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Nomenclature

cannin edited this page Jun 10, 2016 · 1 revision

In order to decrease confusion when talking about SBGN, it is important to use a consistent nomenclature. The following describes what should currently be used.

Language versus notation

SBGN specifications propose symbols, ways to organise them, but also semantic rules to analyse the resulting representations. SBGN "drawings" can be translated into English, but also into computer readable formats. Those specifications really propose true languages. SBGN is therefore made up of three languages.

What are the languages?

PD is a language that permits the description of all the processes taking place in a biological system. The ensemble of all these processes constitute a Description.

ER is a language that permits the description of all the relations involving the entities of a biological system. The ensemble of all these relations constitute a Relationship.

AF is a language that permits the description of the flow of activity in a biological system.

Nomenclature

The three languages of SBGN should be referred to as:

  • the Process Description language
  • the Entity Relationship language
  • the Activity Flow language

abbreviated as:

  • the PD language
  • the ER language
  • the AF language

A specific representation of a biological system in one of the SBGN languages should be referred to as:

  • a Process Description map
  • an Entity Relationship map
  • an Activity Flow map

abbreviated as

  • a PD map
  • an ER map
  • an AF map

The corpus of all SBGN representations should be referred to as:

  • Process Descriptions
  • Entity Relationships
  • Activity Flows

The capitalization is important. PD, ER and AF are names of languages. As such they must be capitalized in English. This is not the case of the accompanying noun (language or map).

Graph, diagram or map?

A graph is a very technical term that belongs to mathematics and is uncommon in biology. Diagram is a concept that encompasses more than just graph. Examples are Venn diagrams for instance. Therefore, we recommend using the term map for SBGN representations. Those representations effectively permit users to travel and orient themselves in a biological system. Map is also the term most frequently used by the different communities, whether in metabolism, signaling or genomics.

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