Python APIs for the Upper Portions of the SW Layer Cake

[by Chimezie Ogbuji]

So, I haven't written about some recent capabilities I've been developing in FuXi. Ultimately, I would like it to be part of a powerful open-source library for semantic web middle-ware development. The current incarnation of this is python-dlp.

The core inference engine ( a RETE-based production system ) has been stable for some time now. FuXi is comprised of the following major modules:

DLP (An implementation of the DLP transformation)
Horn (an API for RIF Basic Logic Dialect)
Rete (the inference engine)
Syntax (Idiomatic APIs for OWL - InfixOWL)

I've written about all but the 2nd item (more on this in another article) and the last in the above list. I've come full circle on APIs for RDF several times, but I now believe that a pure object RDF model (ORM) approach will never be as useful as a object RDF vocabulary model. I.e., an API built for a specific RDF vocablary. The Manchester OWL syntax has quickly become my syntax of choice for OWL and (at the time) I had been toying with an idea of turning it into an API.

Then one day, I had an exchange with Sandro Hawke on IRC about what a Python API for the OWL Abstract Syntax would look like. I had never taken a close look at the abstract syntax until then and immediately came away thinking something more light-weight and idiomatic would be preferable.

I came across a powerful infix operator recipe for Python:

Infix operators

I wrote an initial, standalone module called InfixOWL and put up a wiki which still serves as decent initial documentation for the syntax. I've since moved it into a proper module in FuXi, fixed some bugs and very recently added even more idiomatic APIs.

The module defines the following top-level Python classes:

Individual - Common class for 'type' descriptor
AnnotatibleTerm(Individual) - Common class for 'label' and 'comment' descriptors
Ontology(AnnotatibleTerm) - OWL ontology
Class(AnnotatibleTerm) - OWL Class
OWLRDFListProxy - Common class for class descriptions composed from boolean operators
EnumeratedClass(Class) - Class descriptions consisting of owl:oneOf
BooleanClass(Class,OWLRDFListProxy) - Common class for owl:intersectionOf / owl:unionOf descriptions
Restriction(Class) - OWL restriction
Property(AnnotatibleTerm) - OWL property

Example code speaks much louder than words, so below is a snippet of InfixOWL code which I used to compose (programmatically) the CPR ontology:

CPR   = Namespace('http://purl.org/cpr/0.75#')
INF   = Namespace('http://www.loa-cnr.it/ontologies/InformationObjects.owl#')
EDNS  = Namespace('http://www.loa-cnr.it/ontologies/ExtendedDnS.owl#')
DOLCE = Namespace('http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl#')
OBI   = Namespace('http://obi.sourceforge.net/ontology/OBI.owl#')
SNAP  = Namespace('http://www.ifomis.org/bfo/1.0/snap#')
SPAN  = Namespace('http://www.ifomis.org/bfo/1.0/span#')
REL   = Namespace('http://www.geneontology.org/owl#')
GALEN = Namespace('http://www.co-ode.org/ontologies/galen#')
TIME  = Namespace('http://www.w3.org/2006/time#')
CYC   = Namespace('http://sw.cyc.com/2006/07/27/cyc/')
XML   = Namespace('http://www.w3.org/2001/04/infoset#')
g = Graph()    
g.namespace_manager = namespace_manager
Class.factoryGraph = g
Property.factoryGraph = g
Ontology.factoryGraph = g

cprOntology = Ontology("http://purl.org/cpr/owl")
cprOntology.imports = ["http://obo.sourceforge.net/relationship/relationship.owl",
                       DOLCE,
                       #EDNS,
                       URIRef("http://obi.svn.sourceforge.net/viewvc/*checkout*/obi/ontology/trunk/OBI.owl"),
                       "http://www.w3.org/2006/time#"]
representationOf = Property(CPR['representation-of'],
                            inverseOf=Property(CPR['represented-by']),
                            domain=[Class(CPR['representational-artifact'])],
                            comment=[Literal("...")])
... snip ...
person = Class(CPR.person,
               subClassOf=[Class(SNAP.Object)])
... snip ...
clinician = Class(CPR.clinician)
clinician.comment=Literal("A person who plays the clinician role (typically Nurse, Physician / Doctor,etc.)")
#This expressio is equivalent to cpr:clinician rdfs:subClassOf cpr:person
person+=clinician    
.. snip ..
patientRecord = Class(CPR['patient-record'])
patientRecord.comment=Literal("an electronic document (a representational artifact [REFTERM])  "+
                               "which captures clinically relevant data about a specific patient and "+
                               " is primarily comprised of one or more cpr:clinical-descriptions.")
patientRecord.seeAlso = URIRef("http://ontology.buffalo.edu/bfo/Terminology_for_Ontologies.pdf")
patientRecord.subClassOf = \
    [bytes,
     #Class(CYC.InformationBearingThing),
     CPR['representation-of'] |only| patient,
     REL.OBO_REL_has_proper_part |some| Class(CPR['clinical-description'])]
... snip ...
problemDisj=Class(CPR['pathological-state']) | organismalOccurrent | extraOrganismalOccurrent
problem = Class(CPR['medical-problem'],
                subClassOf=[problemDisj,
                            realizedBy|only|Class(CPR['screening-act']),                                
                            DOLCE['has-quality'] |some| owlTimeQuality])

After the OWL graph is composed, it can be serialized by simply invoking:

g.serialize(format='pretty-xml')

[Chimezie Ogbuji]

via Copia