Neuroinformatics Literature System Oriented To Knowledge Discovery: Design And Preliminary Implementation

The neuroscience research has brought on enormous amounts of diverse data, moreover the experimental technology progress of neuroscience causes the data type of the new neural information to increase unceasingly, which lead to the difficulty for the neuroscientists to grasp all useful information. In addition, many barriers exist in multiple databases access techniques, including mismatches in query languages, access mechanisms, data models and semantic deduction. Therefore it is extremely significant to integrate the neuroscientific information resources.This study aim to design a specific Neuroinformatics Literature System (NILS) for neuroimaging and brain function research, might save the work on data conversions for the researcher and promote data sharing. It can partly solve the conformity problem of isomeric neural information database, form an integrative data platform to integrate this kind of database with relative information, and then it is advantageous to the database information extraction and the knowledge discovery. The main research works are as followed:In order to orient knowledge discovery, data in the studies of multi-level neuroimaging and brain function are integrated, helpful information and knowledge are extracted from the literature, and the primary data for the nerve ontology prototype construction are provided. NILS consists of 8 main function modules: System Maintenance, Literature Renewal, Literature Retrieval, Result Display/Output, Literature Information Analysis, Neuroimaging Integration, Neuroinformation Text Mining and Nerve Ontology Prototype Construction. It makes possible to semiautomatic gather, coordinate, analyze and store data from multiple underlying sources, provides multi-disciplinary and multi-level integrative retrieval service, helps us to establish a network of comprehensive neuroscientific knowledge for fully understanding the brain principle of work. NILS will not only serve as a foundation platform for the future study pattern driven by hypothesis, but also reveal a great variety of implication relations in the literature, which was previously rarely-known.Based on the cluster server of TS10000, a NILS with integration, expansibility and customization is constructed through the technology of object-oriented relational database. Oracle 9i acts as the database management system, and the operating system is Red Hat Linux 7.3. The overall system uses the Browser/Serve frame, the background program was developed on the basis of Java. The query and maintainance of databases was implemented by adopting Java Server Page, JavaBean and other Java web application technology. In the program design, the separate expression operation enhances the maintainability and the extendibility of the system. The unique sub-module design of the literature renewal in the NILS ensures the literature quality, which includes the user-privilege classifying, the handling for duplicate checking, and the examination of submission, the formal storage to database, the responsibility signature and the quantitative statistics. NILS provides three kinds of retrieving channels, as well as gives fourteen different retrieval fields, consisting of title, author, key word and so on. In addition, the system is equipped with logical coordinate retrieval and secondary circulation retrieval. Moreover NILS possesses an EndNote interface, which is a reference software managed by the third party. The retrieval result can be fast imported into the EndNote, which are advantageous for the user to reference and cite NILS's literature data.Combining the domain characteristic of the neuroimaging and brain function research, a Neuroinformatics tree structure index was designed. This tree structure has been used to collect the Neuroinformatics literature and index the literature, regarded as the classified basis in the subject browsing, and also has been applied in constructing nerve ontology prototype. At present this tree structure includes eight kinds of subject heading: nervous system structure, nerve physiology, brain function, molecular neuroscience, nervous system origin, heredity and development, clinical neuroscience, computation neuroscience and others, all subject headings are more than 350.