Trace an interaction declared in EXTENDED_BINARY_SIF to the BioPAX description, visualize the BioPAX representation in the form of a network, and identify the source database record. This gist crosses many aspects of the tools and services offered through Pathway Commons.
This is aimed at a computational audience. If you know what SIF is and you have used curl you should be fine. It would help if you are familiar with BioPAX although this is not essential.
- Access to a command line terminal to run curl
- Chisio BioPAX Editor (ChiBE)
- Desktop application installation required
- sample_extended.sif - An excerpt of an EXTENDED_BINARY_SIF formatted file with a single interaction between RNF14 and UBE2D1
- chibe_biopax.png - Screenshot of the ChiBE rendering of BioPAX for the RNF14-UBE2D1 interaction MEDIATOR_IDS entry
- reactome_pathway.png - Screenshot of the Reactome pathway correspondind to the MEDIATOR_IDS entry
In sample_extended.sif, locate the last column with header MEDIATOR_IDS:
| PARTICIPANT_A | INTERACTION_TYPE | PARTICIPANT_B | PATHWAY_NAMES | ... | MEDIATOR_IDS |
|---|---|---|---|---|---|
| RNF14 | neighbor-of | UBE2D1 | Adaptive Immune System;... | ... | http://identifiers.org/reactome/R-HSA-983157;... |
This contains a set of URIs that represent the Pathway Commons identifier (aka 'ID') of the interaction (or sub-class e.g. MolecularInteraction, Conversion, Control) in BioPAX. Briefly, Pathway Commons detects several common network or pathway patterns in BioPAX and reduces them to SIF. Examine the first URI:
http://identifiers.org/reactome/R-HSA-983157
In this case, the ID in the form of a URI is a URL in that it resolves to a resource (web page) in Reactome. This might not be true of IDs in general.
We will use the Pathway Commons web service from the command line. Perform a GET request
$ curl http://beta.pathwaycommons.org/pc2/get?uri=http://identifiers.org/reactome/R-HSA-983157 > r_hsa_983157.owl You should see something like the following output:
<?xml version="1.0" encoding="UTF-8"?>
<rdf:RDF
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
xmlns:owl="http://www.w3.org/2002/07/owl#"
xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
xmlns:bp="http://www.biopax.org/release/biopax-level3.owl#"
xml:base="http://purl.org/pc2/8/">
<owl:Ontology rdf:about="">
<owl:imports rdf:resource="http://www.biopax.org/release/biopax-level3.owl#" />
</owl:Ontology>...BioPAX is implemented in OWL so we save the body of our request to a file ending in
.owl
We recommend using Chisio BioPAX Editor (ChiBE) which is a desktop editor specifically designed for viewing and editing BioPAX.
Loading the BioPAX output into ChiBE results in the rendering of the associated network show in chibe_biopax.png. This is a rich representation of a multitude of genes, complexes, and processes. In particular, highlighted in the image is RNF14 as part of a set of E3-Ubiquitin-ligases that interact with E2-Ubiquitin complex (containing UBE2D1).
This example highlights the lossy nature of BioPAX to SIF!
The translation from BioPAX to SIF was performed based on an interaction of two complexes involving RNF14 and UBE2D1. In ChiBE, clicking on the higlighted square linking the two complexes displays a record of type Biochemical Reaction with a Reference to a Reactome record. The associated 'Location in Pathway Browser' can be followed to show a record for Interaction of E3 with substrate and E2-Ub complex(Homo sapiens). Clicking this link displays the pathway as in reactome_pathway.png.
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