OboInOwl:Main Page

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We are working on a newer version of this mapping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

Obo Format List

Also of interest:

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?

Tools for the mapping

Protege plugins

OBO Explorer Protege tab: http://www.aiai.ed.ac.uk/~stuart/oboexplorer.tar

OBO Converter Protege tab:

source code http://smi-protege.stanford.edu/svn/obo-converter/trunk/

binaries http://smi-cbio01.stanford.edu/~nigam/OBOConverter.zip

instructions on how to use it at http://protege.cim3.net/cgi-bin/wiki.pl?OBOConverter

OWL Export/Import plugin for OboEdit

That is the development version of the OWL Export/Import plugin for OboEdit . Just download the distribution file, unzip it and copy its content to <OboEdit>/extensions folder. Start OboEdit and you should find the option "OWL Adapter" for loading ontologies, File->Load Terms..., and for saving, File->Save as...

Download plugin.

If you have problems with big ontologies, try to increase the size of the memory available to OboEdit.

URIs

Added a separate page on mapping OBO IDs to URIs:

OboInOwl:URIs

Overview of [Other] Mapping efforts

The spreadsheet below provides a 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