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OntoMaven Repositories and OMG API4KP
Ralph Schäfermeier Adrian Paschke
Freie Universität Berlin
ALIGNED Project Meeting Dec 3
Outline
1 OMG API4KP – An API for Knowledge Platforms
Scope of the Standard
Scenario: The Connected Patient System
Scenario: Semantic Annotation and Discovery of Biodiversity Data
The API4KP Metamodel
Foundations: Monads
Architecture Styles
2 Repositories with OntoMaven
Motivation
Architecture
Selected Plug-Ins
The Terminology Server Scenario with Distributed Knowledge
Repositories
,
FU Berlin, OntoMaven and API4KP, ALIGNED Project Meeting Dec 3, 2015 2
Outline
1 OMG API4KP – An API for Knowledge Platforms
Scope of the Standard
Scenario: The Connected Patient System
Scenario: Semantic Annotation and Discovery of Biodiversity Data
The API4KP Metamodel
Foundations: Monads
Architecture Styles
2 Repositories with OntoMaven
Motivation
Architecture
Selected Plug-Ins
The Terminology Server Scenario with Distributed Knowledge
Repositories
,
FU Berlin, OntoMaven and API4KP, ALIGNED Project Meeting Dec 3, 2015 3
A Meta-API for Knowledge (Reasoning)
Platforms (KPs)
A Meta-API is a platform-independent
model (PIM) for a family of APIs in
specific languages, also called PSMs
(platform-specific models).
API4KP provides a
PIM for the external
APIs of KPs.
Figure: A Monolithic KP Architecture.
FU Berlin, OntoMaven and API4KP, ALIGNED Project Meeting Dec 3, 2015 4
Languages in Scope
Knowledge Representation and Reasoning Languages
Resource Description Framework (RDF)
RDF Schema (RDFS)
Web Ontology Language (OWL)
Common Logic (CL)
Event-Condition-Action RuleML (ECA)
. . .
Data Representation Languages
Extensible Messaging and Presence Protocol (XMPP)
JSON
. . .
,
FU Berlin, OntoMaven and API4KP, ALIGNED Project Meeting Dec 3, 2015 6
Outline
1 OMG API4KP – An API for Knowledge Platforms
Scope of the Standard
Scenario: The Connected Patient System
Scenario: Semantic Annotation and Discovery of Biodiversity Data
The API4KP Metamodel
Foundations: Monads
Architecture Styles
2 Repositories with OntoMaven
Motivation
Architecture
Selected Plug-Ins
The Terminology Server Scenario with Distributed Knowledge
Repositories
,
FU Berlin, OntoMaven and API4KP, ALIGNED Project Meeting Dec 3, 2015 7
The Connected Patient System 0: Overview
Figure: A Distributed KP Architecture for Stream Processing, Clinical Decision
Support (CDS) and Case History Storage.
,
FU Berlin, OntoMaven and API4KP, ALIGNED Project Meeting Dec 3, 2015 8
The Connected Patient System I: Streaming
Data and Query Results
Biomedical devices are available via pub-sub.
Streamed data arrive in multiple formats e.g. XMPP, RDF
Vocabularies are defined in RDFS, OWL, Common Logic (CL).
Healthcare providers submit SPARQL queries through API4KP,
receiving streamed incremental results, updated as new data arrive.
Figure: A Heterogeneous Stream Processing KP Architecture.
,
FU Berlin, OntoMaven and API4KP, ALIGNED Project Meeting Dec 3, 2015 9
The Connected Patient System II: CDS
A Clinical Decision Support System (CDS) is defined using
event-condition-action (ECA) rules submited through API4KP, reacting
to
simple events (e.g. a vital parameter exceeding a threshold)
complex events (e.g. a decreasing trend in the average daily physical
activity)
intervening with alerts and reminders.
A failure of response (through API4KP) to an alert leads to escalation
to another recipient.
Figure: A Clinical Decision Support (CDS) KP Architecture.
,
FU Berlin, OntoMaven and API4KP, ALIGNED Project Meeting Dec 3, 2015 10
The Connected Patient System: Complete
Figure: A Distributed KP Architecture.
,
FU Berlin, OntoMaven and API4KP, ALIGNED Project Meeting Dec 3, 2015 12
Outline
1 OMG API4KP – An API for Knowledge Platforms
Scope of the Standard
Scenario: The Connected Patient System
Scenario: Semantic Annotation and Discovery of Biodiversity Data
The API4KP Metamodel
Foundations: Monads
Architecture Styles
2 Repositories with OntoMaven
Motivation
Architecture
Selected Plug-Ins
The Terminology Server Scenario with Distributed Knowledge
Repositories
,
FU Berlin, OntoMaven and API4KP, ALIGNED Project Meeting Dec 3, 2015 13
GFBio Terminology Server
API4KP
API4KP
SKOS RDF
OWL
Web Services Client
HTTP Server
Semantic Web Repository
(Virtuoso)
HTTP
request
Serialization format
(RDF/XML,JSON,JSON LD,…)
External Web Services
requestor
,
FU Berlin, OntoMaven and API4KP, ALIGNED Project Meeting Dec 3, 2015 14
Outline
1 OMG API4KP – An API for Knowledge Platforms
Scope of the Standard
Scenario: The Connected Patient System
Scenario: Semantic Annotation and Discovery of Biodiversity Data
The API4KP Metamodel
Foundations: Monads
Architecture Styles
2 Repositories with OntoMaven
Motivation
Architecture
Selected Plug-Ins
The Terminology Server Scenario with Distributed Knowledge
Repositories
,
FU Berlin, OntoMaven and API4KP, ALIGNED Project Meeting Dec 3, 2015 15
API4KP Metamodel: Classes
A metamodel is a model about models.
Entities in the universe of a KP fall principally into these classes:
Knowledge Sources - Models of the World
Knowledge Environments - Models of Relationships
Knowledge Operations - the Meta-API, Models of APIs
Knowledge Events
,
FU Berlin, OntoMaven and API4KP, ALIGNED Project Meeting Dec 3, 2015 16
API4KP Metamodel: Classes
Entities in the universe of a KP fall principally into these classes:
Knowledge Sources : source of machine-readable information with
semantics.
Knowledge Environments
Knowledge Operations
Knowledge Events
,
FU Berlin, OntoMaven and API4KP, ALIGNED Project Meeting Dec 3, 2015 16
API4KP Metamodel: Classes
Entities in the universe of a KP fall principally into these classes:
Knowledge Sources
Mutable or Immutable (a.k.a Knowledge Resources)
By level of abstraction (Knowledge Source Level)
Basic or Structured
Knowledge Environments
Knowledge Operations
Knowledge Events
,
FU Berlin, OntoMaven and API4KP, ALIGNED Project Meeting Dec 3, 2015 16
API4KP Metamodel: Classes
Entities in the universe of a KP fall principally into these classes:
Knowledge Sources
Mutable or Immutable (a.k.a Knowledge Resources)
By level of abstraction (Knowledge Source Level)
Item - physical source, e.g. on hard disk or in memory
Manifestation - concrete syntax, e.g. OWL axiom in Manchester syntax
Expression - abstract syntax, e.g. OWL axiom
Asset - equivalence class of Knowledge Expressions, with some equivalence
relation e.g. logical equivalence
Basic or Structured
Knowledge Environments
Knowledge Operations
Knowledge Events
,
FU Berlin, OntoMaven and API4KP, ALIGNED Project Meeting Dec 3, 2015 16
API4KP Metamodel: Classes
Entities in the universe of a KP fall principally into these classes:
Knowledge Sources
Knowledge T Environments : mathematical structure of mappings,
where the domain and codomains of the mappings, called members
of the knowledge environment, are instances of class T.
Knowledge Operations
Knowledge Events
,
FU Berlin, OntoMaven and API4KP, ALIGNED Project Meeting Dec 3, 2015 16
API4KP Metamodel: Classes
Entities in the universe of a KP fall principally into these classes:
Knowledge Sources
Knowledge T Environments
Knowledge Operations : functionality (possibly with side-effects. i.e.
effects beyond the output value returned) having a knowledge
source, environment or operation type in its signature.
Knowledge Events
,
FU Berlin, OntoMaven and API4KP, ALIGNED Project Meeting Dec 3, 2015 16
API4KP Metamodel: Classes
Entities in the universe of a KP fall principally into these classes:
Knowledge Sources
Knowledge Environments
Knowledge Operations
Knowledge Events : successful evaluation or execution of a
knowledge operation by a particular application at a particular time
FU Berlin, OntoMaven and API4KP, ALIGNED Project Meeting Dec 3, 2015 16
Outline
1 OMG API4KP – An API for Knowledge Platforms
Scope of the Standard
Scenario: The Connected Patient System
Scenario: Semantic Annotation and Discovery of Biodiversity Data
The API4KP Metamodel
Foundations: Monads
Architecture Styles
2 Repositories with OntoMaven
Motivation
Architecture
Selected Plug-Ins
The Terminology Server Scenario with Distributed Knowledge
Repositories
,
FU Berlin, OntoMaven and API4KP, ALIGNED Project Meeting Dec 3, 2015 17
Structures Needed in API4KP
The various knowledge representations in the scenario require a variety
of structures.
Descriptions of I/O programs for persistent Knowledge Sources, e.g.
the database of the Case History KP.
Unordered collections for declarative Knowledge Sources,
Ordered collections for order-prioritized Knowledge Sources,
Concurrent sequences for streamed Knowledge Sources,
Descriptions of side-effects for active Knowledge Sources,
Failure-aware types for reliable Knowledge Sources,
Descriptions of state transitions for stateful Knowledge Sources,
,
FU Berlin, OntoMaven and API4KP, ALIGNED Project Meeting Dec 3, 2015 18
Structures Needed in API4KP
The various knowledge representations in the scenario require a variety
of structures.
Descriptions of I/O programs for persistent Knowledge Sources,
Unordered collections for declarative Knowledge Sources, e.g. the
OWL ontology in the Stream Processing KP.
Ordered collections for order-prioritized Knowledge Sources,
Concurrent sequences for streamed Knowledge Sources,
Descriptions of side-effects for active Knowledge Sources,
Failure-aware types for reliable Knowledge Sources,
Descriptions of state transitions for stateful Knowledge Sources,
,
FU Berlin, OntoMaven and API4KP, ALIGNED Project Meeting Dec 3, 2015 18
Structures Needed in API4KP
The various knowledge representations in the scenario require a variety
of structures.
Descriptions of I/O programs for persistent Knowledge Sources,
Unordered collections for declarative Knowledge Sources,
Ordered collections for order-prioritized Knowledge Sources, e.g. the
ECA rulebase in the CDS KP.
Concurrent sequences for streamed Knowledge Sources,
Descriptions of side-effects for active Knowledge Sources,
Failure-aware types for reliable Knowledge Sources,
Descriptions of state transitions for stateful Knowledge Sources,
,
FU Berlin, OntoMaven and API4KP, ALIGNED Project Meeting Dec 3, 2015 18
Structures Needed in API4KP
The various knowledge representations in the scenario require a variety
of structures.
Descriptions of I/O programs for persistent Knowledge Sources,
Unordered collections for declarative Knowledge Sources,
Ordered collections for order-prioritized Knowledge Sources,
Concurrent sequences for streamed Knowledge Sources, e.g. the
input and output streams of the Stream Processing KP.
Descriptions of side-effects for active Knowledge Sources,
Failure-aware types for reliable Knowledge Sources,
Descriptions of state transitions for stateful Knowledge Sources,
,
FU Berlin, OntoMaven and API4KP, ALIGNED Project Meeting Dec 3, 2015 18
Structures Needed in API4KP
The various knowledge representations in the scenario require a variety
of structures.
Descriptions of I/O programs for persistent Knowledge Sources,
Unordered collections for declarative Knowledge Sources,
Ordered collections for order-prioritized Knowledge Sources,
Concurrent sequences for streamed Knowledge Sources,
Descriptions of side-effects for active Knowledge Sources, e.g. the
effects generated by the CDS KP.
Failure-aware types for reliable Knowledge Sources,
Descriptions of state transitions for stateful Knowledge Sources,
,
FU Berlin, OntoMaven and API4KP, ALIGNED Project Meeting Dec 3, 2015 18
Structures Needed in API4KP
The various knowledge representations in the scenario require a variety
of structures.
Descriptions of I/O programs for persistent Knowledge Sources,
Unordered collections for declarative Knowledge Sources,
Ordered collections for order-prioritized Knowledge Sources,
Concurrent sequences for streamed Knowledge Sources,
Descriptions of side-effects for active Knowledge Sources,
Failure-aware types for reliable Knowledge Sources, e.g. a failed
communication from the CDS KP.
Descriptions of state transitions for stateful Knowledge Sources,
,
FU Berlin, OntoMaven and API4KP, ALIGNED Project Meeting Dec 3, 2015 18
Structures Needed in API4KP
The various knowledge representations in the scenario require a variety
of structures.
Descriptions of I/O programs for persistent Knowledge Sources,
Unordered collections for declarative Knowledge Sources,
Ordered collections for order-prioritized Knowledge Sources,
Concurrent sequences for streamed Knowledge Sources,
Descriptions of side-effects for active Knowledge Sources,
Failure-aware types for reliable Knowledge Sources,
Descriptions of state transitions for stateful Knowledge Sources, e.g.
ECA simulations for protocol development.
,
FU Berlin, OntoMaven and API4KP, ALIGNED Project Meeting Dec 3, 2015 18
Structures Needed in API4KP
The various knowledge representations in the scenario require a variety
of structures.
Descriptions of I/O programs for persistent Knowledge Sources,
Unordered collections for declarative Knowledge Sources,
Ordered collections for order-prioritized Knowledge Sources,
Concurrent sequences for streamed Knowledge Sources,
Descriptions of side-effects for active Knowledge Sources,
Failure-aware types for reliable Knowledge Sources,
Descriptions of state transitions for stateful Knowledge Sources,
In functional programming, monads have been created for each of these
cases, providing a concept of equivalence that is isolated from
side-effects and non-determinism, which is critical for conceptual
modeling.
,
FU Berlin, OntoMaven and API4KP, ALIGNED Project Meeting Dec 3, 2015 18
Outline
1 OMG API4KP – An API for Knowledge Platforms
Scope of the Standard
Scenario: The Connected Patient System
Scenario: Semantic Annotation and Discovery of Biodiversity Data
The API4KP Metamodel
Foundations: Monads
Architecture Styles
2 Repositories with OntoMaven
Motivation
Architecture
Selected Plug-Ins
The Terminology Server Scenario with Distributed Knowledge
Repositories
,
FU Berlin, OntoMaven and API4KP, ALIGNED Project Meeting Dec 3, 2015 19
API4KP Distributed Architecture Styles
Direct Strongly-Coupled API4KB Access
OntoMaven, RuleMaven
FU Berlin, OntoMaven and API4KP, ALIGNED Project Meeting Dec 3, 2015 20
API4KP Distributed Architecture Styles
Direct Strongly-Coupled API4KB Access
OntoMaven, RuleMaven
Loosely-coupled Remote Invocation via API4KB Interfaces
Request-Reply Protocols
Remote Procedure Calls
Remote Method Invocation
Distributed Components (OntoMaven with Aspect-Oriented Component
Model)
FU Berlin, OntoMaven and API4KP, ALIGNED Project Meeting Dec 3, 2015 20
API4KP Distributed Architecture Styles
Direct Strongly-Coupled API4KB Access
OntoMaven, RuleMaven
Loosely-coupled Remote Invocation via API4KB Interfaces
Request-Reply Protocols
Remote Procedure Calls
Remote Method Invocation
Distributed Components (OntoMaven with Aspect-Oriented Component
Model)
Decoupled Indirect Communication
Publish Subscribe and Distributed Event Based Systems
Group communication (broadcast/multicast)
Shared Resources (Tuple Spaces, Distributed Shared Memory, . . . )
Asynchronous Messaging (ZeroMQ, Erlang/RabbitMQ, OpenESB, Mule
ESB, . . . )
,
FU Berlin, OntoMaven and API4KP, ALIGNED Project Meeting Dec 3, 2015 20
Participants
Tara Athan, Athan Services (athant.com), West Lafayette, Indiana,
USA, taraathan@gmail.com
Roy Bell, Raytheon, Fort Wayne, Indiana, USA,
Roy_M_Bell@raytheon.com
Elisa Kendall, Thematix Partners LLC, New York, New York, USA,
ekendall@thematix.com
Adrian Paschke, AG Corporate Semantic Web, Freie Universitaet
Berlin, Germany, paschke@inf.fu-berlin.de
Ralph Schaefermeier, AG Corporate Semantic Web, Freie Universitaet
Berlin, Germany, schaef@inf.fu-berlin.de
Davide Sottara, Department of Biomedical Informatics, Arizona State
University, USA, davide.sottara@asu.edu
,
FU Berlin, OntoMaven and API4KP, ALIGNED Project Meeting Dec 3, 2015 21
Outline
1 OMG API4KP – An API for Knowledge Platforms
Scope of the Standard
Scenario: The Connected Patient System
Scenario: Semantic Annotation and Discovery of Biodiversity Data
The API4KP Metamodel
Foundations: Monads
Architecture Styles
2 Repositories with OntoMaven
Motivation
Architecture
Selected Plug-Ins
The Terminology Server Scenario with Distributed Knowledge
Repositories
,
FU Berlin, OntoMaven and API4KP, ALIGNED Project Meeting Dec 3, 2015 24
Ontology Project Life Cycle Management
Avoid manual steps
Reuse/import, rename, refactor, merge, test, deploy, . . .
