Data extraction and ad hoc query of an entity-attribute-value database

Entity--attribute--value (EAV) tables form the major component of several mainstream electronic patient record systems (EPRSs). Such systems have been optimized for real-time retrieval of individual patient data. Data warehousing, on the other hand, involves cross-patient data retrieval based on values of patient attributes, with a focus on ad hoc query. Attribute-centric query is inherently more difficult when data are stored in EAV form than when they are stored conventionally. The authors illustrate their approach to the attribute-centric query problem with ACT/DB, a database for managing clinical trials data. This approach is based on metadata supporting a query front end that essentially hides the EAV/non-EAV nature of individual attributes from the user. The authors' work does not close the query problem, and they identify several complex subproblems that are still to be solved.     

The LabBase system for data management in large scale biology research laboratories

MOTIVATION: The development of laboratory information management systems (LIMSs) for large scale biology research projects can be a challenging problem. Many such projects generate complex datasets via complex procedures that undergo continuous refinement. A key software challenge is to simplify the database-development task so that databases can be built and modified quickly enough to keep pace with changing project-requirements. Results: LabBase extends the facilities offered by relational database systems to simplify the task of creating databases for large scale biology research projects. LabBase provides a structural object data model, similar to ACEDB, and adds to this the concepts of Materials, Steps, and States: Materials are objects representing the identifiable things that participate in a laboratory protocol; Steps are objects reporting the results of a laboratory or analytical procedure; and States are objects denoting places in a laboratory protocol. The system provides a data definition language for succinctly defining laboratory databases, and operations for conveniently storing and retrieving data in such databases. The system also provides support for workflow management. LabBase is implemented in Perl5 and provides a natural interface for laboratory application programs written in Perl. AVAILABILITY: The software is freely available. Contact the authors. CONTACT: nat@jax.org     

A model system for studying the integration of molecular biology databases

MOTIVATION: Integration of molecular biology databases remains limited in practice despite its practical importance and considerable research effort. The complexity of the problem is such that an experimental approach is mandatory, yet this very complexity makes it hard to design definitive experiments. This dilemma is common in science, and one tried-and-true strategy is to work with model systems. We propose a model system for this problem, namely a database of genes integrating diverse data across organisms, and describe an experiment using this model. RESULTS: We attempted to construct a database of human and mouse genes integrating data from GenBank and the human and mouse genome-databases. We discovered numerous errors in these well-respected databases: approximately 15% of genes are apparently missing from the genome-databases; links between the sequence and genome-databases are missing for another 5-10% of the cases; about a third of likely homology links are missing between the genome-databases; 10-20% of entries classified as 'genes' are apparently misclassified. By using a model system, we were able to study the problems caused by anomalous data without having to face all the hard problems of database integration. CONTACT: nat@jax.org     

Medical image collection indexing: shape-based retrieval using KD-trees

The capacity to retrieve images containing objects with shapes similar to a query shape is desirable in medical image databases. We propose a similarity measure and an indexing mechanism for non-rigid comparison of shape which adds this capability to image databases. The (dis-)similarity measure is based on the observations that: (1) the geometry of the same organ in different subjects is not related by a strictly rigid transformation; and (2) the orientation of the organ plays a key role in comparing shape. We propose a similarity measure that computes a non-rigid mapping between curves and uses this mapping to compare oriented shape. We also show how KD-trees can index curves so that retrieval with our similarity measure is efficient. Experiments with real-world data from a database of magnetic resonance images are provided.     

