The AFO Merger allows merging multiple ontologies from Allotrope and/or external sources into a single file.


The AFO Merger offers the following functions. See “–help” for full set of features.

  • Inferencing using HermiT or Pellet selecting different inferencing options (e.g. class hierarchy).
  • Combining inferred triples with merged ontologies to create one combined file (that can be queried as if an inferencing engine was active in order to speed up queries).
  • Querying ontologies based on OWL queries using SPARQL-DL (mapping of SPARQL syntax to OWL-DL).
  • Quick verification of consistency and analysis, explanation of inconsistencies.
  • Modularization of ontologies.
  • Importing terms of external ontologies based on MIREOT standard and following Allotrope style guide.
  • Extract taxonomy modules
  • Extract deprecated terms
  • Use option “–help” to see available features

How to see help and get list of current features?
Execute from command line:

 java -jar afo-merger-x.y.x.jar --help

How to merge two ontologies?
There are multiple options how to specify source ontologies to merge.

  • Specify full paths to ontology files
    You can specify IRIs of ontologies together with their location:
java -jar afo-merger-x.y.x.jar --input "\path\to\ontology1.ttl" "\path\to\ontology2.ttl"
  • Specify full path to local folder of ontologies
    You can specify IRIs of ontologies together with a folder name:
java -jar afo-merger-x.y.x.jar --load "" "" --folder "C:\path\to\folder"

Given folder is searched recursively for TTL files containing specified ontologies

How to combine ontologies with inferred triples?
Use command line for merging ontologies and add option “–combine” in order to create an additional artifact that contains all merged triples of ontologies together with inferred triples. For example:

 java -jar afo-merger-x.y.x.jar --input "\path\to\ontology1.ttl" "\path\to\ontology2.ttl" --combine