Software

The Ontology Abstraction Framework (OAF)

Software

The Ontology Abstraction Framework (OAF) is a free and open-source software system for visually summarizing the structures of ontologies. The OAF enables users to create and explore structural summaries of ontologies called abstraction networks. The OAF is being developed as part of an ongoing research project at the Structural Analysis of Biomedical Ontologies Center (SABOC) in the Computer Science Department at the New Jersey Insitute of Technology. The OAF is playing a key role in SABOC's research into the structure of biomedical ontologies (specifically, the ontologies found in the NCBO BioPortal).

The OAF supports ontologies in Web Ontology Language (OWL), Open Biomedical Ontologies (OBO), and  SNOMED CT RF2 formats. Experimental support for NDF-RT, as represented in Apelon DTS format, is also available. The OAF has two major components: a system for creating, visualizing, and exploring abstraction networks and a hybrid text-diagram concept browser for reviewing the modeling of individual ontology concepts. The OAF is released in three versions (shown on the right). All versions of the OAF include these main components, but additional functionality is available in each version. The theoretical foundations of the OAF are described in:

Ochs C, Geller J, Perl Y, Musen MA.
A unified software framework for deriving, visualizing, and exploring abstraction networks for ontologies.
Journal of Biomedical Informatics. 2016 Aug 31;62:90-105.

The OAF Protege Plugin and OAF for OWL/OBO utilize the OWL API and Protege API.


Excerpt of an abstraction network in the OAF for the NCIt Neoplasm subhierarchy

1.1. Types of Abstraction Networks Supported by the OAF

The OAF supports the following kinds of abstraction networks:

  • Partial-area Taxonomies: Summarize subhierarchies of concepts that are modeled with the same types of defining relationships (e.g., properties in OWL, relationships in OBO, and attribute relationships in SNOMED CT). Concepts are separated into disjoint sets called areas, which contain of concepts with the exact same set of defining relationships. Areas are separated into partial-areas, which summarize subhierarchies of semantically similar concepts in each area.
  • Disjoint Partial-area Taxonomies: When an ontology allows concepts to have multiple parents a given concept may be summarized by multiple partial-areas, according to which subhierarchies it belongs to. A disjoint partial-area taxonomy separates concepts into disjoint sets called disjoint partial-areas, which visually identify points of intersection between partial-areas.
  • Tribal Abstraction Network (TAN): Summarize the intersections between user-selected subhierarchies in an ontology. Concepts are partitioned into disjoint sets called bands, which identify the subhierarchy/subhierarchies a set of concepts belongs to. Bands are partitioned into clusters, which identify subhierarchies of concepts that exist at a specific point of intersection between two or more subhierarchies.
  • Disjoint Tribal Abstraction Networks: As with partial-areas, a given concept may be summarized by multiple clusters. A Disjoint TAN separates concepts into disjoint units called disjoint clusters, which summarize the points of intersection between clusters in a band.
  • Target Abstraction Network (Target AbN): Also called Range AbN (when applied to OWL/OBO ontologies) or Ingredient AbN (when applied to NDF-RT). Summarizes subhierarchies of concepts that serve as targets for defining relationships, along with the source concepts that have relationships pointing to the target concepts.


A Tribal Abstraction Network (TAN) created from a NCIt subhierarchy in the OAF Protege Plugin

1.2. Live Abstraction Networks

A Live Abstraction Network is an abstraction network that updates as an ontology is edited. The Protege Plugin version of the OAF includes in-development functionality for live abstraction networks. As you edit your ontology, the summary provided by the abstraction network will accurately reflect the current state of your ontology. We have tested live abstraction network functionality with each of the above abstraction network types.

Live abstraction networks in the OAF Protege Plugin also include the ability to switch back and forth between abstraction networks created from the asserted relationships of an ontology and the inferred relationships of an ontology.

1.3. Diff Abstraction Networks

A Diff Abstraction Network is an abstraction network that summarizes changes to an ontology's structure. The OAF framework includes programmatic functionality for creating diff abstraction networks for any kind of abstraction network. However, the current user-facing version of the OAF only includes a user interface for Diff Partial-area Taxonomies, which summarize changes to subhierarchies of structurally and semantically similar concepts. Diff partial-area taxonomies can be derived in the standalone versions of the OAF for OWL/OBO and SNOMED CT. Additional diff partial-area taxonomy is available in specific OAF versions.

1.3.1. Live Diff Partial-area Taxonomies

The OAF Protege Plugin includes initial support for Live Diff Partial-area Taxonomies, which summarize changes to your ontology as you are editing it. Live diff partial-area taxonomies can be derived from a fixed version of the ontology or progressively as each edit is applied. Additionally, live diff partial-area taxonomies can be derived using asserted relationships or inferred relationships, and changes can be tracked across both.


Live Diff Partial-area Taxonomy view in the OAF Protege Plugin

1.3.2. Visual Semantic Delta

The OAF for SNOMED CT includes support for Visual Semantic Deltas, which provide concept-level change information.

2. Ontology Abstraction Framework (OAF) Features

All versions of the OAF include two main components: a system for creating, visualizing, and exploring various kinds of abstraction networks and a text-diagram hybrid concept browser. 

2.1. Abstraction Networks in the OAF

Every version of the OAF can derive all of the abstraction networks described above. Each abstraction network can be created for an arbitrary subhierarchy of concepts, as long as the subhierarchy has an appropriate structure. Additionally, the OAF includes various processes for creating/extracting subsets of abstraction networks. A process of aggregation can also be applied to hide nodes that summarize relative few concepts. Each version of the OAF includes also includes custom functionality, described below.

