Development and use of Ontologies Inside the Neuroscience Information Framework: A Practical Approach

Abstract

An initiative of the NIH Blueprint for neuroscience research, the Neuroscience Information Framework (NIF) project advances neuroscience by enabling discovery and access to public research data and tools worldwide through an open source, semantically enhanced search portal. One of the critical components for the overall NIF system, the NIF Standardized Ontologies (NIFSTD), provides an extensive collection of standard neuroscience concepts along with their synonyms and relationships. The knowledge models defined in the NIFSTD ontologies enable an effective concept-based search over heterogeneous types of web-accessible information entities in NIF's production system. NIFSTD covers major domains in neuroscience, including diseases, brain anatomy, cell types, sub-cellular anatomy, small molecules, techniques, and resource descriptors. Since the first production release in 2008, NIF has grown significantly in content and functionality, particularly with respect to the ontologies and ontology-based services that drive the NIF system. We present here on the structure, design principles, community engagement, and the current state of NIFSTD ontologies.

Keywords: neuroscience ontology; ontologies; ontology reuse; semantic search.

Figure 1

Two example bridging OWL modules in NIFSTD (rectangular boxes) that contain class property associations between multiple core modules.

Figure 2

Transition of contributions between the NeuroLex and the NIFSTD.

Figure 3

Structure of contents in a typical NeuroLex category page. (A) The standard input text field for searching the entire NeuroLex wiki contents. (B) Different tabs to display and edit the contents of a particular category page. (C) The structured contents of a category page (e.g., Cerebellum). Boxes corresponding to (D–F) demonstrate the ability of the NeuroLex to automatically assemble related knowledge about a particular category from the edits made in other NeuroLex pages. (G) The list of contributors who made edits to the page. (H) The list of subcategories of a particular category page.

Figure 4

Asserted simple hierarchy of “Cerebellum Purkinje cell.”

Figure 5

Typical NIFSTD restrictions asserted for various neuron types.

Figure 6

After invoking a reasoner NIFSTD Cerebellum Purkinje cell becomes a subclass of four different defined neuron types based on the restrictions specified in Figure 5.

Figure 7

On the left, the increase of NIF contents in terms of the number of federated records (green) and databases (blue). On the right, the increase of community outreach in terms of the number of visitors to the NIF portal.