Software
The Ontology Abstraction Framework (OAF)
The Ontology Abstraction Framework (OAF)
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:
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.
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
OAF Protege Plugin | OAF for OWL/OBO | OAF for SNOMED CT |
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The Bacterial Infectious Disease partial-area taxonomy in the OAF for SNOMED CT
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).
Some consideration when using the OAF Protege Plugin:
4.2. OAF for OWL/OBO
The OAF for OWL/OBO requires Java 8 or better, available here: Download Java.
Some consideration when using the OAF for OWL/OBO:
4.3. OAF for SNOMED CT
The OAF for SNOMED CT requires Java 8 or better, available here: Download Java.
Some consideration when using the OAF for SNOMED CT: