449/README.md
+upstream_sha: 06f0c449
+imported_at: 2026-08-27
 prompt_class: catalogue
 upstream_changes: accepted
 author: upstream
@@ -237,6 +237,7 @@ validated: false
 - [Obsidian Smart Connections](https://github.com/brianpetro/obsidian-smart-connections) - AI-powered note linking and research graph navigation
 - [Research Rabbit](https://www.researchrabbit.ai/) - AI-powered literature discovery and research network mapping
 - [SciWrite](https://github.com/labarba/sciwrite) - Agent skill for AI-assisted scientific manuscript writing review distilled from Stanford's *Writing in the Sciences* course, performing five sequential editorial audit passes on clarity, voice, structure, consistency, and integrity (2026)
+- [PaperSpine](https://github.com/WUBING2023/PaperSpine) - Motivation-driven academic writing system for Claude Code, Codex, OpenClaw, and Hermes CLI that learns from strong papers, builds evidence-aware central-argument blueprints, and rewrites manuscripts with revision matrices and LaTeX-safe audits (4.9K+ stars, MIT License, 2026)
 - [Claude Prism](https://github.com/delibae/claude-prism) - Offline-first scientific writing workspace powered by Claude, integrating LaTeX, Python, and 100+ scientific skills with local execution, Zotero integration, and privacy-focused design (2026)

 ---
@@ -307,6 +308,7 @@ validated: false
 - [Scholar Loop](https://github.com/renee-jia/scholar-loop) - Autonomous multi-agent AI scientist that mirrors a PhD workflow: literature review → grounded hypothesis → real ML experiments → self-critique → write-up; features a deterministic harness with frozen-metric scoring, edit allowlists, and a verified registry to make reward-hacking and hallucination impossible, plus 108 unit tests runnable without API keys or GPUs (461+ stars, MIT License, 2026)
 - [ResearchStudio (Microsoft)](https://github.com/microsoft/ResearchStudio) - AI co-author covering the entire research lifecycle — from an under-specified research direction to a published paper; includes ResearchStudio-Idea for evidence-grounded research ideation and ResearchStudio-Reel for turning finished papers into posters, narrated videos, blogs, and interactive reels; runs as skills on Claude Code and Codex (1.2K+ stars, MIT License, 2026)
 - [Principia](https://github.com/pzqpzq/Principia) - Principle-first scientific idea discovery framework that extracts reusable principles from public literature and private research materials, composes them into traceable Idea Cards with prior-art comparisons, and exports validation-ready research packs; emphasizes inspectable scientific objects, risk disclosure, and falsification paths (ICML 2026, 411+ stars, MIT License)
+- [Imbue Catalyst](https://github.com/imbue-ai/catalyst) - Semi-autonomous AI scientist for scientific theory discovery and verifiable goal solving, using adversarial review-refinement loops and evolution-inspired candidate populations; integrates with Claude Code, Gemini CLI, Antigravity, and Codex harnesses (Imbue, 31+ stars, AGPL-3.0, 2026)

 ### Evaluation & Benchmarking
 - [ScienceAgentBench (ICLR 2025)](https://github.com/OSU-NLP-Group/ScienceAgentBench) - 102 executable tasks from 44 peer-reviewed papers across 4 disciplines with containerized evaluation
@@ -399,6 +401,7 @@ validated: false
 - [Fourier Neural Operator](https://github.com/neuraloperator/neuraloperator) - Learning operators in Fourier space
 - [Poseidon](https://github.com/camlab-ethz/poseidon) - Efficient foundation models for PDEs with pretrained transformer-based neural operators and downstream task fine-tuning pipelines, HuggingFace integration for models and datasets (ETH Zurich CAMLab, arXiv 2024)
 - [GAOT (NeurIPS 2025)](https://github.com/camlab-ethz/GAOT) - Geometry Aware Operator Transformer serving as an efficient and accurate neural surrogate for PDEs on arbitrary domains, combining geometric priors with transformer architectures for scientific computing (ETH Zurich CAMLab, 92+ stars)
+- [TensorMesh (ETH Zurich CAMLab, arXiv 2026)](https://github.com/camlab-ethz/TensorMesh) - Fast, differentiable, JIT-free finite element library for PyTorch enabling GPU-native PDE solving with native autograd, tensorized assembly, and sparse linear algebra; part of the TensorGalerkin framework (218+ stars, Apache 2.0)
 - [PhiFlow](https://github.com/tum-pbs/PhiFlow) - Differentiable PDE solving framework for machine learning with built-in fluid simulation, supporting PyTorch/JAX/TensorFlow backends and enabling neural network training within physical simulations (TUM, MIT License)
 - [exponax](https://github.com/Ceyron/exponax) - Efficient differentiable n-dimensional PDE solvers built on JAX and Equinox, shipping 46+ built-in equations with Fourier spectral methods, exponential time differencing, and full auto-differentiation for physics-based deep learning workflows (MIT, 200+ stars, 2024)

@@ -706,6 +709,7 @@ validated: false
 #### Materials Discovery
 - [GNoME](https://github.com/google-deepmind/materials_discovery) - DeepMind's graph neural network for materials exploration, discovering 2.2M new crystal structures (380K most stable) equivalent to 800 years of traditional research, with 520K+ materials dataset open-sourced (Nature 2023)
 - [FAIRChem (OMat24)](https://github.com/FAIR-Chem/fairchem) - Meta's comprehensive ML ecosystem for materials/chemistry with 118M+ DFT calculations, EquiformerV2 models achieving top Matbench Discovery performance
+- [Skala 1.1 (Microsoft Research, 2026)](https://github.com/microsoft/skala) - Neural network-based exchange-correlation functional for density functional theory (DFT) that surpasses state-of-the-art hybrid functionals in accuracy for main-group thermochemistry, kinetics, and non-covalent interactions at semi-local DFT cost; includes PySCF/GPU4PySCF/ASE bindings and C++/Fortran integrations (248+ stars, MIT License)
 - [All-atom Diffusion Transformers (ADiT)](https://github.com/facebookresearch/all-atom-diffusion-transformer) - Unified latent diffusion transformer that jointly generates periodic crystals and non-periodic molecules, scaling to 500M parameters with SOTA results on QM9, MP20, and GEOM-DRUGS (Meta FAIR, ICML 2025, 310+ stars)
 - [JARVIS](https://github.com/usnistgov/jarvis) - NIST's open-source platform for data-driven atomistic materials design, integrating DFT datasets (JARVIS-DFT), machine learning property prediction (JARVIS-ML), and a comprehensive leaderboard for benchmarking materials AI methods across the periodic table (384+ stars)
 - [NVIDIA ALCHEMI Toolkit](https://github.com/NVIDIA/nvalchemi-toolkit) - Developer toolkit for accelerating training and inference for AI in chemistry and material science, providing optimized GPU-accelerated workflows for molecular and materials machine learning (NVIDIA, 2026)
@@ -744,6 +748,7 @@ validated: false
 - [Neural ODEs](https://github.com/rtqichen/torchdiffeq) - Differential equations with neural networks
 - [Physics-Informed Neural Networks](https://github.com/maziarraissi/PINNs) - Physics-constrained ML
 - [EquiformerV2](https://github.com/atomicarchitects/equiformer_v2) - Improved equivariant Transformer for 3D atomic graphs (ICLR2024)
+- [EquiformerV3](https://github.com/atomicarchitects/equiformer_v3) - Scaling efficient, expressive, and general SE(3)-equivariant graph attention transformers for atomic systems and machine-learned interatomic potentials (MIT License, 2026)
 - [Equiformer](https://github.com/atomicarchitects/equiformer) - Equivariant graph attention Transformer (ICLR2023)
