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ROBOT is licensed under the
BSD 3-Clause License.
Theme by orderedlist

Extract

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

See 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.

The --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 --upper-terms and --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.

NOTE: The 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

Error Messages

Missing MIREOT Term(s) Error

MIREOT requires either --lower-term or --branch-from-term to proceed. --upper-term is optional.

Missing Lower Term(s) Error

If an --upper-term is specified for MIREOT, --lower-term (or terms) must also be specified.

Invalid Method Error

The --method option only accepts: MIREOT, STAR, TOP, and BOT.

Invalid Option Error

The following flags should not be used with STAR, TOP, or BOT methods: