NAME

       go2fmt, go2obo_xml, go2owl, go2rdf_xml, go2obo_text - conversion tool and its wrappers

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>