We need to manipulate our data in finely tuned ways. In order to do this, we must precisely define subgroups of our data.

It's as easy as 1, 2, 3; or, A, B, C. Just think it terms of groups of 1, groups of 2, and groups of 3.

The first three letters of the Greek Alphabet, α, β, and γ (alpha, beta, and gamma, respectively), are used to specify types of relationships between features. Refer to the image below as you read the explanations.

These Greek letters refer to how many relationships exist between certain types of features. Relationship means that two features appear to share at least some of the same space in a genome. In the image above, a relationship is represented by a red line between types of features.

• An α Feature (Alpha Feature) does not have a relationship with any other type of feature. Alpha Features form groups of 1 or α Groups (Alpha Groups). Sometimes, these types of features are referred to as singletons.
   
   
  • An α Locus (Alpha Locus) does not have any relationships with any clones. Some of the locations of α Loci are known and these loci can be placed on an MLG (Molecular Linkage Group).
     
     
  • An α Clone (Alpha Clone) does not have any relationships with any loci nor does it have any relationships with any contigs. The locations of α Clones are not known and these clones cannot be placed on an MLG.
     
     
  • An α Contig (Alpha Contig) is not defined. A contig must have a relationship with a clone in order to exist.
     
     
• A β Feature (Beta Feature) has a relationship with exactly one other type of feature. Beta Features form groups of 2.
   
   
  • A β Locus (Beta Locus) has at least one relationship with a clone, forming a group with exactly two types of features, a β Group (Beta Group). Some of the locations of β Loci are known, in which cases these loci can be placed on MLG's.
     
     
  • A β Clone (Beta Clone) has a relationship with one or more loci, or else it has a relationship with a contig. However, a β Clone does not have relationships with both a locus and a contig. A β Clone forms a group which consists of exactly two types of features, a β Group (Beta Group).
     
     
    • A β₁ Clone (Beta 1 clone) is a β Clone which has a relationship with one or more loci. A β₁ Group (Beta 1 Group) is a group with a locus and a clone. If the location of a β Locus is known, its corresponding β Clone can also be placed.
       
       
    • A β₂ Clone (Beta 2 Clone) is a β Clone which only has a relationship with a contig. A β₂ Group (Beta 2 Group) is a group with a clone and a contig. A β₂ Clone may or may not be able to be placed on an MLG. See Extended Ontology (once it is written) for more information.
       
       
  • A β Contig (Beta Contig) has a relationship with one or more clones, none of which clones have any relationships with any loci. A β Contig forms a group which consists of exactly two types of features, a β Group (Beta Group). A β Contig cannot be placed on an MLG.
     
     
• A γ Feature (Gamma Feature) has relationships, either directly or indirectly, with exactly two other types of features. Gamma Features form groups of 3. All γ Features can be placed on MLG's.
   
   
  • A γ Locus (Gamma Locus) has a relationship with at least one clone which itself has a relationship with a contig, forming a group of exactly three types of features, a γ Group (Gamma Group).
     
     
  • A γ Clone (Gamma Clone) has a relationship with one or more loci and this clone also has a relationship with a contig, forming a group of exactly three types of features, a γ Group (Gamma Group).
     
     
  • A γ Contig (Gamma Contig) has a relationship with one or more clones, at least one of which clones has a relationship with at least one locus, forming a group of exactly three types of features, a γ Group (Gamma Group).
     
     

Resolution of Conflicts. This notation has two apparent conflicts which can be resolved:

• A locus can be in both β and γ groups. It is possible for a locus to be in a γ Group, but also have a relationships with a β₁ Clone. This conflict is resolved by order of importance: A γ Group is more important than a β Group, so the locus in this situation is called a γ Locus. The result of this determination is that it is possible for a β₁ Clone to have a relationship with a γ Locus.
• A contig can be in both β and γ groups. It is possible for a contig to be in a γ Group, but also have a relationship with a β₂ Clone. This conflict is resolved by order of importance: A γ Group is more important than a β Group, so the contig in this situation is called a γ Contig. The result of this determination is that it is possible for a β₂ Clone to have a relationship with a γ Contig.

Soybean Genome Basic Data Sets

Let Σ Features mean all of the features under consideration; Σ Loci mean all of the loci under consideration; Σ Clones mean all of the Clones under consideration; and Σ Contigs mean all of the contigs under consideration.

• Σ Features = Σ Loci ∪ Σ Clones ∪ Σ Contigs
  • Σ Loci ∩ Σ Clones = Ø
  • Σ Loci ∩ Σ Contigs = Ø
  • Σ Clones ∩ Σ Contigs = Ø
• Σ Loci = α Loci ∪ β Loci ∪ γ Loci
  • α Loci ∩ β Loci = Ø
  • α Loci ∩ γ Loci = Ø
  • β Loci ∩ γ Loci = Ø
• Σ Clones = α Clones ∪ β Clones ∪ γ Clones
  • α Clones ∩ β Clones = Ø
  • α Clones ∩ γ Clones = Ø
  • β Clones ∩ γ Clones = Ø
    • β Clones = β₁ Clones ∪ β₂ Clones
      • β₁ Clones ∩ β₂ Clones = Ø
• Σ Contigs = α Contigs ∪ β Contigs ∪ γ Contigs
  • α Contigs = Ø
  • β Contigs ∩ γ Contigs = Ø

The above set equations do not display properly on all browsers. Here is an image of the same equations so that you can be sure that you are getting the correct information.

Extended Ontology

The basic ontology can be extended to make even finer distinctions between types of features. As the image below illustrates, β Groups can have indirect relationships with other β Groups and with γ Groups. This possibility further differentiates β Loci, β₁ Clones, and β₂ Clones.

β Groups with relationships to other β Groups are indicated with single primes. In the cluster where a β Locus has a relationship with a β₁ Clone which, itself, has a relationship with another β Locus, they are designated as two β' Loci and a β'₁ Clone. An illustration of this is at the top of the above figure. Likewise, in a cluster where a β₁ Clone has a relationship to a β Locus which, itself, has a relationship with another β₁ Clone, they are designated as two β'₁ Clones and a β' Locus.

β Groups with relationships to γ groups are indicated with double primes as indicated at the lower part of the above figure. β Groups in this situation are indicated as β'' Loci, β''₁ Clones, and β''₂ Clones.

Soybean Genome Extended Data Sets

Let Σβ Loci mean all of the β Loci under consideration; Σβ₁ Clones mean all of the β₁ Clones under consideration; and Σβ₂ Clones mean all of the β₂ Clones under consideration.

• Σβ Loci = β Loci ∪ β' Loci ∪ β'' Loci
  • β Loci ∩ β' Loci = Ø
  • β Loci ∩ β'' Loci = Ø
  • β' Loci ∩ β'' Loci = Ø
• Σβ₁ Clones = β₁ Clones ∪ β'₁ Clones ∪ β''₁ Clones
  • β₁ Clone ∩ β'₁ Clone = Ø
  • β₁ Clone ∩ β''₁ Clone = Ø
  • β'₁ Clone ∩ β''₁ Clone = Ø
• Σβ₂ Clones = β₂ Clones ∪ β'₂ Clones ∪ β''₂ Clones
  • β₂ Clone ∩ β'₂ Clone = Ø
  • β₂ Clone ∩ β''₂ Clone = Ø
  • β'₂ Clone ∩ β''₂ Clone = Ø