搜索结果：Database : the journal of biological databases and curation

In disseminating scientific and statistical data, on-line databases have almost completely replaced traditional paper-based media such as journals and reference works. Given this, can we measure the impact of a database in the same way that we measure an author's or journal's impact? To do this, we need somehow to represent a database as a set of publications, and databases typically allow a large number of possible decompositions into parts, any of which could be treated as a publication. We show that the definition of the h-index naturally extends to hierarchies, so that if a database admits some kind of hierarchical interpretation we can use this as one measure of the importance of a database; moreover, this can be computed as efficiently as one can compute the normal h-index. This also gives us a decomposition of the database that might be used for other purposes such as giving credit to the curators or contributors to the database. We illustrate the process by analyzing three widely used databases.

The popularity of the Mobile Database is increasing day by day as people need information even on the move in the fast changing world. This database technology permits employees using mobile devices to connect to their corporate networks, hoard the needed data, work in the disconnected mode and reconnect to the network to synchronize with the corporate database. In this scenario, the data is being moved closer to the applications in order to improve the performance and autonomy. This leads to many interesting problems in mobile database research and Mobile Database has become a fertile land for many researchers. In this paper a survey is presented on data and Transaction management in Mobile Databases from the year 2000 onwards. The survey focuses on the complete study on the various types of Architectures used in Mobile databases and Mobile Transaction Models. It also addresses the data management issues namely Replication and Caching strategies and the transaction management functionalities such as Concurrency Control and Commit protocols, Synchronization, Query Processing, Recovery and Security. It also provides Research Directions in Mobile databases.

Consistent query answering is the problem of computing the answers from a database that are consistent with respect to certain integrity constraints that the database as a whole may fail to satisfy. Those answers are characterized as those that are invariant under minimal forms of restoring the consistency of the database. In this context, we study the problem of repairing databases by fixing integer numerical values at the attribute level with respect to denial and aggregation constraints. We introduce a quantitative definition of database fix, and investigate the complexity of several decision and optimization problems, including DFP, i.e. the existence of fixes within a given distance from the original instance, and CQA, i.e. deciding consistency of answers to aggregate conjunctive queries under different semantics. We provide sharp complexity bounds, identify relevant tractable cases; and introduce approximation algorithms for some of those that are intractable. More specifically, we obtain results like undecidability of existence of fixes for aggregation constraints; MAXSNP-hardness of DFP, but a good approximation algorithm for a relevant special case; and intractability but

Data processing systems impose multiple views on data as it is processed by the system. These views include spreadsheets, databases, matrices, and graphs. The common theme amongst these views is the need to store and operate on data as whole sets instead of as individual data elements. This work describes a common mathematical representation of these data sets (associative arrays) that applies across a wide range of applications and technologies. Associative arrays unify and simplify these different approaches for representing and manipulating data into common two-dimensional view of data. Specifically, associative arrays (1) reduce the effort required to pass data between steps in a data processing system, (2) allow steps to be interchanged with full confidence that the results will be unchanged, and (3) make it possible to recognize when steps can be simplified or eliminated. Most database system naturally support associative arrays via their tabular interfaces. The D4M implementation of associative arrays uses this feature to provide a common interface across SQL, NoSQL, and NewSQL databases.

We address the issue of incorporating a particular yet expressive form of integrity constraints (namely, denial constraints) into probabilistic databases. To this aim, we move away from the common way of giving semantics to probabilistic databases, which relies on considering a unique interpretation of the data, and address two fundamental problems: consistency checking and query evaluation. The former consists in verifying whether there is an interpretation which conforms to both the marginal probabilities of the tuples and the integrity constraints. The latter is the problem of answering queries under a "cautious" paradigm, taking into account all interpretations of the data in accordance with the constraints. In this setting, we investigate the complexity of the above-mentioned problems, and identify several tractable cases of practical relevance.

Up-to-date meta-databases are vital for the analysis of biological data. However,the current exponential increase in biological data leads to exponentially increasing meta-database sizes. Large-scale meta-database management is therefore an important challenge for production platforms providing services for biological data analysis. In particular, there is often a need either to run an analysis with a particular version of a meta-database, or to rerun an analysis with an updated meta-database. We present our GeStore approach for biological meta-database management. It provides efficient storage and runtime generation of specific meta-database versions, and efficient incremental updates for biological data analysis tools. The approach is transparent to the tools, and we provide a framework that makes it easy to integrate GeStore with biological data analysis frameworks. We present the GeStore system, an evaluation of the performance characteristics of the system, and an evaluation of the benefits for a biological data analysis workflow.