Serologic and molecular characterization of an abortigenic strain of equine arteritis virus isolated from infective frozen semen and an aborted equine fetus

A virus isolated from an aborted equine fetus was determined to be antigenically distinct from several other strains of equine arteritis virus (EAV) by use of a neutralization assay with a large panel of neutralizing monoclonal antibodies. The virus was readily neutralized by polyclonal equine anti-EAV serum. Comparative nucleotide and amino acid sequence analyses indicated that the virus (WA97) isolated from the aborted fetus was virtually identical to a virus (S1971) isolated from imported semen used to inseminate another mare on the farm. Phylogenetic analysis indicated that the WA97/S1971 virus was more related to European than to North American strains of EAV. These sensitive molecular procedures may be useful for epidemiologic investigations of EAV infections. Screening and certification of stallions and frozen equine semen would prevent dissemination of pathogenic strains of EAV.     

An interactive activation approach to object processing: effects of structural similarity, name frequency, and task in normality and pathology

We present a computational model of the processes involved in retrieving stored semantic and name information from objects, using a simple interactive activation and competition architecture. We simulate evidence showing a cross-over in normal reaction times to make semantic classification and identification responses to objects from categories with either structurally similar or structurally dissimilar exemplars, and that identification times to objects from these two different classes correlate differentially with measures of the structural similarity of objects within the category and the frequency of the object's name. Structural similarity exerts a negative effect on object decision as well as naming, though this effect is larger on naming. Also, on naming, structural similarity interacts with the effects of name frequency, captured in the model by varying the weight on connections from semantic to name units; frequency effects are larger with structurally dissimilar items. In addition, (1) the range of potential errors for objects from these two classes, when responses are elicited before activation reached a stable state, differ--a wider range of errors occur to objects from categories with structurally similar exemplars; and (2) simulated lesions to different locations within the model produce selective impairments to identification but not to semantic classification responses to objects from categories with structurally similar exemplars. We discuss the results in relation to data on visual object processing in both normality and pathology.     

Error checking and graphical representation of multiple-complete-digest (MCD) restriction-fragment maps

Genetic and physical maps display the relative positions of objects or markers occurring within a target DNA molecule. In constructing maps, the primary objective is to determine the ordering of these objects. A further objective is to assign a coordinate to each object, indicating its distance from a reference end of the target molecule. This paper describes a computational method and a body of software for assigning coordinates to map objects, given a solution or partial solution to the ordering problem. We describe our method in the context of multiple-complete-digest (MCD) mapping, but it should be applicable to a variety of other mapping problems. Because of errors in the data or insufficient clone coverage to uniquely identify the true ordering of the map objects, a partial ordering is typically the best one can hope for. Once a partial ordering has been established, one often seeks to overlay a metric along the map to assess the distances between the map objects. This problem often proves intractable because of data errors such as erroneous local length measurements (e.g., large clone lengths on low-resolution physical maps). We present a solution to the coordinate assignment problem for MCD restriction-fragment mapping, in which a coordinated set of single-enzyme restriction maps are simultaneously constructed. We show that the coordinate assignment problem can be expressed as the solution of a system of linear constraints. If the linear system is free of inconsistencies, it can be solved using the standard Bellman-Ford algorithm. In the more typical case where the system is inconsistent, our program perturbs it to find a new consistent system of linear constraints, close to those of the given inconsistent system, using a modified Bellman-Ford algorithm. Examples are provided of simple map inconsistencies and the methods by which our program detects candidate data errors and directs the user to potential suspect regions of the map.     

Lack of association of factor V Leiden and coronary heart disease in individuals with and without diabetes

We have created databases and software applications for the analysis of DNA mutations at the human p53 gene, the human hprt gene and both the rodent transgenic lacI and lacZ loci. The databases themselves are stand-alone dBASE files and the software for analysis of the databases runs on IBM-compatible computers with Microsoft Windows. Each database has a separate software analysis program. The software created for these databases permit the filtering, ordering, report generation and display of information in the database. In addition, a significant number of routines have been developed for the analysis of single base substitutions. One method of obtaining the databases and software is via the World Wide Web. Open the following home page with a Web Browser: http://sunsite.unc.edu/dnam/mainpage. html . Alternatively, the databases and programs are available via public FTP from: anonymous@sunsite.unc.edu. There is no password required to enter the system. The databases and software are found beneath the subdirectory: pub/academic/biology/dna-mutations. Two other programs are available at the site, a program for comparison of mutational spectra and a program for entry of mutational data into a relational database.     

