BioPortal FAQ

Frequently Asked Questions within cBio

General

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

Technical

Questions for cores 1 and 2

OBO Format

Questions about the OBO text and xml formats

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

What tools support Obo-Format?

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

Blip

The following tools have limited support:

• Protege (only for 1.0 - even then, may be problematic?). Requires OBO plugin.

Note that you can load OWL files into Protege-OWL; see below

Why not 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.

Can I convert Obo-format to OWL?

Yes! See

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

==Ontology Metadata

OBD

What is OBD?

OBD is a database for storing data typed using OBO ontologies

Where is it?

In development!

Is there a demo?

See http://www.fruitfly.org/~cjm/obd

Datasets

See the above URL for now