README.md · dwb2023/hgnc_gene

metadata

dataset_info:
  features:
    - name: hgnc_id
      dtype: string
    - name: gene_symbol
      dtype: string
    - name: name
      dtype: string
    - name: locus_group
      dtype: string
    - name: locus_type
      dtype: string
    - name: status
      dtype: string
    - name: location
      dtype: string
    - name: alias_symbol
      dtype: string
    - name: alias_name
      dtype: string
    - name: prev_symbol
      dtype: string
    - name: prev_name
      dtype: string
    - name: gene_group
      sequence: string
    - name: gene_group_id
      sequence: int64
    - name: date_approved_reserved
      dtype: string
    - name: date_symbol_changed
      dtype: string
    - name: date_name_changed
      dtype: string
    - name: date_modified
      dtype: string
    - name: entrez_id
      dtype: string
    - name: ensembl_gene_id
      dtype: string
    - name: vega_id
      dtype: string
    - name: ucsc_id
      dtype: string
    - name: ena
      sequence: string
    - name: refseq_accession
      sequence: string
    - name: ccds_id
      sequence: string
    - name: uniprot_ids
      sequence: string
    - name: pubmed_id
      sequence: int64
    - name: mgd_id
      sequence: string
    - name: rgd_id
      sequence: string
    - name: lsdb
      sequence: string
    - name: omim_id
      sequence: string
    - name: orphanet
      dtype: float64
    - name: merops
      dtype: string
    - name: iuphar
      dtype: string
    - name: cd
      dtype: string
    - name: enzyme_id
      sequence: string
    - name: agr
      dtype: string
    - name: mane_select
      sequence: string
    - name: gencc
      dtype: string
    - name: uuid
      dtype: string
    - name: rna_central_id
      sequence: string
    - name: curator_notes
      sequence: string
    - name: metadata_source
      dtype: string
  splits:
    - name: train
      num_bytes: 56063
      num_examples: 87
  download_size: 49646
  dataset_size: 56063
configs:
  - config_name: default
    data_files:
      - split: train
        path: data/train-*

Dataset Purpose

This dataset provides a mapping table of gene identifiers and metadata, consolidating information from major bioinformatics resources like HGNC, ENSEMBL, NCBI, and IUPHAR. It is optimized for cross-referencing and querying gene-related data in tasks such as synthetic lethality studies and bioinformatics workflows.

Key Usage

Primary Identifier: Use gene_symbol for lookups and integrations.
Provenance Tracking: Refer to the metadata_source column for data origins.
Timeline Analysis: Leverage standardized date columns for temporal insights.

Dataset Structure

The dataset contains the following fields, each of which is essential for understanding the synthetic lethal interactions and genetic relationships in cancer:

