SunnyLin/GCF-GRCh38-p14-genomic
收藏Hugging Face2025-11-17 更新2025-12-20 收录
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https://hf-mirror.com/datasets/SunnyLin/GCF-GRCh38-p14-genomic
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---
tags:
- biology
pretty_name: GCF-GRCh38
size_categories:
- 1M<n<10M
---
## Dataset Summary
This dataset is a processed, tabular representation of the **NCBI RefSeq GFF file** for the human reference genome **GRCh38.p14**. The original GFF (General Feature Format) data, `GCF_000001405.40_GRCh38.p14_genomic.gff`, has been converted to the **Parquet format** for efficient storage and fast querying using libraries like Pandas and Apache Arrow.
The data contains annotations for all genomic features (genes, transcripts, exons, CDS, etc.) on the primary sequences of the GRCh38 human genome assembly.
## Data Structure
The dataset is stored as a single **Parquet** file and can be easily loaded into a Pandas DataFrame.
| Column Name | Data Type | Description | Example Value |
| :--- | :--- | :--- | :--- |
| `seqid` | string | NCBI Accession ID for the sequence (chromosome). **Needs mapping to `chrX` names.** | `NC_000001.11` |
| `source` | string | Source of the feature (e.g., RefSeq, BestRefSeq). | `BestRefSeq` |
| `type` | string | Type of the genomic feature (e.g., `gene`, `transcript`, `exon`, `CDS`). | `gene` |
| `start` | int32 | Feature start position (1-based, inclusive). | `11874` |
| `end` | int32 | Feature end position (1-based, inclusive). | `14409` |
| `score` | string | Score (always `.`) | `.` |
| `strand` | string | Feature strand (`+` for forward, `-` for reverse). | `+` |
| `phase` | string | Phase for CDS features (0, 1, or 2). | `.` |
| `attributes` | string | **Feature attributes, stored as a JSON string/dictionary.** | `{"ID": "gene-DDX11L1", "Dbxref": ["GeneID:100287102", "HGNC:HGNC:37102"]...}` |
## Usage
#### 1. Python (Pandas) Setup
To easily convert the `seqid` (NCBI Accession ID) to the standard chromosome name (`chr1`, `chr2`, etc.), you can use the following mapping dictionary extracted from the GRCh38.p14 assembly report.
```python
ncid2chr = {
'NC_000001.11': 'chr1', 'NC_000002.12': 'chr2', 'NC_000003.12': 'chr3',
'NC_000004.12': 'chr4', 'NC_000005.10': 'chr5', 'NC_000006.12': 'chr6',
'NC_000007.14': 'chr7', 'NC_000008.11': 'chr8', 'NC_000009.12': 'chr9',
'NC_000010.11': 'chr10', 'NC_000011.10': 'chr11', 'NC_000012.12': 'chr12',
'NC_000013.11': 'chr13', 'NC_000014.9': 'chr14', 'NC_000015.10': 'chr15',
'NC_000016.10': 'chr16', 'NC_000017.11': 'chr17', 'NC_000018.10': 'chr18',
'NC_000019.10': 'chr19', 'NC_000020.11': 'chr20', 'NC_000021.9': 'chr21',
'NC_000022.11': 'chr22', 'NC_000023.11': 'chrX', 'NC_000024.10': 'chrY',
'NC_012920.1': 'chrM'
}
```
提供机构：
SunnyLin