 - [TORAX](https://github.com/google-deepmind/torax) - Differentiable tokamak core transport simulator for fusion energy research, coupling PDE solvers with JAX auto-differentiation and neural-network surrogates for fast forward modelling, pulse-design, and trajectory optimization (Google DeepMind, Apache 2.0)
 - [DiffPhysDrone (Nature Machine Intelligence 2025)](https://github.com/HenryHuYu/DiffPhysDrone) - First real quadrotor robot trained end-to-end with differentiable physics for vision-based agile flight, bridging simulation-based learning and real-world deployment with physics-informed neural network controllers (558+ stars)
@@ -804,6 +809,7 @@ validated: false
 - [FarmVibes.AI](https://github.com/microsoft/farmvibes-ai) - Multi-modal geospatial ML platform for agriculture and sustainability, fusing satellite imagery (RGB, SAR, multispectral), drone imagery, weather data, and sensor data for crop identification, carbon footprint estimation, and microclimate prediction (Microsoft Research, MIT License)
 - [PlantCV](https://github.com/danforthcenter/plantcv) - Open-source image analysis toolkit for high-throughput plant phenotyping, extracting morphological, color, and texture traits from RGB, hyperspectral, and thermal imagery with modular Python workflows for crop improvement, stress detection, and plant biology research (Donald Danforth Plant Science Center, 795+ stars, MPL-2.0)
 - [Virdis](https://github.com/Thanas-R/Virdis) - Satellite-powered agricultural and land analytics platform combining Sentinel-2 imagery, Google Earth Engine processing, real-time weather data, soil science databases, and AI-driven crop planning into a unified web dashboard (145+ stars, AGPL-3.0, 2026)
+- [Agribound](https://github.com/montimaj/agribound) - AI-powered field boundary delineation toolkit combining satellite foundation models, embeddings, and global training data for accurate agricultural parcel/field boundary mapping, with Google Earth Engine integration and PyPI distribution (84+ stars, Apache 2.0, 2026)

 #### Ecological Modeling
 - [BioSimulators](https://github.com/biosimulators/Biosimulators) - Biological simulation tools
@@ -831,6 +837,9 @@ validated: false
 ### Structural & Civil Engineering
 - [StructureClaw](https://github.com/structureclaw/structureclaw) - AI-assisted structural engineering workspace for AEC workflows: natural language to structural model, analysis, code-check, and report (171+ stars, MIT License, 2026)

+### Construction & Built Environment Management
+- [OpenConstructionERP](https://github.com/datadrivenconstruction/OpenConstructionERP) - Open-source construction ERP with AI-powered cost matching, BOQ generation, and PDF/CAD/BIM takeoff; 42 regional catalogues, 21 languages, 71 modules (DataDrivenConstruction, 717+ stars, AGPL-3.0, 2026)
+
 ### Architectural Design & BIM
 - [Aedifex](https://github.com/TangSY/aedifex) - Open-source 3D architectural editor with an AI design assistant; build floor plans with walls, doors, windows, and furniture using natural language, with real-time WebGPU-powered previews (TangSY, 59+ stars, MIT License, 2026)

@@ -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/c6f07d90/README.md
-upstream_sha: c6f07d90
-imported_at: 2026-08-31
+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
@@ -75,7 +75,6 @@ Browse and search the resources via the [GitHub Pages UI](https://inoue0426.gith
      - [Drug Target Interaction](#drug-target-interaction)
      - [Compound-Protein Interaction](#compound-protein-interaction)
      - [Molecular Generation](#molecular-generation)
-    - [Protein Property Prediction](#protein-property-prediction)
    - [LLM for Biology](#llm-for-biology)
    - [Foundation Models](#foundation-models)
      - [Single-cell Foundation Models](#single-cell-foundation-models)
@@ -160,7 +159,6 @@ Browse and search the resources via the [GitHub Pages UI](https://inoue0426.gith
 - [GenBank](https://www.ncbi.nlm.nih.gov/genbank/) — NCBI's database of genetic sequences.
 - [UCSC Genome Browser](https://genome.ucsc.edu/) — UCSC's genome browser.
 - [cBioPortal](https://www.cbioportal.org/) — Cancer genomics database; aggregating many patient datasets.
- [OncoKB](https://www.oncokb.org/) — Precision oncology knowledge base of cancer genes, variants, and therapeutic implications.
 - [10x Genomics Dataset](https://www.10xgenomics.com/resources/datasets) — Collection of single-cell datasets.
 - [The Genotype-Tissue Expression (GTEx)](https://gtexportal.org/home/) — Human gene expression and regulation resource.
 - [Dependency Map (DepMap)](https://depmap.org/portal/) — CRISPR-Cas9 screens in cancer cell lines.
@@ -318,7 +316,7 @@ Browse and search the resources via the [GitHub Pages UI](https://inoue0426.gith
 - [CellCharter](https://github.com/CSOgroup/cellcharter) — Identification and characterization of spatial cell niches from spatial transcriptomics using VAEs and Gaussian mixture models.
 - [STAGATE](https://github.com/RucDongLab/STAGATE) — Adaptive graph attention auto-encoder for spatial domain identification in spatial transcriptomics.
 - [NCEM](https://github.com/theislab/ncem) — GNN-based model for learning intercellular communication from spatial graphs of cells.
- [DeepTalk](https://github.com/JiangBioLab/DeepTalk) — Graph attention network for deciphering cell-cell communication from spatial transcriptomics.
+- [DeepTalk](https://github.com/JiangBioLab/DeepTalk) — Graph attention network for deciphering cell-cell communication from spatial transcriptomics data.
 - [COMMOT](https://github.com/zcang/COMMOT) — Optimal transport-based framework for screening cell-cell communication in spatial transcriptomics.
 - [TIGON](https://github.com/yutongo/TIGON) — Neural optimal transport method for reconstructing growth and dynamic trajectories from single-cell transcriptomics.
 - [LINGER](https://github.com/Durenlab/LINGER) — Neural network for gene regulatory network inference from single-cell multiome (RNA+ATAC-seq) data with bulk data pretraining.
@@ -385,10 +383,6 @@ Browse and search the resources via the [GitHub Pages UI](https://inoue0426.gith
 - [ReLeaSE](https://github.com/isayev/ReLeaSE) — Deep reinforcement learning framework for de novo drug design combining a generative and predictive model.
 - [PaccMannRL](https://github.com/PaccMann/paccmann_generator) — Reinforcement learning-based generative model for de novo hit-like anticancer molecule design from transcriptomic data.

-### Protein Property Prediction
-
- [NbBayesLM](https://github.com/FairuzShadmaniShishir/NbBayesLM) — Bayesian neural network integrating protein language model embeddings and physicochemical features to predict nanobody thermostability with uncertainty estimates. [Paper](https://www.frontiersin.org/journals/bioinformatics/articles/10.3389/fbinf.2026.1832968/full)
-
 ### LLM for Biology

 - [AI4Chem/ChemLLM-7B-Chat](https://huggingface.co/AI4Chem/ChemLLM-7B-Chat) — LLM for chemical & molecular science.
@@ -445,7 +439,7 @@ Browse and search the resources via the [GitHub Pages UI](https://inoue0426.gith
 - [GeneCompass](https://github.com/xCompass-AI/GeneCompass) — Large-scale foundation model integrating DNA regulatory sequences and single-cell transcriptomics from 120M+ cells across multiple species for gene regulation prediction.
 - [UnitedNet](https://github.com/LiuLab-Bioelectronics-Harvard/UnitedNet) — Interpretable multi-task deep neural network for single-cell multi-omics integration spanning transcriptomics, chromatin accessibility, and proteomics.
 - [SpatialGlue](https://github.com/zhanglabtools/SpatialGlue) — Graph attention network for spatial multi-omics integration jointly embedding spatial transcriptomics with chromatin accessibility or proteomics.
