How to add an ontology to DRUM?

[dpdoughe]

If I have an ontology in OWL .rdf or extracted terms to .obo format, how can I add this to DRUM? Does DRUM prefer certain ontology file formats?
A related question, would DRUM make use of EXACT, NARROW, etc synonyms in such an ontology?

[wdebeaum]

It's probably easiest to use .obo, since most of the external ontologies we use are in that format. This is what you'd need to do:

0. (optional) Add a rule to the TextTagger Makefile for obtaining the .obo file (the existing ones start here). This is recommended if you want other people to be able to install your version of drum easily.
1. Add your .obo file to the OBO_FILES list here.
2. Somehow map the terms in your .obo file into the TRIPS ontology. There are a couple ways to do this:
   1. If you want to map to more than one TRIPS ontology type, and your .obo file has an isa hierarchy:
      1. Add a rule to the TT Makefile to create a directory full of DSL-format files containing the hierarchy from the .obo file, grouped by term ID number. The existing rules for this start here.
      2. Add a def-obo-resource line in drum-dsl-resources.lisp. This defines a Lisp package for the OBO term IDs to live in, and lets DeepSemLex know how to find the hierarchy DSL files.
      3. Add mappings in DSL format from your OBO term IDs to TRIPS ontology types in drum-mappings.lisp. If you're the author of the .obo file, you can instead include the mappings directly in the .obo file. This was done for bioentities.obo, for example.
   2. Otherwise (if you only want to map to one type, or there's no hierarchy to use), you can just add some code to Drum.pm to determine the TRIPS ontology type for a given OBO term ID. You can add to the if/elsif block that starts here. (The list of TRIPS ontology types to output is called lftypes for historical reasons).

You may also need to add some code to the build scripts get-obo-terms.pl and/or obo-to-dsl.pl, depending on how special your .obo file is.

The online Ontology Mapper/Builder tool may be helpful for figuring out how to map to TRIPS ontology types, though right now it doesn't load .obo files, and there's no converter from .obo to its JSON save format.

[wdebeaum]

Oh, I just remembered: if you're doing 2(i), you also need to add your term ID prefix to this line in Drum.pm (which is part of the if/elsif block I mentioned in 2(ii)).

[dpdoughe]

Would there be a way to open the TRIPS ontology in a tool like Protege? Is the ontology available in OWL format?

[wdebeaum]

There is some code for converting the TRIPS ontology to OWL format in src/OWL/, which you can try to use by running make ontology.owl in that directory. However, that's actually a holdover from an earlier project we did involving parsing WordNet glosses, and hasn't been well maintained. It probably doesn't work 100%. In particular I doubt the list of .lisp files here has been kept up to date with recent additions here, and I think there were some minor hacks to the Java code I had to make in order to get it to build last time, which I might not have committed because they were hacks. It also depends on a specific version of Protege in order to work (3.4.7 IIRC?), and you might have to tell configure where to find Protege.

If, like many people who ask similar questions, all you really want to do is avoid having to learn Lisp in order to deal with the ontology, you might be interested in one of the other XML-formatted versions of the ontology. You can make your own version of the XML files behind the DeepSemLex-based ontology browser webpage, by running make in src/DeepSemLex/code/browser/ (the XML files end up in src/DeepSemLex/data/browser/). You could also make one big DSL XML file using a combination of trips-ont-to-dsl.sh and dsl-to-xml.sh in src/DeepSemLex/code/converters/ (that won't have the lexicon, though). Or you could try to make the XML files behind the older ontology browser webpage using this code.

Writing code to convert one of these XML formats to OWL may or may not be easier than getting the old converter to work.