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: Syntactic Locality Module Extractor (SLME) and Minimum Information to Reference an External Ontology Term (MIREOT).
Each SLME module type takes a “seed” that you specify with
--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.
BOT: The BOT, or BOTTOM, -module contains mainly the terms in the seed, plus all their super-classes and the inter-relations between them. The module is called BOT (or BOTTOM) because it takes a view from the BOTTOM of the class-hierarchy upwards. Modules of this type are typically of a medium size and should be used if there is a need to include all super-classes in the module. This is the most widely used module type - when in doubt, use this one.
TOP: The TOP-module contains mainly the terms in the seed, plus all their sub-classes and the inter-relations between them. The module is called TOP because it takes a view from the TOP of the class-hierarchy downwards. Modules of this type are typically large and should only be used if there is a need to include all sub-classes in the module.
STAR: The STAR-module contains mainly the terms in the seed and the inter-relations between them (not necessarily sub- and super-classes). Modules of this type are typically very small and should be used if the module needs to be of minimal size containing only (or mostly) the classes in the seed file.
For more details see:
ROBOT expects any
--term or IRI in the
--term-file to exist in the input ontology. If none of the input terms exist, the command will fail with an empty terms error. This can be overridden by including
Important note for ontologies that include individuals: When using the SLME method of extraction, all individuals (ABox axioms) and their class types (the TBox axioms they depend on) are included by default. The
extract command provides an
--individuals option to specify what (if any) individuals are included in the output ontology:
--individuals include: all individuals in the input ontology and their class types (default)
--individuals minimal: only the individuals that are a type of a class in the extracted module
--individuals definitions: only the individuals that are used in logical definitions of classes
--individuals exclude: no individuals
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
--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.
To only include all descendants of a term or set of terms, use
--lower-terms are not required when using this option.
Note that if the same IRI is used for both a class and an individual, MIREOT will ignore the individual and only extract the class.
For more details see the MIREOT paper.
When extracting (especially with MIREOT), sometimes the hierarchy can have too many intermediate classes, making it difficult to identify relevant relationships. For example, you may end up with this after extracting
- material anatomical entity - anatomical structure - multicellular anatomical structure - organ - abdomen element - adrenal/interrenal gland - adrenal gland (*) - lateral structure - adrenal gland (*)
By specifying how to handle these intermediates, you can reduce unnecessary intermediate classes:
--intermediates all: default behavior, do not prune the ontology
--intermediates minimal: only include intermediate intermediates with more than one sibling (i.e. the parent class has another child)
--intermediates none: do not include any intermediates
Running this command to extract, inclusively, between ‘material anatomical entity’ and ‘adrenal gland’:
robot extract --method MIREOT \ --input uberon_fragment.owl \ --upper-term UBERON:0000465 \ --lower-term UBERON:0002369 \ --intermediates minimal \ --output results/uberon_minimal.owl
Would result in the following structure:
- material anatomical entity - anatomical structure - adrenal gland (*) - organ - adrenal gland (*)
You can chain this output into reduce to further clean up the structure, as some redundant axioms may appear.
Running the same command, but with
robot extract --method MIREOT \ --input uberon_fragment.owl \ --upper-term UBERON:0000465 \ --lower-term UBERON:0002369 \ --intermediates none \ --output results/uberon_none.owl
Would result in:
- material anatomical entity - adrenal gland
Any term specified as an input term will not be pruned.
extract will include imported ontologies. To exclude imported ontologies, just add
--imports exclude for any non-MIREOT extraction method:
robot extract --method BOT \ --catalog catalog.xml \ --input imports-nucleus.owl \ --term GO:0005739 \ --imports exclude \ --output results/mitochondrion.owl
This only includes what is asserted in
imports-nucleus.owl, which imports
imports-nucleus.owl only includes the term ‘mitochondrion’ (
GO:0005739) and links it to its parent class, ‘intracellular membrane-bounded organelle’ (
nucleus.owl contains the full hierarchy down to ‘intracellular membrane-bounded organelle’. The output module,
mitochondrion.owl, only includes the term ‘mitochondrion’ and this subClassOf statement.
By contrast, including imports returns the full hierarchy down to ‘mitochondrion’, which is asserted in
robot extract --method BOT \ --catalog catalog.xml \ --input imports-nucleus.owl \ --term GO:0005739 \ --imports include \ --output results/mitochondrion-full.owl
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
extract provides an option to annotate extracted terms with
rdfs:isDefinedBy. If the term already has an annotation using this property, the existing annotation will be copied and no new annotation will be added.
robot extract --method BOT \ --input annotated.owl \ --term UBERON:0000916 \ --annotate-with-source true \ --output results/annotated_source.owl
The object of the property is, by default, the base name of the term’s IRI. For example, the IRI for
http://purl.obolibrary.org/obo/GO_0000001) would receive the source
Sometimes classes are adopted by other ontologies, but retain their original IRI. In this case, you can provide the path to a term-to-source mapping file as CSV or TSV.
robot --prefix 'GO: http://purl.obolibrary.org/obo/GO_' \ extract --method BOT \ --input annotated.owl \ --term UBERON:0000916 \ --annotate-with-source true \ --sources source-map.tsv \ --output results/changed_source.owl
The mapping file can either use full IRIs:
Or prefixes, as long as the prefix is valid:
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.
The input for
--imports must be either
--method option only accepts: MIREOT, STAR, TOP, and BOT.
The following flags should not be used with STAR, TOP, or BOT methods:
The input for
--sources must be either CSV or TSV format.
--individuals must be one of:
--intermediates must be one of: