Contents

1 CX data structure

The CX data structure can be divided into three main classes:

1.1 Aspect dependencies

Aspects with IDs:

Aspects, that reference IDs:

2 Data types

CX is a JSON based format, that means that JavaScript data types are used. Those will be mapped to and from R data types as follows:

data type example R data type
boolean “true” logical
double “2.3” numeric
integer “23” integer
long “123456” integer
string “blue” character
list_of_boolean [“true”,“false”] list(logical)
list_of_double [“2.3”,“4.5”] list(numeric)
list_of_integer [“23”,“45”] list(integer)
list_of_long [“23”,“45”] list(integer)
list_of_string [“Marco”,“Polo”] list(character)

3 NDEx conventions

3.1 Handling of Identifiers

All identifiers should be either:

  • \(\lt\)prefix\(\gt\):\(\lt\)id\(\gt\) format
  • a string without " : "
  • a URI

3.2 Citations

It is recomended to use the attribute “citation” on edges or nodes to store citations to specify literature references or other sources of information that are relevant to the network. Citations are primarily described by five dublin core terms. The “dc” prefix is implicitly interpreted as referencing dublin core in the context of the citations aspect.

The five primary dublin core terms defined for citations are:

4 Meta aspects

4.1 metaData

As a transfer format,the owner (sender) is considered to have a complete picture of the network including all metadata and aspects associated with the network. When a sender has the choice of sending an element as either pre- or post-metadata. In RCX both are combined when converting a CX file. The content a the metaData aspect is specified as:

RCX property RCX specifics CX property CX options description
name name Required in pre- and post-metadata The name of the aspect
version default:“1.0” version Required in pre-metadata version of this aspect schema (“1.1.0”, “2.0.0”, etc.)
idCounter auto-generated idCounter Required if the aspect exports IDs Integer (All Element IDs are integers; see node id, edge id, cytoscape groups)
elementCount auto-generated elementCount Optional number (integer) of elements in this aspect
consistencyGroup default:1 consistencyGroup Optional An integer identifier shared by aspects to indicate that they are mutually consistent
properties properties Optional An aspect-defined property list
- not supported checksum Optional (Deprecated) NDEx CX implementation does not support this attribute. This attribute is ignored in NDEx

4.2 status

A complete CX stream ends with a status aspect object. This aspect tells the recipient if the CX is successfully generated by the source.

Note: This aspect is auto-generated in RCX and cannot be changed!

property options values description
success Required “true” or “false” Was the CX successfully generated by the source
error Required string or "" error message or "" if sucess==“true”

5 Core aspects

5.1 nodes

RCX property CX property CX options values description
id @id Required, Unique integer CX internal id, starts at 0, exported to metaData!
name n Optional string node name, eg. “EGFR”, “node 1”
represents r Optional string represents, eg. “HGNC:AKT1”

Note: At least one node has to be present, therefore this aspect is mandatory!

5.2 edges

RCX property CX property CX options values description
id @id Required, Unique integer CX internal id, starts at 0, exported to metaData!
source s Required integer source, reference to CX internal node id
target t Required integer target, reference to CX internal node id
interaction i Optional string intercation, eg. “binds”

5.3 nodeAttributes

RCX property RCX specifics CX property options values description
propertyOf po Required integer property of, reference to CX internal node id
name n Required string attribute name, eg. “weight”, “name”, “selected”
value v Required string or list of strings attribute value(s), eg. [“2”, “0.34”, “2.3”], “Node 6”, “true”
dataType default:“string” d Optional string data type, default “string”
isList default:FALSE d Optional string If set to TRUE, the CX data type will be modified
subnetworkId default:NA s Optional integer reference to CX internal subnetwork id

5.3.1 NDEx conventions

names description
alias alternative identifiers for the node. Same meaning as BioPAX “aliases”
relatedTo identifiers denoting concepts related to the node. Same meaning as BioPAX “relatedTerms”

5.4 edgeAttributes

RCX property RCX specifics CX property options values description
propertyOf po Required integer property of, reference to CX internal edge id
name n Required string attribute name, eg. “weight”, “name”, “selected”
value v Required string or list of strings attribute value(s), eg. [“2”, “0.34”, “2.3”], “Node 6”, “true”
dataType default:“string” d Optional string data type, default “string”
isList default:FALSE d Optional boolean If set to TRUE, the CX data type will be modified
subnetworkId default:NA s Optional integer reference to CX internal subnetwork id

5.5 networkAttributes

RCX property RCX specifics CX property options values description
name n Required string attribute name, eg. “dc:title”
value v Required string or list of strings attribute value(s), eg. "Result of heat
dataType default:“string” d Optional string data type, default “string”
isList default:FALSE d Optional boolean If set to TRUE, the CX data type will be modified
subnetworkId default:NA s Optional integer reference to CX internal subnetwork id

5.5.1 NDEx conventions

names description
name the name of the network
description a description of the network
version NDEx will treat this attribute as the version of the network. Format is not controlled but best practice is to use string conforming to Semantic Versioning.
ndex:sourceFormat used by NDEx to indicate format of an original file imported, can determine semantics as well. The NDEx UI will allow export options based on this value. Applications that alter a network such that it can no longer be exported in the format should remove the value.

