/usr/share/doc/ray/Documentation/GeneOntology.txt is in ray-doc 2.3.1-1.
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The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 | Ray can output gene ontology profiles using a colored de Bruijn approach.
The graph is colored using EMBL_CDS DNA sequences.
Then, Gene Ontology annotations of those DNA sequence are used
to output a profile.
EMBL_CDS <---> Uniprot <---> Gene Ontology
From the manual:
-gene-ontology OntologyTerms.txt Annotations.txt
Provides an ontology and annotations.
OntologyTerms.txt is fetched from http://geneontology.org
Annotations.txt is a 2-column file (EMBL_CDS handle & gene ontology identifier)
See Documentation/GeneOntology.txt
The OntologyTerms.txt file is
http://geneontology.org/ontology/obo_format_1_2/gene_ontology_ext.obo
The annotation file must be derived from Uniprot-GOA
(http://www.ebi.ac.uk/GOA/).
Files created are
<RayOutput>/BiologicalAbundances/_GeneOntology/Terms.xml
<RayOutput>/BiologicalAbundances/_GeneOntology/Terms.tsv
For a script that does everything, see
https://github.com/sebhtml/Paper-Replication-2012
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