Other Alias

go2fmt, go2obo_xml, go2owl, 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 style ontology file and writes out as a different format

-e

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

-p

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

-w|writer

format for output - see below for list

-|xslt

The name or filename of an 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 /xml/xsl/*.xsl will be searched; if is not set, then the perl modules dir where 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

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 terms

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

go_assoc

Annotations of genes or gene products using

Files with prefix ``gene-association.''

obo_text

Files with suffix ``.obo''

This is a new file format replacement for the existing 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 version of the 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

format (default: OWL-DL)

is a W3C standard format for ontologies

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

obj_yaml

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

obj_storable

A dump of the perl GO::Model::Graph object. You need Storable from 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 output format

godb_prestore

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

chadodb_prestore

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

<http://www.godatabase.org/dev>