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gene_network_with_hgnc_symbols

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metadata
dataset_info:
  features:
    - name: identifier
      dtype: string
    - name: gene_symbol
      dtype: string
    - name: name
      dtype: string
    - name: entrez_url
      dtype: string
    - name: ensembl_url
      dtype: string
    - name: uniprot_url
      dtype: string
    - name: iuphar_url
      dtype: string
    - name: kegg_url
      dtype: string
    - name: omim_url
      dtype: string
    - name: orphanet_url
      dtype: string
    - name: location
      dtype: string
  splits:
    - name: train
      num_bytes: 31974
      num_examples: 87
  download_size: 15892
  dataset_size: 31974
configs:
  - config_name: default
    data_files:
      - split: train
        path: data/train-*
license: cc-by-sa-4.0

Dataset Description

This dataset provides a structured representation of gene-related information, incorporating resolvable URLs to key external databases and ontologies. These URLs allow users to directly access detailed information about genes, their relationships, and associated biological properties. The dataset is ideal for bioinformatics research, knowledge graph development, and integrative analyses of genomic data.

Features and Data Structure

The dataset includes the following fields:

  • identifier: A resolvable URL that uniquely identifies the gene in the HGNC database.
  • gene_symbol: The standardized symbol representing the gene (e.g., TP53).
  • name: The full name or description of the gene (e.g., Thymidylate Synthetase).
  • entrez_url: A URL to the gene's entry in the NCBI Entrez Gene database.
  • ensembl_url: A URL to the gene's entry in the Ensembl genome database.
  • uniprot_url: A URL to the gene's entry in the UniProt database, providing protein-specific details.
  • iuphar_url: A URL to the IUPHAR database for pharmacological data related to the gene.
  • kegg_url: A URL to the gene's pathway information in the KEGG database.
  • omim_url: A URL to the OMIM database for genetic disorder associations.
  • orphanet_url: A URL to the Orphanet database for rare disease associations.
  • location: The chromosomal location of the gene (e.g., 18p11.32), indicating its position in the human genome.

Key Adjustments in Terminology

  • Fields like entrez_url, ensembl_url, and others are not simple "identifiers." They are resolvable URLs that link to detailed information within their respective databases.
  • The term URL is explicitly used in the field names to clarify their purpose as lookup resources rather than unique identifiers.

Usage

This dataset enables direct integration with external knowledge bases through the provided URLs, making it a powerful resource for tasks such as:

  1. Data Integration: Map genes across databases by resolving URLs to access detailed metadata.
  2. Knowledge Graph Construction: Use the dataset to establish semantic links between genes, proteins, diseases, and pathways.
  3. Genomic Analysis: Explore chromosomal locations and database-specific annotations for genes of interest.

Example Queries

  • Retrieve genes located on chromosome 18.
  • Access details about a specific gene by resolving its uniprot_url.
  • Explore rare diseases associated with genes by querying orphanet_url.

Citation

If you use this dataset, please cite it as follows:

@dataset{dwb2023_gene_network,
  author = {dwb2023},
  title = {Gene Network with HGNC Symbols V4},
  year = {2025},
  publisher = {Hugging Face Datasets},
  url = {https://huggingface.co/datasets/dwb2023/gene_network_with_hgnc_symbols}
}

Acknowledgements

The dataset integrates information from trusted resources, including HGNC, NCBI Entrez, Ensembl, UniProt, KEGG, OMIM, and Orphanet. We thank these organizations for their significant contributions to genomics research.