NeuroNames 2002

  title={NeuroNames 2002},
  author={Douglas M. Bowden and Mark F. Dubach},
NeuroNames is a nomenclature designed as a tool for indexing digital databases of neuroscientific information.1 It can be used, for example, as the entry point to a digital dictionary of neuroanatomy, to a brain atlas, or to a database of information referenced to specific brain structures. The user can query with terms from many different nomenclatures. One can create a neuroanatomic ontology from NeuroNames by relating an appropriate subset of terms to a conceptual model represented by… 
Creating neuroscience ontologies.
A description of the experience in establishing interoperability between BrainInfo and other neuroscience Web sites and an ontology of 2500 neuroanatomical concepts referenced by 15,000 terms in seven languages are described.
Terminology for Neuroscience Data Discovery: Multi-tree Syntax and Investigator-Derived Semantics
Semantics enabling NIF data discovery were selected by investigators expert in particular systems (vision, olfaction, behavioral neuroscience, neurodevelopment), brain areas (cerebellum, thalamus, hippocampus), preparations, diseases, diseases (neurodegenerative disease), or techniques (microscopy, computation and modeling, neurogenetics).
Integrating databases and expert systems for the analysis of brain structures
Examples of search for information in NHDB system, inferences of relations between cortical structures from equivalent neuroanatomical atlases, reconstruction of functional networks of brain structures from data collated from the literature, translation of connectivity matrices in equivalent parcellation schemes, and evaluations of similarities of brain structure from humans, macaques and rats are presented.
Automated Recognition of Brain Region Mentions in Neuroscience Literature
A corpus of manually annotated brain region mentions is created to facilitate text mining of neuroscience literature and found context windows, lemmatization and abbreviation expansion to be the most informative techniques.
The NIFSTD and BIRNLex Vocabularies: Building Comprehensive Ontologies for Neuroscience
The structure of the NIFSTD, and its predecessor BIRNLex, is reported on, the principles followed in its construction and examples of its use within NIF are provided, to promote easy extension and modification.
The NeuARt II system: a viewing tool for neuroanatomical data based on published neuroanatomical atlases
NeuARt II, the neuroinformatics tool presented here, provides an accurate and powerful way of representing neuroanatomical data in the context of commonly-used brain atlases for visualization, comparison and analysis.
Large-scale extraction of brain connectivity from the neuroscientific literature
Text-mining models are presented to extract and aggregate brain connectivity results from 13.2 million PubMed abstracts and 630 216 full-text publications related to neuroscience, which drastically accelerates connectivity literature review.
Automated Neuroanatomical Relation Extraction: A Linguistically Motivated Approach with a PVT Connectivity Graph Case Study
A linguistically motivated approach based on patterns defined over the constituency and dependency parse trees of sentences is introduced based on the presence of a relation between a pair of brain regions, which enables the creation and analysis of a directional brain region connectivity graph.
Neuroanatomical domain of the foundational model of anatomy ontology
Recent enhancements to the neuroanatomical content of the Foundational Model of Anatomy that models cytoarchitectural and morphological regions of the cerebral cortex, as well as white matter structure and connectivity are described.
A Formal Ontology of Subcellular Neuroanatomy
The structure and content of a formal ontology whose scope is the subcellular anatomy of the nervous system (SAO), covering nerve cells, their parts, and interactions between these parts are described and many applications of this ontology to image annotation, content-based retrieval of structural data, and integration of shared data across scales and researchers are described.


Chapter I A digital Rosetta stone for primate brain terminology
NeuroNames Brain Hierarchy
It is hoped that the systematic construction of the NeuroNames Brain Hierarchy will facilitate use of the most widely accepted definitions of classical neuroanatomy in quantitative computerized neuroimaging applications.
NeuroNames©: Human/Macaque Neuroanatomical Nomenclature.
NeuroNames© is a comprehensive, hierarchical nomenclature of structures found in the human and nonhuman primate brain, designed to serve as a teaching tool, as an entry point to computerized atlases and as an indexing tool to data bases created by modern brain imaging techniques.
Brain Maps: Structure of the Rat Brain
This atlas describes the development of the rat Brain through Cytoarchitecture, followed by a detailed description of Nervous System Development, and annotated Nomenclature Tables (tables and annotations in parallel), covering basic cell groups and Gross Anatomical Features of the Rat CNS.
A Stereotaxic Template Atlas of the Macaque Brain for Digital Imaging and Quantitative Neuroanatomy
A stereotaxic brain atlas of the longtailed macaque (Macaca fascicularis) is presented in a format suitable for use as a template atlas and facilitates comparison of brains of different nonhuman primate species by providing a template brain against which to compare size and internal variability.
Primate brain maps : structure of the macaque brain
Primate Brain Maps is an invaluable tool and reference work for everyone working in primate brain research, but also a unique source of information for all those in the fields of neuroanatomy and neuroinformatics.
Atlas of the Human Brain
This greatly enlarged new edition of Atlas of the Human Brain provides the most detailed and accurate delineations of brain structure available and includes features which assist in the new fields of neuroscience - functional imaging, resting state imaging and tractography.
A stereotaxic atlas of the brain of the cynomolgus monkey (Macaca fascicularis)
Outline drawings of representative frontal sections of the Macaca fascicularis brain are presented in stereotaxic coordinates, based on photographs of unstained frozen sections of three formalin‐fixed brains in which stainless steel needles were inserted to mark the horizontal zero and several anteroposterior positions.
Correlation and revised nomenclature of ventral nuclei in the thalamus of human and monkey.
  • E. Jones
  • Biology
    Stereotactic and functional neurosurgery
  • 1990
The application of histochemical and immunocytochemical methods to the human thalamus, when allied with traditional staining methods, permits a clearer definition of the borders between many nuclei and a nomenclature that is applicable to both monkeys and humans introduced.
Correlative Anatomy of the Nervous System
The medical neurologist and neurosurgeon will find it indispensable as an authoritative source of information and a guide to the pertinent literature.