dwb2023/uniprot_gene_lookup

Dataset Card for UniProt Gene Lookup

Dataset Details

Dataset Description

This dataset is a lookup table of gene information curated from the reviewed entries of UniProtKB/Swiss-Prot. The dataset contains the protein-coding gene data, curated by expert biocurators to ensure high-quality and experimentally validated information. It is designed to assist researchers in mapping genes to corresponding protein sequences, functional annotations, and associated metadata.

• Curated by: The UniProt Consortium (European Bioinformatics Institute (EBI), Georgetown University, University of Delaware, Swiss Institute of Bioinformatics (SIB)).
• Language(s) (NLP): Not applicable (This dataset focuses on biological data).
• License: Creative Commons Attribution 4.0 International (CC BY 4.0)【7†source】.

Dataset Sources

• Repository: UniProtKB (Query: reviewed:true).
• Paper: "UniProt: the Universal Protein Knowledgebase in 2023," Nucleic Acids Research, Vol. 51, D523–D531【7†source】.
• Demo: Not available.

Uses

Direct Use

This dataset is suitable for biological research, particularly in bioinformatics, genomics, and proteomics. It can be used for gene annotation, protein function prediction, and understanding gene-protein relationships.

Out-of-Scope Use

This dataset may not be suitable for natural language processing tasks or non-biological fields. Misuse could include applications that do not consider the scientific validity or limitations of the curated gene annotations.

Dataset Structure

The dataset is structured as a tab-separated values (TSV) file containing gene identifiers, protein sequences, functional annotations, and associated metadata.

Dataset Creation

Curation Rationale

This dataset was created to provide researchers with a high-quality resource for gene-to-protein mapping, emphasizing experimentally verified annotations. It helps streamline bioinformatics workflows by providing reliable data that reduces the need for extensive literature searches.

Source Data

Data Collection and Processing

The data was collected from UniProtKB/Swiss-Prot, the reviewed section of UniProt. The dataset is curated by expert biocurators who continuously update it based on new scientific literature and computational predictions.

Who are the source data producers?

The source data producers include the UniProt Consortium, which integrates biological knowledge from multiple external resources and community contributions.

Bias, Risks, and Limitations

This dataset may have limitations in terms of coverage for less-studied organisms or gene variants that have not been experimentally validated. Researchers should consider potential biases in gene annotations, especially for organisms with fewer studies.

Recommendations

Researchers are advised to cross-check the dataset with the latest scientific literature and use it as a supplementary tool rather than a definitive source for gene annotations.

Citation

Please cite the dataset using the following BibTeX:

@article{UniProt2023,
  author = {The UniProt Consortium},
  title = {UniProt: the Universal Protein Knowledgebase in 2023},
  journal = {Nucleic Acids Research},
  year = {2023},
  volume = {51},
  number = {D1},
  pages = {D523--D531},
  doi = {10.1093/nar/gkac1052},
  url = {https://www.uniprot.org/uniprotkb?query=reviewed:true}
}

Dataset Card Authors

• Don Branson

Dataset Card Contact

• dwb2023