- [MIDAS](https://github.com/labomics/midas) — Mosaic integration and differential accessibility model for single-cell multi-omics that handles arbitrary missing-modality combinations across transcriptomics, chromatin accessibility, and proteomics.
+- [MIDAS](https://github.com/labomics/midas) — Mosaic integration and differential accessibility model for single-cell multi-omics data that handles arbitrary missing-modality combinations across transcriptomics, chromatin accessibility, and proteomics.
 - [Concerto](https://github.com/melobio/Concerto-reproducibility) — Contrastive self-supervised learning framework for single-cell multimodal data integration, batch correction, and reference-query mapping.
 - [scButterfly](https://github.com/BioX-NKU/scButterfly) — Dual-aligned variational autoencoder for single-cell cross-modality translation between paired and unpaired multiomics data.
 - [JAMIE](https://github.com/Oafish1/JAMIE) — Joint variational autoencoder for multimodal single-cell data imputation and embedding.
@@ -527,7 +521,6 @@ If you use this list in papers, slides, or documentation, please cite this repos
 To keep quality high, additions should meet all of the following:

 - The resource is trustworthy and relevant to computational biology.
- The resource has clear value to the scope and audience of this collection; highly specialized resources with limited relevance beyond a narrow application context may be declined even when technically sound.
 - The primary link points to an official source (official docs, organization site, maintained repository, or official dataset page).
 - The resource has evidence of technical substance: ideally a peer-reviewed paper; at minimum a preprint or official technical documentation.
 - The description is factual and concise (no marketing copy).
@@ -2,9 +2,9 @@
 title: "Cspell"
 task: ""
 lineage_type: import
-upstream_source: https://github.com/inoue0426/awesome-computational-biology/blob/c6f07d90/cspell.json
-upstream_sha: c6f07d90
-imported_at: 2026-08-31
+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
@@ -59,7 +59,6 @@ validated: false
    "eukaryotic",
    "metabolites",
    "OMIM",
-    "OncoKB",
    "Mendelian",
    "DisGeNET",
    "GWAS",
@@ -172,9 +171,7 @@ validated: false
    "bowang",
    "ctheodoris",
    "OpenAI",
-    "GPT",
-    "nanobody",
-    "thermostability"
+    "GPT"
  ],
  "ignorePaths": [
    "node_modules/**"
@@ -2,9 +2,9 @@
 title: "Resources"
 task: ""
 lineage_type: import
-upstream_source: https://github.com/inoue0426/awesome-computational-biology/blob/c6f07d90/data/resources.json
-upstream_sha: c6f07d90
-imported_at: 2026-08-31
+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
@@ -899,20 +899,10 @@ validated: false
    ],
    "tasks": [],
    "modalities": [
-      "single-cell-rna-seq",
-      "genomics"
+      "Genomics"
    ],
    "organism": [],
-    "api": false,
-    "entities": [
-      "cell",
-      "gene"
-    ],
-    "documentation": "https://www.10xgenomics.com/resources/datasets",
-    "last_checked": "2026-08-08",
-    "metadata_sources": [
-      "https://www.10xgenomics.com/resources/datasets"
-    ]
+    "api": false
  },
  {
    "id": "alphafold_protein_structure_database",
@@ -925,20 +915,10 @@ validated: false
    ],
    "tasks": [],
    "modalities": [
-      "molecular-structure",
-      "protein-sequence"
+      "Protein"
    ],
    "organism": [],
-    "api": false,
-    "entities": [
-      "protein"
-    ],
-    "documentation": "https://alphafold.ebi.ac.uk/api-docs",
-    "last_checked": "2026-08-08",
-    "metadata_sources": [
-      "https://alphafold.ebi.ac.uk/",
-      "https://alphafold.ebi.ac.uk/api-docs"
-    ]
+    "api": false
  },
  {
    "id": "bindingdb",
@@ -952,20 +932,11 @@ validated: false
    ],
    "tasks": [],
    "modalities": [
-      "chemical-structure",
-      "molecular-structure"
+      "Protein",
+      "Small Molecule"
    ],
    "organism": [],
-    "api": false,
-    "entities": [
-      "molecule",
-      "protein"
-    ],
-    "documentation": "https://www.bindingdb.org/rwd/bind/index.jsp",
-    "last_checked": "2026-08-08",
-    "metadata_sources": [
-      "https://www.bindingdb.org/rwd/bind/index.jsp"
-    ]
+    "api": false
  },
  {
    "id": "biocyc",
@@ -978,20 +949,10 @@ validated: false
    ],
    "tasks": [],
    "modalities": [
-      "genomics"
+      "Pathway"
    ],
    "organism": [],
-    "api": false,
-    "entities": [
-      "gene",
-      "pathway",
-      "organism"
-    ],
-    "documentation": "https://biocyc.org/",
-    "last_checked": "2026-08-08",
-    "metadata_sources": [
-      "https://biocyc.org/"
-    ]
+    "api": false
  },
  {
    "id": "biogrid",
@@ -1008,16 +969,7 @@ validated: false
      "Protein"
    ],
    "organism": [],
-    "api": false,
-    "entities": [
-      "gene",
-      "protein"
-    ],
-    "documentation": "https://thebiogrid.org/",
-    "last_checked": "2026-08-08",
-    "metadata_sources": [
-      "https://thebiogrid.org/"
-    ]
+    "api": false
  },
  {
    "id": "cancer_cell_line_encyclopedia",
@@ -1031,22 +983,11 @@ validated: false
    ],
    "tasks": [],
    "modalities": [
-      "genomics",
-      "transcriptomics"
+      "Gene Expression",
+      "Small Molecule"
    ],
    "organism": [],
-    "api": false,
-    "entities": [
-      "cell",
-      "gene",
-      "disease",
-      "drug"
-    ],
-    "documentation": "https://sites.broadinstitute.org/ccle/",
-    "last_checked": "2026-08-08",
-    "metadata_sources": [
-      "https://sites.broadinstitute.org/ccle/"
-    ]
+    "api": false
  },
  {
    "id": "catalogue_of_somatic_mutations_in_cancer_cosmic",
@@ -1059,20 +1000,10 @@ validated: false
    ],
    "tasks": [],
    "modalities": [
-      "genomics"
+      "Genomics"
    ],
    "organism": [],
-    "api": false,
-    "entities": [
-      "disease",
-      "gene",
-      "variant"
-    ],
-    "documentation": "https://cancer.sanger.ac.uk/cosmic",
-    "last_checked": "2026-08-08",
-    "metadata_sources": [
-      "https://cancer.sanger.ac.uk/cosmic"
-    ]
+    "api": false
  },
  {
    "id": "cath_database",
@@ -1085,19 +1016,10 @@ validated: false
    ],
    "tasks": [],
    "modalities": [
-      "molecular-structure",
-      "protein-sequence"
+      "Protein"
    ],
    "organism": [],
-    "api": false,
-    "entities": [
-      "protein"
-    ],
-    "documentation": "https://www.cathdb.info/",
-    "last_checked": "2026-08-08",
-    "metadata_sources": [
-      "https://www.cathdb.info/"
-    ]
+    "api": false
  },
  {
    "id": "cbioportal",
@@ -1110,23 +1032,10 @@ validated: false
    ],
    "tasks": [],
    "modalities": [
-      "genomics",
-      "clinical"
+      "Genomics"
    ],
    "organism": [],
-    "api": false,
-    "entities": [
-      "disease",
-      "gene",
-      "variant"
-    ],
-    "github": "https://github.com/cBioPortal/cbioportal",
-    "documentation": "https://www.cbioportal.org/",
-    "last_checked": "2026-08-08",
-    "metadata_sources": [
