Frequently Asked Questions within cBio

This FAQ is currently in alpha - please be patient...

General

cBio

What is cBio

What does cBio stand for?

OBO

What is OBO?

Where are the ontologies?

Currently on http://obo.sourceforge.net

Soon to be moving to the cBio site

How do I submit an ontology?

The current protocol is:

send an email to the obo-discuss mailing list, even if the ontology is in planning stages

If the ontology satisfies basic criteria, we will add it to the OBO metadata and it will appear on the OBO site

Soon we will have an ontology submission service on the cBio website

Ontology Content

Building Ontologies

How do I go about building an ontology?

What is the OBO Gold standard?

==Current Ontologies

incomplete is-a paths

Many OBO ontologies are currently incomplete with respect to all classes/terms having an is-a parent. Many tools (including OBO-Edit and AmiGO) deliberately allow the conflation of relations when presenting the ontology as a DAG or a tree to the user. However, other tools (including Protege and SWOOP) do not. This means that some OBO ontologies can look unusual when viewed with these other tools (lots of classes appear at the root level).

This is currently being addressed by the maintainers of OBO ontologies. An effort is underway to complete the is-a parentage in the GO cellular component ontology (biological process will be more difficult). The Plant Ontology Consortium are completing the is-a parentage in the plant anatomical structure ontology.

Until this work is complete, some OBO ontologies may look unusual when viewed in conventional ontology browsing and editing tools. With some of these tools, there may be some configurations which allow other relations to be conflated with the is-a relation when presenting the ontology as a DAG or tree view.

One option is to automatically create an is-a parent to the ontology root for every non-root class/term which lacks any is-a parents. Note that this may create inconsistencies in the ontology if the genuine is-a parent is somewhere deeper in the ontology hierarchy; nevertheless this step may be necessary before presenting some OBO ontologies to tools such as reasoners.

Technical

Questions for cores 1 and 2

OBO Format

Questions about the OBO text and xml formats

What is OBO Format?

Is OBO Format different from the old GO format?

Yes. The old dag-edit format (i.e. the one in which indentation was used to denote the GO hierarchy) is STRONGLY deprecated.

Where can I find the spec?

You can find details on the 1.0 spec on the GO home page

The 1.2 spec is in preparation, and will be released to coincide with the first production OBO-Edit release before the end of 2005

Why not use an XML format?

There is also an obo-xml format. See

http://www.godatabase.org/dev/xml

Currently only available as DTD. Relax-NG and XSD coming soon.

What tools support Obo-Format?

The following are *ontology* tools that support the OBO format. There are many other tools for the analysis of gene ontology data which also happen to read the OBO format - see http://www.geneontology.org/GO.tools.shtml for a list

OBO-Edit: (naturally!). You should use this rather than DAG-Edit (DAG-Edit still supports obo-1.0 format), as DAG-Edit is deprecated as of 2006.

COBRA: developed by Stuart Aitken as part of http://www.xspan.org. COBRA is a java ontology editor/viewer for aligning ontologies

go-perl: http://search.cpan.org/~cmungall/go-perl

Using Protege with OBO ontologies

You have two options here - use the Protege OBO plugin, or convert to a format which Protege understands.

The OBO plugin was developed at the University of Washington, and is no longer supported.

You can convert any obo-format file to OWL and use Protege-OWL (but not Protege-classic); see the next entry.

Note that when you look at many of the OBO ontologies in Protege (classic or Protege-OWL) you will see that there are large amounts of classes apparently at the root level. This is because OBO ontologies have historically not been complete with respect to all classes having a superclass (is-a parent). This is currently being addressed. See the FAQ entry on this subject.

Can I convert Obo-format to OWL?

Yes. At this present time, the best way of foing this is to use the xslts included in go-perl. Download and install: http://search.cpan.org/~cmungall/go-perl/ Then run the script

  go2owl myontology.obo

This functionality will soon be available from oboedit

For more details on the mapping, see:

http://www.fruitfly.org/~cjm/obol/doc/mapping-obo-to-owl.html

OK, but can I just download OBO ontologies as OWL without doing the conversion myself?

You can, at least for some OBO ontologies. This is an experimental service, and will eventually be subsumed into the services provided by cBio:

http://www.fruitfly.org/~cjm/obo-download

Can I convert Obo-format files to Protege-classic?

Not yet. In theory it should not be hard to provide an XSL for this. The reverse transformation may be more difficult.

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