Edit this page | Blame

Types of Data in GeneNetwork


  • assigned:
  • priority:
  • status: open
  • type: documentation
  • keywords: gn-uploader, uploader, genenetwork, documentation, doc, docs, data, data type, types of data


There are five (5) main types of data in GeneNetwork

  • Classical Phenotypes (PublishData)
  • High Content Data
  • Genotype Data
  • Cofactors and Attributes
  • Metadata

Classical Phenotypes

This is usually low-content data e.g. body weight, tail length, etc.

This is currently saved in the `Publish*` tables in the database.

This data is saved as is i.e. not log-transformed

High Content Data

This includes mainly molecular data such as

  • mRNA assay data
  • genetic expression data
  • probes
  • tissue type and data

These data are saved in the `ProbeSet*` database tables (and other closely related tables like the `Tissue*` tables - fred added this: verify).

These could be saved in the database in a log-tranformed form - verify.

How do you check for log-transformation in the data?

Genotype Data

This is core data, and all other data seem to rely on its existence.

Useful for:

  • correlations, cofactor and PheWAS computations.
  • mapping purposes
  • search and display
  • editing and curation

Cofactors and Attributes

This data can be alphanumeric (mix of numerical and non-numerical) data.

It is not intended for mapping.


This data should (ideally) always accompany any and all of the data types above. It provides contextual information regarding the data it accompanies, and is useful for search, and other contextualising operations.

It is alphanumeric data, and mostly cannot be used for numeric computations.

(made with skribilo)