The mouse genome informatics (MGI) resource, an in-depth resource for the genetics, genomics and biology of the laboratory mouse, provides free access to integrated data on diverse biological attributes, ranging from sequence to phenotype and disease model representation. MGI advances translational research through an integrated data platform that facilitates acquisition, explicit representation, and semantic querying and interpretation of multi-parametric genome-scale datasets, and fosters interoperability across different model organism systems and disparate data sources. To this end, MGI employs a set of logically rigorous, dynamic, and cross-referenceable ontologies to unambiguously describe current biological knowledge, expedite manual curation, and advance the informatics capacity to execute complex data mining tasks relevant to comparative and functional genomics. Major bio-ontologies developed and implemented at MGI include the gene ontology (GO), Mammalian Phenotype (MP) ontology, and adult mouse anatomical (MA) Dictionary, reviewed in this paper. All these share a common generic vocabulary infrastructure, and utilize identical annotation tools and web-based browsers to reinforce ontology-centric curation and support ontology-driven querying of the vocabularies and the associated knowledgebase.

Biology is a vast domain. The Mouse Genome Informatics (MGI) system, which focuses on the biology of the laboratory mouse, covers only a small, carefully chosen slice. Nevertheless, we deal with data of immense variety, deep complexity, and exponentially growing volume. Our role as an integration nexus is to add value by combining data sets of diverse types and origins, eliminating redundancy and resolving conflicts. We briefly describe some of the issues we face and approaches we have adopted to the integration problem.

Data integration is key to knowledge discovery in the age of genomics and represents a major, long-standing challenge for the genome informatics community. Integration of data across heterogeneous genome databases requires the identification of common data entities and mechanisms to ensure referential integrity and persistence of these common entities even as our understanding of their biological properties changes. The Mouse Genome Informatics (MGI) database group employs multiple strategies for achieving data integration and maintaining inter-connectedness with other databases, including: (1) the use of permanent, unique accession IDs for identifying core data entities, (2) the application of nomenclature standards for naming genes and strains of mice, and (3) the development and implementation of controlled vocabularies and ontologies to ensure semantic consistency of biological concepts within and across model organism databases.

Describes the design and implementation of QBlSM (Query By Interactive, Spatial Multimedia), a prototype for querying and visualizing 3D spatial data. The first application is in an area in medical research, in particular, Functional Brain Mapping. The system is built on top of the Starburst DBMS extended to handle spatial data types, specifically, scalar fields and arbitrary regions of space within such fields. The authors list the requirements of the application, discuss the logical and physical database design issues, and present timing results from their prototype. They observed that the DBMS' early spatial filtering results in significant performance savings because the system response time is dominated by the amount of data retrieved, transmitted, and rendered.>

E is an extension of C++ designed for writing software systems to support persistent applica- tions.Originally designed as a language for implementing database systems, E has evolved into a general persistent programming language E was the first C++ extension to support transparent persistence, the first C++ implementation to support generic classes, and remains the only C++ extension to provide general-purpose lterators, In addition to its contributions to the C + + programming domain, work on E has made several contributions to the field of persmtent languages in general, including several distinct implementations of persistence.Thm paper describes the main features of E and shows through examples how E addresses many of the problems that arise in building persistent systems.

CACL is a protection scheme for objects that offers a simple and flexible model of protection and has an efficient, software-only implementation.The model, based on Access Control Lists (ACLs) integrated with the type system, allows owners to control who may invoke which methods on which objects, permits cooperation between mutually suspicious principals, allows ownership of objects to be transferred safely, prevents unwanted propagation of authority between principals, and allows changes to the authorization information to take effect on the next method invocation.The implementation, based on the integration of Capabilities with method dispatch, avoids the overhead of access checking in the majority of invocations, at the cost of space for extra dispatch vectors.CACL offers a viable mechanism for finegrained protection in an object-oriented database system.

article Aspects: extending objects to support multiple, independent roles Share on Authors: Joel Richardson IBM Almaden Research Center, San Jose, California IBM Almaden Research Center, San Jose, CaliforniaView Profile , Peter Schwarz IBM Almaden Research Center, San Jose, California IBM Almaden Research Center, San Jose, CaliforniaView Profile Authors Info & Claims ACM SIGMOD RecordVolume 20Issue 2June 1991 pp 298–307https://doi.org/10.1145/119995.115839Online:01 April 1991Publication History 124citation521DownloadsMetricsTotal Citations124Total Downloads521Last 12 Months7Last 6 weeks0 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteGet Access

The goal of the EXODUS extensible DBMS project is to enable the rapid development of a wide spectrum of high-performance, application-specific database systems EXODUS provides certain kernel facilities for use by all applications and a set of tools to aid the database implementor (DBI) in generating new database system software. Some of the DBI's work is supported by EXODUS tools which generate database components from a specification. However, components such as new abstract data types, access methods, and database operations must be explicitly coded by the DBI. This paper analyzes the major programming problems faced by the DBI, describing the collection of programming language constructs that EXODUS provides for simplifying the DBI's task. These constructs have been embedded in the E programming language, an extension of C++ designed specifically for implementing DBMS software.