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Use Cases for Genes

The following use cases were developed by the Genes group.

This use cases apply to the following biological types: Gene.


As a user, I would like to find as many gene resources as possible when looking by gene entity/name/identifier (ID).


As a user, when I look for a gene, I would like to get a quick summary with information regarding gene entities. Such summary should contain at least the data sources, IDs, names and organisms for the gene entity. Additionally, it could contain alternatively spliced transcript, sequence, citations, protein structure and gene features such as genetic variants (SNPs and mutations), regulatory features (promoter regions, enhancers, transcription factor binding sites, sites for methylation):

  1. Search for a gene or transcript (to include IDs, names, synonyms)
  2. Enable discovery by indexing on free text description
  3. Enable direct access, resolution of gene entity
  4. Allow restriction to specific isoforms (alternatively spliced transcripts)
  5. Search according to a disease linked to that gene, author
  6. Allow restriction to where the gene belongs to (human, mouse – which strain, wheat, etc)

As a user, I want to be able to distinguish what is a gene, what is a transcript, whether the gene is protein coding or not, whether it is associated with diseases or other phenotypes, where it has orthologues in other species or paralogs, duplicated versions in the same organism. I also want to be able to gather genetic variation information from as many variation and genomic resources as possible; this would be useful, for instance, to create visualisation tools or to enrich other pages/databases.

The following is a non-exhaustive list of external resources containing gene related information: