OBO Download Matrix

Formats

The following formats are generated. See below for caveats. All indexed ontologies can be downloaded en-masse for any one particular format, see download section below. The format metadata spec can be found Here

• obo
  -- The Obo text format. If this is not the source format, this is generated using flat2obo (part of obo-edit)
• obo_xml
  -- The Obo XML format. Generated using go-perl
• go_ont
  -- The old deprecated go DAG format. Generated using go-perl
• owl
  -- See W3 OWL page for details. Generated from obo-xml using oboxml_to_owl.xsl. See OboInOwl for details of mapping. All obo files converted to owl are made available using the http://purl.org/obo/ URI scheme; for example http://purl.org/obo/GO
• chadoxml
  -- See Chado-XML pages. This format can be loaded into a Chado-schema database using a generic loader such as DBStag.
• godb_prestore
  -- This format can be loaded into a GO DB schema database using a generic loader such as DBStag.
• go_rdf
  -- GO RDF XML format. May soon be deprecated in favour of the OWL export.
• tbl
  -- Simple table-based format
• prolog
  -- Prolog database. Can be reasoned over using a prolog engine. See obol and blip.
• owl-classified-by-pellet
  -- result of running the OWL through the peller classifier. Potentially includes missing subclasses
• obo-classified-by-oboedit
  -- result of running the obo through the oboedit reasoner. Potentially includes missing is_a and relationship links. For best results, see the logical definitions files.

Reports

The following reports are generated from each of the ontologies that are indexable

• validation_report
  -- reports redundant relationships between classes. This report will be extended to report inconsistences obtained by using a reasoning engine
• error_report
  -- reports any syntax errors
• stats
  -- Ontology statistics

Download

All the above are available for download on an ftp site:

• ftp://ftp.fruitfly.org/pub/obo

Compressed tar files are available for the entire download matrix, and also on a per-format basis. No historic archive is maintained, beyond what is provided by the projects managing the individual ontologies

Metadata

Metadata derived from the above ontologies can be downloaded as an xml file here:

• obo-all/ontology_index.xml -- XML
• obo-all/ontology_index.rdf -- RDF

Statistics

Statistics on each indexable ontology is performed as part of the creation of this resource. Individual statistics files are available, per-ontology, above.

• stats.tbl -- tab delimited text
• stats.html -- DHTML table (click on columns to sort)

The tab-delimited version can be used with unix tools such as sort and grep, or imported into an application like Excel.

You can also download stats from previous versions in the archive

Alignment

You can download a basic all-vs-all text alignment of classes in the indexed OBO files above. This is based on text matching using names and synonyms.

• ftp://ftp.fruitfly.org/pub/obo/reports

This file is updated irregularly and may be out of sync with the above files

Browsing and querying

As yet there is no way to browse all the ontologies as a whole. In future we may provide this using a tool such as AmiGO.

Caveats

• This web page should be considered alpha. The contents may change in the future. The URL is not stable, and caution should be exercised when linking to it
• Not every obo ontology is indexed. Currently we index (deprecated) GO and Obo formatted files. There may be problems with GO formatted files. This is a deprecated format (note: everyone has now switched to obo or another suported format). Ontology maintainers should switch to Obo format.
• Many ontologies reside on sourceforge. Sometimes an ontology will not download correctly because of a sourceforge glitch. If this happens, the ontology will be omitted from the list above, or the ontology from the previous week will be used. Eventually we would like a more robust way of handling this
• Some ontologies such as evoc are supplied as a bundle of separate ontologies. Unfortunately, we do not yet index these. We also do not index ontologies that are not available as a simple one-file download from a URL
• We endeavour to produce this on a weekly basis. System problems may prevent us from doing this. The production of these files is automated, unexpected problems may occur. We hope to make this a more reliable process in the future
• This resource is derived automatically from information submitted to the obo site maintainers. This site is not a substitute for any data or formats made available by the individual ontology providers. The purpose of this site is to make available as much of OBO as possible in a uniform fashion for a variety of formats. For any serious analysis, you should perform the file format conversion yourself using the ontology provided directly by the ontology provider. See main OBO site for obtaining this information.
• The MeSH file should be treated with caution. The source mesh.obo file treats links in MeSH as is_a relations, which is incorrect. This means that the resulting OWL file uses owl:subClassOf, which is also incorrect
• The NCBI Taxonomy transformation treats this resource as an ontology of organism types. The taxonomic rank (species, genus, order, family, phylum, etc) is treated as a term property_value. These are translated to annotationProperties in the owl version. See note below on term property_values with oboedit.

  Also note that due to the presence of {} characters in the NCBI Taxonomy you will need oboedit1.1 or oboedit1.100-beta12 or higher, due to a bug in previous versions.

• In the Obo generated from OWL, owl AnnotationProperties are converted into oboedit class properties. You will need OBO-Edit 1.003-beta1 to be able to load the ontology without errors. A quick hack is also to simply run

                    grep -v ^property_value: in.obo > out.obo
                  

  This will also lose property values for instances, but these are not currently displayed in oboedit anyway. (will be visible in a future version)
• This page is semantic-web friendly! Try viewing it with Piggy Bank

How this site works

This site is generated using the tools available in the obo sourceforge cvs, under obo/website/utils