Histone Sequence Database: sequences, structures, post-translational modifications and genetic loci

The Histone Sequence Database is an annotated and searchable collection of all available histone and histone fold sequences and structures. Particular emphasis has been placed on documenting conflicts between similar sequence entries from a number of source databases, conflicts that are not necessarily documented in the source databases themselves. New additions to the database include compilations of post-translational modifications for each of the core and linker histones, as well as genomic information in the form of map loci for the human histone gene complement, with the genetic loci linked to Online Mendelian Inheritance in Man (OMIM). The database is freely accessible through the World Wide Web at either http://genome.nhgri.nih.gov/histones/ or http://www.ncbi.nlm.nih. gov/Baxevani/HISTONES     

Databases and software for the analysis of mutations in the human p53 gene, the human hprt gene and the lacZ gene in transgenic rodents

We have created databases and software applications for the analysis of DNA mutations in the human p53 gene, the human hprt gene and the rodent transgenic lacZ locus. The databases themselves are stand-alone dBase files and the software for analysis of the databases runs on IBM- compatible computers. The software created for these databases permits filtering, ordering, report generation and display of information in the database. In addition, a significant number of routines have been developed for the analysis of single base substitutions. One method of obtaining the databases and software is via the World Wide Web (WWW). Open home page http://sunsite.unc.edu/dnam/mainpage.ht ml with a WWW browser. Alternatively, the databases and programs are available via public ftp from anonymous@sunsite.unc.edu. There is no password required to enter the system. The databases and software are found in subdirectory pub/academic/biology/dna-mutations. Two other programs are available at the WWW site, a program for comparison of mutational spectra and a program for entry of mutational data into a relational database.     

SPROUT—A Modeling Language for SEED

An important capability of the SEED system is rapid generation of internal design representations, including design alternatives, that can be evaluated in terms of a broad range of criteria. It consists of modules that must communicate with each other and remain extensible. From a software engineering perspective, there exists no single programming language or database management system, commercial or research-based, that provides all the needed support. In this paper, we describe the SPROUT modeling language, the cornerstone of efforts to bridge this gap. It supports the specification of a system information model, which contains a building product model as a subset. Developments are discussed that lead to the current language design as well as the support for case-based design, persistent storage of objects, management of versions and alternatives, and communication between different SEED modules (i.e., agents). Emphasis is placed on the automatic generation of computer programs and database schemas from a SPROUT specification. Lastly, this effort is compared to other comparable efforts including PDES∕STEP.     

Expression cloning and humoral immune response to the nucleocapsid and membrane proteins of equine arteritis virus

To provide a convenient and sensitive method for the detection of equine arteritis virus (EAV)-specific serum antibodies, we developed an immunoblot assay employing the EAV nucleocapsid (N) and membrane (M) proteins expressed in a procaryotic expression vector (pMAL-c2) for the production of recombinant maltose-binding (MBP) fusion proteins (MBP-N and MBP-M). The antigenic reactivity of the recombinant fusion proteins and their Xa factor cleavage EAV products was confirmed by immunoblot using horse antisera to EAV. Some horse sera, however, showed immune reactivity to the MBP fusion partner protein. Based on a total of 32 horse sera analyzed for the presence of EAV antibodies by immunoblot, using the MBP-N or -M fusion proteins and the Xa factor cleavage EAV products, and in the serum neutralization test, there was 100% concordance between the assays. Sera from horses experimentally infected with EAV were reactive in the immunoblot test with both the MBP-N and the MBP-M fusion proteins by day 14 after EAV exposure. The reactivity continued to the end of the experiment at day 145 after infection. This immune reactivity correlated with the detection of neutralizing antibodies in the serum samples. Based on these findings, the recombinant N and M proteins might be useful for serodetection of EAV-infected animals.     

