The NIFSTD and BIRNLex vocabularies: building comprehensive ontologies for neuroscience

Abstract

A critical component of the Neuroscience Information Framework (NIF) project is a consistent, flexible terminology for describing and retrieving neuroscience-relevant resources. Although the original NIF specification called for a loosely structured controlled vocabulary for describing neuroscience resources, as the NIF system evolved, the requirement for a formally structured ontology for neuroscience with sufficient granularity to describe and access a diverse collection of information became obvious. This requirement led to the NIF standardized (NIFSTD) ontology, a comprehensive collection of common neuroscience domain terminologies woven into an ontologically consistent, unified representation of the biomedical domains typically used to describe neuroscience data (e.g., anatomy, cell types, techniques), as well as digital resources (tools, databases) being created throughout the neuroscience community. NIFSTD builds upon a structure established by the BIRNLex, a lexicon of concepts covering clinical neuroimaging research developed by the Biomedical Informatics Research Network (BIRN) project. Each distinct domain module is represented using the Web Ontology Language (OWL). As much as has been practical, NIFSTD reuses existing community ontologies that cover the required biomedical domains, building the more specific concepts required to annotate NIF resources. By following this principle, an extensive vocabulary was assembled in a relatively short period of time for NIF information annotation, organization, and retrieval, in a form that promotes easy extension and modification. We report here on the structure of the NIFSTD, and its predecessor BIRNLex, the principles followed in its construction and provide examples of its use within NIF.

Fig. 1

Terminology spreadsheet for automated import of the IUPHAR ion channel database. This direct import was used to create OWL classes, annotations and related properties, under NIFSTD Molecule. Further description of this process is described in the “Results” section

Fig. 2

The semantic domains covered in the NIFSTD v0.5 OWL ontology. Each of the domains specified within the ovals are covered by a separate OWL module (see Table 1). The umbrella file http://purl.org/nif/ontology/nif.owl imports each of these modules when opened in Protégé. These domains are covered either through import of the corresponding BIRNLex module, a module constructed by NIF or a direct import of an existing ontology (see key for color code). Each of the modules, in turn, may cover multiple subdomains, some of which are shown in the rectangular boxes. NS = nervous system

Fig. 3

View of some mammalian thalamic brain regions in NIFSTD. a Core “is a” hierarchy for “Regional part of diencephalon”; b Partonomy of diencephalon computed using OWL ObjectProperties and restrictions that relate the regional part of thalamus to the thalamus. Only a portion of the classes covering thalamic entities is shown here

Fig. 4

Graph view of Nav Sodium Channel representation in NIFSTD. NIF Molecule defines the relationships among the macromolecule Nav 1.4 sodium channel (bold oval), its auxiliary subunit (Nav Beta), the channel and pore regions (aa sequence), the gene encoding these sequences (SCNA4 gene) and its corresponding chromosome location. The different shadings indicate that the concepts come from different hierarchies within the NIF molecule module. Unlabeled arrows represent “is a” relationship, e.g., Nav1.4 Sodium channel is a Type 1 Sodium channel

Fig. 5

Graph view of Alpha 2A Adrenoceptor G-protein coupled receptor (bold oval) representation in NIFSTD Molecule. Through the classes and relationships within NIFSTD Molecule, the macromolecule is related to its ligand, mRNA and ultimately the chromosome containing the DNA sequence through additional relationships. The different shadings indicate that the concepts come from different hierarchies within the NIF molecule module. Unlabeled arrows represent “is a” relationship, e.g., e.g., Alpha 2a Adrenoreceptor is a Type 2 Adrenoreceptor

Fig. 6

Example of cross-domain relations that can be built among NIFSTD modules (NOTE: Current NIFSTD has yet to add expressed_in relations)

Fig. 7

Sample search of the NIF using the NIFSTD vocabularies to expand and refine the search. Query results from the NIF Registry, a human curated database of neuroscience relevant sites on the web, are shown