Two of the most common ways of processing and manipulating OWL ontologies are through an ontology editing environment (e.g. Protege or TopBraid) or via a programmatic interface, such as the OWL API. A complementary method is to use an OWL-aware command line shell. Posh, the Prolog OWL Shell is an interactive toplevel readeval-print-loop interface that provides powerful capabilities for querying and transforming ontologies. It includes a bridge to the OWLAPI and to multiple OWL reasoners, and allows a mixture of closed-world rule-based querying on top of open world reasoning. It also provides an interface to POPL, the Prolog Ontology Processing Language. Posh is available from http://blipkit.wordpress.com/posh
Powerful and feature-rich java libraries such as Jena and the OWLAPI[
Posh is a simple wrapper for the Thea library[
This puts the user into an enhanced prolog REPL shell with provides expected features such as readline support and history.
A little knowledge of prolog syntax helps - variables are indicated by a
leading upper case character or underscore, and queries are terminated by a “.”.
Posh makes use of prolog’s infix operators to define a Manchester Syntax[
The following query finds all subclass axioms whose second argument is an existential restriction using the connected to property (in other words, it finds the connected parts of a fly): ?- q X < connected_to some Y.
The < operator is shorthand for SubClassOf (posh favors brevity at the possible expense of obfuscation). We can query more specifically for all asserted connections to the antennal lobe, getting back a singe axiom as an answer: ?- q X < connected_to some ’antennal lobe’. ’cortex of antennal lobe’<connected_to some ’antennal lobe’.
This illustrates a useful configurable feature whereby labels in queries are substituted for the corresponding IRI; this is very handy for bio-ontologies where the convention is to use numeric IDs.
A standard SELECT-WHERE type construct is also supported: ?- q X where X < connected_to some ’antennal lobe’. ’cortex of antennal lobe’. 2.1
Posh comes bundled with jars for Pellet[
A\=annotationAssertion(_,_,_)))]. ?- q {X < connected_to some ’antennal lobe’}.
Annotations are not given to the reasoner, and after initialization the reasoner is queried for the contents of the curly braces. Closed-world prolog queries can be freely mixed with open-world reasoner queries. We can use the prolog negationas-failure operator to find all neuron classes that are not known to be restricted to the head: ?- q X where {X < neuron},\+{X < part_of some head}.
Users can write their own prolog predicates and mix these in with their
queries, or they can take advantage of powerful SWI-Prolog library[
Posh also makes use of a new extension of Thea called the Prolog Ontology
Process Language. This is similar to OPPL2[
POPL directives can be issued directly from within an interactive Posh session. For exampe, the following command will rewrite all overlaps SomeValuesFrom expressions to use a nested class expression: overlaps some Y ===> has_part some part_of some Y.
(any OWL expression can be used here, arbitrary levels deep).
The same thing can be done using the powerful visitor pattern in the OWL API, albeit at the cost of more lines of code.
The following example adds equivalence axioms wherever two classes have the same label: add X==Y where X label N, Y label N, X\=Y.
Here the predicate label/2 is a convenience wrapper for rdfs:label triples. We are not restricted to built-in predicates, and can easily define our own. For example, if we wanted to add equivalence axioms for all class pairs whose stemmed labels match, we can define a predicate using the porter stem predicate from the SWI prolog NLP library: stemmed_label(X,N) :- X label N1, porter_stem(N1,N). shares_stemmed_label(X,Y) :- stemmed_label(X,N),stemmed_label(Y,N),X\=Y.
This can then be consulted and used in the following POPL directive: add X==Y where shares_stemmd_label(X,Y). 3
Posh occupies something of a niche in the ecosystem of OWL tooling. Upstanding
software engineers are likely to favour solid java APIs, and ontology power users
can make use of an increasing number of plugins for their ontology development
environment of choice. In particular, the new SPARQL-DL[
Furthermore, REPLs to the java OWL API are available in a number of
scripting languages from Groovy to Lisp, exemplified in toolkits such as El
Vira[
In the spirit of what was once the hacking language of choice for bioinformaticians, Perl3, an alternative acronym for Posh is the “Pathologically Obfuscated Semantic Hacker”. Posh aims to fill a similar niche, allowing powerful ontology operations to be scripted quickly and easily. 4
Posh is a powerful and somewhat ad-hoc shell that allows prolog, OWL reasoning and unix operations to be mashed up interactively on the command line. It is available as part of the Thea library4, but to obtain the latest version please see the main Posh page (http://blipkit.wordpress.com/posh/) which also includes a collection of examples and a companion guide to the examples in this note.