The simple interaction format is convenient for building a graph from a list of interactions. It also makes it easy to combine different interaction sets into a larger network, or add new interactions to an existing data set.
A . If a tab ‘\t' character is found in the first line of the file. The SIF is treated as tab delimited, otherwise it is parsed as a whitespace delimited file.
B . In NDEx, each line in a SIF network file is mapped to a NDEx edge object. The "relationship type" field in that line maps to the predicate of that edge. Each edge has one source node and one or more target nodes depend on the number of target nodes in that line.
C . Each node field in the SIF file is mapped to an NDEx node object. If the value of the "node field" is a URI or CURIE formated string, the NDEx server will create a BaseTerm object based on the string and then create a Node to represent that base term. If the value of the "node field" is a simple literal text, no BaseTerm will be created, only a Node will be created and the "name" attribute of the node will have the value of the "node field".
D . If the SIF file is an Extended Binary SIF file, a header line will define columns that are treated in the following manner:
1 . the "INTERACTION_PUBMED_ID" field will be used to create linked Citation objects.
2 . "PARTICIPANT_NAME" field will be used to populate the "name" attribute of the node.
3 . "UNIFICATION_XREF" field will be used to create an alias of a node.
4 . "RELATIONSHIP_XREF" field will be used to create related terms of a node.
5 . The "NAME" field in the Extended Binary SIF Property header will be use to set the name of the network. "ORGANISM" and "URI DATASOURCE" are treated as properties of the network.
OpenBEL (www.openbel.org) is the public standard for the BEL language. It is designed to represent scientific findings by capturing causal and correlative relationships in context, where context can include information about the biological and experimental system in which the relationships were observed, the supporting publications cited and the curation process used.
A BEL document is a set of statements represent specific assertions from cited information resources. Statements are, in most cases, triples with context annotations. The most common type of context annotation are specialized structures to cite specific supporting evidence from knowledge sources, but a more general mechanism allows the annotation of biological contexts such as species, cell type, or cell line. When encoded as a network, a BEL document may have multiple edges of the same type between two nodes, each edge representing a different assertion from a different citation.
BEL documents are not primarily intended as a format for biological inference, but rather as a means to store reusable facts in a form that is well suited to the assembly of purpose-built biological models. Assembly can be automated or may be the result of manual selection and incorporation of findings to produce a specialized model. The choice of assembly algorithm and parameters will lead to different output models for the same input BEL documents.
A particular form of assembled biological model suitable for some types of qualitative causal reasoning and for visualization is the "Knowledge Assembly Model" (KAM). NDEx networks are in principle capable of expressing KAM structures, but as of NDEx v1.2, there are no examples of KAMs in NDEx.
BEL is distinct from many other biological representation schemes in that it employs a system in which all concepts referenced in statements, such as protein abundances, complexes, modified proteins, or reactions are represented by functional composition of terms. This system is supported directly in NDEx networks using FunctionTerm network elements.
BEL documents are expressed in:
– XBEL, an XML format.
– BELScript, a line-oriented text format designed for human readability and composition.
– BEL RDF
NDEx currently supports import and export utilities for XBEL. The following section describes the rules used to transform BEL documents to and from NDEx Networks and XBEL .
XBEL is an XML format in which XML nodes representing BEL statements are grouped by nested nodes that set the biological and citation context annotations for each statement that they contain. The context annotations from outer contexts apply to the statements of inner contexts unless specifically contradicted by annotations in inner contexts.
The following rules are applied based on the type of XML node processed:
name, description and version are mapped to Network.name, Network.description and Network.version respectively.
"copyright", "contactInfo" and "Disclaimer" are stored as network properties.
Author list in AuthorGroup are flattened and each author name is stored as an individual property in the network. LicenseGroup is stored in the similar way.
NamespaceGroup
Elements are stored as Namespace objects in NDEx network.
annotationDefinitionGroup
internalAnnotationDefinition
the "id" attribute is mapped to a Namespace object.
"description" and "usage" are stored as properties in the Namespace object.
"listAnnotation" elements are flattened and stored as properties in the Namespace object.
annotationDefinitionGroup
Each element is stored as a Namespace object in the Network.
statementGroup
If element "name" or "comment" exists in statement group.
if a citation exists in the annotationGroup at the same level, "name" and "comment" are treated as properties of the citation.
if a support exists in the annotationGroup at the same level, "name" and "comment" are treated as properties of the support.
otherwise "comment" are stored as properties for each statement in the current statementGroup and it will be also passed on to the next level of statementGroup. "name" will be ignored in this case.
annotationGroup
evidence is mapped to a Support object in the Network.
citation is mapped to a Citation object in the Network.
annotations are stored as NDExPropertyValuePair objects on each edge (or node if the statement is mapped to a orphan node).
statement
Case 1: statement has subject, object, and predicate
statement maps to NDEx Edge element
Case 2: statement does NOT have object
statement maps to NDEx Node element
node may be an "orphan" with no edges, or possibly other edges will reference the node.
Case 3: statement object is a statement expression, S2
statement object is encoded by a node that represents a ReifiedEdgeTerm
The ReifiedEdgeTerm references an edge that is created based on S2
A comment attribute of a statement is stored as a property of the Network element that it is mapped to, i.e. either an edge or node.
The XGMML standard is defined by the Cytoscape application. The version of XGMML exported by different versions of Cytoscape are annotated with version strings. The current version of Cytoscape produces an XML document in which the <graph> element has a property of cy:documentVersion="3.0″
Properties of a network in XGMML are stored in several places within the document. Some of these properties are shared by all XGMML files.
The main <graph> element has the following properties in XGMML 3.0:
The <graph> element also has these constant properties, common to all XGMML 3.0 files. Note that the URI for the XGMML namespace does not respond as of the NDEx v1.2 release.
Within the <graph> element is an attribute: <att name="networkMetadata"> This contains RDF that expresses properties of the network using standard ontologies, especially Dublin Core. Properties typically include:
An XGMML network may have additional attribute <att> elements within the <graph> element.
In XGMML 1.1, a number of graphics properties of the entire network are expressed as attributes, such as
<att type="real" name="GRAPH_VIEW_ZOOM" value="0.41322728443244305″/>
In XGMML 3.0, a separate <graphics> element within the <graph> element separates the graphic <att> elements of the network from other attributes.
XGMML->NDEx
NDEx->XGMML
NDEx uses BioPAX paxtools to parse each imported BioPAX network into an org.biopax.paxtools.model.Model object, and then transforms the Paxtools Model object into an NDEx network.
Translation Rules: