Difference between revisions of "BioPortal FAQ"
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| + | ===What is the OBO Gold standard?=== | ||
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Not yet. In theory it should not be hard to provide an XSL for this. The reverse transformation may be more difficult. | 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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==OBD== | ==OBD== | ||
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See the above URL for now | See the above URL for now | ||
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Revision as of 18:17, 5 December 2005
Frequently Asked Questions within cBio
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?
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
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
- 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