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.\" ========================================================================
.\"
.IX Title "GO2FMT 1"
.TH GO2FMT 1 "2010-05-28" "perl v5.12.3" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
.\" way too many mistakes in technical documents.
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.SH "NAME"
go2fmt.pl
go2obo_xml
go2owl
go2rdf_xml
go2obo_text
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 2
\&  go2fmt.pl \-w obo_xml \-e errlog.xml ontology/*.ontology
\&  go2fmt.pl \-w obo_xml \-e errlog.xml ontology/gene_ontology.obo
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
parses any \s-1GO/OBO\s0 style ontology file and writes out as a different
format
.SS "\s-1ARGUMENTS\s0"
.IX Subsection "ARGUMENTS"
\fI\-e \s-1ERRFILE\s0\fR
.IX Subsection "-e ERRFILE"
.PP
writes parse errors in \s-1XML\s0 \- defaults to \s-1STDERR\s0
(there should be no parse errors in well formed files)
.PP
\fI\-p \s-1FORMAT\s0\fR
.IX Subsection "-p FORMAT"
.PP
determines which parser to use; if left unspecified, will make a guess
based on file suffix. See below for formats
.PP
\fI\-w|writer \s-1FORMAT\s0\fR
.IX Subsection "-w|writer FORMAT"
.PP
format for output \- see below for list
.PP
\fI\-|xslt \s-1XSLT\s0\fR
.IX Subsection "-|xslt XSLT"
.PP
The name or filename of an \s-1XSLT\s0 transform
.PP
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
.PP
.Vb 1
\&  go2fmt.pl \-xslt oboxml_to_owl go.obo
.Ve
.PP
If the name is specified, then first of all \f(CW$GO_ROOT\fR/xml/xsl/*.xsl
will be searched; if \s-1GO_ROOT\s0 is not set, then the perl modules dir
where \s-1GO\s0 is installed will be searched (the xslts will be installed
here automatically if you follow the normal install process)
.SS "\-use_cache"
.IX Subsection "-use_cache"
If this switch is specified, then caching mode is turned on.
.PP
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 \*(L".cache\*(R" suffix.
.PP
The next time you parse the file, this program will automatically
check for the existence of the \*(L".cache\*(R" 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.
.PP
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
.SS "\s-1FORMATS\s0"
.IX Subsection "FORMATS"
writable formats are
.IP "go_ont" 4
.IX Item "go_ont"
Files with suffix \*(L".ontology\*(R"
.Sp
These store the ontology DAGs
.IP "go_def" 4
.IX Item "go_def"
Files with suffix \*(L".defs\*(R"
.IP "go_xref" 4
.IX Item "go_xref"
External database references for \s-1GO\s0 terms
.Sp
Files with suffix \*(L"2go\*(R" (eg ec2go, metacyc2go)
.IP "go_assoc" 4
.IX Item "go_assoc"
Annotations of genes or gene products using \s-1GO\s0
.Sp
Files with prefix \*(L"gene-association.\*(R"
.IP "obo_text" 4
.IX Item "obo_text"
Files with suffix \*(L".obo\*(R"
.Sp
This is a new file format replacement for the existing \s-1GO\s0 flat file
formats. It handles ontologies, definitions and xrefs (but not
associations)
.IP "obo_xml" 4
.IX Item "obo_xml"
Files with suffix \*(L".obo.xml\*(R" or \*(L".obo\-xml\*(R"
.Sp
This is the \s-1XML\s0 version of the \s-1OBO\s0 flat file format above
.IP "prolog" 4
.IX Item "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
.IP "tbl" 4
.IX Item "tbl"
simple (lossy) tabular representation
.IP "summary" 4
.IX Item "summary"
can be used on both ontology files and association files
.IP "pathlist" 4
.IX Item "pathlist"
shows all paths to the root
.IP "owl" 4
.IX Item "owl"
\&\s-1OWL\s0 format (default: OWL-DL)
.Sp
\&\s-1OWL\s0 is a W3C standard format for ontologies
.Sp
You will need the \s-1XSL\s0 files from the full go-dev distribution to run
this; see the \s-1XML\s0 section in <http://www.godatabase.org/dev>
.IP "obj_yaml" 4
.IX Item "obj_yaml"
a \s-1YAML\s0 representation of a GO::Model::Graph object
.IP "obj_storable" 4
.IX Item "obj_storable"
A dump of the perl GO::Model::Graph object. You need Storable
from \s-1CPAN\s0 for this to work. This is intended to cache objects on the
filesystem, for fast access. The obj_storable representation may not
be portable
.IP "text_html" 4
.IX Item "text_html"
A html-ified \s-1OBO\s0 output format
.IP "godb_prestore" 4
.IX Item "godb_prestore"
\&\s-1XML\s0 that maps directly to the \s-1GODB\s0 relational schema
(can then be loaded using stag\-storenode.pl)
.IP "chadodb_prestore" 4
.IX Item "chadodb_prestore"
\&\s-1XML\s0 that maps directly to the Chado relational schema
(can then be loaded using stag\-storenode.pl)
.SS "\s-1DOCUMENTATION\s0"
.IX Subsection "DOCUMENTATION"
<http://www.godatabase.org/dev>