Pass documentation and configuration information
FU Berlin, OntoMaven and API4KP, ALIGNED Project Meeting Dec 3, 2015 25
Ontology Project Life Cycle Management
Avoid manual steps
Reuse/import, rename, refactor, merge, test, deploy, . . .
Pass documentation and configuration information
Work collaboratively, but support local development
Remote and local repositories (even without Internet connection)
FU Berlin, OntoMaven and API4KP, ALIGNED Project Meeting Dec 3, 2015 25
Ontology Project Life Cycle Management
Avoid manual steps
Reuse/import, rename, refactor, merge, test, deploy, . . .
Pass documentation and configuration information
Work collaboratively, but support local development
Remote and local repositories (even without Internet connection)
Automatically process resources
Manage dependencies and development + deployment properties
FU Berlin, OntoMaven and API4KP, ALIGNED Project Meeting Dec 3, 2015 25
Ontology Project Life Cycle Management
Avoid manual steps
Reuse/import, rename, refactor, merge, test, deploy, . . .
Pass documentation and configuration information
Work collaboratively, but support local development
Remote and local repositories (even without Internet connection)
Automatically process resources
Manage dependencies and development + deployment properties
Share ontology resources across projects
Ontology artifacts including metadata, documentation, tests, . . .
,
FU Berlin, OntoMaven and API4KP, ALIGNED Project Meeting Dec 3, 2015 25
Outline
1 OMG API4KP – An API for Knowledge Platforms
Scope of the Standard
Scenario: The Connected Patient System
Scenario: Semantic Annotation and Discovery of Biodiversity Data
The API4KP Metamodel
Foundations: Monads
Architecture Styles
2 Repositories with OntoMaven
Motivation
Architecture
Selected Plug-Ins
The Terminology Server Scenario with Distributed Knowledge
Repositories
,
FU Berlin, OntoMaven and API4KP, ALIGNED Project Meeting Dec 3, 2015 26
OntoMaven – Apache Maven Extension
Ontology Artifacts
Managed by groupID, artifactID, and version
FU Berlin, OntoMaven and API4KP, ALIGNED Project Meeting Dec 3, 2015 27
OntoMaven – Apache Maven Extension
Ontology Artifacts
Managed by groupID, artifactID, and version
Ontology Repositories
Local and remote repositories used to store artifacts (ontologies,
plug-ins, resources, test suites etc.)
FU Berlin, OntoMaven and API4KP, ALIGNED Project Meeting Dec 3, 2015 27
OntoMaven – Apache Maven Extension
Ontology Artifacts
Managed by groupID, artifactID, and version
Ontology Repositories
Local and remote repositories used to store artifacts (ontologies,
plug-ins, resources, test suites etc.)
OntoMaven Plug-ins
Implement the ontology project life cycle management functionalities
Goals provide interfaces bundled to life cycle phases
FU Berlin, OntoMaven and API4KP, ALIGNED Project Meeting Dec 3, 2015 27
OntoMaven – Apache Maven Extension
Ontology Artifacts
Managed by groupID, artifactID, and version
Ontology Repositories
Local and remote repositories used to store artifacts (ontologies,
plug-ins, resources, test suites etc.)
OntoMaven Plug-ins
Implement the ontology project life cycle management functionalities
Goals provide interfaces bundled to life cycle phases
Project Ontology Model
POM.xml – Declarative project description and configuration
,
FU Berlin, OntoMaven and API4KP, ALIGNED Project Meeting Dec 3, 2015 27
POM.xml
<project>
<modelVersion>...</modelVersion>
<groupId>...</groupId>
<artifactId>...</artifactId>
<version>...</version>
...
</project>
,
FU Berlin, OntoMaven and API4KP, ALIGNED Project Meeting Dec 3, 2015 28
The Maven Repository Architecture
Image source: http://tutorials.jenkov.com/maven/maven-tutorial.html ,
FU Berlin, OntoMaven and API4KP, ALIGNED Project Meeting Dec 3, 2015 29
Outline
1 OMG API4KP – An API for Knowledge Platforms
Scope of the Standard
Scenario: The Connected Patient System
Scenario: Semantic Annotation and Discovery of Biodiversity Data
The API4KP Metamodel
Foundations: Monads
Architecture Styles
2 Repositories with OntoMaven
Motivation
Architecture
Selected Plug-Ins
The Terminology Server Scenario with Distributed Knowledge
Repositories
,
FU Berlin, OntoMaven and API4KP, ALIGNED Project Meeting Dec 3, 2015 30
OntoMaven – Selected Plug-Ins
Import Dependency Management
Documentation
Versioning
Testing with Test Suites
Aspect-Oriented Development and Module Selection
. . .
,
FU Berlin, OntoMaven and API4KP, ALIGNED Project Meeting Dec 3, 2015 31
Import and Dependency Management Plug-In
???.owl
Import
Ontology
Parse Ontology
exist?
Return Result List
(List of imported and
not imported Ontologies)
yes
no
save? end
Save Ontology
in Local
Repository
yes
no
Create
XMLCatalog
Return
Result List
(List of local
ontologies and
XMLCatalog with
local references)
Figure: Importation of an ontology into the local repository.
,
FU Berlin, OntoMaven and API4KP, ALIGNED Project Meeting Dec 3, 2015 32
Ontology Artifacts
Archiva
Repostory
Manager
Dependencies
,
FU Berlin, OntoMaven and API4KP, ALIGNED Project Meeting Dec 3, 2015 33
Ontology Artifacts in Remote Repository
<profiles> <profile>
<id>2</id>
<activation> <activeByDefault>true</activeByDefault>
</activation>
<repositories> <repository>
<snapshots> <enabled>true</enabled> </snapshots>
<id>snapshots</id>
<name>OntoMaven Snapshot Repository</name>
<url>http://www.corporate−semantic−web.de/repository/
snapshots/</url>
...
</profiles>
<dependencies> <dependency>
<groupId>xfront.com.owl.ontologies</groupId>
<artifactId>Camera−OWL−Ontology</artifactId>
<version>1.0−SNAPSHOT</version> <type>owl</type>
</dependency> </dependencies>
,
FU Berlin, OntoMaven and API4KP, ALIGNED Project Meeting Dec 3, 2015 34
Report Plug-In – Documentation
<description>here’s the description of an ontology
</description>
<organization>
<name>Corporate Semantic Web, Freie Universitaet
Berlin</name>
<url>http://www.corporate−semantic−web.de</url>
</organization>
<inceptionYear>2013</inceptionYear>
<licenses> <license>
<name>LGPL−3.0</name>
<url>http://www.gnu.org/licenses/lgpl.txt</url>
</license></licenses>
<developers> <developer>
<name>Adrian Paschke</name>
<email>paschke@inf.fu−berlin.d</email>
<organization>Corporate Semantic Web</
organization>
<organizationUrl>http://www.corporate−semantic−
web.de/
</organizationUrl>
<roles> <role>developer</role> </roles>
</developer></developers>
,
FU Berlin, OntoMaven and API4KP, ALIGNED Project Meeting Dec 3, 2015 35
Ontology Report
,
FU Berlin, OntoMaven and API4KP, ALIGNED Project Meeting Dec 3, 2015 36
Technical Report
,
FU Berlin, OntoMaven and API4KP, ALIGNED Project Meeting Dec 3, 2015 37
Visualization Report
,
FU Berlin, OntoMaven and API4KP, ALIGNED Project Meeting Dec 3, 2015 38
Versioning Plug-In – SVont
Plug-In SVN Command Description
checkout Check out working copy from project
achieve
status Status of the working copy
diff Diff between two revisions or paths
commit Commit working copy to repository
info Info about repository and working copy
Iteration nIteration n-1…Iteration 2Iteration 1
Version 1
Version 1
Version 2.1Version 2
Version 1 Version 1
Version 2.x
Version 3 Version 3.1
Version 4
,
FU Berlin, OntoMaven and API4KP, ALIGNED Project Meeting Dec 3, 2015 39
OntoMaven – Plug-In Goal ”diff“
-------------------------- DIFF INFORMATION ------------------------
Ontology File : ...............camera.owl
================== ACTUAL CHANGES ==================================
Axioms were added to the repository, or deleted from the working copy.
SubClassOf(<http://www.xfront.com/ontologies/camera/#Money> owl:Thing)
Declaration(Class(<http://www.xfront.com/ontologies/camera/#Money>))
====================================================================
------------------ MORE INFO ---------------------------------------
The above changes of the OWL classes are dependent on the axioms:
currency <------ DataProperty (Domain)
cost <------ ObjectProperty (Range)
--------------------------------------------------------------------
,
FU Berlin, OntoMaven and API4KP, ALIGNED Project Meeting Dec 3, 2015 40
SVont – Subversion for Ontologies
,
FU Berlin, OntoMaven and API4KP, ALIGNED Project Meeting Dec 3, 2015 41
SVont – Commit Workflow
Client
SVoNt Server
SVN Server SVoNt Extension
Precommit
Hook
commit
Error
Consistency
Check
consistent
Change	
Detection
changes
Change	Writer
Change	
Log
Process
Commit
Process
Commit
no yes
no
yes
Ontology File
,
FU Berlin, OntoMaven and API4KP, ALIGNED Project Meeting Dec 3, 2015 42
Test Plug-In – Test Cases for KBs
§ Test Cases constrain the possible models and approximate the intended models of
the knowledge base
§ Queries are used to test the rule base
§ A test case is defined by T := {X, A, N}, where
§ assertion base (input data, e.g. facts )
§ a formula denoting a test query
§ N := + , – a positive or negative label
§ Semantics
§ |=TC compatibility relation
§ Mod association function between sets of formulas and sets of models
§ Σ model selection function
for T:={X, A, +} and for T:={X,A,-}
§ CR(X) deductive closure of X. Decidable inference operator based on formal proofs
LX ⊆
LA∈
)(R)(Mod(X),m:Mmiff)A,(X,|M 0TC0 AModm∈⇒∑∈∈∀+=
)(R)(Mod(X),m:Mmiff)A,(X,|M 0TC0 AModm∉⇒∑∈∈∃−=
)(XCA R∈)(XCA R∉
+
Intended
Model
Partial
Model
+ +
-
Test Cases (+,-)
inconsistent:
+
Intended
Model
+ +
-
Test Cases (+,-)
consistent:
-
,
FU Berlin, OntoMaven and API4KP, ALIGNED Project Meeting Dec 3, 2015 43
POM.xml Test Plug-In Configuration
<plugin>
<groupId>de.csw.MvnOnt</groupId>
<artifactId>MvnOwlTest</artifactId>
<version>1.0−SNAPSHOT</version>
<configuration><owlfile>owl/1a.owl</owlfile></configuration>
<executions><execution><goals><goal>owltest</goal>
</goals></execution></executions>
</plugin>
<plugin>
<groupId>de.csw.MvnOnt</groupId>
<artifactId>MvnOwlEntailment</artifactId>
<version>1.0−SNAPSHOT</version>
<configuration>
<premise_file>owl/1a.owl</premise_file>
<conclusion_file>owl/1aconclusion.owl</conclusion_file>
</configuration><executions><execution>
<goals><goal>owlentailment</goal></goals>
</execution></executions></plugin></plugins> ,
FU Berlin, OntoMaven and API4KP, ALIGNED Project Meeting Dec 3, 2015 44
Aspect-Oriented Ontologies
Aspect definition
by quantification
Query Manual annotation/
selected editing
context in tool
Original ontology
Ontology with
aspect annotations
Aspect-based
module selection
Aspect names
or descriptions
Ontology
module
Ontology module selection
as an OntoMaven goal
,
FU Berlin, OntoMaven and API4KP, ALIGNED Project Meeting Dec 3, 2015 45
Declarative Module Selection with Aspects
and OntoMaven
nual annotation/
ected editing
text in tool
Ontology with
aspect annotations
Aspect-based
module selection
Aspect names
or descriptions
Ontology
module
Ontology module selection
as an OntoMaven goal
<userAspects>
<aspect>http://example.org/reputation#Reputation123</aspect>
<aspect>http://example.org/provenance#prov_789</aspect>
<aspect>http://example.org/time#TimeInterval1</aspect>
</userAspects>
,
FU Berlin, OntoMaven and API4KP, ALIGNED Project Meeting Dec 3, 2015 46
Outline
1 OMG API4KP – An API for Knowledge Platforms
Scope of the Standard
Scenario: The Connected Patient System
Scenario: Semantic Annotation and Discovery of Biodiversity Data
The API4KP Metamodel
Foundations: Monads
Architecture Styles
2 Repositories with OntoMaven
Motivation
Architecture
Selected Plug-Ins
The Terminology Server Scenario with Distributed Knowledge
Repositories
,
FU Berlin, OntoMaven and API4KP, ALIGNED Project Meeting Dec 3, 2015 47
Terminology Server Scenario with OntoMaven
Ontologies,
vocabularies and
external sources
configurable as
OntoMaven
dependencies.
Easy to add new
resources.
Fast deployment of
test instances with
different knowledge
sources.
Context-based
deployment of
knowledge
components with
aspect-orientation.
API4KP
API4KP
SKOS RDF
OWL
Web Services Client
HTTP Server
Semantic Web Repository
(Virtuoso)
HTTP
request
Serialization format
(RDF/XML,JSON,JSON LD,…)
External Web Services
requestor
Local
repository
Local
repository
Local
repository
Central
repository
OntoMaven
OntoMavenexternaldependencies
<pom>
Compontents
• contracts
• provided and required
interfaces
,
FU Berlin, OntoMaven and API4KP, ALIGNED Project Meeting Dec 3, 2015 48
Summary
The Terminology Server scenario encompasses a number of
architectural paradigms and KR requirements addressed by API4KP.
API4KP shows high ontological completeness and clarity with respect
to the Bunge-Wand-Weber reference model.
FU Berlin, OntoMaven and API4KP, ALIGNED Project Meeting Dec 3, 2015 49
Summary
The Terminology Server scenario encompasses a number of
architectural paradigms and KR requirements addressed by API4KP.
API4KP shows high ontological completeness and clarity with respect
to the Bunge-Wand-Weber reference model.
OntoMaven automates and supports the life cycle management of
ontology projects and ontology artifacts
Declarative description in POM defining project conventions and APIs
Additional resource directories
Plug-in configuration
Artifact libraries
Repository and deployment configuration
Aspect-orientation for context-based knowledge resource selection
. . .
API4KP and OntoMaven allow integration and exchange of
heterogeneous and distributed knowledge and data sources
in a declarative fashion
along with metadata, interface descriptions, and test cases
,
FU Berlin, OntoMaven and API4KP, ALIGNED Project Meeting Dec 3, 2015 49
Related Publications I
R. Schäfermeier, L. Krus, and A. Paschke, “An aspect-oriented extension to the owl api –
specifying and composing views of owl ontologies using ontology aspects and java
annotations,” in KEOD 2015: 7th International Conference on Knowledge Engineering
and Ontology Development, vol. 2, pp. 187–194, 2015.
A. Paschke, “Provalets - OSGi-based Prova Agents for Rule-Based Data Access,” in
Proceedings of the 14th International Conference on Ontologies, Databases and
Applications of Semantics (ODBASE) 2015, Rhodes, Greece, October 26-30, 2015, 2015.
T. Athan, R. Bell, E. F. Kendall, A. Paschke, and D. Sottara, “API4KP metamodel: A
meta-api for heterogeneous knowledge platforms,” in Rule Technologies: Foundations,
Tools, and Applications - 9th International Symposium, RuleML 2015, Berlin, Germany,
August 2-5, 2015, Proceedings, p. 144–160, 2015.
A. Paschke, T. Athan, D. Sottara, E. F. Kendall, and R. Bell, “A representational analysis of
the API4KP metamodel,” in Formal Ontologies Meet Industry - 7th International
Workshop, FOMI 2015, Berlin, Germany, August 5, 2015, Proceedings, p. 1–12, 2015.
A. Paschke and R. Schäfermeier, “Aspect OntoMaven — Aspect-Oriented Ontology
Development and Configuration With OntoMaven,” in 3rd Workshop on Formal Semantics
for the Future Enterprise (FSFE 2015), Business Information Systems Workshops
(W. Abramowicz, ed.), vol. 228, Springer, 2015.
,
FU Berlin, OntoMaven and API4KP, ALIGNED Project Meeting Dec 3, 2015 50
Related Publications II
R. Schäfermeier and A. Paschke, Verteilte und agile Ontologieentwicklung, pp. 341–358.
X.media.press, Springer Berlin Heidelberg, 2015.
R. Schäfermeier and A. Paschke, “Aspect-Oriented Ontologies: Dynamic Modularization
Using Ontological Metamodeling,” in Proceedings of the 8th International Conference on
Formal Ontology in Information Systems (FOIS 2014), pp. 199 – 212, IOS Press, 2014.
R. Schäfermeier, T. Athan, and A. Paschke, “Common Logic Importation Resolution
Implemented in OntoMaven,” in Proceedings of the 8th International Workshop on
Modular Ontologies @FOIS 2014" (WoMO 2014), 2014.
A. Paschke, “OntoMaven: Maven-based Ontology Development and Management of
Distributed Ontology Repositories,” arXiv:1309.7341 [cs], Sept. 2013.
R. Schäfermeier, “Aspect-Oriented Ontology Development,” in Business Information
Systems Workshops (W. Abramowicz, ed.), no. 160 in Lecture Notes in Business
Information Processing, pp. 208–219, Springer Berlin Heidelberg, 2013.
