UC Davis/UC San Diego Human Brain Project

Project 1: Informatics

The objective of this Informatics project is to build a scalable information system infrastructure that provides software tools and uses data produced by Projects 2-4 in the construction of a primate lateral geniculate database, which will serve as a prototype for later construction of a Program-specific thalamic database.  This Informatics project is utilizing concepts and methodologies in metadata management, data integration, thesaurus creation, data annotation models, and information retrieval schemes for graphical and non-graphical neuroscientific data sets.  The Neuroscience Information Repository is based on an object-relational database system infrastructure that stores content-dependent metadata, concept-oriented, indexing metadata (data annotations), and links of these metadata to the primary data sets distributed between Projects 2-4.  The metadata will be used to access, manage, and extend graphical and non-graphical data generated by the projects in a Web-based transparent and uniform fashion.  Tools are being developed for project members and the general Neuroscience community that can be used annotate graphical and non-graphical semistructured information with concepts (neuroconcepts) obtained from a concept-oriented controlled terminology system.

More specifically,  we are developing these tools and functions:

  1. A terminology server for creating and managing project specific thesauri (NeuroThesauri) will be developed, including tools (NeuArt) to annotate graphical and non-graphical project specific data based on neuroconcepts specified in these Thesauri;
  2. The Neuroscience Information Repository (NIR) has been designed and currently being implemented to record and manage image and project specific metadata in an image registry and metadata component;
  3. Web-based Information retrieval schemes against the terminology server and NIR for retrieving graphical and non-graphical data sets from project sites in a uniform and transparent fashion are being developed;
  4. Application-specific tools being used and developed in Projects 2-4 will be integrated on top of NIR, allowing the Projects and the Neuroscience community to access and utilize these tools as part of NIR, which will provide a unique Web-based portal to the repository of primate lateral geniculate data and eventually to a wider Neuroscience database.

Contributions of Project 1 to the program as a whole

This project is the recipient of data that come in varied and application-specific formats from Projects 2-4; it synthesizes, coordinates, integrates these data and converts them into a smaller number of formats supported by the NIR; it will develop and support the data formats on which all secondary or derived data processing and interactive operations will be performed on the program-specific data; it is developing methods for exchanging the program-specific data with other databases of neuroscience information.

Specific contributions of Project 1

Taking advantage of new insights in informatics, this project will develop an information system that will integrate the project-specific datasets and build project- and program-specific metadata with the capacity to annotate in graphical and textual form and to import data in diverse formats from other neuroscience data repositories. It is building a prototype Neuroscience Information Repository based on data about the primate lateral geniculate nucleus (LGN) and its connections.

This Project will thus:

  1. Receive data generated by Projects 2-4, integrate these data and use them in building a database of the primate LGN that will form a prototype Information System;
  2. Develop a scalable NIR for acquisition, storage, manipulation, and retrieval of morphological, physiological, molecular, cytological, circuitry, functional, and behavioral information about the LGN, using a federated network architecture;
  3. Combine the various software tools being developed in Projects 2-4 into an integrated package capable of use in widely varying formats;
  4. Using the LGN database and associated tools as a model, develop and implement an integrated data model and cooperative tools that permit diverse neuroscientific groups to archive, index, retrieve, and exchange heterogeneous neuroscientific information. In both the short and the long term, the information system and associated tools will support data linkages that allow users to create and work with group-specific and integrated neuroscience vocabularies (NeuroThesauri)

Project 1 status

Several core components and concepts described in the Informatics project have been published . First prototypes described in these works have been implemented. This includes in particular a query protocol, jTerm, to access concepts recorded in a terminology server using a Web-based interface.  The terminology server used is currently to be populated with approximately 500 program specific neuroconcepts and terms that Dr. Fred Gorin has assembled and structured.

The NeuArt tool has been redesigned and implemented in Java. The tool now provides users with functionality to annotate image data using neuroconcepts from a terminology server. For this, jTerm has been integrated into NeuArt.  Currently, NeuArt can be used to annotate image data from projects 2 and 4 (XANAT database). NeuArt also provides a tool that enables  annotation to be exported in XML format. A data annotation tool for text data is currently under development at the Database and Information Systems Group at UC Davis. Both annotation tools will provide core components in this program.

A first prototype of NIR has been set up on an Oracle8i database. Simple Web-based interfaces to record (image) metadata are currently under development.

Personnel

Principal Investigator: Fredric A. Gorin, UC Davis
Co-PI: Leo M. Chalupa, UC Davis
Co-PI: Patrick Fitch ,UC Davis
Co-PI: Michael Gertz ,UC Davis
Co-PI: Bernd Hamann, UC Davis
Co-PI: Michael Hogarth, UC Davis
Co-PI: Edward G. Jones ,UC Davis
Co-PI: Harvey J. Karten, UC San Diego
Co-PI: Bruno S. Olshausen, UC Davis
Co-PI: Richard Walters ,UC Davis
 
Page reference:  http://neuroscience.ucdavis.edu/HBP/project1.html;
Last update: 08/23/2002
Copyright: University of California