go2obo_xml(1) conversion tool and its wrappers

Other Alias

go2fmt, go2owl, go2rdf_xml, go2obo_text


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


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



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


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

-|xslt XSLT

The name or filename of an XSLT transform

This can either be an absolute path to a file anywhere on the filesystem, or it can just be the name of the xslt; eg

  go2fmt.pl -xslt oboxml_to_owl go.obo

If the name is specified, then first of all $GO_ROOT/xml/xsl/*.xsl will be searched; if GO_ROOT is not set, then the perl modules dir where GO is installed will be searched (the xslts will be installed here automatically if you follow the normal install process)


If this switch is specified, then caching mode is turned on.

With caching mode, the first time you parse a file, then an additional file will be exported in a special format that is fast to parse. This file will have the same filename as the original file, except it will have the ``.cache'' suffix.

The next time you parse the file, this program will automatically check for the existence of the ``.cache'' file. If it exists, and is more recent than the file you specified, this is parsed instead. If it does not exist, it is rebuilt.

This will bring a speed improvement for b<some> of the output formats below (such as pathlist). Most output formats work with event-based parsing, so caching the object brings no benefit and will in fact be slower than bypassing the cache


writable formats are
Files with suffix ``.ontology''

These store the ontology DAGs

Files with suffix ``.defs''
External database references for GO terms

Files with suffix ``2go'' (eg ec2go, metacyc2go)

Annotations of genes or gene products using GO

Files with prefix ``gene-association.''

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)

Files with suffix ``.obo.xml'' or ``.obo-xml''

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

prolog facts - you will need a prolog compiler/interpreter to use these. You can reason over these facts using Obol or the forthcoming Bio-LP project
simple (lossy) tabular representation
can be used on both ontology files and association files
shows all paths to the root
OWL format (default: OWL-DL)

OWL is a W3C standard format for ontologies

You will need the XSL files from the full go-dev distribution to run this; see the XML section in <http://www.godatabase.org/dev>

a YAML representation of a GO::Model::Graph object
A dump of the perl GO::Model::Graph object. You need Storable from CPAN for this to work. This is intended to cache objects on the filesystem, for fast access. The obj_storable representation may not be portable
A html-ified OBO output format
XML that maps directly to the GODB relational schema (can then be loaded using stag-storenode.pl)
XML that maps directly to the Chado relational schema (can then be loaded using stag-storenode.pl)