-      "https://www.cbioportal.org/",
-      "https://github.com/cBioPortal/cbioportal"
-    ]
+    "api": false
  },
  {
    "id": "cellminer_cross_database_cellminercdb",
@@ -1183,20 +1092,10 @@ validated: false
    ],
    "tasks": [],
    "modalities": [
-      "chemical-structure"
+      "Small Molecule"
    ],
    "organism": [],
-    "api": false,
-    "entities": [
-      "compound",
-      "molecule",
-      "protein"
-    ],
-    "documentation": "https://www.ebi.ac.uk/chembl/",
-    "last_checked": "2026-08-08",
-    "metadata_sources": [
-      "https://www.ebi.ac.uk/chembl/"
-    ]
+    "api": false
  },
  {
    "id": "chemspider",
@@ -1225,19 +1124,10 @@ validated: false
    ],
    "tasks": [],
    "modalities": [
-      "clinical"
+      "Clinical"
    ],
    "organism": [],
-    "api": false,
-    "entities": [
-      "disease",
-      "drug"
-    ],
-    "documentation": "https://clinicaltrials.gov/",
-    "last_checked": "2026-08-08",
-    "metadata_sources": [
-      "https://clinicaltrials.gov/"
-    ]
+    "api": false
  },
  {
    "id": "comparative_toxicogenomics_database",
@@ -1251,20 +1141,11 @@ validated: false
    ],
    "tasks": [],
    "modalities": [
-      "knowledge-graph"
+      "Gene",
+      "Small Molecule"
    ],
    "organism": [],
-    "api": false,
-    "entities": [
-      "compound",
-      "gene",
-      "disease"
-    ],
-    "documentation": "https://ctdbase.org/",
-    "last_checked": "2026-08-08",
-    "metadata_sources": [
-      "https://ctdbase.org/"
-    ]
+    "api": false
  },
  {
    "id": "critical_assessment_of_structure_prediction_casp",
@@ -1293,21 +1174,10 @@ validated: false
    ],
    "tasks": [],
    "modalities": [
-      "single-cell-rna-seq",
-      "transcriptomics"
+      "Single Cell"
    ],
    "organism": [],
-    "api": false,
-    "entities": [
-      "cell",
-      "gene",
-      "tissue"
-    ],
-    "documentation": "https://cellxgene.cziscience.com/",
-    "last_checked": "2026-08-08",
-    "metadata_sources": [
-      "https://cellxgene.cziscience.com/"
-    ]
+    "api": false
  },
  {
    "id": "davis_kinase_inhibitors_db",
@@ -1338,21 +1208,10 @@ validated: false
    ],
    "tasks": [],
    "modalities": [
-      "genomics"
+      "Genomics"
    ],
    "organism": [],
-    "api": false,
-    "entities": [
-      "cell",
-      "gene",
-      "disease",
-      "drug"
-    ],
-    "documentation": "https://depmap.org/portal/",
-    "last_checked": "2026-08-08",
-    "metadata_sources": [
-      "https://depmap.org/portal/"
-    ]
+    "api": false
  },
  {
    "id": "dgidb",
@@ -1366,19 +1225,11 @@ validated: false
    ],
    "tasks": [],
    "modalities": [
-      "knowledge-graph"
+      "Gene",
+      "Small Molecule"
    ],
    "organism": [],
-    "api": false,
-    "entities": [
-      "drug",
-      "gene"
-    ],
-    "documentation": "https://www.dgidb.org/",
-    "last_checked": "2026-08-08",
-    "metadata_sources": [
-      "https://www.dgidb.org/"
-    ]
+    "api": false
  },
  {
    "id": "diseases",
@@ -1441,21 +1292,10 @@ validated: false
    ],
    "tasks": [],
    "modalities": [
-      "knowledge-graph"
+      "Knowledge Graph"
    ],
    "organism": [],
-    "api": false,
-    "entities": [
-      "drug",
-      "disease",
-      "gene",
-      "pathway"
-    ],
-    "github": "https://github.com/SuLab/DrugMechDB",
-    "last_checked": "2026-08-08",
-    "metadata_sources": [
-      "https://github.com/SuLab/DrugMechDB"
-    ]
+    "api": false
  },
  {
    "id": "drug_repurposing_hub",
@@ -1468,20 +1308,10 @@ validated: false
    ],
    "tasks": [],
    "modalities": [
-      "chemical-structure"
+      "Small Molecule"
    ],
    "organism": [],
-    "api": false,
-    "entities": [
-      "drug",
-      "protein",
-      "disease"
-    ],
-    "documentation": "https://repo-hub.broadinstitute.org/repurposing",
-    "last_checked": "2026-08-08",
-    "metadata_sources": [
-      "https://repo-hub.broadinstitute.org/repurposing"
-    ]
+    "api": false
  },
  {
    "id": "drugbank",
@@ -1519,20 +1349,10 @@ validated: false
    ],
    "tasks": [],
    "modalities": [
-      "chemical-structure"
+      "Small Molecule"
    ],
    "organism": [],
-    "api": false,
-    "entities": [
-      "drug",
-      "protein",
-      "disease"
-    ],
-    "documentation": "https://drugcentral.org/",
-    "last_checked": "2026-08-08",
-    "metadata_sources": [
-      "https://drugcentral.org/"
-    ]
+    "api": false
  },
  {
    "id": "drugtargetcommons",
@@ -1545,19 +1365,10 @@ validated: false
    ],
    "tasks": [],
    "modalities": [
-      "chemical-structure"
+      "Small Molecule"
    ],
    "organism": [],
-    "api": false,
-    "entities": [
-      "drug",
-      "protein"
-    ],
-    "documentation": "https://drugtargetcommons.fimm.fi/",
-    "last_checked": "2026-08-08",
-    "metadata_sources": [
-      "https://drugtargetcommons.fimm.fi/"
-    ]
+    "api": false
  },
  {
    "id": "encode",
@@ -2125,22 +1936,6 @@ validated: false
    "organism": [],
    "api": false
  },
-  {
-    "id": "oncokb",
-    "name": "OncoKB",
-    "type": "database",
-    "url": "https://www.oncokb.org/",
-    "description": "Precision oncology knowledge base of cancer genes, variants, and therapeutic implications.",
-    "tags": [
-      "genome"
-    ],
-    "tasks": [],
-    "modalities": [
-      "Genomics"
-    ],
-    "organism": [],
-    "api": false
-  },
  {
    "id": "open_targets_platform",
    "name": "Open Targets Platform",
@@ -2588,18 +2383,10 @@ validated: false
    ],
    "tasks": [],
    "modalities": [
-      "protein-sequence"
+      "Protein"
    ],
    "organism": [],
-    "api": false,
-    "entities": [
-      "protein"
-    ],
-    "documentation": "https://www.uniprot.org/",
-    "last_checked": "2026-08-08",
-    "metadata_sources": [
-      "https://www.uniprot.org/"
-    ]
+    "api": false
  },
  {
    "id": "uniref",
@@ -4208,7 +3995,7 @@ validated: false
    "name": "MIDAS",
    "type": "model",
    "url": "https://github.com/labomics/midas",
-    "description": "Mosaic integration and differential accessibility model for single-cell multi-omics that handles arbitrary missing-modality combinations across transcriptomics, chromatin accessibility, and proteomics.",
+    "description": "Mosaic integration and differential accessibility model for single-cell multi-omics data that handles arbitrary missing-modality combinations across transcriptomics, chromatin accessibility, and proteomics.",
    "tags": [
      "foundation-models",
      "multi-omics-foundation-models",
@@ -4479,24 +4266,6 @@ validated: false
    "organism": [],
    "api": false
  },
-  {
-    "id": "nbbayeslm",
-    "name": "NbBayesLM",
-    "type": "model",
-    "url": "https://github.com/FairuzShadmaniShishir/NbBayesLM",
-    "description": "Bayesian neural network integrating protein language model embeddings and physicochemical features to predict nanobody thermostability with uncertainty estimates. [Paper](https://www.frontiersin.org/journals/bioinformatics/articles/10.3389/fbinf.2026.1832968/full)",
