NeuroNames: an ontology for the BrainInfo portal to neuroscience on the web

Abstract

BrainInfo ( http://braininfo.org ) is a growing portal to neuroscientific information on the Web. It is indexed by NeuroNames, an ontology designed to compensate for ambiguities in neuroanatomical nomenclature. The 20-year old ontology continues to evolve toward the ideal of recognizing all names of neuroanatomical entities and accommodating all structural concepts about which neuroscientists communicate, including multiple concepts of entities for which neuroanatomists have yet to determine the best or 'true' conceptualization. To make the definitions of structural concepts unambiguous and terminologically consistent we created a 'default vocabulary' of unique structure names selected from existing terminology. We selected standard names by criteria designed to maximize practicality for use in verbal communication as well as computerized knowledge management. The ontology of NeuroNames accommodates synonyms and homonyms of the standard terms in many languages. It defines complex structures as models composed of primary structures, which are defined in unambiguous operational terms. NeuroNames currently relates more than 16,000 names in eight languages to some 2,500 neuroanatomical concepts. The ontology is maintained in a relational database with three core tables: Names, Concepts and Models. BrainInfo uses NeuroNames to index information by structure, to interpret users' queries and to clarify terminology on remote web pages. NeuroNames is a resource vocabulary of the NLM's Unified Medical Language System (UMLS, 2011) and the basis for the brain regions component of NIFSTD (NeuroLex, 2011). The current version has been downloaded to hundreds of laboratories for indexing data and linking to BrainInfo, which attracts some 400 visitors/day, downloading 2,000 pages/day.

Figure 1

The BrainInfo Portal, as a communication channel, is similar to conventional portals in that it has a repository of links to documents on the Web. It differs from conventional portals in that: 1) information in the repository is organized according to an ontology that allows indexing of documents based on the concepts rather than the words therein; 2) the portal interacts with users to interpret and disambiguate queries; and 3) a curator continuously updates the portal ontology with new terms, new concepts and the addresses of web pages that define and illustrate them.

Figure 2. Elements of a Scientific Ontology Include Words, Concepts, Models and Entities

Words are character strings, which are names representing concepts, models and the entities they represent. Names are linked to definitions of concepts and models. The contents of models are combinations of concepts and of smaller models represented by their names in lists, hierarchies and system diagrams. Entities are the objects and combinations of objects represented by concepts and models. (Images are represented here because, while they are not considered components of an ontology, they are equally or more important than words for communication of anatomical concepts.)

Figure 3. NeuroNames is an informatics tool

for resolving ambiguities in exchanges of information. In neuroanatomy the same structural concept, or model composed of structural concepts, can have multiple names and the same name can represent multiple concepts. A given model includes multiple concepts and the same concept can occur in multiple models. Different scientists can hold different concepts of the same structural entity and can model a complex entity in different ways.

Figure 4. NeuroNames Ontology of the Nervous System

A hypothetical set of brain models (one human, one macaque and two rat models) are integrated with a subset of concepts from the NeuroNames ontology to illustrate relations among reference concepts (embossed or yellow), referred concepts (italicized or light blue) and models (capitalized or white). CNS: central nervous system; HB: hindbrain; MB: midbrain; FB: forebrain; NS: nervous system; sn_a-e: subnuclei of solitary nucleus in two hypothetical atlases of the rat brain. Dashed lines indicated intervening levels of hierarchy. Arrows indicate identity of referred concepts in models with their reference concepts. All instances of ‘brain’ in italicized or light blue share the standard name and definition of the reference concept ‘brain’ in embossed or yellow letters. The coding of subnuclei sn_a-c in Rat Brain 1 as reference concepts and of sn_a and sn_c as referred concepts in Rat Brain 2 indicates that the concepts were first found, coded and defined in the ontology from the Rat Brain 1 atlas.

Figure 5. Relations of area 9 of Brodmann (guenon)

to eight areas reported by other investigators to be the same as, or to overlap, that area of cortex. Note that the Vogts based their judgment as to equivalence of their structures on cytoarchitecture, i.e., similarity of internal structure. Walker and Mauss judged their structures equivalent on the basis of topology, i.e., similarity of shape and location. The method used to identify a structure is an essential component of its scientific definition.

Figure 6. Names, Concepts and Models Tables

form the ontologic core of some 80 tables in the database schema of BrainInfo.

Figure 7. BrainInfo Response to Query ‘arcuate nucleus’

Six names for three concepts. Red (dashed) ovals: ‘arcuate nucleus’ as homonym for three different concepts. Blue (solid) ovals: Five synonyms for the same concept ‘arcuate nucleus of the hypothalamus’. [Page modified from BrainInfo (2010d).]

Figure 8. BrainInfo’s Central Directory for ventral posteromedial nucleus

(standard name for arcuate nucleus of the thalamus). Central Directories for some 2500 structures provide hyperlinks to most kinds of information that a user may seek.

Figure 9. The NeuroNames ontology aids interpretation of other websites

The user sought information about the hippocampus (as a synonym of ‘CA fields’). BrainInfo has retrieved the page at USC’s Brain Information Management System (BAMS, 2010), which provides information about the structure using the terminology ‘Ammon Horn’, ‘CA1’, ‘CA2’ and ‘CA3’ (green dark ovals). BrainInfo indicates terms for which the user should look (red light oval).