A developmental ontology for the mammalian brain based on the prosomeric model

•We have used the prosomeric model to create a modern ontology of mammalian brain structures. •This ontology is based chiefly on gene expression during development. •This ontology will be useful to the field of neuroinformatics. In the past, attempts to create a hierarchical classification of brain structures (an ontology) have been limited by the lack of adequate data on developmental processes. Recent studies on gene expression during brain development have demonstrated the true morphologic interrelations of different parts of the brain. A developmental ontology takes into account the progressive rostrocaudal and dorsoventral differentiation of the neural tube, and the radial migration of derivatives from progenitor areas, using fate mapping and other experimental techniques. In this review, we used the prosomeric model of brain development to build a hierarchical classification of brain structures based chiefly on gene expression. Because genomic control of neural morphogenesis is remarkably conservative, this ontology should prove essentially valid for all vertebrates, aiding terminological unification. In the past, attempts to create a hierarchical classification of brain structures (an ontology) have been limited by the lack of adequate data on developmental processes. Recent studies on gene expression during brain development have demonstrated the true morphologic interrelations of different parts of the brain. A developmental ontology takes into account the progressive rostrocaudal and dorsoventral differentiation of the neural tube, and the radial migration of derivatives from progenitor areas, using fate mapping and other experimental techniques. In this review, we used the prosomeric model of brain development to build a hierarchical classification of brain structures based chiefly on gene expression. Because genomic control of neural morphogenesis is remarkably conservative, this ontology should prove essentially valid for all vertebrates, aiding terminological unification. the caudal subdivision of the forebrain that joins the midbrain to the secondary prosencephalon; it contains three major alar domains (pretectum, thalamus, and prethalamus), as well as the corresponding tegmental regions. an approach to the analysis of brain structure based on the merging of concepts drawn from evolution and embryonic development. the study of connections within the central nervous system (‘odos’ is Greek for a road). transverse unitary subdivisions of the neural tube that share a common dorsoventral structure (floor, basal, alar, and roof plates), but each have differential molecular identities and fates; they comprise the secondary prosencephalon, diencephalon (prosomeres), the midbrain (mesomeres), and the hindbrain (rhombomeres). Greek for the genesis of being: the process of development. a formal conceptualization of the structure of a knowledge base, usually in the form of a hierarchical classification. major subdivision of the telencephalon, usually visualized as covering and surrounding the subpallium; in mammals, it gives rise to the cerebral cortex and several claustroamygdaloid pallial nuclei. Greek for forebrain: the part of the brain that appears at the rostral end of the neural tube. the rostral major subdivision of the developing forebrain that separates from the diencephalon caudally (early in development, both are encompassed within the primary prosencephalon); the secondary prosencephalon includes the telencephalon, the eye, and the hypothalamus. a major subdivision of the telencephalon usually visualized topographically as lying under the pallium, at the brain ‘base’ it generates the so-called ‘basal ganglia’, including the striatum, pallidum, diagonal-basal area, and preoptic area. a meaningful higher-level unit of biological structure, comprising segments that share a general character (e.g., the Drosophila thorax tagma as opposed to the abdominal tagma). a dorsal subdivision of the secondary prosencephalon that forms the pallium and subpallium. a system for describing and representing position relative to external references. a system for describing the relative position of the components of a structure irrespective of external references and any nondisruptive deformations; topology attends exclusively to the invariant neighborhood relations between the components.