Map_interspecies_interactions.md

Map_interspecies_interactions

Bio::EnsEMBL::EGPipeline::PipeConfig::Map_interspecies_interactions_conf

Storing pathogen-host interactions data from different source DBs including PHI-base into Ensembl Interspecies interactions DB

Prerequisites

A registry file with the urls of the interspecies_interactions_db, the ncbi_tax, and meta_db database servers specified.

A .csv file from the source_DB from whioch the interactions are sourced.

A .obo file with the descritption of the controlled terms used to describe different aspects of the interactions (optional)

How to run

init_pipeline.pl Bio::EnsEMBL::EGPipeline::PipeConfig::Map_interspecies_interactions_conf \
    -pipeline_url $EHIVE_URL
    -reg_file $REGISTRY 
    -obo_file $OBO_FILE
    -source_db $SOURCE_DB
    -inputfile $INPUT_DB_FILE

Parameters / Options

option	default value	meaning
-reg_file		Different format than the one previously used in the perl eHive pipeline. This one centralises the url DB details for some databases that the pipeline is going to access. Specifically: interactions_db_url, ncbi_tax_url and meta_db_url
-input_file		path to the prepared PHI-base current snapshot
-obo_file		optional path to any .obo file containing controlled vocabulary or ontologies used to describe the interactions properties
-source_db		name of the sourceDB from where we are importing data.ie.- 'PHI-base'

Notes

N.B. The pipeline is still under construction. The first block (populating interactions to our interactionsDB) is operational but will undergo further modifications. A second part to this pipeline will extrapolate new interactions using Ensembl resources.