Field Name	Description
hgnc_id	HGNC ID. A unique ID created by the HGNC for every approved symbol.
gene_symbol	The HGNC approved gene symbol. Equates to the "Approved symbol" field within the gene symbol report.
name	HGNC approved name for the gene. Equates to the "Approved name" field within the gene symbol report.
locus_group	A group name for a set of related locus types as defined by the HGNC (e.g. non-coding RNA).
locus_type	The locus type as set by the HGNC.
status	Status of the symbol report, which can be either "Approved" or "Entry Withdrawn".
location	Cytogenetic location of the gene (e.g. 2q34).
alias_symbol	Other symbols used to refer to this gene as seen in the "Alias symbols" field in the gene symbol report.
alias_name	Other names used to refer to this gene as seen in the "Alias names" field in the gene symbol report.
prev_symbol	Gene symbols previously approved by the HGNC for this gene. Equates to the "Previous symbols" field within the gene symbol report.
prev_name	Gene names previously approved by the HGNC for this gene. Equates to the "Previous names" field within the gene symbol report.
gene_group	The gene group name as set by the HGNC and seen at the top of the gene group reports.
gene_group_id	ID used to designate a gene group the gene has been assigned to.
date_approved_reserved	The date the entry was first approved.
date_symbol_changed	The date the approved symbol was last changed.
date_name_changed	The date the approved name was last changed.
date_modified	Date the entry was last modified.
entrez_id	NCBI gene ID. Found within the "Gene resources" section of the gene symbol report.
ensembl_gene_id	Ensembl gene ID. Found within the "Gene resources" section of the gene symbol report.
vega_id	Vega gene ID. Found within the "Gene resources" section of the gene symbol report.
ucsc_id	UCSC gene ID. Found within the "Gene resources" section of the gene symbol report.
ena	International Nucleotide Sequence Database Collaboration (GenBank, ENA and DDBJ) accession number(s). Found within the "Nucleotide resources" section of the gene symbol report.
refseq_accession	RefSeq nucleotide accession(s). Found within the "Nucleotide resources" section of the gene symbol report.
ccds_id	Consensus CDS ID. Found within the "Nucleotide resources" section of the gene symbol report.
uniprot_ids	UniProt protein accession. Found within the "Protein resource" section of the gene symbol report.
pubmed_id	Pubmed and Europe Pubmed Central PMID(s).
mgd_id	Mouse genome informatics database ID. Found within the "Homologs" section of the gene symbol report.
rgd_id	Rat genome database gene ID. Found within the "Homologs" section of the gene symbol report.
lsdb	The name of the Locus Specific Mutation Database and URL for the gene.
omim_id	Online Mendelian Inheritance in Man (OMIM) ID
orphanet	Orphanet ID
merops	ID used to link to the MEROPS peptidase database
iuphar	The objectId used to link to the IUPHAR/BPS Guide to PHARMACOLOGY database.
cd	Symbol used within the Human Cell Differentiation Molecule database for the gene
enzyme_id	ENZYME EC accession number
agr	The HGNC ID that the Alliance of Genome Resources (AGR) have linked to their record of the gene.
mane_select	NCBI and Ensembl transcript IDs/acessions including the version number for one high-quality representative transcript per protein-coding gene.
gencc	The HGNC ID used within the GenCC database as the unique identifier of their gene reports within the GenCC database.
uuid	Unique identifier (not in original description, but present in the JSON list)
rna_central_id	RNA Central ID (not in original description, but present in the JSON list)
curator_notes	Curator notes (not in original description, but present in the JSON list)
metadata_source	source of the metadata

Citation

Please cite the original dataset using the following format:

BibTeX:

@article{10.1093/nar/gkac888,
    author = {Seal, Ruth L and Braschi, Bryony and Gray, Kristian and Jones, Tamsin E M and Tweedie, Susan and Haim-Vilmovsky, Liora and Bruford, Elspeth A},
    title = "{Genenames.org: the HGNC resources in 2023}",
    journal = {Nucleic Acids Research},
    volume = {51},
    number = {D1},
    pages = {D1003-D1009},
    year = {2022},
    month = {10},
    abstract = "{The HUGO Gene Nomenclature Committee (HGNC) assigns unique symbols and names to human genes. The HGNC database (www.genenames.org) currently contains over 43 000 approved gene symbols, over 19 200 of which are assigned to protein-coding genes, 14 000 to pseudogenes and nearly 9000 to non-coding RNA genes. The public website, www.genenames.org, displays all approved nomenclature within Symbol Reports that contain data curated by HGNC nomenclature advisors and links to related genomic, clinical, and proteomic information. Here, we describe updates to our resource, including improvements to our search facility and new download features.}",
    issn = {0305-1048},
    doi = {10.1093/nar/gkac888},
    url = {https://doi.org/10.1093/nar/gkac888},
    eprint = {https://academic.oup.com/nar/article-pdf/51/D1/D1003/48441239/gkac888.pdf},
}

Dataset Card Authors

Author: dwb2023

Dataset Card Contact

Contact: dwb2023