-    "tags": [
-      "protein-property-prediction"
-    ],
-    "tasks": [
-      "Protein Property Prediction"
-    ],
-    "modalities": [
-      "Protein"
-    ],
-    "organism": [],
-    "api": false
-  },
  {
    "id": "neodti",
    "name": "NeoDTI",
@@ -5675,23 +5444,9 @@ validated: false
    "tasks": [
      "Preprocessing"
    ],
-    "modalities": [
-      "dna-sequence",
-      "protein-sequence"
-    ],
+    "modalities": [],
    "organism": [],
-    "api": false,
-    "entities": [
-      "gene",
-      "protein"
-    ],
-    "github": "https://github.com/biopython/biopython",
-    "documentation": "https://biopython.org/wiki/Documentation",
-    "last_checked": "2026-08-08",
-    "metadata_sources": [
-      "https://github.com/biopython/biopython",
-      "https://biopython.org/"
-    ]
+    "api": false
  },
  {
    "id": "casper",
@@ -5721,22 +5476,9 @@ validated: false
    "tasks": [
      "Preprocessing"
    ],
-    "modalities": [
-      "spatial-transcriptomics"
-    ],
+    "modalities": [],
    "organism": [],
-    "api": false,
-    "entities": [
-      "cell",
-      "tissue"
-    ],
-    "github": "https://github.com/CSOgroup/cellcharter",
-    "documentation": "https://cellcharter.readthedocs.io/",
-    "last_checked": "2026-08-08",
-    "metadata_sources": [
-      "https://github.com/CSOgroup/cellcharter",
-      "https://cellcharter.readthedocs.io/"
-    ]
+    "api": false
  },
  {
    "id": "cellchat",
@@ -5750,20 +5492,9 @@ validated: false
    "tasks": [
      "Preprocessing"
    ],
-    "modalities": [
-      "single-cell-rna-seq"
-    ],
+    "modalities": [],
    "organism": [],
-    "api": false,
-    "entities": [
-      "cell",
-      "gene"
-    ],
-    "github": "https://github.com/sqjin/CellChat",
-    "last_checked": "2026-08-08",
-    "metadata_sources": [
-      "https://github.com/sqjin/CellChat"
-    ]
+    "api": false
  },
  {
    "id": "celltypist",
@@ -5775,24 +5506,11 @@ validated: false
      "preprocessing-tools"
    ],
    "tasks": [
-      "cell-type-annotation"
-    ],
-    "modalities": [
-      "single-cell-rna-seq"
+      "Preprocessing"
    ],
+    "modalities": [],
    "organism": [],
-    "api": false,
-    "entities": [
-      "cell",
-      "gene"
-    ],
-    "github": "https://github.com/Teichlab/celltypist",
-    "documentation": "https://celltypist.readthedocs.io/",
-    "last_checked": "2026-08-08",
-    "metadata_sources": [
-      "https://github.com/Teichlab/celltypist",
-      "https://celltypist.readthedocs.io/"
-    ]
+    "api": false
  },
  {
    "id": "chatspatial",
@@ -5854,30 +5572,16 @@ validated: false
    "tasks": [
      "Preprocessing"
    ],
-    "modalities": [
-      "chemical-structure",
-      "molecular-structure"
-    ],
+    "modalities": [],
    "organism": [],
-    "api": false,
-    "entities": [
-      "molecule",
-      "protein"
-    ],
-    "github": "https://github.com/deepchem/deepchem",
-    "documentation": "https://deepchem.readthedocs.io/",
-    "last_checked": "2026-08-08",
-    "metadata_sources": [
-      "https://github.com/deepchem/deepchem",
-      "https://deepchem.readthedocs.io/"
-    ]
+    "api": false
  },
  {
    "id": "deeptalk",
    "name": "DeepTalk",
    "type": "toolkit",
    "url": "https://github.com/JiangBioLab/DeepTalk",
-    "description": "Graph attention network for deciphering cell-cell communication from spatial transcriptomics.",
+    "description": "Graph attention network for deciphering cell-cell communication from spatial transcriptomics data.",
    "tags": [
      "preprocessing-tools"
    ],
@@ -6092,21 +5796,9 @@ validated: false
    "tasks": [
      "Preprocessing"
    ],
-    "modalities": [
-      "chemical-structure"
-    ],
+    "modalities": [],
    "organism": [],
-    "api": false,
-    "entities": [
-      "molecule"
-    ],
-    "github": "https://github.com/rdkit/rdkit",
-    "documentation": "https://www.rdkit.org/docs/",
-    "last_checked": "2026-08-08",
-    "metadata_sources": [
-      "https://github.com/rdkit/rdkit",
-      "https://www.rdkit.org/docs/"
-    ]
+    "api": false
  },
  {
    "id": "scanpy",
@@ -6120,22 +5812,9 @@ validated: false
    "tasks": [
      "Preprocessing"
    ],
-    "modalities": [
-      "single-cell-rna-seq"
-    ],
+    "modalities": [],
    "organism": [],
-    "api": false,
-    "entities": [
-      "cell",
-      "gene"
-    ],
-    "github": "https://github.com/scverse/scanpy",
-    "documentation": "https://scanpy.readthedocs.io/en/stable/",
-    "last_checked": "2026-08-08",
-    "metadata_sources": [
-      "https://github.com/scverse/scanpy",
-      "https://scanpy.readthedocs.io/en/stable/"
-    ]
+    "api": false
  },
  {
    "id": "scenic",
@@ -6197,23 +5876,9 @@ validated: false
    "tasks": [
      "Preprocessing"
    ],
-    "modalities": [
-      "single-cell-rna-seq",
-      "multi-omics"
-    ],
+    "modalities": [],
    "organism": [],
-    "api": false,
-    "entities": [
-      "cell",
-      "gene"
-    ],
-    "github": "https://github.com/scverse/scvi-tools",
-    "documentation": "https://docs.scvi-tools.org/",
-    "last_checked": "2026-08-08",
-    "metadata_sources": [
-      "https://github.com/scverse/scvi-tools",
-      "https://docs.scvi-tools.org/"
-    ]
+    "api": false
  },
  {
    "id": "seqbench",
@@ -6243,22 +5908,9 @@ validated: false
    "tasks": [
      "Preprocessing"
    ],
-    "modalities": [
-      "single-cell-rna-seq"
-    ],
+    "modalities": [],
    "organism": [],
-    "api": false,
-    "entities": [
-      "cell",
-      "gene"
-    ],
-    "github": "https://github.com/satijalab/seurat",
-    "documentation": "https://satijalab.org/seurat/",
-    "last_checked": "2026-08-08",
-    "metadata_sources": [
-      "https://github.com/satijalab/seurat",
-      "https://satijalab.org/seurat/"
-    ]
+    "api": false
  },
  {
    "id": "squidpy",
@@ -6272,22 +5924,9 @@ validated: false
    "tasks": [
      "Preprocessing"
    ],
-    "modalities": [
-      "spatial-transcriptomics"
-    ],
+    "modalities": [],
    "organism": [],
-    "api": false,
-    "entities": [
-      "cell",
-      "tissue"
-    ],
-    "github": "https://github.com/scverse/squidpy",
-    "documentation": "https://squidpy.readthedocs.io/",
-    "last_checked": "2026-08-08",
-    "metadata_sources": [
-      "https://github.com/scverse/squidpy",
-      "https://squidpy.readthedocs.io/"
-    ]
+    "api": false
  },
  {
    "id": "stagate",
@@ -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/c6f07d90/data/resources.yml
-upstream_sha: c6f07d90
-imported_at: 2026-08-31
+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
@@ -1183,17 +1183,6 @@ resources:
    organism: []
    api: false

-  - id: oncokb
-    name: "OncoKB"
-    type: database
-    url: https://www.oncokb.org/
-    description: "Precision oncology knowledge base of cancer genes, variants, and therapeutic implications."
