The reuse of ontology terms creates links between data, making the ontology and the data more valuable. But often you want to reuse just a subset of terms from a target ontology, not the whole thing. Here we take the filtered ontology from the previous step and extract a “STAR” module for the term ‘adrenal cortex’ and its supporting terms:
robot extract --method STAR \ --input filtered.owl \ --term-file uberon_module.txt \ --output results/uberon_module.owl
uberon_module.txt for an example of a term file. Terms should be listed line by line, and comments can be included with
#. Individual terms can be specified with
--term followed by the CURIE.
--method options fall into two groups: Minimal Information for Reuse of External Ontology Term (MIREOT) and Syntactic Locality Module Extractor (SLME).
For MIREOT, both “upper” (ancestor) and “lower” (descendant) limits can be specified, like this:
robot extract --method MIREOT \ --input uberon_fragment.owl \ --upper-term "obo:UBERON_0000465" \ --lower-term "obo:UBERON_0001017" \ --lower-term "obo:UBERON_0002369" \ --output results/uberon_mireot.owl
To specify upper and lower term files, use
--lower-terms. The upper terms are the upper boundaries of what will be extracted. If no upper term is specified, all terms up to the root (
owl:Thing) will be returned. The lower term (or terms) is required; this is the limit to what will be extracted, e.g. no descendants of the lower term will be included in the result.
extract command works on the input ontology, not its imports. To extract from imports you should first merge.
For more details see:
You can also include ontology annotations from the input ontology with
--copy-ontology-annotations true. By default, this is false.
robot extract --method BOT \ --input annotated.owl \ --term UBERON:0000916 \ --copy-ontology-annotations true \ --output results/annotated_module.owl
MIREOT requires either
--branch-from-term to proceed.
--upper-term is optional.
--upper-term is specified for MIREOT,
--lower-term (or terms) must also be specified.
--method option only accepts: MIREOT, STAR, TOP, and BOT.
The following flags should not be used with STAR, TOP, or BOT methods: