Table 1 Glossary

is-a relationship

The subsumption relationship underlying the hierarchy of an ontology is called is-a relationship

A hierarchical is-a relationship connecting the concept Regulatory Gene to the concept Gene in Fig. 1a

Lateral relationship

The non-hierarchical semantic relationship is called lateral relationship, in contrast to the hierarchical is-a relationship. It is called “role” in NCIt and “attribute relationship” in SNOMED CT

The NCIt concept Antigen Gene in Fig. 1a is defined by its lateral relationship (or role) Gene Plays Role In Process with the value Immune Response Process

Area

An area is a group of all the concepts having exactly the same set of lateral relationship types

Figure 1b has an area colored in blue and labeled as Gene Plays Role In Process, summarizing four concepts

Partial-area

A partial-area is a subunit in an area defined by a root concept describing the semantic of the partial-area, including also its all descendant concepts within the area sharing the same semantic

Figure 1c has a partial-area labeled as Antigen Gene (4) in the right blue area

Small partial-area

A partial-area is small if its size is not larger than a bound b, where b is a small number, typically lower or equal to 10

The partial-area MicroRNA Gene (2) in the left blue area in Fig. 1c is a small partial-area with size 2