-    tags: [genome]
-    tasks: []
-    modalities: [Genomics]
-    organism: []
-    api: false
-
  - id: open_targets_platform
    name: "Open Targets Platform"
    type: database
@@ -2254,7 +2243,7 @@ resources:
    name: "MIDAS"
    type: model
    url: https://github.com/labomics/midas
-    description: "Mosaic integration and differential accessibility model for single-cell multi-omics that handles arbitrary missing-modality combinations across transcriptomics, chromatin accessibility, and proteomics."
+    description: "Mosaic integration and differential accessibility model for single-cell multi-omics data that handles arbitrary missing-modality combinations across transcriptomics, chromatin accessibility, and proteomics."
    tags: [foundation-models, multi-omics-foundation-models, single-cell-foundation-models]
    tasks: [Foundation Model]
    modalities: [Multi-Omics, Single Cell]
@@ -2393,17 +2382,6 @@ resources:
    organism: []
    api: false

-  - id: nbbayeslm
-    name: "NbBayesLM"
-    type: model
-    url: https://github.com/FairuzShadmaniShishir/NbBayesLM
-    description: "Bayesian neural network integrating protein language model embeddings and physicochemical features to predict nanobody thermostability with uncertainty estimates. [Paper](https://www.frontiersin.org/journals/bioinformatics/articles/10.3389/fbinf.2026.1832968/full)"
-    tags: [protein-property-prediction]
-    tasks: [Protein Property Prediction]
-    modalities: [Protein]
-    organism: []
-    api: false
-
  - id: neodti
    name: "NeoDTI"
    type: model
@@ -3002,7 +2980,7 @@ resources:
    name: "DeepTalk"
    type: toolkit
    url: https://github.com/JiangBioLab/DeepTalk
-    description: "Graph attention network for deciphering cell-cell communication from spatial transcriptomics."
+    description: "Graph attention network for deciphering cell-cell communication from spatial transcriptomics data."
    tags: [preprocessing-tools]
    tasks: [Preprocessing]
    modalities: []
@@ -2,9 +2,9 @@
 title: "Resources"
 task: ""
 lineage_type: import
-upstream_source: https://github.com/inoue0426/awesome-computational-biology/blob/c6f07d90/docs/data/resources.json
-upstream_sha: c6f07d90
-imported_at: 2026-08-31
+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
@@ -899,20 +899,10 @@ validated: false
    ],
    "tasks": [],
    "modalities": [
-      "single-cell-rna-seq",
-      "genomics"
+      "Genomics"
    ],
    "organism": [],
-    "api": false,
-    "entities": [
-      "cell",
-      "gene"
-    ],
-    "documentation": "https://www.10xgenomics.com/resources/datasets",
-    "last_checked": "2026-08-08",
-    "metadata_sources": [
-      "https://www.10xgenomics.com/resources/datasets"
-    ]
+    "api": false
  },
  {
    "id": "alphafold_protein_structure_database",
@@ -925,20 +915,10 @@ validated: false
    ],
    "tasks": [],
    "modalities": [
-      "molecular-structure",
-      "protein-sequence"
+      "Protein"
    ],
    "organism": [],
-    "api": false,
-    "entities": [
-      "protein"
-    ],
-    "documentation": "https://alphafold.ebi.ac.uk/api-docs",
-    "last_checked": "2026-08-08",
-    "metadata_sources": [
-      "https://alphafold.ebi.ac.uk/",
-      "https://alphafold.ebi.ac.uk/api-docs"
-    ]
+    "api": false
  },
  {
    "id": "bindingdb",
@@ -952,20 +932,11 @@ validated: false
    ],
    "tasks": [],
    "modalities": [
-      "chemical-structure",
-      "molecular-structure"
+      "Protein",
+      "Small Molecule"
    ],
    "organism": [],
-    "api": false,
-    "entities": [
-      "molecule",
-      "protein"
-    ],
-    "documentation": "https://www.bindingdb.org/rwd/bind/index.jsp",
-    "last_checked": "2026-08-08",
-    "metadata_sources": [
-      "https://www.bindingdb.org/rwd/bind/index.jsp"
-    ]
+    "api": false
  },
  {
    "id": "biocyc",
@@ -978,20 +949,10 @@ validated: false
    ],
    "tasks": [],
    "modalities": [
-      "genomics"
+      "Pathway"
    ],
    "organism": [],
-    "api": false,
-    "entities": [
-      "gene",
-      "pathway",
-      "organism"
-    ],
-    "documentation": "https://biocyc.org/",
-    "last_checked": "2026-08-08",
-    "metadata_sources": [
-      "https://biocyc.org/"
-    ]
+    "api": false
  },
  {
    "id": "biogrid",
@@ -1008,16 +969,7 @@ validated: false
      "Protein"
    ],
    "organism": [],
-    "api": false,
-    "entities": [
-      "gene",
-      "protein"
-    ],
-    "documentation": "https://thebiogrid.org/",
-    "last_checked": "2026-08-08",
-    "metadata_sources": [
-      "https://thebiogrid.org/"
-    ]
+    "api": false
  },
  {
    "id": "cancer_cell_line_encyclopedia",
@@ -1031,22 +983,11 @@ validated: false
    ],
    "tasks": [],
    "modalities": [
-      "genomics",
-      "transcriptomics"
+      "Gene Expression",
+      "Small Molecule"
    ],
    "organism": [],
-    "api": false,
-    "entities": [
-      "cell",
-      "gene",
-      "disease",
-      "drug"
-    ],
-    "documentation": "https://sites.broadinstitute.org/ccle/",
-    "last_checked": "2026-08-08",
-    "metadata_sources": [
-      "https://sites.broadinstitute.org/ccle/"
-    ]
+    "api": false
  },
  {
    "id": "catalogue_of_somatic_mutations_in_cancer_cosmic",
@@ -1059,20 +1000,10 @@ validated: false
    ],
    "tasks": [],
    "modalities": [
-      "genomics"
+      "Genomics"
    ],
    "organism": [],
-    "api": false,
-    "entities": [
-      "disease",
-      "gene",
-      "variant"
-    ],
-    "documentation": "https://cancer.sanger.ac.uk/cosmic",
-    "last_checked": "2026-08-08",
-    "metadata_sources": [
-      "https://cancer.sanger.ac.uk/cosmic"
-    ]
+    "api": false
  },
  {
    "id": "cath_database",
@@ -1085,19 +1016,10 @@ validated: false
    ],
    "tasks": [],
    "modalities": [
-      "molecular-structure",
-      "protein-sequence"
+      "Protein"
    ],
    "organism": [],
-    "api": false,
-    "entities": [
-      "protein"
-    ],
-    "documentation": "https://www.cathdb.info/",
-    "last_checked": "2026-08-08",
-    "metadata_sources": [
-      "https://www.cathdb.info/"
-    ]
+    "api": false
  },
  {
    "id": "cbioportal",
@@ -1110,23 +1032,10 @@ validated: false
    ],
    "tasks": [],
    "modalities": [
-      "genomics",
-      "clinical"
+      "Genomics"
    ],
    "organism": [],
-    "api": false,
-    "entities": [
-      "disease",
-      "gene",
-      "variant"
-    ],
-    "github": "https://github.com/cBioPortal/cbioportal",
-    "documentation": "https://www.cbioportal.org/",
-    "last_checked": "2026-08-08",
-    "metadata_sources": [
-      "https://www.cbioportal.org/",
-      "https://github.com/cBioPortal/cbioportal"
-    ]
+    "api": false
  },
  {
    "id": "cellminer_cross_database_cellminercdb",
@@ -1183,20 +1092,10 @@ validated: false
    ],
    "tasks": [],
    "modalities": [
-      "chemical-structure"
+      "Small Molecule"
    ],
    "organism": [],
-    "api": false,
-    "entities": [
-      "compound",
-      "molecule",
-      "protein"
-    ],
-    "documentation": "https://www.ebi.ac.uk/chembl/",
-    "last_checked": "2026-08-08",
-    "metadata_sources": [
-      "https://www.ebi.ac.uk/chembl/"
-    ]
+    "api": false
  },
  {
    "id": "chemspider",
@@ -1225,19 +1124,10 @@ validated: false
    ],
    "tasks": [],
    "modalities": [
-      "clinical"
+      "Clinical"
    ],
    "organism": [],
-    "api": false,
-    "entities": [
-      "disease",
-      "drug"
-    ],
-    "documentation": "https://clinicaltrials.gov/",
-    "last_checked": "2026-08-08",
-    "metadata_sources": [
-      "https://clinicaltrials.gov/"
-    ]
+    "api": false
  },
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    "id": "comparative_toxicogenomics_database",
@@ -1251,20 +1141,11 @@ validated: false
    ],
    "tasks": [],
    "modalities": [
-      "knowledge-graph"
+      "Gene",
+      "Small Molecule"
    ],
    "organism": [],
-    "api": false,
-    "entities": [
-      "compound",
-      "gene",
-      "disease"
-    ],
-    "documentation": "https://ctdbase.org/",
-    "last_checked": "2026-08-08",
-    "metadata_sources": [
-      "https://ctdbase.org/"
-    ]
+    "api": false
  },
  {
    "id": "critical_assessment_of_structure_prediction_casp",
@@ -1293,21 +1174,10 @@ validated: false
    ],
    "tasks": [],
    "modalities": [
-      "single-cell-rna-seq",
-      "transcriptomics"
+      "Single Cell"
    ],
    "organism": [],
-    "api": false,
-    "entities": [
-      "cell",
-      "gene",
-      "tissue"
-    ],
-    "documentation": "https://cellxgene.cziscience.com/",
-    "last_checked": "2026-08-08",
-    "metadata_sources": [
-      "https://cellxgene.cziscience.com/"
-    ]
+    "api": false
  },
  {
    "id": "davis_kinase_inhibitors_db",
@@ -1338,21 +1208,10 @@ validated: false
    ],
    "tasks": [],
    "modalities": [
-      "genomics"
+      "Genomics"
    ],
    "organism": [],
-    "api": false,
-    "entities": [
-      "cell",
-      "gene",
-      "disease",
-      "drug"
-    ],
-    "documentation": "https://depmap.org/portal/",
-    "last_checked": "2026-08-08",
-    "metadata_sources": [
-      "https://depmap.org/portal/"
-    ]
+    "api": false
  },
  {
    "id": "dgidb",
@@ -1366,19 +1225,11 @@ validated: false
    ],
    "tasks": [],
    "modalities": [
-      "knowledge-graph"
+      "Gene",
+      "Small Molecule"
    ],
    "organism": [],
-    "api": false,
-    "entities": [
-      "drug",
-      "gene"
-    ],
-    "documentation": "https://www.dgidb.org/",
-    "last_checked": "2026-08-08",
-    "metadata_sources": [
-      "https://www.dgidb.org/"
-    ]
+    "api": false
  },
  {
    "id": "diseases",
@@ -1441,21 +1292,10 @@ validated: false
    ],
    "tasks": [],
    "modalities": [
-      "knowledge-graph"
+      "Knowledge Graph"
    ],
    "organism": [],
-    "api": false,
-    "entities": [
-      "drug",
-      "disease",
-      "gene",
-      "pathway"
-    ],
-    "github": "https://github.com/SuLab/DrugMechDB",
-    "last_checked": "2026-08-08",
-    "metadata_sources": [
-      "https://github.com/SuLab/DrugMechDB"
-    ]
+    "api": false
  },
  {
    "id": "drug_repurposing_hub",
@@ -1468,20 +1308,10 @@ validated: false
    ],
    "tasks": [],
    "modalities": [
-      "chemical-structure"
+      "Small Molecule"
    ],
    "organism": [],
-    "api": false,
-    "entities": [
-      "drug",
-      "protein",
-      "disease"
-    ],
-    "documentation": "https://repo-hub.broadinstitute.org/repurposing",
-    "last_checked": "2026-08-08",
-    "metadata_sources": [
-      "https://repo-hub.broadinstitute.org/repurposing"
-    ]
+    "api": false
  },
  {
    "id": "drugbank",
@@ -1519,20 +1349,10 @@ validated: false
    ],
    "tasks": [],
    "modalities": [
-      "chemical-structure"
+      "Small Molecule"
    ],
    "organism": [],
-    "api": false,
-    "entities": [
-      "drug",
-      "protein",
-      "disease"
-    ],
-    "documentation": "https://drugcentral.org/",
-    "last_checked": "2026-08-08",
-    "metadata_sources": [
-      "https://drugcentral.org/"
-    ]
+    "api": false
  },
  {
    "id": "drugtargetcommons",
@@ -1545,19 +1365,10 @@ validated: false
    ],
    "tasks": [],
    "modalities": [
-      "chemical-structure"
+      "Small Molecule"
    ],
    "organism": [],
-    "api": false,
-    "entities": [
-      "drug",
-      "protein"
-    ],
-    "documentation": "https://drugtargetcommons.fimm.fi/",
-    "last_checked": "2026-08-08",
-    "metadata_sources": [
-      "https://drugtargetcommons.fimm.fi/"
-    ]
+    "api": false
  },
  {
    "id": "encode",
@@ -2125,22 +1936,6 @@ validated: false
    "organism": [],
    "api": false
  },
-  {
-    "id": "oncokb",
-    "name": "OncoKB",
-    "type": "database",
-    "url": "https://www.oncokb.org/",
-    "description": "Precision oncology knowledge base of cancer genes, variants, and therapeutic implications.",
-    "tags": [
-      "genome"
-    ],
-    "tasks": [],
-    "modalities": [
-      "Genomics"
-    ],
-    "organism": [],
-    "api": false
-  },
  {
    "id": "open_targets_platform",
    "name": "Open Targets Platform",
@@ -2588,18 +2383,10 @@ validated: false
    ],
    "tasks": [],
    "modalities": [
-      "protein-sequence"
+      "Protein"
    ],
    "organism": [],
-    "api": false,
-    "entities": [
-      "protein"
-    ],
-    "documentation": "https://www.uniprot.org/",
-    "last_checked": "2026-08-08",
-    "metadata_sources": [
-      "https://www.uniprot.org/"
-    ]
+    "api": false
  },
  {
    "id": "uniref",
@@ -4208,7 +3995,7 @@ validated: false
    "name": "MIDAS",
    "type": "model",
    "url": "https://github.com/labomics/midas",
-    "description": "Mosaic integration and differential accessibility model for single-cell multi-omics that handles arbitrary missing-modality combinations across transcriptomics, chromatin accessibility, and proteomics.",
+    "description": "Mosaic integration and differential accessibility model for single-cell multi-omics data that handles arbitrary missing-modality combinations across transcriptomics, chromatin accessibility, and proteomics.",
    "tags": [
      "foundation-models",
      "multi-omics-foundation-models",
@@ -4479,24 +4266,6 @@ validated: false
    "organism": [],
    "api": false
  },
-  {
-    "id": "nbbayeslm",
-    "name": "NbBayesLM",
-    "type": "model",
-    "url": "https://github.com/FairuzShadmaniShishir/NbBayesLM",
-    "description": "Bayesian neural network integrating protein language model embeddings and physicochemical features to predict nanobody thermostability with uncertainty estimates. [Paper](https://www.frontiersin.org/journals/bioinformatics/articles/10.3389/fbinf.2026.1832968/full)",
-    "tags": [
-      "protein-property-prediction"
-    ],
-    "tasks": [
-      "Protein Property Prediction"
-    ],
-    "modalities": [
-      "Protein"
-    ],
-    "organism": [],
-    "api": false
-  },
  {
    "id": "neodti",
    "name": "NeoDTI",
@@ -5675,23 +5444,9 @@ validated: false
    "tasks": [
      "Preprocessing"
    ],
-    "modalities": [
-      "dna-sequence",
-      "protein-sequence"
-    ],
+    "modalities": [],
    "organism": [],
-    "api": false,
-    "entities": [
-      "gene",
-      "protein"
-    ],
-    "github": "https://github.com/biopython/biopython",
-    "documentation": "https://biopython.org/wiki/Documentation",
-    "last_checked": "2026-08-08",
-    "metadata_sources": [
-      "https://github.com/biopython/biopython",
-      "https://biopython.org/"
-    ]
+    "api": false
  },
  {
    "id": "casper",
@@ -5721,22 +5476,9 @@ validated: false
    "tasks": [
      "Preprocessing"
    ],
-    "modalities": [
-      "spatial-transcriptomics"
-    ],
+    "modalities": [],
    "organism": [],
-    "api": false,
-    "entities": [
-      "cell",
-      "tissue"
-    ],
-    "github": "https://github.com/CSOgroup/cellcharter",
-    "documentation": "https://cellcharter.readthedocs.io/",
-    "last_checked": "2026-08-08",
-    "metadata_sources": [
-      "https://github.com/CSOgroup/cellcharter",
-      "https://cellcharter.readthedocs.io/"
-    ]
+    "api": false
  },
  {
    "id": "cellchat",
@@ -5750,20 +5492,9 @@ validated: false
    "tasks": [
      "Preprocessing"
    ],
-    "modalities": [
-      "single-cell-rna-seq"
-    ],
+    "modalities": [],
    "organism": [],
-    "api": false,
-    "entities": [
-      "cell",
-      "gene"
-    ],
-    "github": "https://github.com/sqjin/CellChat",
-    "last_checked": "2026-08-08",
-    "metadata_sources": [
-      "https://github.com/sqjin/CellChat"
-    ]
+    "api": false
  },
  {
    "id": "celltypist",
@@ -5775,24 +5506,11 @@ validated: false
      "preprocessing-tools"
    ],
    "tasks": [
-      "cell-type-annotation"
-    ],
-    "modalities": [
-      "single-cell-rna-seq"
+      "Preprocessing"
    ],
+    "modalities": [],
    "organism": [],
-    "api": false,
-    "entities": [
-      "cell",
-      "gene"
-    ],
-    "github": "https://github.com/Teichlab/celltypist",
-    "documentation": "https://celltypist.readthedocs.io/",
-    "last_checked": "2026-08-08",
-    "metadata_sources": [
-      "https://github.com/Teichlab/celltypist",
-      "https://celltypist.readthedocs.io/"
-    ]
+    "api": false
  },
  {
    "id": "chatspatial",
@@ -5854,30 +5572,16 @@ validated: false
    "tasks": [
      "Preprocessing"
    ],
-    "modalities": [
-      "chemical-structure",
-      "molecular-structure"
-    ],
+    "modalities": [],
    "organism": [],
-    "api": false,
-    "entities": [
-      "molecule",
-      "protein"
-    ],
-    "github": "https://github.com/deepchem/deepchem",
-    "documentation": "https://deepchem.readthedocs.io/",
-    "last_checked": "2026-08-08",
-    "metadata_sources": [
-      "https://github.com/deepchem/deepchem",
-      "https://deepchem.readthedocs.io/"
-    ]
+    "api": false
  },
  {
    "id": "deeptalk",
    "name": "DeepTalk",
    "type": "toolkit",
    "url": "https://github.com/JiangBioLab/DeepTalk",
-    "description": "Graph attention network for deciphering cell-cell communication from spatial transcriptomics.",
+    "description": "Graph attention network for deciphering cell-cell communication from spatial transcriptomics data.",
    "tags": [
      "preprocessing-tools"
    ],
@@ -6092,21 +5796,9 @@ validated: false
    "tasks": [
      "Preprocessing"
    ],
-    "modalities": [
-      "chemical-structure"
-    ],
+    "modalities": [],
    "organism": [],
-    "api": false,
-    "entities": [
-      "molecule"
-    ],
-    "github": "https://github.com/rdkit/rdkit",
-    "documentation": "https://www.rdkit.org/docs/",
-    "last_checked": "2026-08-08",
-    "metadata_sources": [
-      "https://github.com/rdkit/rdkit",
-      "https://www.rdkit.org/docs/"
-    ]
+    "api": false
  },
  {
    "id": "scanpy",
@@ -6120,22 +5812,9 @@ validated: false
    "tasks": [
      "Preprocessing"
    ],
-    "modalities": [
-      "single-cell-rna-seq"
-    ],
+    "modalities": [],
    "organism": [],
-    "api": false,
-    "entities": [
-      "cell",
-      "gene"
-    ],
-    "github": "https://github.com/scverse/scanpy",
-    "documentation": "https://scanpy.readthedocs.io/en/stable/",
-    "last_checked": "2026-08-08",
-    "metadata_sources": [
-      "https://github.com/scverse/scanpy",
-      "https://scanpy.readthedocs.io/en/stable/"
-    ]
+    "api": false
  },
  {
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@@ -6197,23 +5876,9 @@ validated: false
    "tasks": [
      "Preprocessing"
    ],
-    "modalities": [
-      "single-cell-rna-seq",
-      "multi-omics"
-    ],
+    "modalities": [],
    "organism": [],
-    "api": false,
-    "entities": [
-      "cell",
-      "gene"
-    ],
-    "github": "https://github.com/scverse/scvi-tools",
-    "documentation": "https://docs.scvi-tools.org/",
-    "last_checked": "2026-08-08",
-    "metadata_sources": [
-      "https://github.com/scverse/scvi-tools",
-      "https://docs.scvi-tools.org/"
-    ]
+    "api": false
  },
  {
    "id": "seqbench",
@@ -6243,22 +5908,9 @@ validated: false
    "tasks": [
      "Preprocessing"
    ],
-    "modalities": [
-      "single-cell-rna-seq"
-    ],
+    "modalities": [],
    "organism": [],
-    "api": false,
-    "entities": [
-      "cell",
-      "gene"
-    ],
-    "github": "https://github.com/satijalab/seurat",
-    "documentation": "https://satijalab.org/seurat/",
-    "last_checked": "2026-08-08",
-    "metadata_sources": [
-      "https://github.com/satijalab/seurat",
-      "https://satijalab.org/seurat/"
-    ]
+    "api": false
  },
  {
    "id": "squidpy",
@@ -6272,22 +5924,9 @@ validated: false
    "tasks": [
      "Preprocessing"
    ],
-    "modalities": [
-      "spatial-transcriptomics"
-    ],
+    "modalities": [],
    "organism": [],
-    "api": false,
-    "entities": [
-      "cell",
-      "tissue"
-    ],
-    "github": "https://github.com/scverse/squidpy",
-    "documentation": "https://squidpy.readthedocs.io/",
-    "last_checked": "2026-08-08",
-    "metadata_sources": [
-      "https://github.com/scverse/squidpy",
-      "https://squidpy.readthedocs.io/"
-    ]
+    "api": false
  },
  {
    "id": "stagate",