Comparison of algorithms for dissimilarity-based compound selection

Dissimilarity-based compound selection has been suggested as an effective method for selecting structurally diverse subsets of chemical databases. This article reports a comparison of several maximum-dissimilarity and sphere-exclusion algorithms for dissimilarity-based selection. The effectiveness of the algorithms is quantified by the numbers of biological activity classes identified in subsets selected from the World Drugs Index database, and by the numbers of active compounds identified in feedback searches of this database. The experiments demonstrate the general effectiveness and efficiency of the MaxMin algorithm.     

On naming a giraffe a zebra: Picture naming errors across different object categories.

Two experiments examined naming to deadline for picture of objects from categories with structurally similar or dissimilar exemplars. In Exp 1, a wider range of naming errors were made for objects from structurally similar categories, consistent with those items having a broader set of structural neighbors. Also, only visual?+?semantic errors were made to structurally similar objects, whereas modal errors for some structurally dissimilar objects were either purely visual or purely semantically related to targets. In Exp 2, the names of visual?+?semantic primes occurred as perseverative responses to objects from both category types. The data fit a cascade model of picture naming, in which errors under deadline reflect the rate-limiting processes affecting naming. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

Measurement of plasma total homocysteine by HPLC with coulometric detection

Vertebrate MitBASE is a specialized database where all the vertebrate mitochondrial DNA entries from primary databases are collected, revised and integrated with new information emerging from the literature. Variant sequences are also analyzed, aligned and linked to reference sequences. Data related to the same species and fragment can be viewed over the WWW. The database has a flexible interface and a retrieval system to help non-expert users and contains information not currently available in the primary databases. Vertebrate MitBASE is now available through the MitBASE home page at URL: http://www.ebi.ac.uk/htbin/Mitbase/mitb ase.pl. This work is part of a larger project, MitBASE which is a network of databases covering the full panorama of knowledge on mitochondrial DNA from protists to human sequences.     

Enzyme-linked immunosorbent assay for serological survey of equine arteritis virus in racehorses

To examine antibodies against equine arteritis virus (EAV), an enzyme-linked immunosorbent assay (ELISA) using purified virus antigen was developed. The results of ELISA were compared with those of serum neutralization (SN) tests. The ELISA absorbance values and the SN titers in sera collected weekly from EAV-infected horses showed a similar pattern. The ELISA could detect antibody to EAV in horses experimentally infected with not only a homologous virus strain, which was used as the ELISA antigen, but also a heterologous strain. Using the ELISA, serum samples collected in 1996 from racehorses in three prefectures (Hokkaido, Ibaraki, and Shiga) were examined and there was no evidence of recent EAV infection among these racehorse populations in Japan. The ELISA should be a simple and highly specific method for rapid screening of EAV infection in racehorses.     

A strategy for database interoperation

To realize the full potential of biological databases (DBs) requires more than the interactive, hypertext flavor of database interoperation that is now so popular in the bioinformatics community. Interoperation based on declarative queries to multiple network-accessible databases will support analyses and investigations that are orders of magnitude faster and more powerful than what can be accomplished through interactive navigation. I present a vision of the capabilities that a query-based interoperation infrastructure should provide, and identify assumptions underlying, and requirements of, this vision. I then propose an architecture for query-based interoperation that includes a number of novel components of an information infrastructure for molecular biology. These components include a knowledge base that describes relationships among the conceptualizations used in different biological databases, a module that can determine the DBs that are relevant to a particular query, a module that can translate a query and its results from one conceptualization to another, a collection of DB drivers that provide uniform physical access to different database management systems, a suite of translators that can interconvert among different database schema languages, and a database that describes the network location and access methods for biological databases. A number of the components are translators that bridge the heterogeneities that exist between biological DBs at several different levels, including the conceptual level, the data model, the query language, and data formats.