5.6 cartesianLayout

Cartesian layout elements store coordinates of nodes.

RCX property CX property options values description
node node Required integer reference to CX internal node id
x x Required numeric x coordinate
y y Required numeric y coordinate
z z Optional numeric z coordinate
view view Optional integer reference to CX internal reference to CX internal subnetwork id of type view

6 Cytoscape aspects

See Cytoscape Styles on how styles are created in Cytoscape. The following aspects are based on how Cytoscape defines the visual representation of networks. For further information see Using Visual Properies in RCy3, which gives an overview of how to handle Visual properties in R automation.

6.1 cyGroups

RCX property CX property options values description
id @id Required, Unique integer CX internal id, starts at 0, exported to metaData!
n n Required string name of this group
nodes nodes Optional list of integer the nodes making up the group, reference to CX internal node id
externalEdges external_edges Optional list of integer the external edges making up the group, reference to CX internal edge id
internalEdges internal_edges Optional list of integer the internal edges making up the group, reference to CX internal edge id
collapsed collapsed Optional boolean indicate whether the group is displayed as a single node

6.2 CyVisualProperties

6.2.1 CyVisualProperties (CX)

CX property options values description
properties_of Required string, dictionary to indicate the element type these properties belong to, allowed values are: “network”, “nodes:default”, “edges:default”, “nodes”, “edges”
applies_to Required integer the identifier of the element these properties apply to, reference to CX internal node id or edge id
view Optional integer reference to CX internal subnetwork id of type view
properties Optional named list of strings pairs of the actual properties, e.g. “NODE_BORDER_STROKE” : “SOLID”, “NODE_BORDER_WIDTH” : “1.5”, “NODE_FILL_COLOR” : “#FF3399”
dependencies Required named list of strings pairs of the dependencies, e.g. “nodeCustomGraphicsSizeSync” : “true”, “nodeSizeLocked” : “false”
mappings Optional named list of named list of strings, dictionary e.g. “NODE_BORDER_WIDTH” : {“type” : “DISCRETE”, “definition” : “COL=required,T=boolean,K=0=true,V=0=10.0”}

The JSON object model for the cyVisualProperties aspect is not suitable to be proper represented in R data structures, therefore it is split up into the main aspect and several sub-aspects. The R structure looks as follows:

CyVisualProperties
├──network = CyVisualProperty
├──nodes = CyVisualProperty
├──edges = CyVisualProperty
├──defaultNodes = CyVisualProperty
└──defaultEdges = CyVisualProperty

CyVisualProperty
├──properties = CyVisualPropertyProperties
│   ├──name
│   └──value 
├──dependencies = CyVisualPropertyDependencies
│   ├──name
│   └──value 
├──mappings = CyVisualPropertyMappings
│   ├──name
│   ├──type
│   └──definition 
├──appliesTo = <reference to subnetwork id>
└──view = <reference to subnetwork id>

6.2.2 CyVisualProperties (RCX)

RCX property options values description
network Optional list of CyVisualProperty represents “property_of”=“network” of CyVisualProperties
nodes Optional list of CyVisualProperty represents “property_of”=“nodes:default” of CyVisualProperties
edges Optional list of CyVisualProperty represents “property_of”=“edges” of CyVisualProperties
defaultNodes Optional list of CyVisualProperty represents “property_of”=“nodes:default” of CyVisualProperties
defaultEdges Optional list of CyVisualProperty represents “property_of”=“edges:default” of CyVisualProperties

6.2.2.1 CyVisualProperty

RCX property RCX specifics options values description
properties default:NA Optional CyVisualPropertyProperties represents “property_of”=“network” of CyVisualProperties
depencdencies default:NA Optional CyVisualPropertyDependencies represents “property_of”=“nodes:default” of CyVisualProperties
mappings default:NA Optional CyVisualPropertyMappings represents “property_of”=“edges” of CyVisualProperties
appliesTo default:NA Optional integer reference to CX internal subnetwork id
view default:NA Optional integer reference to CX internal subnetwork id of type view

6.2.2.2 CyVisualPropertyProperties

RCX property options values description
name Required string name of the property, e.g. “NODE_PAINT” or “EDGE_VISIBLE”
value Required string value of the property, e.g. “#FF0000” or “true”

6.2.2.3 CyVisualPropertyDependencies

RCX property options values description
name Required string name of the dependency, e.g. “nodeCustomGraphicsSizeSync” or “nodeSizeLocked”
value Required string value of the dependency, e.g. “true” or “false”

