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We are working on a newer version of this mapping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:

 OBO Explorer Tab

OBO Converter Protege tab:

 source code OBO Converter Tab
 binaries OBO Converter Tab
 instructions on how to use it at OBO Converter Tab

OboEdit OWL plugin

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...

OboEdit OWL 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