Loads gene association files that link GO terms to genes or proteins.
genes, proteins, GO terms, publications, GO evidence
The data is available from http://www.geneontology.org
There is an optional configuration file that let’s you determine which type of object you create, and which identifier field you set. If your annotation file annotates genes and uses the primary identfier, these are the default values and you do not need to update the configuration file.
parameter | definition | possible values |
---|---|---|
typeAnnotated | class of what is being annotated | gene (default) or protein |
identifier | which field to set | primaryIdentifier (default), symbol, or primaryAccession |
readcolumn [1] | which column to use for identifier | identifier (default) or symbol |
[1] | See http://www.geneontology.org/GO.format.gaf-2_0.shtml for column descriptioins |
# an example entry
7165.typeAnnotated=protein
7165.identifier=primaryAccession
project XML example
<source name="go-annotation" type="go-annotation">
<property name="src.data.dir" location="/data/go-annotation"/>
<property name="ontologyPrefix" value="GO"/>
</source>