SWO-EDAM Merge: Converting EDAM from OBO to OWL (original) (raw)

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#subset_annotation 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

About Allyson Lister

Find me at https://orcid.org/0000-0002-7702-4495 and https://www.eng.ox.ac.uk/people/allyson-lister/

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