OboInOwl:Main Page

2006-09-14T09:55:55Z

Stuart: /* Progress */

=OboInOwl=

This wiki is for discussing the mapping between Obo1.2 format and OWL

And you can find the first version of this mapping here:

http://www.godatabase.org/dev/doc/mapping-obo-to-owl.html

We are working on a newer version of this mapping

=Mail Lists=

[https://lists.sourceforge.net/lists/listinfo/obo-format Obo Format List]

Also of interest:

[https://lists.sourceforge.net/lists/listinfo/obo-crossproducts Obo Cross-Product List]

=Progress=

I've overhauled the obo2owl mapping. I've pretty much followed Alan's
recommendations (I made a lot of purely internal changes to the xslt too though which should make it much clearer). Hope these work for you Stuart. Sorry about the churn
- but this will definitely be worth it in the end.

Example OWL file can be found here (also attached):

http://geneontology.cvs.sourceforge.net/*checkout*/geneontology/go-dev/xml/examples/gotest.owl

(note that this example includes a cross-product example)

The OWL is generated from either of the following:

http://geneontology.cvs.sourceforge.net/*checkout*/geneontology/go-dev/xml/examples/gotest.obo
http://geneontology.cvs.sourceforge.net/*checkout*/geneontology/go-dev/xml/examples/gotest.obo-xml

The XSL can be found here:

http://geneontology.cvs.sourceforge.net/*checkout*/geneontology/go-dev/xml/xsl/obo2owl.xsl
http://geneontology.cvs.sourceforge.net/*checkout*/geneontology/go-dev/xml/xsl/obo2owl_obo_in_owl_metamodel.xsl

The XSL actually serves as fairly reasonable documentation about what's going on - but we'll also come up with a friendlier description once it's finalised

You can convert the obo-xml directly with the xslt. If you want to
convert from obo you'll need the latest version of go-perl (from cvs)

Here are the changes and things still pending:

Adopted Alan Ruttenberg's metamodel changes (see obo-format list)

split into 2 separate xsl files

subset (ontology views) now more consistent with obo
* the oboInOwl class is SubsetDef
* this does not appear in the owl:Ontology section, it stands alone
(subsets can be used across ontologies)

namespace changes -
* the metamodel is now called oboInOwl
(the format is owned by GO, so this maps to a GO URI)
* the default ontology content namespace is now bioont
(the URI for this will be some bioontologies.org URI)
* slashes not hashes or underscores
- example: rdf:about="oboContent/GO/0000001"

fixed rdf:about/resource/ID issues
- ID is never used
- about and resource now used in correct places

CHECKED

- validates as DL in http://phoebus.cs.man.ac.uk:9999/OWL/Validator
- works in SWOOP
- works in Protege-OWL (but looks odd)

TODO

do we need an equivalentClass for intersectionOf?
SWOOP saves this without

decide on final URI scheme
- Can we make the URIs less verbose? Use entities - or is this frowned on?

new obo tags for obsoletion
handling obsoletes

decide on whether the oboInOwl metamodel should be exported as
part of the content export, or linked to separately;
and if linked to separately, do we need an owl:imports?

Added by SA: here is a link to the OBO Explorer Protege tab:

http://www.aiai.ed.ac.uk/~stuart/oboexplorer.tar

=URIs=

Added a separate page on mapping OBO IDs to URIs:

[[OboInOwl:URIs]]

=Overview of [Other] Mapping efforts=

Below is a quick summary of the various OBO to OWL conversion efforts that I am aware of. Email me (nigam .AT. stanford.edu) with additions/deletions as you come across them.

==Spreadsheet comparing mappings==

Publically viewable:

* http://spreadsheets.google.com/ccc?key=pWN_4sBrd9l1Umn1LN8WuQQ

Editable (contact us to add your mapping & edit):

* http://spreadsheets.google.com/ccc?key=o06770842196506107736.4732937099693365844

[[Image:OBOtoOWL.png]]

NCBO Wiki - User contributions [en]

OboInOwl:Main Page