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

-|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)

-use_cache

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

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

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

tbl

simple (lossy) tabular representation

summary

can be used on both ontology files and association files

pathlist

shows all paths to the root

owl

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>

obj_yaml

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

obj_storable

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

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>