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Creating composite cross-species ontologies

The uberon:merge-species command is intended to replace OWLTools’s --merge-species-ontology command. It is a core component of the pipeline that creates Uberon’s “composite” cross-species products (such as composite-metazoan).

Usage

The syntax is similar to that of the original OWLTools command:

robot uberon:merge-species -i <FILE> -t <TAXON> -s <SUFFIX> -o <FILE>

except that the -q, --include-property option must be repeated for each property to include (that is, use -q RO:0002202 -q RO:0002496) instead of -q RO:0002202 RO:0002496).

The command offers additional features that were not available in the original OWLTools command. They are all disabled by default, use the following options to enable them:

  • -d, --remove-declarations: delete class declarations for classes that have been merged;
  • -x, --extended-translation: translate more types of class expression than just ObjectSomeValuesFrom;
  • -g, --translate-gcas: translate general class axioms that refer to a class that has been merged;
  • -G, --remove-gcas: delete (instead of translating) general class axioms that refer to a class that has been merged.

Batch mode

For convenience, the command also supports a “batch mode”, enabled with the -b, --batch-file option, to create a composite ontology involving several species in a single step. The batch file should be a TSV file where each line represents a species, and:

  • the first column indicates the taxon ID (equivalent to the -t option);
  • the second column indicates the suffix to append to term labels (equivalent to the -s option);
  • the third column indicates the properties to unfold on (comma-separated; equivalent to the -p option);
  • and the fourth column indicates the object properties to include (comma-separated; equivalent to the -q option).

All columns except the first are optional.

For example, if batch.tsv is a file containing the following:

NCBITaxon:9606	human	RO:0002162	RO:0002202,RO:0002496,RO:0002497
NCBITaxon:10090	mouse	RO:0002162	RO:0002202,RO:0002496,RO:0002497

then the following command:

robot uberon:merge-species -i source.owl --batch-file batch.tsv -o output.owl

is equivalent to:

robot uberon:merge-species -i source.owl \
                           -t NCBITaxon:9606 \
                           -s human \
                           -p RO:0002162 \
                           -q RO:0002202 -q RO:0002496 -q BFO:0000051 \
      uberon:merge-species -t NCBITaxon:10090 \
                           -s mouse \
                           -p RO:0002162 \
                           -q RO:0002202 -q RO:0002496 -q BFO:0000051 \
                           -o output.owl