BODB
From USCBPWiki
Project Overview
Advances in neuroscientific research have led to a flood of information that can only be structured and navigated with the aid of databases and the technology of the World Wide Web. As one contribution to channeling this flood we are developing BODB, in which the aim is to facilitate the interchange between those developing new brain models and new experiments. The current ideas are that the system (1) houses capsules of neuroscientific literature information that will facilitate comparison and integration of original articles; (2) provides a standard form and its repository for entering BOPs, Brain Operating Principles – the gist of the brain mechanisms that abstract away from their heterogeneities, as a way to organize experiments, models and technological spin-off of brain mechanisms; (3) provides a standard form and its repository for entering Model summaries; (4) supplies a sharing point for the data in (1,2,3) among users to enhance the knowledge development; (5) provides a repository of experimental data with a standard structure, and the experimental-data and cross-experiment data analysis tools (currently our focus is on brain imaging data); and (6) provides a means to connect the related documents together and a practical entry-searching tool to enhance the accessibility of information.
These features are intended for both brain modelers and brain experimenters. The experimental data and analysis tools will be used by the brain modeler in extracting knowledge and developing new models, and by the experimenter in designing further experimental protocols. Furthermore, the BOP and Model entries will supply knowledge for the modeler to construct new models, and provide the experimenter suggestions to contrive new experiments. Consequently, the implementation and integration of these features would enhance a theory-experiment cycle (Arbib,2001).
Our current version of BODB combines features of an SDB (Summary Database) and Model Repository (as in Brain Models on the Web [BMW]) (Bischoff-Grethe, Spoelstra & Arbib, 2001), supplemented with a variety of new features. The system is basically comprised of data entities for storing article information, brain operating principles and models, brain-imaging experimental data, and, finally , their relations.
From Figure 1, we start by describing Article Information. These functions as a set of bibliographies, keeping information on publications cited in other entries in BODB. As usual, each item in Article Information is categorized into one of 7 types: journal, book, chapter, thesis, conference, electronic, and unpublished.
The second entity, Brain Operating Principle (BOP), originated from the observation that key concepts concerning brain mechanisms are sometimes implicit in many references but integrated in none. The Brain Operating Principle entity is designed to serve as a repository for maintaining structured and succinct concepts about “how the brain (or a key – functional or structural – subsystem) works”, whether extracted and generalized from empirical data, or exemplified in computational models. We designed this entity with the m:n relationship linking to Article information since one brain operating principle could be derived from many articles, while one article could be a source of information for two or more principles.
The third entity, Model, is designed to function as a repository for descriptions of computational models of brain mechanisms with fields available to provide linkages to actual implementations, simulations, documentation and descriptions. We designed this entity, too, with the m:n relationship linking to Article information. Another m:n relationship links the Model and Brain Operating Principle entities because one model could be derived from many principles, as one principle could be exemplified in many models. Since one model could be synthesized from other models, the other m:n self-relationship is also supplied to this entity.
The next fundamental entity is Brain Region. This entity contains names and hierarchies of regions of the human brain, currently based on Brain Imaging data from the Research Imaging Center, The University of Texas Health Science Center at San Antonio. These brain region names are used to categorize entries related to specific human brain regions, enhancing entry-search capability.
The last entity is Brain Imaging Experimental Data. Currently, this entity functions primarily as a repository for tables of brain-imaging experimental data. To augment this feature, we adapted the Talairach Daemon (TD) developed by the San Antonio group as well as ideas from USCBP’s own NeuARt project (Dashti et al., 2001) to enable the user to graphically compare and contrast the experimental data on brain-slice images. A 1:m relationship from this entity to the Article Information entity is added because one article could have two or more experiment sets. As, an m:n relationship to brain region is applied in the sense that one experiment set could refer to two or more brain regions.
In addition to the basic entities we described so far, we added a set of tables that are responsible for maintaining block diagrams for models and anatomical relationships, etc., with supplementary information such as box area (coordinates) and box name. These diagrams not only help the user visualize Model entries, but also provide connections between Models via hierarchical relations.
As shown in Diagram 1, connections among entities not only allow the user to go back and forth between entries via their relations, but provide options for cross search as well (e.g. search models by related brain operating principles). The current version of BODB provides searches and their options as listed in Table 1.
