koio

KOIO - The Knowledge Object Implementation Ontology

KOIO is a domain ontology that tells us what a Knowledge Object is as an artifact. It describes Knowledge Objects and their parts as they are implemented. For this reason, KOIO generally serves as an evolving formal and explicit model of Knowledge Objects. It can be used to describe the parts of many computable biomedical knowledge (CBK) artifacts found in the wild. In addition, KOIO functions as a formal specification for linked metadata relevant for describing, annotating, packaging, and handling CBK artifacts.

The Knowledge Systems Lab (KSL) at the University of Michigan began work on KOIO in 2016 and continues to evolve KOIO over time. KSL’s general approach is to keep KOIO concise, connected, and common.

To keep it concise, only a very small number of new terms describing key parts known to be valuable to CBK stakeholders are included in KOIO. These KOIO-defined terms include “Knowledge”, “Service”, and “Test”. As a model of Knowledge Objects, KOIO supports multiplicity of these parts meaning that a Knowledge Object may have one or more elements of knowledge plus multiple corresponding services and tests. KOIO enables the lifecycles and provenance of the key individual parts of Knowledge Objects to be tracked and documented independently.

The key parts of Knowledge Objects defined in KOIO are logically connected to terms from the upper-level Basic Formal Ontology (BFO). In addition, KOIO adopts terms from the Information Artifact Ontology (IAO) and the Software Ontology (SWO) wherever possible.

Finally, KOIO tries to leave implementation details out so that it can serve as a common ontology for describing nearly all CBK artifacts, regardless of the platforms or applications that support and incorporate them.

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KOIO ontology is currently used in the Knowledge Grid (KGrid) poject for creating knowledge objects.

About this repository

The KOIO repository is used for evolving, sharing, and managing KOIO. KOIO formally defines the structure of Knowledge Objects using linked data representations made available in canonical OWL files.

KOIO comes in several versions indicated by folders labeled with version numbers. In addition several legacy contexts and examples of knwoledge objects conforming to various versions of KOIO are included. The other folders and files generaly pertain to the current working version of KOIO which has yet to be released.

Downloads

Documentation for latest release

The KOIO ontology documentation could be found at https://kgrid.org/koio/2.1/docs/

For more detail about the current release please see the slides at https://drive.google.com/file/d/19DmeYajmh0Wxll7hOjfbEfO_mnDvkSL8/view?usp=drive_link.

Knowledge Systems Laboratory (KSL)

KSL is an R&D lab in the Department of Learning Health Sciences at the University of Michigan Medical School. KSL created KOIO in 2016-17. It was first conceived as part of the Knowledge Grid (KGrid) project for devising better socio-technical knowledge infrastructure components for learning health systems. By 2023-24, KOIO came to be seen as an important KSL deliverable in its own right.

Development roles and rules

Here are the roles of people who will contribute in the development of this ontology and the rules that they should follow:

Roles (workflow)

Rules

Namespace

Classes

Knowledge Object

A Knowledge Object is an Information Artifact capable of serving a role as the atomic unit of computable knowledge and therefore comprised of at least one Knowledge Object Implementation.
IRI https://kgrid.org/koio#KnowledgeObject
Is defined by https://kgrid.org/koio/2.1/docs/
Term status: stable

Knowledge

Knowledge is information or understanding about a subject, obtained through experience or study.
IRI https://kgrid.org/koio#Knowledge
Is defined by https://kgrid.org/koio/2.1/docs/
Term status: stable

Service

A Service is a defined function or capability provided by a software system. Each Service provides a way to use or interact with a KnowledgeObject, facilitating access and utilization of the Knowledge encapsulated within the KnowledgeObject. A Service is a specification of what a self-contained piece of software does.
IRI https://kgrid.org/koio#Service
Is defined by https://kgrid.org/koio/2.1/docs/
Term status: stable

Test

A test is an information content entity conveying a systematic procedure to assess specific aspects of software performance, functionality, or security. Tests are created to ensure that the software meets specified requirements or to identify any defects.
IRI https://kgrid.org/koio#Test
Is defined by https://kgrid.org/koio/2.1/docs/
Term status: stable

Implementation

An implementation is a computer or machine processable file that is or informs a series of instructions that can be directly interpreted or executed.
IRI https://kgrid.org/koio#Implementation
Is defined by https://kgrid.org/koio/2.1/docs/
Term status: stable

Information Artifact

An Information Artifact is an Artifact that is the IndependentContinuant bearer created as the result of one or more intentional processes. Examples: uniprot, the english language, the contents of this document or a printout of it, the temperature measurements from a weather balloon. For more information, see the project home page at https://github.com/information-artifact-ontology/IAO.
IRI https://kgrid.org/koio#InformationArtifact
Is defined by https://kgrid.org/koio/2.1/docs/
Term status: stable

Object Properties

depends on

Indicates that a service uses a specific knowledge.
IRI https://kgrid.org/koio#dependsOn
Is defined by https://kgrid.org/koio/2.1/docs/
Term status: stable
Has domain: Service
Has range: Knowledge

has interface

Provides a method of asserting what type of interactions are possible for the class in question. The interface must be from the ‘software interface’ hierarchy.
IRI https://kgrid.org/koio#hasInterface
Is defined by https://kgrid.org/koio/2.1/docs/
Term status: stable
Has domain: Service
Has range: Software Interface

is implemented by

It is the relationship between an algorithm and a piece of software which includes an implementation of that software for use when the software is executed. IRI https://kgrid.org/koio#isImplementedBy
Is defined by https://kgrid.org/koio/2.1/docs/
Term status: stable
Has domain: Test, Service, Knowledge
Has range: Implementation

has documentation

Is a property that indicates an association between a knowledge object, knowledge, or service and documentation that describes, relates to, or provides information about each of these things.
IRI https://kgrid.org/koio#hasDocumentation
Is defined by https://kgrid.org/koio/2.1/docs/
Term status: stable
Has domain:Test, Service, Knowledge, Implementation, Knowledge Object
Has range: Information Artifact

has knowledge

indicates that a Knowledge Object contains or is associated with specific Knowledge.
IRI https://kgrid.org/koio#hasKnowledge
Is defined by https://kgrid.org/koio/2.1/docs/
Term status: stable
Has domain: Knowledge Object
Has range: Knowledge

has service

It is a relation that holds between a whole KnowledgeObject and its Service part(s). Denotes that a KnowledgeObject includes or provides a specific Service.
IRI https://kgrid.org/koio#hasService
Is defined by https://kgrid.org/koio/2.1/docs/
Term status: stable
Has domain: Knowledge Object
Has range: Service

has test

It is a property that links a knowledge object, service, or knowledge to a specific test designed to evaluate its functionality, performance, or reliability. This property signifies that the component has an associated test to verify or validate its behavior.
IRI https://kgrid.org/koio#hasTest
Is defined by https://kgrid.org/koio/2.1/docs/
Term status: stable
Has domain: Knowledge Object, Service, Knowledge
Has range: Test

Appendix A—Generate JSON_LD Context File From KOIO OWL File Using owl2jsonld Tool

owl2jsonld is a tool that generate a JSON-LD @context for concepts (classes and properties) found in the specified OWL or RDFS ontology.

  1. Install Java 
    # JAVA installation on Linux
sudo apt update
sudo apt install default-jre

  2. Download the Tool: You can download the owl2jsonld tool from its GitHub repository. The official releases include an uberjar (standalone JAR) that bundles all dependencies and can be used as a command-line tool.

  3. Run the JAR File and create the context.json form the owl file: 
    java -jar owl2jsonld-0.2.1-standalone.jar file:///path/to/owl/file/koio.owl -o context.json

Note: path to owl file must be an IRI starting with file://.