GO2FMT(1p)

💖 NAME 💖

okay bestie, welcome to the GO2FMT(1p) manual! this is all about go2fmt, go2obo_xml, go2owl, go2rdf_xml, and go2obo_text — a conversion tool and its wrappers. periodt. ✨

🌈 SYNOPSIS 🌈

go2fmt.pl -w obo_xml -e errlog.xml ontology/*.ontology
go2fmt.pl -w obo_xml -e errlog.xml ontology/gene_ontology.obo

💅 DESCRIPTION 💅

okay so it parses any GO/OBO style ontology file and writes out as a different format. slay. 💅

🧠 ARGUMENTS 🧠

• -e ERRFILE — writes parse errors in XML. defaults to STDERR (there should be no parse errors in well formed files, no cap).
• -p FORMAT — determines which parser to use; if left unspecified, it 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 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 📚

okay bestie, the docs are at <http://www.godatabase.org/dev>. go off. 👑

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💖 and that's the whole manual! this page came from perl v5.36.0, dated 2023-12-18, and it's the GO2FMT(1p) manual. mwah! ✨💅