Curated databases have become important sources of information across scientific disciplines, and due to the manual work of experts, often become important reference works. Features such as provenance tracking, archiving, and data citation are widely regarded as important features for curated databases, but implementing such features is challenging, and small database projects often lack the resources to do so. A scientific database application is not just the database itself, but also an ecosystem of web applications to display the data, and applications supporting data curation. Supporting advanced curation features requires changing all of these components, and there is currently no way to provide such capabilities in a reusable way. Cross-tier programming languages have been proposed to simplify the creation of web applications, where developers write an application in a single, uniform language. Consequently, database queries and updates can be written in the same language as the rest of the program, and at least in principle, it should be possible to provide curation features reusably via program transformations. As a first step, it is important to establish that realistic cu

We investigate the query evaluation problem for fixed queries over fully dynamic databases, where tuples can be inserted or deleted. The task is to design a dynamic algorithm that immediately reports the new result of a fixed query after every database update. We consider queries in first-order logic (FO) and its extension with modulo-counting quantifiers (FO+MOD), and show that they can be efficiently evaluated under updates, provided that the dynamic database does not exceed a certain degree bound. In particular, we construct a data structure that allows to answer a Boolean FO+MOD query and to compute the size of the result of a non-Boolean query within constant time after every database update. Furthermore, after every update we are able to immediately enumerate the new query result with constant delay between the output tuples. The time needed to build the data structure is linear in the size of the database. Our results extend earlier work on the evaluation of first-order queries on static databases of bounded degree and rely on an effective Hanf normal form for FO+MOD recently obtained by Heimberg, Kuske, and Schweikardt (LICS 2016).

Annotated speech corpora are databases consisting of signal data along with time-aligned symbolic `transcriptions'. Such databases are typically multidimensional, heterogeneous and dynamic. These properties present a number of tough challenges for representation and query. The temporal nature of the data adds an additional layer of complexity. This paper presents and harmonises two independent efforts to model annotated speech databases, one at Macquarie University and one at the University of Pennsylvania. Various query languages are described, along with illustrative applications to a variety of analytical problems. The research reported here forms a part of several ongoing projects to develop platform-independent open-source tools for creating, browsing, searching, querying and transforming linguistic databases, and to disseminate large linguistic databases over the internet.

Biologists are increasingly using databases for storing and managing their data. Biological databases typically consist of a mixture of raw data, metadata, sequences, annotations, and related data obtained from various sources. Current database technology lacks several functionalities that are needed by biological databases. In this paper, we introduce bdbms, an extensible prototype database management system for supporting biological data. bdbms extends the functionalities of current DBMSs to include: (1) Annotation and provenance management including storage, indexing, manipulation, and querying of annotation and provenance as first class objects in bdbms, (2) Local dependency tracking to track the dependencies and derivations among data items, (3) Update authorization to support data curation via content-based authorization, in contrast to identity-based authorization, and (4) New access methods and their supporting operators that support pattern matching on various types of compressed biological data types. This paper presents the design of bdbms along with the techniques proposed to support these functionalities including an extension to SQL. We also outline some open issues i

Graph neural networks (GNNs) are powerful deep learning models for graph-structured data, demonstrating remarkable success across diverse domains. Recently, the database (DB) community has increasingly recognized the potentiality of GNNs, prompting a surge of researches focusing on improving database systems through GNN-based approaches. However, despite notable advances, There is a lack of a comprehensive review and understanding of how GNNs could improve DB systems. Therefore, this survey aims to bridge this gap by providing a structured and in-depth overview of GNNs for DB systems. Specifically, we propose a new taxonomy that classifies existing methods into two key categories: (1) Relational Databases, which includes tasks like performance prediction, query optimization, and text-to-SQL, and (2) Graph Databases, addressing challenges like efficient graph query processing and graph similarity computation. We systematically review key methods in each category, highlighting their contributions and practical implications. Finally, we suggest promising avenues for integrating GNNs into Database systems.

This paper explores the effect that changing access patterns has on the performance of database management systems. Changes in access patterns play an important role in determining the efficiency of key performance optimization techniques, such as dynamic clustering, prefetching, and buffer replacement. However, all existing benchmarks or evaluation frameworks produce static access patterns in which objects are always accessed in the same order repeatedly. Hence, we have proposed the Dynamic Evaluation Framework (DEF) that simulates access pattern changes using configurable styles of change. DEF has been designed to be open and fully extensible (e.g., new access pattern change models can be added easily). In this paper, we instantiate DEF into the Dynamic object Evaluation Framework (DoEF) which is designed for object databases, i.e., object-oriented or object-relational databases such as multi-media databases or most XML databases.The capabilities of DoEF have been evaluated by simulating the execution of four different dynamic clustering algorithms. The results confirm our analysis that flexible conservative re-clustering is the key in determining a clustering algorithm's ability

The use of the iris as a biometric identifier has increased dramatically over the last 30 years, prompting privacy and security concerns about the use of iris images in research. It can be difficult to acquire iris image databases due to ethical concerns, and this can be a barrier for those performing biometrics research. In this paper, we describe and show how to create a database of realistic, biometrically unidentifiable colored iris images by training a diffusion model within an open-source diffusion framework. Not only were we able to verify that our model is capable of creating iris textures that are biometrically unique from the training data, but we were also able to verify that our model output creates a full distribution of realistic iris pigmentations. We highlight the fact that the utility of diffusion networks to achieve these criteria with relative ease, warrants additional research in its use within the context of iris database generation and presentation attack security.

