Blip BlogThe syntax for posh has changed in the latest release on the “posh” branch. Previously “q”, “l” and other shortcut commands were unary predicates. This caused a few problems when combining with other programs. Now there is a single generic infix predicate “\” for all shortcut commands. The first argument in the command. E.g q\’wing’. [...]
The current implementation of Thea makes use of the SWI-Prolog semweb package as means of parsing OWL encoded as RDF/XML, according to the Mapping to RDF Graphs specification. After the triples have been translated into owl2_model facts such as EquivalentClasses/1, they are discarded. This is somewhat analagous to how the java OWLAPI views RDF – [...]
Ontologies such as the FMA represent reference anatomical entities. Many actual existing anatomical entities would not be classified in reference anatomical ontologies, due to widespread variation found in nature. This applies across multiple scales and modalities: genes and proteins are typically represented using some reference structure, pathways are abstractions that conveniently ignore all the messy [...]
My slides and paper for POSH are now online: Manuscript: owled2011_submission_15.pdf Slides: POSH (slideshare)
Posh (Prolog OWL Shell) is a command line utility that wraps the Thea OWL library to allow for advanced querying and processing of ontologies, combining the power of prolog and OWL reasoning. Installation Install SWI Download and install SWI-Prolog (http://swi-prolog.org). This is a simple point and click procedure for most platforms. If you want to [...]
Thea2 now wraps OWLAPI v3. Support is provided for pellet and hermit out of the box. There is now also additional command line support. download and install SWI-Prolog download Thea2 (for now you have to git clone and get the owlapi3 branch) Add Thea2 to your path: (assuming you install in ~/thea2) export PATH=”$PATH:$HOME/thea2″ You [...]
SWI, like most prologs provides fast first-argument indexing. Accessing a large database of facts via other arguments can be very slow, as a sequential scan is used. SWI provides index/1, but it doesn’t appear to be very effective. The index_util module provides faster indexing by rewriting fact clauses to provide multiple entry points. From the [...]
blip includes a generic grammar/writer for the graphviz language ‘dot’. dot is actually quite powerful, and allows for specification of boxes inside boxes. For example, the following blip command line call: blip -r fma ontol-subset -n Heart -cr subclass -to display will generate and display a png such as this: The ontol/conf directory specifies a [...]
The mis-named “tabling” module (should really be called “memoize”) now allows for persisting memoized calls to a file. See: http://github.com/cmungall/blipkit/blob/master/packages/blipcore/tabling.pro (docs up on the pldoc server soon). To see how this works, consider the transitive closure of the subclass/2 fact, as defined in the ontol_db schema: subclassT(X,Y):- subclass(X,Y). subclassT(X,Y):- subclass(X,Z),subclassT(Z,Y). if you end up using [...]
previously the layout was blipkit/ packages/ blip/ [LIBRARY] This has been simplified to: blipkit/ packages/ [LIBRARY]/ Some URLs in some of the previous posts should be modified accordingly In addition, each sub-library now has a standard organization: [LIBRARY]/ conf/ — configuration modules t/ — plunit tests (.plt files) data/ — data for tests examples/ — [...]
