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Exporting to the Simple Interaction Format (SIF)

Introduction:

By default, all interaction networks and pathways in Pathway Commons are stored in the BioPAX exchange format. However, a number of web service commands, including get_neighbors and get_record_by_cpath_id, support the export of interaction networks to the Simple Interaction Format (SIF). SIF was originally created for use with Cytoscape, the open source bioinformatics software platform for visualizing molecular interaction networks. SIF is simple to parse, and easy to load into Cytoscape and other third-party applications.

SIF Format:

The SIF export from Pathway Commons is formatted as:

physical_entity_id <relationship type> physical_entity_id

where physical_entity_id is a valid primary ID in Pathway Commons, and <relationship type> is one of the interaction inference rules specified below.

Inference Rules:

It is not possible to fully translate a BioPAX formatted network (which is capable of storing rich biological semantics, including multi-participant relationships) into a SIF binary network (which is only capable of storing pairwise interactions between physical entities). We therefore infer pairwise SIF relationships from more complex BioPAX relationships using a set of rules. In general, this translation is lossy. Nonetheless, this SIF network remains useful for certain types of bioinformatic applications that require pairwise interaction input.

For those commands that support SIF export, users can specify an optional binary_interaction_rule argument. This is a comma separated list of inference rules (see table below) that are applied when binary interactions are requested. If not specified, all binary interaction rules will be applied.

binary_interaction_rule	Original BioPAX Interaction	Inferred Set of Pairwise Interaction
COMPONENT_OF: The first entity is a component of the second entity, which is a complex. This interaction is transient in the sense that A component_of B and B component_of C implies A component_of C. This interaction is directed.

CO_CONTROL: This rule infers an interaction if the first and second entities have control over the same process. This interaction is undirected.

INTERACTS_WITH: The entities participate in an interaction. Controllers are not included. This interaction is undirected.

IN_SAME_COMPONENT: Two entities belong to the same molecular complex. This does not necessarily mean they interact directly. In a complex with n molecules, this rule will create a clique composed of n(n-1)/2 interactions. This interaction is undirected.

METABOLIC_CATALYSIS: The first entity catalyzes a reaction that either consumes or produces the second entity. This interaction is directed.

REACTS_WITH: The entities participate in a conversion as substrates or products. Controllers are not included. This interaction is undirected.

SEQUENTIAL_CATALYSIS: The entities catalyze two conversions that are connected via a common molecule, e.g. the first entity produces a substrate that is consumed by the second entity. This interaction is directed.

STATE_CHANGE: The first entity controls a reaction that changes the state of the second entity, e.g. by phosphorylation or other posttranslational modification, or by a change in subcellular location. This interaction is directed.

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Retrieving Physical Entity Details:

In the SIF export defined above, physical entities are identified with physical_entity_id(s), and not with standard gene names or external identifiers. To retrieve the identity of each physical entity, you must make a Pathway Commons and use the get_record_by_cpath_id. In this case, you specify one or more internal IDs, and set output=biopax. This enables you to retrieve the full physical entity information, in BioPAX format.