Collating and Curating Neuroanatomical Nomenclatures: Principles and Use of the Brain Architecture Knowledge Management System (BAMS)

Abstract

Terms used to describe nervous system parts and their interconnections are rife with synonyms, partial correspondences, and even homonyms, making effective scientific communication unnecessarily difficult. To address this problem a new Topological Relations schema for the Relations module of BAMS (Brain Architecture Knowledge Management System) was created. It includes a representation of the qualitative spatial relations between nervous system parts defined in different neuroanatomical nomenclatures or atlases and is general enough to record data and metadata from the literature, regardless of description level or species. Based on this foundation a Projections Translations inference engine was developed for the BAMS interface that automatically translates neuroanatomical projection (axonal inputs and outputs) reports across nomenclatures from translated information. To make BAMS more useful to the neuroscience community three things were done. First, we implemented a simple schema for validation of the translated neuroanatomical projections. Second, more than 1,000 topological relations between brain gray matter regions for the rat were inserted, along with associated details. Finally, a case study was performed to enter all historical or legacy published information about terminology related to one relatively complex gray matter region of the rat. The bed nuclei of the stria terminalis (BST) were chosen and 21 different nomenclatures from 1923 to present were collated, along with 284 terms for parts (gray matter differentiations), 360 qualitative topological relations between parts, and more than 7,000 details about spatial relations between parts, all of which was annotated with appropriate metadata. This information was used to construct a graphical "knowledge map" of relations used in the literature to describe subdivisions of the rat BST.

Keywords: data mining; databases; neuroanatomical projections; neuroanatomy; neuroinformatics.

Figure 1

The ER structure of the new Topological Relations module of BAMS. The Brain Parts and the Topological Relations modules are shown in dotted boxes.

Figure 2

The result of a search in BAMS for topological relations by regions defined in different neuroanatomical nomenclatures (inset; it can be accessed directly at the URL: http://brancusi. usc.edu/bkms/brain/search_bname_con.php). The result of the search will include the related regions, their nomenclatures, and associated annotated and metadata. The link “Additional metadata” will lead to details related to the comparison method, shown in Figure 3 (see Text for details).

Figure 3

Users can further access details of the comparison process shown in Figure 2, and of the precision of comparison that are collated from the associated reference. See Text for details.

Figure 4

Metadata stored in the “Definition specification” table, which can be associated with a nervous system region recorded in BAMS are listed together with its definition. This example refers to the part BST2, defined by Geeraedts et al. (1990).

Figure 5

An example of neuroanatomical Projections Translations inference engine output. The screenshot lists the inferred projections of BSTrh defined in rat Swanson (2004) nomenclature. The topologically-based Projections Translations inference engine first lists all nervous system regions related with the region of interest and defined in different nomenclatures. The second table is made of those regions that receive neuroanatomical projections recorded in their original nomenclatures and translated into the one of interest (Swanson, 2004), links to details of the translated projections, and of the topological relations between original and translated regions. See Text for details.

Figure 6

The reconstructed and translated projections matrix of the anterior division of the rat BST, as defined in Swanson (2004) nomenclature. The inset shows a magnified portion of the matrix.

Figure 7

The updated BAMS Ontology (http://retzius. usc.edu/bkms/bams-ontology.html) includes neuroanatomical terms defined in different rat nervous system nomenclatures, and their relations with concepts. The ontology can be browsed online, and downloaded as an XML file, found at the same URL.

Figure 8

Example of validation of the process of neuroanatomical projections translation. A portion of the projections pattern of BSTDL (Moga–Fulwiler–Saper nomenclature), which is the result of translation of projections of BTov (Swanson, nomenclature) is validated both automatically (code EO) by projections reports mapped onto the original nomenclature (Moga–Fulwiler–Saper), and manually, by experts (code IE). See Text for details.

Figure 9

Graphical display of BST-related terms defined in 15 nomenclatures, and their semantic relations (“the knowledge map”). The graph was obtained using GraphViz's Neato tool (Gansner and North, ; Bota and Swanson, 2007b). A higher resolution version of this Figure can be found at the URL: http://brancusi.usc.edu/bkms/bst-relations.png. The inset of the Figure shows the semantical grouping of terms BSTov (Swanson 92/98/04; Ju/Swanson), BSTDL defined in Moga-89 nomenclature, BSTLD in Paxinos/Watson-98, and two related amygdalar nuclei defined in the deOlmos-85 nomenclature.