2.2. OAF Concept Browser

Every version of the OAF includes a concept browser based on our previously developed Neighborhood Auditing Tool (NAT) for the Unified Medical Lanauge System (UMLS). This browser provides a text-diagram hybrid view of an ontology. The OAF Concept Browser was designed to facilitate the auditing of ontology content by domain experts. The OAF Concept Browser includes functionality for marking perceived errors in an ontology. To access this functionality, create or open an "Audit Set." When an audit set is loaded errors can be reported by right clicking on a concept or relationship.


Tetralogy of Fallot displayed in OAF Concept Browser for SNOMED CT

3. Comparison of OAF Versions

OAF Protege Plugin OAF for OWL/OBO OAF for SNOMED CT
  • Support for OWL/OBO ontologies in Protege 5.2
  • Integrated into the Protege ontology editing environment
  • OAF and Concept Browser included in tabs
  • Live Abstraction Networks, which update as an ontology is edited
  • Derive abstraction networks using asserted or inferred relationships
  • Live Diff Partial-area Taxonomy ontology view, which summarizes structural changes as an ontology is edited
  • Standalone OAF version
  • Support for OWL/OBO ontologies
  • Support for Diff Partial-area Taxonomies
  • Support for Import Subtaxonomies, which summarize concepts originating from a specific reused ontology
  • Standalone OAF version
  • Support for SNOMED CT RF1/RF2 formats
  • Support for stated and inferred relationships
  • Support for Visual Semantic Delta, which computes concept-specific change information

 


The Bacterial Infectious Disease partial-area taxonomy in the OAF for SNOMED CT

4. Installing and Running the OAF

4.1. OAF Protege Plugin

The OAF Protege Plugin requires Protege 5.2 or newer (desktop version). The newest version of Protege can be downloaded at the  Protege website. The OAF Plugin for Protege 5 can be downloaded through Protege's plugins list or installed manually (description below).

  1. Download OAF Plugin for Protege 5 (above)
  2. Locate the local directory Protege was installed in
  3. Place the oaf-protege.jar file in Protege's plugins folder
  4. Start Protege
  5. Open an ontology
  6. To view the OAF Abstraction Network tool click on: "Window -> Tabs -> Ontology Abstraction Network (OAF)"
  7. To view the OAF Class Browser click on: "Window -> Tabs -> Ontology Abstraction Network (OAF) Class Browser"
  8. To include a Live Diff Partial-area Taxonomy view click on: "Windows -> Views -> Ontology Views -> OAF Live Diff Taxonomies". 
  9. It is recommended that you include the Live Diff Partial-area Taxonomy view in Protege's entities tab.

Some consideration when using the OAF Protege Plugin:

  • The default Java Heap space specified for Protege may be too small when large ontologies/large abstraction networks are displayed. The minimum heap space can be increased manually.
  • The OAF Abstraction Network tool and OAF Class Browser will use the asserted hierarachical relationships of an ontology until a reasoner is applied. When a reasoner is running the inferred hierarchical relationships are utilized.

4.2. OAF for OWL/OBO

The OAF for OWL/OBO requires Java 8 or better, available here: Download Java.

  1. Download OAF for OWL/OBO (above)
  2. Extract the contents of oaf-owl.zip to an easy-to-find directory. The Desktop is recommended.
  3. Navigate to where you exacted the contents of oaf-owl.zip
  4. If you are using Windows, double click on "run oaf.bat" to launch the complete OAF and "run class browser" to run only the OAF Class Browser. If you are not using Windows, double click on oaf-owl.jar.
  5. Click on Open an Ontology (.owl/.obo) and select an appropriate ontology file. The ontology will be loaded into the OAF.

Some consideration when using the OAF for OWL/OBO:

  • The OAF for OWL/OBO uses the asserted relationships of an ontology. There is currently no support for reasoning in the standalone OAF for OWL/OBO, though it is planned as a future feature.

4.3. OAF for SNOMED CT

The OAF for SNOMED CT requires Java 8 or better, available here: Download Java.

  1. Download OAF for SNOMED CT (above)
  2. Extract the contents of oaf-snomed.zip to an easy-to-find directory. The Desktop is recommended.
  3. Navigate to where you exacted the contents of oaf-snomed.zip
  4. If you are using Windows, double click on "run oaf.bat" to launch the complete OAF for SNOMED CT and "run concept browser" to run only the OAF Concept Browser. If you are not using Windows, double click on oaf-snomed.jar.
  5. Click on "Select Folder Containing SNOMED CT Release(s) and select a folder that contains one or more International SNOMED CT releases
  6. The releases will be listed in the drop down box to the right of the button. Select a release and then click "Load".

Some consideration when using the OAF for SNOMED CT:

  • Currently the OAF for SNOMED CT supports the International Release of SNOMED CT. It can be in RF1 or RF2 format. Support for country-specific releases is planned (though it may currently work with some US Extension releases).
  • The OAF for SNOMED CT requires that SNOMED CT release files are in the appropriate directory. For example, the July 2016 international release should be located in a folder named "SnomedCT_RF2Release_INT_20160731" (the same folder that is included in the International Release download from the NLM UTS: https://www.nlm.nih.gov/healthit/snomedct/international.html