Append ontology to a World

[Gilberto Lobo]

Hi everyone,

I done some research and didn't found any solution egarding my situation. Here it is:

I have two ontologies CloudOntology.owl and IaaS.owl, the thing is that CloudOntology has a dependency on IaaS.owl and I can't figure out how to load both ontologies on a World or any other valid solution that also sync the reasoner.

I have both ontologies owl files locally on my computer

I'm posting the code for better explanation:

from owlready2 import *
from pprint import pprint


class SparqlQuery:

    def __init__(self):
        onto_path.append("/home/gilberto/PycharmProjects/cloud_ontology/Ontology/")
       
        onto = get_ontology("CloudOntology.owl")
        onto2 = get_ontology("IaaS.owl")
        onto.imported_ontologies.append(onto2)

        # Here I was trying using a World, I always get an error trying to load CloudOntology.owl
        # But I always succeed when loading IaaS.owl alone
        # my_world = World()
        # my_world.get_ontology("CloudOntology.owl").load()

        # Here I get the following:
        # This is my onto:  get_ontology("CloudOntology.owl#")
        # This is my ontology imports:  [get_ontology("IaaS.owl#")]
        print("This is my onto: ", onto)
        print("This is my ontology imports: ", onto.imported_ontologies)

        # Here is where I got stuck, it seems I can't sync my reasoner unless it is a World
        # sync_reasoner(onto)  # reasoner is started and synchronized here
        # self.graph = onto.as_rdflib_graph()

    # Just a method for querying the ontology
    def search(self):
        # Search query is given here
        # Base URL of your ontology has to be given here
        query = """ PREFIX ab: <http://www.owl-ontologies.com/CloudOntology.owl>
                SELECT ?s ?p ?o
                WHERE {
                ?s ?p ?o .
                } """
        print(query)
        # query is being run
        resultsList = self.graph.query(query)

        # creating json object
        response = []
        for item in resultsList:
            # print("\t\tItem >\t\t\t\t\t\t\t\t", item)

            s = str(item['s'].toPython())
            s = re.sub(r'.*#', "", s)

            p = str(item['p'].toPython())
            p = re.sub(r'.*#', "", p)

            o = str(item['o'].toPython())
            o = re.sub(r'.*#', "", o)

            response.append({'s': s, 'p': p, 'o': o})

        return response


runQuery = SparqlQuery()
# response = runQuery.search()

# pprint(response)  # just to show the output



I also searched alot on the documentation, but I didn't found out how to solve this. I'm sure its just me not knowing how to do the code properly, but can anyone help me with this?

Thanks in advance.

[Jiba]

Hi,

By default, Owlready uses a single world called "default_world". This should be fine for your application. You can just load ontologies with get_ontology(...).load(), and call the reasoner with sync_reasoner() (without parameter, it uses default_world).

Jiba

[Gilberto Lobo]

Hy Jiba,

first, thanks for the really quick answer, I'm gonna try this.

Regards.

[Gilberto Lobo]

I changed my code to this:

from owlready2 import *
from pprint import pprint


class SparqlQuery:

    def __init__(self):
        onto_path.append("/home/gilberto/PycharmProjects/cloud_ontology/Ontology/")

        default_world.get_ontology("CloudOntology.owl").load()

        sync_reasoner()  # reasoner is started and synchronized here

        self.graph = default_world.as_rdflib_graph()


Now I was getting this error message:

* Owlready2 * Warning: optimized Cython parser module 'owlready2_optimized' is not available, defaulting to slower Python implementation
* Owlready2 * Running HermiT...
    java -Xmx2000M -cp /home/gilberto/PycharmProjects/cloud_ontology/venv/lib/python3.6/site-packages/owlready2/hermit:/home/gilberto/PycharmProjects/cloud_ontology/venv/lib/python3.6/site-packages/owlready2/hermit/HermiT.jar org.semanticweb.HermiT.cli.CommandLine -c -O -D -I file:////tmp/tmpfm1v8ow_
Traceback (most recent call last):
  File "/home/gilberto/PycharmProjects/cloud_ontology/sparql_query.py", line 46, in <module>
    runQuery = SparqlQuery()
  File "/home/gilberto/PycharmProjects/cloud_ontology/sparql_query.py", line 12, in __init__
    sync_reasoner()  # reasoner is started and synchronized here
  File "/home/gilberto/PycharmProjects/cloud_ontology/venv/lib/python3.6/site-packages/owlready2/reasoning.py", line 126, in sync_reasoner_hermit
    output = subprocess.check_output(command, stderr = subprocess.STDOUT)
  File "/usr/lib/python3.6/subprocess.py", line 336, in check_output
    **kwargs).stdout
  File "/usr/lib/python3.6/subprocess.py", line 418, in run
    output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command '['java', '-Xmx2000M', '-cp', '/home/gilberto/PycharmProjects/cloud_ontology/venv/lib/python3.6/site-packages/owlready2/hermit:/home/gilberto/PycharmProjects/cloud_ontology/venv/lib/python3.6/site-packages/owlready2/hermit/HermiT.jar', 'org.semanticweb.HermiT.cli.CommandLine', '-c', '-O', '-D', '-I', 'file:////tmp/tmpfm1v8ow_']' returned non-zero exit status 1.

