Interaction Exporter

This project infers interactions between molecules from reactome.org database.

Introduction

The Reactome database does not primarily focus on molecular interactions, but such data can be derived from the molecular reactions and complexes annotated.

Two molecules are reported as interactors, if:

1. they are components of the same complex/polymer
2. they are inputs of the same reaction
3. one of them is the catalyst of a reaction and the other one is an input of that reaction.

Interactions are not oriented: if a interacts with b, then b interacts with a, so only one interaction is exported. However, duplicated interaction can appear since uniqueness is only warranted at the level of Reactome stable identifiers. If two Reactome objects with different stable identifiers point to the same protein, it is not considered as duplicated.

Installation

Download the source code

git clone https://github.com/reactome/interaction-exporter.git

Use maven to create the executable

mvn clean package -f pom.xml

A target/interaction-exporter-exec.jar will be created.

Usage

java -jar interaction-exporter-exec.jar [--help] 
	(-h|--host) <host> (-b|--port) <port> (-u|--user) <user> (-p|--password) <password>
	(-o|--output) <output>
	[(-m|--maxUnitSize) <maxUnitSize>] 
	[(-s|--species) <species>] [(-O|--object) <object>]
	[(-t|--simpleEntitiesPolicy)  <simpleEntitiesPolicy>]
	[(-v|--verbose)[:<verbose>]]

Parameters

name	flag	description
help	--help	prints the help
host	-h, --host	The neo4j host (default: localhost)
port	-b, --port	The neo4j port (default: 7474)
user	-u, --user	The neo4j user (default: neo4j)
password	-p, --password	The neo4j password (default: neo4j)
max unit size	-m, --maxUnitSize	The maximum size of complexes/sets from which interactions are considered significant. (default: 4)
species	-s, --species	1 or more species from which the interactions will be fetched. ALL to export all of the species (default: Homo sapiens)
object	-O, --object	1 or more objects to export interactions under these objects, species will be ignored.
simple entities policy	-t, --simpleEntitiesPolicy	Set if simple entities are exported as well: ALL, NONE or NON_TRIVIAL. (default: NON_TRIVIAL)
output prefix	-o, --output	Prefix of the output files
verbose	-v, --verbose	Requests verbose output

Note

The "output prefix" is used to concatenate the provided filename with two extensions: ".psi-mitab.txt" and ".tab-delimited.txt". Therefore, when the output parameter is

-o path/to/folder/filename

There will be two files generated in the folder: "filename.psi-mitab.txt" and "filename.tab-delimited.txt".

Methods

To see a detailed explanation of how we extract interactions from Reactome see the wiki: https://github.com/reactome/interaction-exporter/wiki/Methods

PSI-MITAB output

Results are exported using PSI-MITAB version 27 (https://github.com/HUPO-PSI/miTab/blob/master/PSI-MITAB27Format.md).

column	name	multiplicity	value, as (db):(id):(text)	source
1, 2	interactor unique identifier	1	(ChEBI, reactome, uniprotkb):(*)	uniprotkb for proteins, ChEBI for small molecules, reactome as default
3, 4	interactor alternative identifiers	0..*	(*):(*)	any other identifier
5, 6	interactor aliases	0..*	(reactome):(*):(name)	entity.names if !name.contains("\n") && !name.contains(":")
7	interaction detection methods	1	(psi-mi):(MI:0364):(inferred by curator)	constant
8	first author	1..*	(*)	context.literatureReferences.author, by default Fabregat et al. (2015)
9	publication identifier	1..*	(*)	context.literatureReferences.pubmedIdentifier. By default pubmed:24243840
10, 11	interactor taxonomy	1..*	(taxid):(*)	interactor.species
12	Interaction types	1	(psi-mi):(*):(*)	physical for complex/polymer/inputs, reaction.catalyst.activity for reactions
13	Source databases	1	(psi-mi):(MI:0467):(reactome)	constant
14	Interaction identifiers	1	(reactome):(*)	context.stId
15	Confidence score	1	(reactome-score):(*)	0.4 if context is inferred, otherwise 0.5
16	Complex expansion	0..1	(psi-mi):(MI:1061):(matrix expansion)	matrix expansion for complex/polymer/input. empty for catalyst interactions
17, 18	Biological roles	1	(psi-mi):(MI:0499, MI:0501, MI:0502):(enzyme, enzyme target, unspecified role)	unspecified for complex/polymer/inputs. enzyme/enzyme target for catalyst/input pairs
19, 20	Experimental roles	1	(psi-mi):(MI:0499):(unspecified role)	constant
21, 22	Interactors type	0..1	(psi-mi):(*):(*)	biopolymer, complex, desoxyribonucleic acid, protein, ribonucleic acid, small molecule
23, 24	interactors Xref	1..*	(go):(*):(*)	interactors.compartments
25	interaction Xref	1..*	(go):(*):(*)	context.compartments, context.catalyst.activity
26, 27	interactors annotations	0	-	empty
28	interaction annotations	0	-	empty
29	interaction taxonomy	1	(taxid):(*):(*)	context.species
30	interaction parameters	0	-	empty
31	Creation date	0..1	(*)	context.created
32	Update date	0..1	(*)	context.modified
33, 34	interactors checksum	0	-	empty
35	interaction checksum	0	-	empty
36	negative	1	false	false
37, 38	interactors features	0..*	(*):(*):(*)	TranslationalModification in interactor.hasModifiedResidue
39, 40	interactors stoichiometry	1	(*)	(n, n) for complex/input. (0, n) for olygomer. (0, 0) for polymer. (1, n) for catalyst/input
41, 42	interactor identification method	1	(psi-mi):(MI:0364):(inferred by curator)	constant

TSV format

A lighter format with minimum information. We highly encourage using PSI-MITAB standard format.

column	name	multiplicity	value	source
1, 4	interactor uniprot id	1..*	(ChEBI, reactome, uniprotkb):(*)	uniprotkb for proteins, ChEBI for small molecules, reactome as default
2, 5	interactor esembl id	0..*	(ENSEMBL):(*)	identifiers matching ENSG#######
3, 6	interactor EntrezGene	0..*	(EntrezGene):(*)	identifiers matching EntrezGene:#####
7	Interaction type	0..1	(complex, reaction)	context.class (empty if not complex or reaction)
8	Interaction context	1	(*)	context.stId
9	Pubmed references	0..*	(*)	context.literatureReferences