go2obo_xmlp - Online in the Cloud

PROGRAM:

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>

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