Process finished with exit code 1

I ran the debug tool in Pycharm setting a flag when I sync the reasoner, in the stdout got the following exception:

'Exception in thread "main" org.semanticweb.owlapi.model.OWLRuntimeException: org.coode.owlapi.rdfxml.parser.TranslatedUnloadedImportException: org.semanticweb.owlapi.model.UnloadableImportException: Could not load imported ontology: <http://www.owl-ontologies.com/IaaS.owl> Cause: Server returned HTTP response code: 429 for URL: http://www.owl-ontologies.com/IaaS.owl\norg.semanticweb.owlapi.model.UnloadableImportException: Could not load imported ontology: <http://www.owl-ontologies.com/IaaS.owl> Cause: Server returned HTTP response code: 429 for URL: http://www.owl-ontologies.com/IaaS.owl [...]

So I figured that it was trying to fetch the IaaS ontology from the url http://www.owl-ontologies.com/IaaS.owl so I headed to my ontology, and saw the line that was causing my troubles:

 <owl:Ontology rdf:about="">
    <owl:imports rdf:resource="http://www.owl-ontologies.com/IaaS.owl"/>
 </owl:Ontology>

I have the IaaS.owl locally in my computer in the path that I setted on the onto_path, any advice on how can I load this dependency locally? I don't want it to look for it in the web.

And thanks again for the help.

[Gilberto Lobo]

I've managed to do that by substituting the import line by the local path as follows:

before:
 <owl:Ontology rdf:about="">
    <owl:imports rdf:resource="http://www.owl-ontologies.com/IaaS.owl"/>
 </owl:Ontology>

after:
 <owl:Ontology rdf:about="">
    <owl:imports rdf:resource="file:///home/gilberto/PycharmProjects/cloud_ontology/Ontology/IaaS.owl"/>
 </owl:Ontology>

And again, thanks for the help.

[Jiba]

Hi,

I think you need to load the second ontology in Python before calling the reasonner, using :

        default_world.get_ontology("http://www.owl-ontologies.com/IaaS.ow").load()

Jiba

[Gilberto Lobo]

Hi,

I tried to do so, I added the code to Python as you said:

class SparqlQuery:

    def __init__(self):
        onto_path.append("/home/gilberto/PycharmProjects/cloud_ontology/Ontology/")

        default_world.get_ontology("CloudOntology.owl").load()
        default_world.get_ontology("http://www.owl-ontologies.com/IaaS.owl").load()

        pprint(default_world.search(iri = "*"))

        sync_reasoner()  # reasoner is started and synchronized here

        self.graph = default_world.as_rdflib_graph()