R. Schäfermeier and A. Paschke, “Towards a Unified Approach to Modular Ontology
Development Using the Aspect-Oriented Paradigm,” in 7th International Workshop on
Modular Ontologies (WoMO) 2013, p. 73, 2013.
A. Paschke, “OntoMaven API4KB - A Maven-based API for Knowledge Bases,” in SWAT4LS,
2013.
,
FU Berlin, OntoMaven and API4KP, ALIGNED Project Meeting Dec 3, 2015 51
Related Publications III
A. Paschke, “OntoMaven: Maven-based Ontology Development and Management of
Distributed Ontology Repositories,” 2013.
,
FU Berlin, OntoMaven and API4KP, ALIGNED Project Meeting Dec 3, 2015 52

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OntoMaven Repositories and OMG API4KP

  • 1. OntoMaven Repositories and OMG API4KP Ralph Schäfermeier Adrian Paschke Freie Universität Berlin ALIGNED Project Meeting Dec 3
  • 2. Outline 1 OMG API4KP – An API for Knowledge Platforms Scope of the Standard Scenario: The Connected Patient System Scenario: Semantic Annotation and Discovery of Biodiversity Data The API4KP Metamodel Foundations: Monads Architecture Styles 2 Repositories with OntoMaven Motivation Architecture Selected Plug-Ins The Terminology Server Scenario with Distributed Knowledge Repositories , FU Berlin, OntoMaven and API4KP, ALIGNED Project Meeting Dec 3, 2015 2
  • 3. Outline 1 OMG API4KP – An API for Knowledge Platforms Scope of the Standard Scenario: The Connected Patient System Scenario: Semantic Annotation and Discovery of Biodiversity Data The API4KP Metamodel Foundations: Monads Architecture Styles 2 Repositories with OntoMaven Motivation Architecture Selected Plug-Ins The Terminology Server Scenario with Distributed Knowledge Repositories , FU Berlin, OntoMaven and API4KP, ALIGNED Project Meeting Dec 3, 2015 3
  • 4. A Meta-API for Knowledge (Reasoning) Platforms (KPs) A Meta-API is a platform-independent model (PIM) for a family of APIs in specific languages, also called PSMs (platform-specific models). API4KP provides a PIM for the external APIs of KPs. Figure: A Monolithic KP Architecture. FU Berlin, OntoMaven and API4KP, ALIGNED Project Meeting Dec 3, 2015 4
  • 5. Languages in Scope Knowledge Representation and Reasoning Languages Resource Description Framework (RDF) RDF Schema (RDFS) Web Ontology Language (OWL) Common Logic (CL) Event-Condition-Action RuleML (ECA) . . . Data Representation Languages Extensible Messaging and Presence Protocol (XMPP) JSON . . . , FU Berlin, OntoMaven and API4KP, ALIGNED Project Meeting Dec 3, 2015 6
  • 6. Outline 1 OMG API4KP – An API for Knowledge Platforms Scope of the Standard Scenario: The Connected Patient System Scenario: Semantic Annotation and Discovery of Biodiversity Data The API4KP Metamodel Foundations: Monads Architecture Styles 2 Repositories with OntoMaven Motivation Architecture Selected Plug-Ins The Terminology Server Scenario with Distributed Knowledge Repositories , FU Berlin, OntoMaven and API4KP, ALIGNED Project Meeting Dec 3, 2015 7
  • 7. The Connected Patient System 0: Overview Figure: A Distributed KP Architecture for Stream Processing, Clinical Decision Support (CDS) and Case History Storage. , FU Berlin, OntoMaven and API4KP, ALIGNED Project Meeting Dec 3, 2015 8
  • 8. The Connected Patient System I: Streaming Data and Query Results Biomedical devices are available via pub-sub. Streamed data arrive in multiple formats e.g. XMPP, RDF Vocabularies are defined in RDFS, OWL, Common Logic (CL). Healthcare providers submit SPARQL queries through API4KP, receiving streamed incremental results, updated as new data arrive. Figure: A Heterogeneous Stream Processing KP Architecture. , FU Berlin, OntoMaven and API4KP, ALIGNED Project Meeting Dec 3, 2015 9
  • 9. The Connected Patient System II: CDS A Clinical Decision Support System (CDS) is defined using event-condition-action (ECA) rules submited through API4KP, reacting to simple events (e.g. a vital parameter exceeding a threshold) complex events (e.g. a decreasing trend in the average daily physical activity) intervening with alerts and reminders. A failure of response (through API4KP) to an alert leads to escalation to another recipient. Figure: A Clinical Decision Support (CDS) KP Architecture. , FU Berlin, OntoMaven and API4KP, ALIGNED Project Meeting Dec 3, 2015 10
  • 10. The Connected Patient System: Complete Figure: A Distributed KP Architecture. , FU Berlin, OntoMaven and API4KP, ALIGNED Project Meeting Dec 3, 2015 12
  • 11. Outline 1 OMG API4KP – An API for Knowledge Platforms Scope of the Standard Scenario: The Connected Patient System Scenario: Semantic Annotation and Discovery of Biodiversity Data The API4KP Metamodel Foundations: Monads Architecture Styles 2 Repositories with OntoMaven Motivation Architecture Selected Plug-Ins The Terminology Server Scenario with Distributed Knowledge Repositories , FU Berlin, OntoMaven and API4KP, ALIGNED Project Meeting Dec 3, 2015 13
  • 12. GFBio Terminology Server API4KP API4KP SKOS RDF OWL Web Services Client HTTP Server Semantic Web Repository (Virtuoso) HTTP request Serialization format (RDF/XML,JSON,JSON LD,…) External Web Services requestor , FU Berlin, OntoMaven and API4KP, ALIGNED Project Meeting Dec 3, 2015 14
  • 13. Outline 1 OMG API4KP – An API for Knowledge Platforms Scope of the Standard Scenario: The Connected Patient System Scenario: Semantic Annotation and Discovery of Biodiversity Data The API4KP Metamodel Foundations: Monads Architecture Styles 2 Repositories with OntoMaven Motivation Architecture Selected Plug-Ins The Terminology Server Scenario with Distributed Knowledge Repositories , FU Berlin, OntoMaven and API4KP, ALIGNED Project Meeting Dec 3, 2015 15
  • 14. API4KP Metamodel: Classes A metamodel is a model about models. Entities in the universe of a KP fall principally into these classes: Knowledge Sources - Models of the World Knowledge Environments - Models of Relationships Knowledge Operations - the Meta-API, Models of APIs Knowledge Events , FU Berlin, OntoMaven and API4KP, ALIGNED Project Meeting Dec 3, 2015 16
  • 15. API4KP Metamodel: Classes Entities in the universe of a KP fall principally into these classes: Knowledge Sources : source of machine-readable information with semantics. Knowledge Environments Knowledge Operations Knowledge Events , FU Berlin, OntoMaven and API4KP, ALIGNED Project Meeting Dec 3, 2015 16
  • 16. API4KP Metamodel: Classes Entities in the universe of a KP fall principally into these classes: Knowledge Sources Mutable or Immutable (a.k.a Knowledge Resources) By level of abstraction (Knowledge Source Level) Basic or Structured Knowledge Environments Knowledge Operations Knowledge Events , FU Berlin, OntoMaven and API4KP, ALIGNED Project Meeting Dec 3, 2015 16
  • 17. API4KP Metamodel: Classes Entities in the universe of a KP fall principally into these classes: Knowledge Sources Mutable or Immutable (a.k.a Knowledge Resources) By level of abstraction (Knowledge Source Level) Item - physical source, e.g. on hard disk or in memory Manifestation - concrete syntax, e.g. OWL axiom in Manchester syntax Expression - abstract syntax, e.g. OWL axiom Asset - equivalence class of Knowledge Expressions, with some equivalence relation e.g. logical equivalence Basic or Structured Knowledge Environments Knowledge Operations Knowledge Events , FU Berlin, OntoMaven and API4KP, ALIGNED Project Meeting Dec 3, 2015 16
  • 18. API4KP Metamodel: Classes Entities in the universe of a KP fall principally into these classes: Knowledge Sources Knowledge T Environments : mathematical structure of mappings, where the domain and codomains of the mappings, called members of the knowledge environment, are instances of class T. Knowledge Operations Knowledge Events , FU Berlin, OntoMaven and API4KP, ALIGNED Project Meeting Dec 3, 2015 16
  • 19. API4KP Metamodel: Classes Entities in the universe of a KP fall principally into these classes: Knowledge Sources Knowledge T Environments Knowledge Operations : functionality (possibly with side-effects. i.e. effects beyond the output value returned) having a knowledge source, environment or operation type in its signature. Knowledge Events , FU Berlin, OntoMaven and API4KP, ALIGNED Project Meeting Dec 3, 2015 16
  • 20. API4KP Metamodel: Classes Entities in the universe of a KP fall principally into these classes: Knowledge Sources Knowledge Environments Knowledge Operations Knowledge Events : successful evaluation or execution of a knowledge operation by a particular application at a particular time FU Berlin, OntoMaven and API4KP, ALIGNED Project Meeting Dec 3, 2015 16
