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Oort Options
Oort is highly configurable. This page describes the options you can use to customize your release files. Most of these options should be usable from either the command line or the GUI.
This is in the main panel in the GUI. All generated files are placed in this directory
Command line: --outdir DIR
Configures which reasoner to use.
- ELK
- JCel
- HermiT
- Pellet
A full description of the capabilities of different reasoners is outside the scope of this documentation. Please refer to the documentation for each reasoner for full details.
In general, for most ontologies whose source is obo-format, ELK is the recommended reasoner. ELK is very fast, but does not support all of OWL2. However, anything that can be expressed in obo-format (provided macros are not used) can be expressed in the subset of OWL2 used by ELK. Therefore, ELK is the best choice for most obo-format ontologies.
The reasoner is used to generate inferred axioms that are asserted back into the ontology. All files generated as part of the release process (apart from the non-classified ones, see below) have been reasoned over. Providing your users with a pre-reasoned ontology is strongly recommended.
Note that if the input ontology does not contain any equivalence axioms (or "cross-products") then pre-reasoning will not generate any new axioms (but it will remove redundant ones).
A file with suffix -reasoner-report.txt is generated as part of the reasoning process.
Command line: --reasoner REASONER
REASONER can be replaced by the following options:
- elk
- jcel
- hermit
- pellet
The current default reasoner is HermiT.
If set, then a release is generated, even if problems are encountered
Command line: --force
Makes files with suffix non-classified in obo and owl.
These ontologies are generated prior to the reasoning step. The axioms in the ontology should directly match those in the input ontology (often called the "editors version").
We recommend that you provide all users with ontologies that have been reasoned over. This option is provided such that advanced users who want to perform their own reasoning can do this.
Command line: --asserted
Generates a basic / simple ontology from the pre-reasoned input ontology.
The basic ontology is designed for legacy obo-format applications that make certain unwarranted assumptions about ontologies.
See the OBO-Format spec section OBO sublanguages for an explanation of what is omitted when generating a basic ontology.
- A single ID-space (i.e. no MIREOTs, no external links)
- Equivalence axioms (cross-products) removed
- the isa hierarchy is complete w.r.t entailments from the source ontology
Command line: --simple
By default, Oort will not overwrite an existing release
Command line: --allow-overwrite
Command line: --skip-ontology-checks
By default Oort will iterate through all subsets (aka slims) and generate a separate subset ontology. It will perform "gap filling" for missing intermediate terms, filling in the most appropriate relationship.
Currently this can take a long time, so it can optionally be skipped
Command line: --no-subsets
OORT supports a catalog.xml file (as in Protege), to handle redirects for OWL import statements. The catalog.xml may contain absolute and relative paths. Relative paths are resolved in reference to the catalog.xml file location.
Command line: --catalog-xml
When using Oort to merge in external ontologies, Oort assumes that the core ontology has a single ID space, and that the resulting merged ontology should contain all classes in this ID space, together with the reference closure.
This can be overridden by explicitly stating one or more URI prefixes.
Command line: --prefix URIPREFIX (multiple)
Note that ELK makes this somewhat redundant
Command line: --enforceEL
Note that ELK makes this somewhat redundant
Command line: --makeEL
See the OBO-Format spec section 4.4.2 Header Macros
Command line: --expand-xrefs
See the OBO-Format spec section 7 OWL Macros
Command line: --expand-macros or --expand-macros-inplace
Many ontologies use a MIREOT strategy, where a subset of an external ontology or ontologies is merged into the main ontology (as opposed to imported, using owl:imports).
Oort allows you to regenerate this subset using its own algorithm. The algorithm can be described intuitively as taking the source ontology and following the closure of each class in the source ontology, including these classes, plus all axioms belonging to this class (so long as these axioms do not "dangle".
See Mooncat Docs (part of OWLTools)
When the re-mireot option is specified, the existing MIREOTed classes are "flushed"
Command line: --re-mireot
By default, all classes declared in the main ontology are preserved. This can be provided explicitly by passing one or more ontology prefixes (command line only) using --prefix BASEURI
Determines which asserted SubClassOf (isa) links can be "justified" (i.e. re-inferred) by the reasoner. Writes results as part of reasoner report.
This is a very useful curator guide for ontologies such as the GO which have historically manually asserted the isa hierarchy, and are transitioning to an automated approach.
The algorithm is:
- Prior to reasoning, remove all SubClassOf axioms, if that axiom holds between two classes that have logical definitions (Equivalence axioms)
- Reason as normal
- For each removed axiom, see if it has been inferred by the reasoner
- no: report as "exists, not-entailed". Place back in ontology prior to release
- yes: report as "exist, entailed".
This is a simplified version of GULO. See:
Kohler, S., Bauer, S., Mungall, C., Carletti, G., Smith, C., Schofield, P., Gkoutos, G., et al. (2011). Improving ontologies by automatic reasoning and evaluation of logical definitions. BMC Bioinformatics, 12(1), 418
Command line: --justify
Command line: --allow-equivalent-pairs