go::handlers::godb_prestore(3pm) [debian man page]

GO::Handlers::godb_prestore(3pm)			User Contributed Perl Documentation			  GO::Handlers::godb_prestore(3pm)

NAME

	 GO::Handlers::godb_prestore - transforms OBO XML to GODB XML

SYNOPSIS

DESCRIPTION

       This is a transform for turning OBO XML events into XML events that are isomorphic to the GO Database (ie XML element names match GO DB
       table and column names).

       This transformation is suitable for direct loading into a db using the generic DBIx::DBStag loader (see http://stag.sourceforge.net)

       This perl transform may later be replaced by an XSL transform (for speed)

PUBLIC METHODS -
perl v5.14.2							    2013-02-07					  GO::Handlers::godb_prestore(3pm)

GO2FMT(1p)						User Contributed Perl Documentation						GO2FMT(1p)

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>

perl v5.14.2							    2013-02-07								GO2FMT(1p)