Other Aliasgo2fmt, go2obo_xml, go2owl, go2obo_text
go2fmt.pl -w obo_xml -e errlog.xml ontology/*.ontology
go2fmt.pl -w obo_xml -e errlog.xml ontology/gene_ontology.obo
DESCRIPTIONparses 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
format for output - see below for list
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_cacheIf 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
FORMATSwritable 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)