InterPro

InterMine has two InterPro data sources. One that loads the protein domains, e.g. name and description and one that loads the relationship between the proteins and domains.

Types of data loaded

protein domains, e.g. name and description

How to download the data

ftp://ftp.ebi.ac.uk/pub/databases/interpro/interpro.xml.gz

How to load the data into your mine

project XML example

<source name="interpro" type="interpro">

<property name="src.data.dir" location="/data/interpro"/>

</source>

InterPro to protein

This source queries for proteins already in the database and loads related protein domains. So this source must be run after UniProt.

Types of data loaded

protein domains, their relationship to the protein and protein domain region

How to download the data

ftp://ftp.ebi.ac.uk/pub/databases/interpro/protein2ipr.dat.gz ftp://ftp.ebi.ac.uk/pub/databases/interpro/match_complete.dat.gz

How to load the data into your mine

project XML example

<!-- has to be after UniProt because only loads protein domains for loaded proteins -->

<source name="protein2ipr" type="protein2ipr">

<property name="src.data.dir" location="/data/interpro"/>

<property name="src.data.dir.includes" value="protein2ipr.dat"/>

<property name="protein2ipr.organisms" value="9606"/>

<property name=”osAlias” value=”os.production”/>

</source>