Update README.md

README.md

@@ -1,5 +1,10 @@
 ---
 license: cc-by-nc-4.0
+tags:
+- genomics
+- ESKAPE pathogens
+- bioinformatics
+- ProkBERT
 dataset_info:
   features:
   - name: contig_id
@@ -36,3 +41,47 @@ configs:
   - split: ESKAPE
     path: data/ESKAPE-*
 ---
+
+# Dataset Card for ESKAPE Genomic Features Dataset
+
+## Dataset Description
+
+This dataset includes genomic segments from ESKAPE pathogens, characterized by various genomic features such as coding sequences (CDS), intergenic regions, ncRNA, and pseudogenes. It was analyzed to understand the representations captured by models like ProkBERT-mini, ProkBERT-mini-c, and ProkBERT-mini-long.
+
+### Data Fields
+
+- `contig_id`: Identifier of the contig.
+- `segment_id`: Unique identifier for each genomic segment.
+- `strand`: DNA strand of the segment (`+` or `-`).
+- `seq_start`: Starting position of the segment in the contig.
+- `seq_end`: Ending position of the segment in the contig.
+- `segment_start`: Starting position of the segment in the sequence.
+- `segment_end`: Ending position of the segment in the sequence.
+- `label`: Genomic feature category (e.g., CDS, intergenic).
+- `segment_length`: Length of the genomic segment.
+- `Nsegment`: [Additional description needed].
+- `segment`: Genomic sequence of the segment.
+
+### UMAP Embeddings and Silhouette Scores
+
+The dataset was used to assess the zero-shot capabilities of the ProkBERT models in predicting genomic features. UMAP technique was employed to reduce dimensionality and derive embeddings, which were then evaluated using silhouette scores. The embeddings and scores reveal the models' proficiency in differentiating between genomic features and capturing the genomic structure of ESKAPE pathogens.
+
+## Dataset Creation
+
+The dataset is compiled from the RefSeq database and other sources, focusing on ESKAPE pathogens. Redundancy in sequences is reduced using the CD-HIT algorithm.
+
+## Considerations for Using the Data
+
+This dataset is pivotal for genomic research and bioinformatics, particularly for understanding the genomic structure of ESKAPE pathogens and their representation in embedding spaces.
+
+## Additional Information
+
+### Dataset Curators
+
+Curated by [Your Team/Institution Name].
+
+### Licensing Information
+
+Creative Commons Attribution Non-Commercial 4.0 International.
+
+### Citation Information