Hierarchical description of a gene network structure

Gene networks have complex hierarchical structure both organism and cell levels.For formalised description of gene networks structure a special language  was developed. The syntax of this language in the Backus-Naur form is given bellow.

compartment ::= compartment

                {

                  <compartment_id>;

                  <alias>;

                  <color>;

                  <size>;

                  <shape>;

                  entities

                  {

                    <entity_list>

                  }

                  relations

                  {

                    <relation_list>

                  }

                }



compartment_id ::= <string>

alias          ::= alias=<string>

color          ::= color=<number>,<number>,<number>

size           ::= size=(<number>,<number>)

shape          ::= shape= rectangle|round_rectangle|ellipse 



entity_list ::= <entity_description>|

                <entity_list>;<entity_description>



entity_description ::= <coordinate><entity_type><entity_id>

                       |<equalence_group>

                       |<compartment>



coordinate  ::= (<number>,<number>)

entity_type ::= ‘<’cell|gene|rna|protein|process|substance‘>’

entyti_id   ::= <string> 



equalence_group ::= (<entity_id_list>) 

entity_id_list  ::= <entity_id>|<entyty_id_list>,<entity_id>



relation_list ::= <relation_id>|<relation_list>,<relation_id> 

Syntax of specialized language for hierarchical description of gene network structure.  in Backus-Naur form

Any gene network is considered as a compartment, This main compartment can contains other compartments where gene network components are located.

The description of each compartment contains its identifier (compartment_id), synonymous name (alias). Three options (color, size, and shape) specify the compartment image on the diagram.

The entities located in the compartment are described in the entity list (entity_list). The entity description (entity_description) includes the entity image coordinates on the diagram (coordinate), entity type (entity_type), and identifier (entity_id).

The child compartments (that are located inside of this parent compartment) are also described in this section. It provides hierarchical description of the gene network structure.

The proposed format allows generalizing the data obtained from different species. As a result, the diagram may contain several equivalent objects (for example, homologous genes or proteins from different species). Such equivalent entities are described as equivalence group (equivalence_group) and represented on the diagram by a single image.

At last, the relationships (relation_list) between the components of a gene network are listed.

Since the described language is rather complicated, users deals only with the graphic interfaces that allows visualize and explore (GeneNet Viewer) as well as edit (GeneNet Data Input GUI) gene network diagrams. The interfaces can generate and interpret the code in the language.