ROBOT

- - - - - - - - - -
view on github
getting started
common errors
chaining commands
global options
makefile
- - - - - - - - - -
annotate
convert
diff
extract
filter
materialize
merge
mirror
query
reason
reduce
relax
remove
repair
report
template
unmerge
validate
verify
- - - - - - - - - -
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.

NOTE: The extract command works on the input ontology, not its imports. To extract from imports you should first merge.

The --method options fall into two groups: Syntactic Locality Module Extractor (SLME) and Minimum Information to Reference an External Ontology Term (MIREOT).

Syntactic Locality Module Extractor (SLME)

Each SLME module type takes a “seed” that you specify with --term and --term-file options. From the seed it builds a module with a “signature” that includes the seed plus any other terms required so that any logical entailments are preserved between entities (classes, properties and individuals) in the signature. For example, if an ontology implies that A is a subclass of B, and the seed contains A and B, then the module will also imply that A is a subclass of B. In other words, the module will contain all the axioms needed to provide the same entailments for the seed terms (and resulting signature) as the full ontology would.

For more details see:

MIREOT

The MIREOT method preserves the hierarchy of the input ontology (subclass and subproperty relationships), but does not try to preserve the full set of logical entailments. 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.

For more details see the MIREOT paper.

Ontology Annotations

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: