Update README.md

README.md

@@ -1,3 +1,133 @@
----
-license: mit
----
+---
+license: mit
+language:
+- en
+dataset_info:
+  - name: Orthoformer
+    description: Large-scale datasets for training and evaluating the Orthoformer foundation model for orthology and protein family representation learning.
+    config_name: default
+    splits:
+      - name: foundation_model_dataset
+        num_examples: 3000000
+      - name: Downstream_Tasks_dataset
+      - name: Orthoformer_eval_dataset
+tags:
+- protein
+- orthology
+- foundation-model
+- bioinformatics
+- embeddings
+---
+
+# Orthoformer Datasets
+
+## 📌 Overview
+
+**Orthoformer** is a large-scale genomics dataset designed to support **function-centric foundation modeling** of microbial and viral genomes.
+
+Unlike conventional sequence-based models that infer biological roles from nucleotide or protein context, Orthoformer represents each genome by its **orthologous group composition and abundance**, treating **functional units rather than sequences** as the basic biological vocabulary.
+
+The dataset was constructed from approximately **three million prokaryotic and viral genomes**, each encoded as a high-dimensional functional profile capturing:
+
+- biochemical identity  
+- gene family dynamics  
+- evolutionary conservation  
+- pathway-scale metabolic capacity  
+
+These representations enable learning a **functional embedding space** that provides an **alignment-free measure of genomic similarity**, supporting robust taxonomy, phylogenetic analysis, and detection of functional convergence across microbial lineages.
+
+The same functional embeddings generalize beyond evolutionary structure to predict:
+
+- biosynthetic gene cluster abundance  
+- ecological niche differentiation  
+- organism-level phenotypes  
+- marker-gene associations  
+
+Together, the Orthoformer dataset establishes a **function-first framework for microbial genomics**, offering a scalable alternative to sequence-centric datasets for studying microbial evolution, function, and ecology.
+
+
+---
+
+## 📂 Dataset Structure
+
+The repository is organized into three functional splits:
+
+| Split | Purpose | Description |
+|------|--------|-------------|
+| `foundation_model_dataset` | Pretraining | Large-scale collection of microbial and viral genomes represented by orthologous group composition and abundance, used for self-supervised function-centric foundation model training |
+| `Downstream_Tasks_dataset` | Fine-tuning | Labeled genome-level datasets for functional, metabolic, and ecological prediction tasks, including niche, biosynthetic capacity, and phenotype inference |
+| `Orthoformer_eval_dataset` | Evaluation | Benchmark datasets for evaluating functional embeddings on taxonomy, phylogeny, functional convergence, and biological consistency |
+
+---
+
+## 📊 Dataset Statistics
+
+| Split | Size | Max Sequence Length |
+|------|------|--------------------|
+| foundation_model_dataset | ~3M sequences | 2048 |
+| Downstream_Tasks_dataset | Task dependent | Task dependent |
+| Orthoformer_eval_dataset | Benchmarks | Task dependent |
+
+---
+
+## 🚀 Accessing the Dataset
+
+You can download the dataset via Hugging Face using **Git + Xet (recommended for large files)**:
+
+```bash
+# Install git-xet (Linux)
+curl -sSf https://raw.githubusercontent.com/huggingface/xet-core/main/git_xet/install.sh | sh
+git xet install
+
+# Clone the dataset
+git clone https://huggingface.co/datasets/jackkuo/Orthoformer
+````
+
+If you only want the metadata without large files:
+
+```bash
+GIT_LFS_SKIP_SMUDGE=1 git clone https://huggingface.co/datasets/jackkuo/Orthoformer
+```
+
+---
+
+## 🧬 Intended Use
+
+The Orthoformer dataset is intended for training and evaluating **foundation models for microbial functional genomics**, including:
+
+- Functional embedding of microbial and viral genomes  
+- Alignment-free phylogeny and taxonomy  
+- Functional convergence and evolutionary analysis  
+- Metabolic and pathway-level phenotype prediction  
+- Biosynthetic gene cluster and ecological niche inference  
+
+It is specifically designed for **function-centric modeling**, where orthologous gene groups are treated as the fundamental representation units instead of raw nucleotide or amino acid sequences.
+
+---
+
+## 📜 License
+
+This dataset is released under the **MIT License**.
+
+---
+
+## 📖 Citation
+
+If you use this dataset, please cite:
+
+```bibtex
+@dataset{xxx,
+  title = {Orthoformer: xxx},
+  author = {xxx},
+  year = {2025},
+}
+```
+
+---
+
+## 🔗 Related Resources
+
+* **Model**: [https://huggingface.co/jackkuo/Orthoformer](https://huggingface.co/jackkuo/Orthoformer)
+* **Code**: [https://github.com/JackKuo666/Orthoformer](https://github.com/JackKuo666/Orthoformer)
+
+---