Skip to main content

Table 1 Term definitions used in the paper

From: Metabolic and signalling network maps integration: application to cross-talk studies and omics data analysis in cancer

Graphical standards and exchange formats
 XML format Markup language that defines a set of rules for encoding documents used to store and transport data by describing the content in terms of what data is being described.
 SBGN Systems Biology Graphical Notation (SBGN) is a standard graphical syntax for representation of biological processes and interactions. SBGN is compatible with multiple pathway drawing and analytical tools,
 SBML Systems Biology Markup Language (SBML) is a representation format, based on XML, for communicating and storing computational models of biological processes. It is a free and open standard language with widespread software support,
 Standard identifier (ID) Community-accepted nomenclature for scientific naming of biomolecules as genes, proteins, chemicals, drugs etc. The sources for standard IDs are repositories as UNIPROT, CHEB, HUGO,
 Data and models exchange formats Standard formats for data and models to facilitate networks and software intercompatibility. There are two major standard networks exchange formats, BIOPAX for complex networks and SIF for simple binary interactions. The CellDesigner xml format is a commonly-used exchange format compatible with multiple network analysis tools.
Signalling and metabolic network map
 Map Diagram of detailed molecular interactions with meaningful layout reflecting a certain biological process, which is graphically represented in CellDesigner tool.
 Map module (in ACSN) Part of the map representing a sequence of molecular interactions responsible for execution of a particular function.
 Metabolic pathway Subsystem (in ReconMap 2.0) Set of reactions forming a metabolic function.
Set of metabolic reactions associated to (representing) a specific metabolic pathway.
 Map node Graphical representation of a molecule on the map.
 Map entity and alias Unique representation of a molecule on the map. As each molecule can be present multiple times on a map, each individual representation is called an alias of the entity. This definition corresponds to the CellDesigner feature.
Networks merging procedure
 Voronoi cell Individual shape allocated to a seed from the Voronoi method. Each cell is a space that contains only the seed and can be used to generate points inside without overlapping with close seeds.
 Voronoi tessellation A partitioning of a plane into regions based on distance to points in a specific subset of the plane. That set of points (called seeds) is specified beforehand, and for each seed there is a corresponding region consisting of all points closer to that seed than to any other. These regions are called Voronoi cells. In our case, each seed is a molecule or a reaction’s central glyph.
 Centroid Barycenter of a cluster.
 Merging function of BiNoM Function allowing taking two or more CellDesigner maps and merging them in one unique map. This function modifies each entities’ id and alias but keeps the name, coordinates and notes.
 Semantic zoom A mechanism providing several map views with different levels of details depiction achieved by gradual exclusion of details while zooming out. It simplifies navigation through large maps of molecular interactions by providing several levels of details, resembling navigation through geographical maps. Exploring the map from a detailed toward a top-level view is achieved by gradual exclusion and modification (simplification and abstraction) of details. One of the main principles of semantic zooming is in that every detail which is shown on the map at a current zoom level, should be readable.
 Marker Symbol indicating location of chosen objects on the map; adapted from Google maps.
 Pop-up bubble Small window that opens by clicking on marker. Contains short description and hyperlinks related to the marked entity.
 Annotation post Detailed map entity annotation created in CellDesigner by map manager. The annotation is converted to Annotation post and displayed in the associated blog by NaviCell.