#Cytoscape supported file type manual
Assembly can be automated or may be the result of manual selection and incorporation of findings to produce a specialized model. 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.īEL 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. 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. Statements are, in most cases, triples with context annotations. 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.Ī BEL document is a set of statements represent specific assertions from cited information resources. OpenBEL ( is the public standard for the BEL language. "ORGANISM" and "URI DATASOURCE" are treated as properties of the network. The "NAME" field in the Extended Binary SIF Property header will be use to set the name of the network. "RELATIONSHIP_XREF" field will be used to create related terms of a node.ĥ. "UNIFICATION_XREF" field will be used to create an alias of a node.Ĥ. "PARTICIPANT_NAME" field will be used to populate the "name" attribute of the node.ģ. the "INTERACTION_PUBMED_ID" field will be used to create linked Citation objects.Ģ. If the SIF file is an Extended Binary SIF file, a header line will define columns that are treated in the following manner:ġ. 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".ĭ. 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. Each node field in the SIF file is mapped to an NDEx node object. Each edge has one source node and one or more target nodes depend on the number of target nodes in that line.Ĭ. The "relationship type" field in that line maps to the predicate of that edge. In NDEx, each line in a SIF network file is mapped to a NDEx edge object. The SIF is treated as tab delimited, otherwise it is parsed as a whitespace delimited file.ī.
If a tab ‘\t' character is found in the first line of the file. It also makes it easy to combine different interaction sets into a larger network, or add new interactions to an existing data set.Ī.
The simple interaction format is convenient for building a graph from a list of interactions. It is maintained by the NDEx Server and currently cannot be changed by the user.Each network has a "sourceFormat" attribute that records the format in which it was imported or otherwise created.Handling of Network File Formats For All Network Types
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