In GeneNetwork (GN), data is grouped into specific discrete categories. Let's dive into the currently implemented scheme:

• Species: This category groups data based on different species, like humans, mice, or plants.
• Set/Group (InbredSet): This groups data according to a group of genetically similar organisms.
• DatasetType: This classifies data according to it's type. There are three main types: Genotypes, Molecular Traits, and Phenotypes.

The aforementioned classification scheme is inspired by GN's menu structure which forms the skeleton of the proposed classification. You can query metadata about this classification: "gn:ResourceClassificationScheme". This classification scheme has 3 levels:

• gnc:DatasetType
• gnc:Set
• gn:Species

Here's a depper look at each level:

• gnc:DatasetType: This level encompasses subcategories like "gnc:Probeset," "gnc:Genotype," and "gnc:Phenotype."
• gnc:Set: This level includes all the members listed in the InbredSet table.
• gn:Species: This level consists of all the members from the Species table.

The beauty of this system is that most of the resources in GN can be accurately categorized using it. Instead of using specific properties like "gnt:belongsToSpecies" or "gnt:belongsToSet," we can utilize the xkos[0] approach. For instance, to classify a resource, we can use the concept of xkos and apply the relationship "xkos:classifiedUnder." Here's an example of a resource that has been classified:

gn:Gtexv8_sto_0220 xkos:classifiedUnder gnc:Probeset .
gn:Gtexv8_sto_0220 xkos:classifiedUnder gn:setGtex_v8

This means that the resource "gn:Gtexv8_sto_0220" is classified under the category "gnc:Probeset" and also under the set "gn:setGtex_v8."

To query this classification using SPARQL, we can use the following code snippet:

PREFIX xkos: <http://rdf-vocabulary.ddialliance.org/xkos#>
PREFIX gnc: <http://genenetwork.org/category/>
PREFIX gn: <http://genenetwork.org/id/>

SELECT * WHERE {
  gn:Gtexv8_sto_0220 xkos:classifiedUnder ?datasetType .
  gn:Gtexv8_sto_0220 xkos:classifiedUnder ?set .
  gnc:DatasetType skos:member ?datasetType .
  gnc:Set skos:member ?set .
}

• [0] XKOS: An SKOS extension for representing statistical classifications.

• Classification Scheme

• DataSet Types

• Species

• Set