  • 21. Outline 1 OMG API4KP – An API for Knowledge Platforms Scope of the Standard Scenario: The Connected Patient System Scenario: Semantic Annotation and Discovery of Biodiversity Data The API4KP Metamodel Foundations: Monads Architecture Styles 2 Repositories with OntoMaven Motivation Architecture Selected Plug-Ins The Terminology Server Scenario with Distributed Knowledge Repositories , FU Berlin, OntoMaven and API4KP, ALIGNED Project Meeting Dec 3, 2015 17
  • 22. Structures Needed in API4KP The various knowledge representations in the scenario require a variety of structures. Descriptions of I/O programs for persistent Knowledge Sources, e.g. the database of the Case History KP. Unordered collections for declarative Knowledge Sources, Ordered collections for order-prioritized Knowledge Sources, Concurrent sequences for streamed Knowledge Sources, Descriptions of side-effects for active Knowledge Sources, Failure-aware types for reliable Knowledge Sources, Descriptions of state transitions for stateful Knowledge Sources, , FU Berlin, OntoMaven and API4KP, ALIGNED Project Meeting Dec 3, 2015 18
  • 23. Structures Needed in API4KP The various knowledge representations in the scenario require a variety of structures. Descriptions of I/O programs for persistent Knowledge Sources, Unordered collections for declarative Knowledge Sources, e.g. the OWL ontology in the Stream Processing KP. Ordered collections for order-prioritized Knowledge Sources, Concurrent sequences for streamed Knowledge Sources, Descriptions of side-effects for active Knowledge Sources, Failure-aware types for reliable Knowledge Sources, Descriptions of state transitions for stateful Knowledge Sources, , FU Berlin, OntoMaven and API4KP, ALIGNED Project Meeting Dec 3, 2015 18
  • 24. Structures Needed in API4KP The various knowledge representations in the scenario require a variety of structures. Descriptions of I/O programs for persistent Knowledge Sources, Unordered collections for declarative Knowledge Sources, Ordered collections for order-prioritized Knowledge Sources, e.g. the ECA rulebase in the CDS KP. Concurrent sequences for streamed Knowledge Sources, Descriptions of side-effects for active Knowledge Sources, Failure-aware types for reliable Knowledge Sources, Descriptions of state transitions for stateful Knowledge Sources, , FU Berlin, OntoMaven and API4KP, ALIGNED Project Meeting Dec 3, 2015 18
  • 25. Structures Needed in API4KP The various knowledge representations in the scenario require a variety of structures. Descriptions of I/O programs for persistent Knowledge Sources, Unordered collections for declarative Knowledge Sources, Ordered collections for order-prioritized Knowledge Sources, Concurrent sequences for streamed Knowledge Sources, e.g. the input and output streams of the Stream Processing KP. Descriptions of side-effects for active Knowledge Sources, Failure-aware types for reliable Knowledge Sources, Descriptions of state transitions for stateful Knowledge Sources, , FU Berlin, OntoMaven and API4KP, ALIGNED Project Meeting Dec 3, 2015 18
  • 26. Structures Needed in API4KP The various knowledge representations in the scenario require a variety of structures. Descriptions of I/O programs for persistent Knowledge Sources, Unordered collections for declarative Knowledge Sources, Ordered collections for order-prioritized Knowledge Sources, Concurrent sequences for streamed Knowledge Sources, Descriptions of side-effects for active Knowledge Sources, e.g. the effects generated by the CDS KP. Failure-aware types for reliable Knowledge Sources, Descriptions of state transitions for stateful Knowledge Sources, , FU Berlin, OntoMaven and API4KP, ALIGNED Project Meeting Dec 3, 2015 18
  • 27. Structures Needed in API4KP The various knowledge representations in the scenario require a variety of structures. Descriptions of I/O programs for persistent Knowledge Sources, Unordered collections for declarative Knowledge Sources, Ordered collections for order-prioritized Knowledge Sources, Concurrent sequences for streamed Knowledge Sources, Descriptions of side-effects for active Knowledge Sources, Failure-aware types for reliable Knowledge Sources, e.g. a failed communication from the CDS KP. Descriptions of state transitions for stateful Knowledge Sources, , FU Berlin, OntoMaven and API4KP, ALIGNED Project Meeting Dec 3, 2015 18
  • 28. Structures Needed in API4KP The various knowledge representations in the scenario require a variety of structures. Descriptions of I/O programs for persistent Knowledge Sources, Unordered collections for declarative Knowledge Sources, Ordered collections for order-prioritized Knowledge Sources, Concurrent sequences for streamed Knowledge Sources, Descriptions of side-effects for active Knowledge Sources, Failure-aware types for reliable Knowledge Sources, Descriptions of state transitions for stateful Knowledge Sources, e.g. ECA simulations for protocol development. , FU Berlin, OntoMaven and API4KP, ALIGNED Project Meeting Dec 3, 2015 18
  • 29. Structures Needed in API4KP The various knowledge representations in the scenario require a variety of structures. Descriptions of I/O programs for persistent Knowledge Sources, Unordered collections for declarative Knowledge Sources, Ordered collections for order-prioritized Knowledge Sources, Concurrent sequences for streamed Knowledge Sources, Descriptions of side-effects for active Knowledge Sources, Failure-aware types for reliable Knowledge Sources, Descriptions of state transitions for stateful Knowledge Sources, In functional programming, monads have been created for each of these cases, providing a concept of equivalence that is isolated from side-effects and non-determinism, which is critical for conceptual modeling. , FU Berlin, OntoMaven and API4KP, ALIGNED Project Meeting Dec 3, 2015 18
  • 30. Outline 1 OMG API4KP – An API for Knowledge Platforms Scope of the Standard Scenario: The Connected Patient System Scenario: Semantic Annotation and Discovery of Biodiversity Data The API4KP Metamodel Foundations: Monads Architecture Styles 2 Repositories with OntoMaven Motivation Architecture Selected Plug-Ins The Terminology Server Scenario with Distributed Knowledge Repositories , FU Berlin, OntoMaven and API4KP, ALIGNED Project Meeting Dec 3, 2015 19
  • 31. API4KP Distributed Architecture Styles Direct Strongly-Coupled API4KB Access OntoMaven, RuleMaven FU Berlin, OntoMaven and API4KP, ALIGNED Project Meeting Dec 3, 2015 20
  • 32. API4KP Distributed Architecture Styles Direct Strongly-Coupled API4KB Access OntoMaven, RuleMaven Loosely-coupled Remote Invocation via API4KB Interfaces Request-Reply Protocols Remote Procedure Calls Remote Method Invocation Distributed Components (OntoMaven with Aspect-Oriented Component Model) FU Berlin, OntoMaven and API4KP, ALIGNED Project Meeting Dec 3, 2015 20
  • 33. API4KP Distributed Architecture Styles Direct Strongly-Coupled API4KB Access OntoMaven, RuleMaven Loosely-coupled Remote Invocation via API4KB Interfaces Request-Reply Protocols Remote Procedure Calls Remote Method Invocation Distributed Components (OntoMaven with Aspect-Oriented Component Model) Decoupled Indirect Communication Publish Subscribe and Distributed Event Based Systems Group communication (broadcast/multicast) Shared Resources (Tuple Spaces, Distributed Shared Memory, . . . ) Asynchronous Messaging (ZeroMQ, Erlang/RabbitMQ, OpenESB, Mule ESB, . . . ) , FU Berlin, OntoMaven and API4KP, ALIGNED Project Meeting Dec 3, 2015 20
  • 34. Participants Tara Athan, Athan Services (athant.com), West Lafayette, Indiana, USA, taraathan@gmail.com Roy Bell, Raytheon, Fort Wayne, Indiana, USA, Roy_M_Bell@raytheon.com Elisa Kendall, Thematix Partners LLC, New York, New York, USA, ekendall@thematix.com Adrian Paschke, AG Corporate Semantic Web, Freie Universitaet Berlin, Germany, paschke@inf.fu-berlin.de Ralph Schaefermeier, AG Corporate Semantic Web, Freie Universitaet Berlin, Germany, schaef@inf.fu-berlin.de Davide Sottara, Department of Biomedical Informatics, Arizona State University, USA, davide.sottara@asu.edu , FU Berlin, OntoMaven and API4KP, ALIGNED Project Meeting Dec 3, 2015 21
  • 35. Outline 1 OMG API4KP – An API for Knowledge Platforms Scope of the Standard Scenario: The Connected Patient System Scenario: Semantic Annotation and Discovery of Biodiversity Data The API4KP Metamodel Foundations: Monads Architecture Styles 2 Repositories with OntoMaven Motivation Architecture Selected Plug-Ins The Terminology Server Scenario with Distributed Knowledge Repositories , FU Berlin, OntoMaven and API4KP, ALIGNED Project Meeting Dec 3, 2015 24
  • 36. Ontology Project Life Cycle Management Avoid manual steps Reuse/import, rename, refactor, merge, test, deploy, . . . Pass documentation and configuration information FU Berlin, OntoMaven and API4KP, ALIGNED Project Meeting Dec 3, 2015 25
  • 37. Ontology Project Life Cycle Management Avoid manual steps Reuse/import, rename, refactor, merge, test, deploy, . . . Pass documentation and configuration information Work collaboratively, but support local development Remote and local repositories (even without Internet connection) FU Berlin, OntoMaven and API4KP, ALIGNED Project Meeting Dec 3, 2015 25
  • 38. Ontology Project Life Cycle Management Avoid manual steps Reuse/import, rename, refactor, merge, test, deploy, . . . Pass documentation and configuration information Work collaboratively, but support local development Remote and local repositories (even without Internet connection) Automatically process resources Manage dependencies and development + deployment properties FU Berlin, OntoMaven and API4KP, ALIGNED Project Meeting Dec 3, 2015 25
  • 39. Ontology Project Life Cycle Management Avoid manual steps Reuse/import, rename, refactor, merge, test, deploy, . . . Pass documentation and configuration information Work collaboratively, but support local development Remote and local repositories (even without Internet connection) Automatically process resources Manage dependencies and development + deployment properties Share ontology resources across projects Ontology artifacts including metadata, documentation, tests, . . . , FU Berlin, OntoMaven and API4KP, ALIGNED Project Meeting Dec 3, 2015 25
  • 40. Outline 1 OMG API4KP – An API for Knowledge Platforms Scope of the Standard Scenario: The Connected Patient System Scenario: Semantic Annotation and Discovery of Biodiversity Data The API4KP Metamodel Foundations: Monads Architecture Styles 2 Repositories with OntoMaven Motivation Architecture Selected Plug-Ins The Terminology Server Scenario with Distributed Knowledge Repositories , FU Berlin, OntoMaven and API4KP, ALIGNED Project Meeting Dec 3, 2015 26
  • 41. OntoMaven – Apache Maven Extension Ontology Artifacts Managed by groupID, artifactID, and version FU Berlin, OntoMaven and API4KP, ALIGNED Project Meeting Dec 3, 2015 27
  • 42. OntoMaven – Apache Maven Extension Ontology Artifacts Managed by groupID, artifactID, and version Ontology Repositories Local and remote repositories used to store artifacts (ontologies, plug-ins, resources, test suites etc.) FU Berlin, OntoMaven and API4KP, ALIGNED Project Meeting Dec 3, 2015 27
  • 43. OntoMaven – Apache Maven Extension Ontology Artifacts Managed by groupID, artifactID, and version Ontology Repositories Local and remote repositories used to store artifacts (ontologies, plug-ins, resources, test suites etc.) OntoMaven Plug-ins Implement the ontology project life cycle management functionalities Goals provide interfaces bundled to life cycle phases FU Berlin, OntoMaven and API4KP, ALIGNED Project Meeting Dec 3, 2015 27
  • 44. OntoMaven – Apache Maven Extension Ontology Artifacts Managed by groupID, artifactID, and version Ontology Repositories Local and remote repositories used to store artifacts (ontologies, plug-ins, resources, test suites etc.) OntoMaven Plug-ins Implement the ontology project life cycle management functionalities Goals provide interfaces bundled to life cycle phases Project Ontology Model POM.xml – Declarative project description and configuration , FU Berlin, OntoMaven and API4KP, ALIGNED Project Meeting Dec 3, 2015 27
  • 46. The Maven Repository Architecture Image source: http://tutorials.jenkov.com/maven/maven-tutorial.html , FU Berlin, OntoMaven and API4KP, ALIGNED Project Meeting Dec 3, 2015 29
  • 47. Outline 1 OMG API4KP – An API for Knowledge Platforms Scope of the Standard Scenario: The Connected Patient System Scenario: Semantic Annotation and Discovery of Biodiversity Data The API4KP Metamodel Foundations: Monads Architecture Styles 2 Repositories with OntoMaven Motivation Architecture Selected Plug-Ins The Terminology Server Scenario with Distributed Knowledge Repositories , FU Berlin, OntoMaven and API4KP, ALIGNED Project Meeting Dec 3, 2015 30
  • 48. OntoMaven – Selected Plug-Ins Import Dependency Management Documentation Versioning Testing with Test Suites Aspect-Oriented Development and Module Selection . . . , FU Berlin, OntoMaven and API4KP, ALIGNED Project Meeting Dec 3, 2015 31
  • 49. Import and Dependency Management Plug-In ???.owl Import Ontology Parse Ontology exist? Return Result List (List of imported and not imported Ontologies) yes no save? end Save Ontology in Local Repository yes no Create XMLCatalog Return Result List (List of local ontologies and XMLCatalog with local references) Figure: Importation of an ontology into the local repository. , FU Berlin, OntoMaven and API4KP, ALIGNED Project Meeting Dec 3, 2015 32
  • 50. Ontology Artifacts Archiva Repostory Manager Dependencies , FU Berlin, OntoMaven and API4KP, ALIGNED Project Meeting Dec 3, 2015 33
  • 51. Ontology Artifacts in Remote Repository <profiles> <profile> <id>2</id> <activation> <activeByDefault>true</activeByDefault> </activation> <repositories> <repository> <snapshots> <enabled>true</enabled> </snapshots> <id>snapshots</id> <name>OntoMaven Snapshot Repository</name> <url>http://www.corporate−semantic−web.de/repository/ snapshots/</url> ... </profiles> <dependencies> <dependency> <groupId>xfront.com.owl.ontologies</groupId> <artifactId>Camera−OWL−Ontology</artifactId> <version>1.0−SNAPSHOT</version> <type>owl</type> </dependency> </dependencies> , FU Berlin, OntoMaven and API4KP, ALIGNED Project Meeting Dec 3, 2015 34
  • 52. Report Plug-In – Documentation <description>here’s the description of an ontology </description> <organization> <name>Corporate Semantic Web, Freie Universitaet Berlin</name> <url>http://www.corporate−semantic−web.de</url> </organization> <inceptionYear>2013</inceptionYear> <licenses> <license> <name>LGPL−3.0</name> <url>http://www.gnu.org/licenses/lgpl.txt</url> </license></licenses> <developers> <developer> <name>Adrian Paschke</name> <email>paschke@inf.fu−berlin.d</email> <organization>Corporate Semantic Web</ organization> <organizationUrl>http://www.corporate−semantic− web.de/ </organizationUrl> <roles> <role>developer</role> </roles> </developer></developers> , FU Berlin, OntoMaven and API4KP, ALIGNED Project Meeting Dec 3, 2015 35
  • 53. Ontology Report , FU Berlin, OntoMaven and API4KP, ALIGNED Project Meeting Dec 3, 2015 36
  • 54. Technical Report , FU Berlin, OntoMaven and API4KP, ALIGNED Project Meeting Dec 3, 2015 37
  • 55. Visualization Report , FU Berlin, OntoMaven and API4KP, ALIGNED Project Meeting Dec 3, 2015 38
  • 56. Versioning Plug-In – SVont Plug-In SVN Command Description checkout Check out working copy from project achieve status Status of the working copy diff Diff between two revisions or paths commit Commit working copy to repository info Info about repository and working copy Iteration nIteration n-1…Iteration 2Iteration 1 Version 1 Version 1 Version 2.1Version 2 Version 1 Version 1 Version 2.x Version 3 Version 3.1 Version 4 , FU Berlin, OntoMaven and API4KP, ALIGNED Project Meeting Dec 3, 2015 39
  • 57. OntoMaven – Plug-In Goal ”diff“ -------------------------- DIFF INFORMATION ------------------------ Ontology File : ...............camera.owl ================== ACTUAL CHANGES ================================== Axioms were added to the repository, or deleted from the working copy. SubClassOf(<http://www.xfront.com/ontologies/camera/#Money> owl:Thing) Declaration(Class(<http://www.xfront.com/ontologies/camera/#Money>)) ==================================================================== ------------------ MORE INFO --------------------------------------- The above changes of the OWL classes are dependent on the axioms: currency <------ DataProperty (Domain) cost <------ ObjectProperty (Range) -------------------------------------------------------------------- , FU Berlin, OntoMaven and API4KP, ALIGNED Project Meeting Dec 3, 2015 40