Images have become an important data source in many scientific and commercial domains. Analysis and exploration of image collections often requires the retrieval of the best subregions matching a given query. The support of such content-based retrieval requires not only the formulation of an appropriate scoring function for defining relevant subregions but also the design of new access methods that can scale to large databases. In this paper, we propose a solution to this problem of querying significant image subregions. We design a scoring scheme to measure the similarity of subregions. Our similarity measure extends to any image descriptor. All the images are tiled and each alignment of the query and a database image produces a tile score matrix. We show that the problem of finding the best connected subregion from this matrix is NP-hard and develop a dynamic programming heuristic. With this heuristic, we develop two index based scalable search strategies, TARS and SPARS, to query patterns in a large image repository. These strategies are general enough to work with other scoring schemes and heuristics. Experimental results on real image datasets show that TARS saves more than 87

Reference population databases are an essential tool in variant and gene interpretation. Their use guides the identification of pathogenic variants amidst the sea of benign variation present in every human genome, and supports the discovery of new disease-gene relationships. The Genome Aggregation Database (gnomAD) is currently the largest and most widely used publicly available collection of population variation from harmonized sequencing data. The data is available through the online gnomAD browser (https://gnomad.broadinstitute.org/) that enables rapid and intuitive variant analysis. This review provides guidance on the content of the gnomAD browser, and its usage for variant and gene interpretation. We introduce key features including allele frequency, per-base expression levels, constraint scores, and variant co-occurrence, alongside guidance on how to use these in analysis, with a focus on the interpretation of candidate variants and novel genes in rare disease.

Graph databases (GDB) have recently been arisen to overcome the limits of traditional databases for storing and managing data with graph-like structure. Today, they represent a requirement for many applications that manage graph-like data, like social networks. Most of the techniques, applied to optimize queries in graph databases, have been used in traditional databases, distribution systems... or they are inspired from graph theory. However, their reuse in graph databases should take care of the main characteristics of graph databases, such as dynamic structure, highly interconnected data, and ability to efficiently access data relationships. In this paper, we survey the query optimization techniques in graph databases. In particular, we focus on the features they have introduced to improve querying graph-like data.

Commercial application of facial recognition demands robustness to a variety of challenges such as illumination, occlusion, spoofing, disguise, etc. Disguised face recognition is one of the emerging issues for access control systems, such as security checkpoints at the borders. However, the lack of availability of face databases with a variety of disguise addons limits the development of academic research in the area. In this paper, we present a multimodal disguised face dataset to facilitate the disguised face recognition research. The presented database contains 8 facial add-ons and 7 additional combinations of these add-ons to create a variety of disguised face images. Each facial image is captured in visible, visible plus infrared, infrared, and thermal spectra. Specifically, the database contains 100 subjects divided into subset-A (30 subjects, 1 image per modality) and subset-B (70 subjects, 5 plus images per modality). We also present baseline face detection results performed on the proposed database to provide reference results and compare the performance in different modalities. Qualitative and quantitative analysis is performed to evaluate the challenging nature of disgui

Disconnection of mobile clients from server, in an unclear time and for an unknown duration, due to mobility of mobile clients, is the most important challenges for concurrency control in mobile database with client-server model. Applying pessimistic common classic methods of concurrency control (like 2pl) in mobile database leads to long duration blocking and increasing waiting time of transactions. Because of high rate of aborting transactions, optimistic methods aren`t appropriate in mobile database. In this article, OPCOT concurrency control algorithm is introduced based on optimistic concurrency control method. Reducing communications between mobile client and server, decreasing blocking rate and deadlock of transactions, and increasing concurrency degree are the most important motivation of using optimistic method as the basis method of OPCOT algorithm. To reduce abortion rate of transactions, in execution time of transactions` operators a timestamp is assigned to them. In other to checking commitment ordering property of scheduler, the assigned timestamp is used in server on time of commitment. In this article, serializability of OPCOT algorithm scheduler has been proved by

Vector databases have emerged as key enablers for bridging intelligent applications with unstructured data, providing generic search and management support for embedding vectors extracted from the raw unstructured data. As multiple data users can share the same database infrastructure, multi-tenancy support for vector databases is increasingly desirable. This hinges on an efficient filtered search operation, i.e., only querying the vectors accessible to a particular tenant. Multi-tenancy in vector databases is currently achieved by building either a single, shared index among all tenants, or a per-tenant index. The former optimizes for memory efficiency at the expense of search performance, while the latter does the opposite. Instead, this paper presents Curator, an in-memory vector index design tailored for multi-tenant queries that simultaneously achieves the two conflicting goals, low memory overhead and high performance for queries, vector insertion, and deletion. Curator indexes each tenant's vectors with a tenant-specific clustering tree and encodes these trees compactly as sub-trees of a shared clustering tree. Each tenant's clustering tree adapts dynamically to its unique v