6.2.2.4 CyVisualPropertyMappings

The JSON objects or the form {"NODE_BORDER_WIDTH" : {"type" : "DISCRETE", "definition" : "COL=required,T=boolean,K=0=true,V=0=10.0"}} are split up as follows:

RCX property options values description
name Required string name of the property, e.g. “NODE_BORDER_WIDTH”
type Required string value of the property, e.g. “DISCRETE”
definition Required string value of the property, e.g. “COL=required,T=boolean,K=0=true,V=0=10.0”

6.3 cyHiddenAttributes

RCX property RCX specifics CX property options values description
name n Required string name of this hidden attribute
value v Required string or list of strings attribute value(s), eg. “layoutAlgorithm”
dataType default:“string” d Optional string data type, default “string”
isList default:FALSE d Optional boolean If set to TRUE, the CX data type will be modified
subnetworkId default:NA s Optional integer reference to CX internal subnetwork id

6.4 cyNetworkRelations

RCX property RCX specifics CX property options values description
child c Required integer child network, reference to CX internal subnetwork id
parent default:NA p Optional integer parent network, reference to CX internal subnetwork id
name name Optional string the name of the child network; if missing, default is reader-dependent
isView default:FALSE r Optional boolean relationship type, default “subnetwork”

6.5 cySubNetworks

RCX property CX property options values description
id @id Required, Unique integer CX internal id, starts at 0, exported to metaData!
nodes nodes Optional list of integer or “all” the nodes making up the group, reference to CX internal node id
edges edges Optional list of integer or “all” the edges making up the group, reference to CX internal edge id

6.6 cyTableColum

These elements are used to represent Cytoscape table column labels and types. Its main use is to disambiguate empty table columns.

RCX property RCX specifics CX property options values description
name n Required string name of the column; usually the different attributes of nodes, edges and networks
appliesTo “nodes”, “edges”, or “networks” applies_to Required string: “node_table”, “edge_table”, or “network_table” indicates the Cytoscape table this applies to
dataType default:“string” d Optional string data type, default “string”
isList default:FALSE d Optional boolean If set to TRUE, the CX data type will be modified
subnetworkId default:NA s Optional integer reference to CX internal subnetwork id

Note: Cytoscape does not currently support table columns for the root network, but this is option is included here for consistency

7 Deprecated aspects

property description
ndexStatus NDEx server will no longer generate this aspect from the server side. Network last updated before the v2.4.0 release will still have this aspect. Users can use the “Get Network Summary” API function to get the status and other information of a network.
citations We recommend using the attribute “citation” on edges or nodes to store citations.
nodeCitations We recommend using the attribute “citation” on nodes to store citations.
edgeCitations We recommend using the attribute “citation” on edges to store citations.
Supports We recommend using the attribute “supports” on edges or nodes.
nodeSupports We recommend using the attribute “supports” on nodes.
edgeSupports We recommend using the attribute “supports” on edges.
functionTerms No recommendations for alternative representation.
reiefiedEdges No recommendations for alternative representation.
@context We recommend using the attribute “@context” on networks. The value of this attribute is a serialized string from a JSON dictionary that has a prefix as its key and a URL as its value. @context maps terms to IRIs. Terms are case sensitive.
provenanceHistory The server will just treat this as an opaque aspect. For recording the origin and significant events of this network, we recommend to use network attributes to store them. We recommend using prov:wasGeneratedBy and prov:wasDerivedFrom for the event and the list of contributing network URLs.

Note: Starting from v2.4.0, NDEx server will no longer generate these aspects from the server side. Networks last updated before the v2.4.0 release will still have these aspects.

8 Session info

sessionInfo()
## R version 4.2.1 (2022-06-23)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 20.04.5 LTS
## 
## Matrix products: default
## BLAS:   /home/biocbuild/bbs-3.16-bioc/R/lib/libRblas.so
## LAPACK: /home/biocbuild/bbs-3.16-bioc/R/lib/libRlapack.so
## 
## locale:
##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=en_GB              LC_COLLATE=C              
##  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
##  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
##  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
## [1] BiocStyle_2.26.0
## 
## loaded via a namespace (and not attached):
##  [1] bookdown_0.29       digest_0.6.30       R6_2.5.1           
##  [4] jsonlite_1.8.3      magrittr_2.0.3      evaluate_0.17      
##  [7] stringi_1.7.8       cachem_1.0.6        rlang_1.0.6        
## [10] cli_3.4.1           jquerylib_0.1.4     bslib_0.4.0        
## [13] rmarkdown_2.17      tools_4.2.1         stringr_1.4.1      
## [16] xfun_0.34           yaml_2.3.6          fastmap_1.1.0      
## [19] compiler_4.2.1      BiocManager_1.30.19 htmltools_0.5.3    
## [22] knitr_1.40          sass_0.4.2