  • 58. SVont – Subversion for Ontologies , FU Berlin, OntoMaven and API4KP, ALIGNED Project Meeting Dec 3, 2015 41
  • 59. SVont – Commit Workflow Client SVoNt Server SVN Server SVoNt Extension Precommit Hook commit Error Consistency Check consistent Change Detection changes Change Writer Change Log Process Commit Process Commit no yes no yes Ontology File , FU Berlin, OntoMaven and API4KP, ALIGNED Project Meeting Dec 3, 2015 42
  • 60. Test Plug-In – Test Cases for KBs § Test Cases constrain the possible models and approximate the intended models of the knowledge base § Queries are used to test the rule base § A test case is defined by T := {X, A, N}, where § assertion base (input data, e.g. facts ) § a formula denoting a test query § N := + , – a positive or negative label § Semantics § |=TC compatibility relation § Mod association function between sets of formulas and sets of models § Σ model selection function for T:={X, A, +} and for T:={X,A,-} § CR(X) deductive closure of X. Decidable inference operator based on formal proofs LX ⊆ LA∈ )(R)(Mod(X),m:Mmiff)A,(X,|M 0TC0 AModm∈⇒∑∈∈∀+= )(R)(Mod(X),m:Mmiff)A,(X,|M 0TC0 AModm∉⇒∑∈∈∃−= )(XCA R∈)(XCA R∉ + Intended Model Partial Model + + - Test Cases (+,-) inconsistent: + Intended Model + + - Test Cases (+,-) consistent: - , FU Berlin, OntoMaven and API4KP, ALIGNED Project Meeting Dec 3, 2015 43
  • 61. POM.xml Test Plug-In Configuration <plugin> <groupId>de.csw.MvnOnt</groupId> <artifactId>MvnOwlTest</artifactId> <version>1.0−SNAPSHOT</version> <configuration><owlfile>owl/1a.owl</owlfile></configuration> <executions><execution><goals><goal>owltest</goal> </goals></execution></executions> </plugin> <plugin> <groupId>de.csw.MvnOnt</groupId> <artifactId>MvnOwlEntailment</artifactId> <version>1.0−SNAPSHOT</version> <configuration> <premise_file>owl/1a.owl</premise_file> <conclusion_file>owl/1aconclusion.owl</conclusion_file> </configuration><executions><execution> <goals><goal>owlentailment</goal></goals> </execution></executions></plugin></plugins> , FU Berlin, OntoMaven and API4KP, ALIGNED Project Meeting Dec 3, 2015 44
  • 62. Aspect-Oriented Ontologies Aspect definition by quantification Query Manual annotation/ selected editing context in tool Original ontology Ontology with aspect annotations Aspect-based module selection Aspect names or descriptions Ontology module Ontology module selection as an OntoMaven goal , FU Berlin, OntoMaven and API4KP, ALIGNED Project Meeting Dec 3, 2015 45
  • 63. Declarative Module Selection with Aspects and OntoMaven nual annotation/ ected editing text in tool Ontology with aspect annotations Aspect-based module selection Aspect names or descriptions Ontology module Ontology module selection as an OntoMaven goal <userAspects> <aspect>http://example.org/reputation#Reputation123</aspect> <aspect>http://example.org/provenance#prov_789</aspect> <aspect>http://example.org/time#TimeInterval1</aspect> </userAspects> , FU Berlin, OntoMaven and API4KP, ALIGNED Project Meeting Dec 3, 2015 46
  • 64. Outline 1 OMG API4KP – An API for Knowledge Platforms Scope of the Standard Scenario: The Connected Patient System Scenario: Semantic Annotation and Discovery of Biodiversity Data The API4KP Metamodel Foundations: Monads Architecture Styles 2 Repositories with OntoMaven Motivation Architecture Selected Plug-Ins The Terminology Server Scenario with Distributed Knowledge Repositories , FU Berlin, OntoMaven and API4KP, ALIGNED Project Meeting Dec 3, 2015 47
  • 65. Terminology Server Scenario with OntoMaven Ontologies, vocabularies and external sources configurable as OntoMaven dependencies. Easy to add new resources. Fast deployment of test instances with different knowledge sources. Context-based deployment of knowledge components with aspect-orientation. API4KP API4KP SKOS RDF OWL Web Services Client HTTP Server Semantic Web Repository (Virtuoso) HTTP request Serialization format (RDF/XML,JSON,JSON LD,…) External Web Services requestor Local repository Local repository Local repository Central repository OntoMaven OntoMavenexternaldependencies <pom> Compontents • contracts • provided and required interfaces , FU Berlin, OntoMaven and API4KP, ALIGNED Project Meeting Dec 3, 2015 48
  • 66. Summary The Terminology Server scenario encompasses a number of architectural paradigms and KR requirements addressed by API4KP. API4KP shows high ontological completeness and clarity with respect to the Bunge-Wand-Weber reference model. FU Berlin, OntoMaven and API4KP, ALIGNED Project Meeting Dec 3, 2015 49
  • 67. Summary The Terminology Server scenario encompasses a number of architectural paradigms and KR requirements addressed by API4KP. API4KP shows high ontological completeness and clarity with respect to the Bunge-Wand-Weber reference model. OntoMaven automates and supports the life cycle management of ontology projects and ontology artifacts Declarative description in POM defining project conventions and APIs Additional resource directories Plug-in configuration Artifact libraries Repository and deployment configuration Aspect-orientation for context-based knowledge resource selection . . . API4KP and OntoMaven allow integration and exchange of heterogeneous and distributed knowledge and data sources in a declarative fashion along with metadata, interface descriptions, and test cases , FU Berlin, OntoMaven and API4KP, ALIGNED Project Meeting Dec 3, 2015 49
  • 68. Related Publications I R. Schäfermeier, L. Krus, and A. Paschke, “An aspect-oriented extension to the owl api – specifying and composing views of owl ontologies using ontology aspects and java annotations,” in KEOD 2015: 7th International Conference on Knowledge Engineering and Ontology Development, vol. 2, pp. 187–194, 2015. A. Paschke, “Provalets - OSGi-based Prova Agents for Rule-Based Data Access,” in Proceedings of the 14th International Conference on Ontologies, Databases and Applications of Semantics (ODBASE) 2015, Rhodes, Greece, October 26-30, 2015, 2015. T. Athan, R. Bell, E. F. Kendall, A. Paschke, and D. Sottara, “API4KP metamodel: A meta-api for heterogeneous knowledge platforms,” in Rule Technologies: Foundations, Tools, and Applications - 9th International Symposium, RuleML 2015, Berlin, Germany, August 2-5, 2015, Proceedings, p. 144–160, 2015. A. Paschke, T. Athan, D. Sottara, E. F. Kendall, and R. Bell, “A representational analysis of the API4KP metamodel,” in Formal Ontologies Meet Industry - 7th International Workshop, FOMI 2015, Berlin, Germany, August 5, 2015, Proceedings, p. 1–12, 2015. A. Paschke and R. Schäfermeier, “Aspect OntoMaven — Aspect-Oriented Ontology Development and Configuration With OntoMaven,” in 3rd Workshop on Formal Semantics for the Future Enterprise (FSFE 2015), Business Information Systems Workshops (W. Abramowicz, ed.), vol. 228, Springer, 2015. , FU Berlin, OntoMaven and API4KP, ALIGNED Project Meeting Dec 3, 2015 50
  • 69. Related Publications II R. Schäfermeier and A. Paschke, Verteilte und agile Ontologieentwicklung, pp. 341–358. X.media.press, Springer Berlin Heidelberg, 2015. R. Schäfermeier and A. Paschke, “Aspect-Oriented Ontologies: Dynamic Modularization Using Ontological Metamodeling,” in Proceedings of the 8th International Conference on Formal Ontology in Information Systems (FOIS 2014), pp. 199 – 212, IOS Press, 2014. R. Schäfermeier, T. Athan, and A. Paschke, “Common Logic Importation Resolution Implemented in OntoMaven,” in Proceedings of the 8th International Workshop on Modular Ontologies @FOIS 2014" (WoMO 2014), 2014. A. Paschke, “OntoMaven: Maven-based Ontology Development and Management of Distributed Ontology Repositories,” arXiv:1309.7341 [cs], Sept. 2013. R. Schäfermeier, “Aspect-Oriented Ontology Development,” in Business Information Systems Workshops (W. Abramowicz, ed.), no. 160 in Lecture Notes in Business Information Processing, pp. 208–219, Springer Berlin Heidelberg, 2013. R. Schäfermeier and A. Paschke, “Towards a Unified Approach to Modular Ontology Development Using the Aspect-Oriented Paradigm,” in 7th International Workshop on Modular Ontologies (WoMO) 2013, p. 73, 2013. A. Paschke, “OntoMaven API4KB - A Maven-based API for Knowledge Bases,” in SWAT4LS, 2013. , FU Berlin, OntoMaven and API4KP, ALIGNED Project Meeting Dec 3, 2015 51
  • 70. Related Publications III A. Paschke, “OntoMaven: Maven-based Ontology Development and Management of Distributed Ontology Repositories,” 2013. , FU Berlin, OntoMaven and API4KP, ALIGNED Project Meeting Dec 3, 2015 52