SWO-EDAM Merge: Converting EDAM from OBO to OWL

The majority of the work described in this post was performed by Jon Ison.

One-time changes made in the EDAM OBO file

  • Various subsets of terms within EDAM were defined using the http://edamontology.org#subsetannotation type. The following subsets are defined (with the last four in the list already defined in EDAM):
    • edam
    • bioinformatics
    • data
    • operations
    • formats
    • topics
  • The http://www.ebi.ac.uk/efo/definition_editor annotation property was added to all EDAM classes/properties that have definition. This provides authorship in a manner in line with the method already employed within SWO.
  • Created the same obsolete parent class within EDAM as is used within SWO (http://www.w3.org/2002/07/owl#DeprecatedClass).
  • The OWLAPI library (and therefore Protege 4.1) does not currently convert the OBO trailing modifier to OWL (see Protein interaction network rendering). The solution is to convert the trailing modifiers to new custom annotation fields. While {since} and {note} can be converted to custom annotation fields {min_cardinality} and {max_cardinality} can’t, but these should just be deprecated or deleted as appropriate, as they have been of limited value. In some instances, {since} can be directly replaced with the EFO annotation label http://www.ebi.ac.uk/efo/obsoleted_in_version. If possible, something like created_in_version (if it exists) should be used for the other instances of {since}. {note} cannot be replaced by the standard rdfs comment annotation label as this label is supposed to be reserved for comments about the term or definition itself.
  • The “EDAM” idspace has been explicitly added to all properties (and usages of those properties) within the OBO file prior to conversion using a global search and replace. This is because, although the following two lines exist to describe the default namespace for properties within EDAM, it seems the conversion to OWL doesn’t pick this up and creates an incorrect OWL-based namespace for them all.
    idspace: EDAM http://edamontology.org/ “EDAM Relations and Concept Attributes”
    default-relationship-id-prefix: EDAM
  • Convert the EDAM OBO file into a single OWL file using Protege 4.1
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3 Responses to SWO-EDAM Merge: Converting EDAM from OBO to OWL

  1. Pingback: SWO-EDAM Merge: Overview « SWOP

  2. Maroua says:

    Thank you for this great work, but i can’t convert EDAM ontology from obo to owl :(, would you please send me the EDAM owl file!? thank you.

    • Hi – sorry for the delay in replying. I’m happy to point you to the OWL file that we’re using in the SWO merge. If you go to the following page on our SourceForge site: http://theswo.svn.sourceforge.net/viewvc/theswo/trunk/dev/ontologydev/ you can browse the current OWL files for both EDAM and SWO. If you download all edam_*.owl files and then load edam_core.owl into Protege or any other OWL-aware ontology editor, you’ll be able to use and browse EDAM in OWL.

      By the way, this file was generated using Protege 4.1’s conversion feature. If you open the OBO file in Protege 4.1, you can then choose to save the file as OWL, in a format such as RDF/XML. There were a few further manual tweaks to reach the file linked above, but broadly, that is how the conversion was performed.

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