#
#  A merged human interactome
#
#     by Andrew Garrow, Yeyejide Adeleye and Guy Warner
#     Unilever, Safety and Environmental Assurance Center
#
#  contact Andrew.Garrow@Unilever.com
#
# ------------------------------------------



1.Introduction
--------------

The merged human interactome combines human interactions reported in IntAct, DIP, 
BIND and HPRD, in addition to papers by Rual (PMID: 16189514), Stelzl (PMID: 16169070) 
and Marcotte (PMID: 15892868). 

The merge process uses several steps including:
 
(i) parsing data out of initial PSI-MI (.mif xml) formats 
(ii) mapping of various disparate gene/protein IDs to entrez gene IDs 
(iii) breaking up of complexes
(iv) combining interactions and annotation if they contain the same two interaction IDs and 
(v) output including annotation files. 

Further details are available on request from Andrew.Garrow@unilever.com








2. Files and Folders
--------------------


	a) gene_symbols.na

Node attributes file giving gene names associated with various entrez 
gene ids. Custom mapping files can be generated using 
http://www.gene.ucl.ac.uk/cgi-bin/nomenclature/gdlw.pl


	b) human_interactome_type.sif

The interactome in sif (simple interaction format) format. Node IDs are 
entrez gene IDs whilst numbers in the middle are interaction IDs as 
required for linking with annotation files.


	c) human_interactome.tab

The interactome, with key annotations in tab delimited format.






3. Column header interpretation
-------------------------------

Unique ID A:			entrez gene ID of interactor A
Unique ID B:			entrez gene ID of interactor B
Alternative ID A:		gene name for interactor A
Alternative ID B:		gene name for interactor B
Aliases A:			a respective uniprot ID of interactor A (others available in interactor files)
Aliases B:			a respective uniprot ID of interactor B
Interaction detection methods:	methods used for identification of interaction as described in source files
First author surnames:		will be used to describe who identified each interaction
Pubmed IDs:			associated pubmed articles
Species A:			species associted with interactor A
Species B:			species associted with interactor B
Interactor types:		interactor types
Source database:		source datasets
Interaction ID:			unique ID for each interaction
Interaction labels:		labels associated with each interaction
Cross-references:		cross-reference (IDs) for various databases (only when available)
Associated Files:		source files
Experiment files:		files where associated experiments are described
Experiment labels:		labels for experiments (when available)
Different techniques:		number of different associated experimental techniques
Different Pubmed articles:	number of different associated pubmed articles
Different sources:		number of different associated sources
Weight:				above 3 divided by 3