Got a diferent log message, a huge one, here's some lines of it:
* Owlready2 * Running HermiT...
    java -Xmx2000M -cp /home/gilberto/PycharmProjects/cloud_ontology/venv/lib/python3.6/site-packages/owlready2/hermit:/home/gilberto/PycharmProjects/cloud_ontology/venv/lib/python3.6/site-packages/owlready2/hermit/HermiT.jar org.semanticweb.HermiT.cli.CommandLine -c -O -D -I file:////tmp/tmptbmsmwvp
* Owlready2 * HermiT took 2.448326587677002 seconds
* Owlready * Reparenting CloudOntology.Ecision: {CloudOntology.CloudServiceName} => {CloudOntology.BusinessPerformanceManagement, CloudOntology.Financial_Risk_Management, CloudOntology.SaaSProvider, CloudOntology.CloudServiceName, CloudOntology.BusinessPlan}
* Owlready * Reparenting CloudOntology.Fundingroadmap: {CloudOntology.CloudServiceName} => {CloudOntology.Analysis_Statement_Report, IaaS.US_Canada, CloudOntology.SaaSProvider, CloudOntology.CloudServiceName, CloudOntology.Collaboration, CloudOntology.BusinessPlan, CloudOntology.Accounting}
* Owlready * Reparenting CloudOntology.Iplanner: {CloudOntology.CloudServiceName} => {CloudOntology.Budget_Management, CloudOntology.Project_Management, CloudOntology.Financial_Risk_Management, CloudOntology.SaaSProvider, CloudOntology.CloudServiceName, CloudOntology.Collaboration, IaaS.Europe_and_UK, CloudOntology.Document_Management, CloudOntology.BusinessPlan}
* Owlready * Reparenting CloudOntology.EGrid_OS: {CloudOntology.CloudServiceName} => {CloudOntology.EDI-_Electronic_Data_Interchange, CloudOntology.VMI_-_Vendor_Managed_Inventori, CloudOntology.ERP-Enterprise_Recource_Plannig, CloudOntology.Inventory_Management, CloudOntology.CloudServiceName, CloudOntology.SaaSProvider, CloudOntology.SCM_-_Supply_Chain_Management}
* Owlready * Reparenting CloudOntology.Zoho: {CloudOntology.CloudServiceName} => {CloudOntology.BI-Management, CloudOntology.Email_Archiving, CloudOntology.ASP, CloudOntology.JSP, CloudOntology.Collaboration, CloudOntology.Invoice_Sales_Ordering, CloudOntology.Billing, CloudOntology.Personal_Notes, IaaS.HTTP_REST, CloudOntology.Sales_Automation, CloudOntology.Address_Books, CloudOntology.Project_Portfolio_Management, CloudOntology.Sales_Management, CloudOntology.BI_Reports, CloudOntology.SaaSProvider, CloudOntology.CRM-Custommer_Relationship_Management, CloudOntology.Contact_Management, CloudOntology.PHP, CloudOntology.Task_Management_Assignment, CloudOntology.Analysis_Statement_Report, CloudOntology.VMI_-_Vendor_Managed_Inventori, CloudOntology.Support_Services, CloudOntology.CloudServiceName, CloudOntology.Productivity_Suite, CloudOntology.Calander, CloudOntology.Appointments_and_Scheduling, CloudOntology.PaaSProvider, CloudOntology.LeadManagement, IaaS.US_Canada, CloudOntology.Project_Management, CloudOntology.Help_Desk, CloudOntology.Time_Tracking}
* Owlready * Reparenting CloudOntology.WorkXpressCRM: {CloudOntology.CloudServiceName} => {CloudOntology.Facility_Management, CloudOntology.Production_Scheduling, CloudOntology.Asset_Management, CloudOntology.LeadManagement, CloudOntology.VMI_-_Vendor_Managed_Inventori, CloudOntology.ERP-Enterprise_Recource_Plannig, CloudOntology.Inventory_Management, CloudOntology.CloudServiceName, CloudOntology.SaaSProvider, CloudOntology.IT_Management, CloudOntology.CRM-Custommer_Relationship_Management, CloudOntology.Application_LifeCycle_Management, CloudOntology.WorkForce_Management, CloudOntology.Accounting}
* Owlready * Reparenting CloudOntology.Deposco: {CloudOntology.CloudServiceName} => {CloudOntology.Facility_Management, IaaS.US_Canada, CloudOntology.VMI_-_Vendor_Managed_Inventori, CloudOntology.WMS-_Warehouse_Management_System, CloudOntology.ERP-Enterprise_Recource_Plannig, CloudOntology.BI_Reports, CloudOntology.Inventory_Management, CloudOntology.CloudServiceName, CloudOntology.SaaSProvider, CloudOntology.SCM_-_Supply_Chain_Management}
* Owlready * Reparenting CloudOntology.Xtertain: {CloudOntology.CloudServiceName} => {CloudOntology.Facility_Management, CloudOntology.VMI_-_Vendor_Managed_Inventori, CloudOntology.ERP-Enterprise_Recource_Plannig, CloudOntology.Inventory_Management, CloudOntology.CloudServiceName, CloudOntology.SaaSProvider}
* Owlready * Reparenting CloudOntology.Purchase: {CloudOntology.Financial} => {CloudOntology.AvailableServices_Inthe_Cloud, CloudOntology.Financial}

And goes on... Does that mean that the dependencies where loaded?

Thanks again.

[Jiba]

Hi,

It seems that everything is Ok now.

The long message is the inferrence done by the reasoner.
For example, the following:

* Owlready * Reparenting CloudOntology.Purchase: {CloudOntology.Financial} => {CloudOntology.AvailableServices_Inthe_Cloud, CloudOntology.Financial}

Means that the class CloudOntology.Purchase was a child of CloudOntology.Financial, and is now a child of both CloudOntology.AvailableServices_Inthe_Cloud and CloudOntology.Financial.


You can remove these messages by calling the reasoner as follows:

        sync_reasoner(debug = 0)

Jiba

[Gilberto Lobo]

Thanks again Jiba, for all the help and promptness.