Usage

Usage: boomer [options]
  --usage  <bool>
        Print usage and exit
  --help | -h  <bool>
        Print help message and exit
  --output | -o  <output files/dir name>
        Name used for folder to ouput clique JSON files; also basename for ontology and Markdown output files.
  --ptable | -t  <filename>
        TSV file containing table of mappings with probabilities.
  --ontology | -a  <filename>
        OWL file containing all asserted/background axioms.
  --prefixes | -p  <filename>
        YAML dictionary of prefix-to-expansion mappings for all prefixes used in the ptable. These namespaces are also used to check for new within-namespace equivalences.
  --window-count | -w  <positive integer>
        Number of groups to split a clique of mappings into when shuffling between greedy search runs. Windows maintain their order; mappings within a window are shuffled.
  --runs | -r  <positive integer>
        Number of separate shuffled runs to conduct for each greedy search.
  --exhaustive-search-limit | -e  <positive integer>
        Maximum size clique for exhaustive search algorithm. Larger cliques use greedy search.
  --output-internal-axioms | -e  <bool>
        Include axioms used to enforce proper subclass relationships (e.g. generated disjoint sibling classes) in OWL output (default false).
  --restrict-output-to-prefixes | -e  <prefix strings (max of 2)>
        Generate output only for cliques where a mapping between these two namespaces was resolved as something other than its highest probability option.

Running

A pre-built copy of Boomer can downloaded from the releases page, e.g., https://github.com/INCATools/boomer/releases/download/v0.1/boomer-0.1.tgz. After unzipping the archive you should see a bin and a lib folder. Keep these together in the same folder, and add the bin folder to your path.

The current command-line interface is specialized for the term mapping use case (see options above).

To run Boomer, you must have Java installed. To set the JVM heap size (usually necessary for processing larger files), use an environment variable:

export JAVA_OPTS=-Xmx10G

Example command line (from https://github.com/geneontology/go-rhea-boom/blob/master/Makefile)

boomer --ptable probs.tsv --ontology go-rhea.ofn --window-count 1 --runs 100 --prefixes prefixes.yaml --output rhea-boom --exhaustive-search-limit 14 --restrict-output-to-prefixes=GO --restrict-output-to-prefixes=RHEA