NAME

go2fmt.pl go2obo_xml go2owl go2rdf_xml go2obo_text

SYNOPSIS

  go2fmt.pl -w obo_xml -e errlog.xml ontology/*.ontology
  go2fmt.pl -w obo_xml -e errlog.xml ontology/gene_ontology.obo

DESCRIPTION

parses any GO/OBO style ontology file and writes out as a different format

ARGUMENTS

-e ERRFILE

writes parse errors in XML - defaults to STDERR (there should be no parse errors in well formed files)

-p FORMAT

determines which parser to use; if left unspecified, will make a guess based on file suffix. See below for formats

-w|writer FORMAT

format for output - see below for list

FORMATS

writable formats are

go_ont

Files with suffix ".ontology"

These store the ontology DAGs

go_def

Files with suffix ".defs"

go_xref

External database references for GO terms

Files with suffix "2go" (eg ec2go, metacyc2go)

go_assoc

Annotations of genes or gene products using GO

Files with prefix "gene-association."

obo_text

Files with suffix ".obo"

This is a new file format replacement for the existing GO flat file formats. It handles ontologies, definitions and xrefs (but not associations)

obo_xml

Files with suffix ".obo.xml" or ".obo-xml"

This is the XML version of the OBO flat file format above

prolog

creates a prolog database file (for use with the OBO project)

tbl

simple (lossy) tabular representation

summary

can be used on both ontology files and association files

pathlist

shows all paths to the root

obj_yaml

a YAML representation of a GO::Model::Graph object

text_html

A html-ified OBO output format

godb_prestore

XML that maps directly to the GODB relational schema (can then be loaded using stag-storenode.pl)

chadodb_prestore

XML that maps directly to the Chado relational schema (can then be loaded using stag-storenode.pl)

DOCUMENTATION

http://www.godatabase.org/dev