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PubChem (https://pubchem.ncbi.nlm.nih.gov) is a public repository for information on chemical substances and their biological activities, launched in 2004 as a component of the Molecular Libraries Roadmap Initiatives of the US National Institutes of Health (NIH). For the past 11 years, PubChem has grown to a sizable system, serving as a chemical information resource for the scientific research community. PubChem consists of three inter-linked databases, Substance, Compound and BioAssay. The Substance database contains chemical information deposited by individual data contributors to PubChem, and the Compound database stores unique chemical structures extracted from the Substance database. Biological activity data of chemical substances tested in assay experiments are contained in the BioAssay database. This paper provides an overview of the PubChem Substance and Compound databases, including data sources and contents, data organization, data submission using PubChem Upload, chemical structure standardization, web-based interfaces for textual and non-textual searches, and programmatic access. It also gives a brief description of PubChem3D, a resource derived from theoretical three-dimensional structures of compounds in PubChem, as well as PubChemRDF, Resource Description Framework (RDF)-formatted PubChem data for data sharing, analysis and integration with information contained in other databases.

A. ANTECHAMBER. Database Systems. The Main Principles. Functionalities. Complexity and Diversity. Past and Future. Ties with This Book. Bibliographic Notes. Theoretical Background. Some Basics. Languages, Computability, and Complexity. Basics from Logic. The Relational Model. The Structure of the Relational Model. Named versus Unnamed Perspectives. Notation. Bibliographic Notes. B. BASICS: RELATIONAL QUERY LANGUAGES. Conjunctive Queries. Getting Started. Logic-Based Perspectives. Query Composition and Views. Algebraic Perspectives. Adding Union. Bibliographic Notes. Exercises. Adding Negation: Algebra and Calculus. The Relational Algebras. Nonrecursive Datalog with Negation. The Relational Calculus. Syntactic Restrictions for Domain Independence. Aggregate Functions. Digression: Finite Representations of Infinite Databases. Bibliographic Notes. Exercises. Static Analysis and Optimization. Issues in Practical Query Optimization. Global Optimization. Static Analysis of the Relational Calculus. Computers with Acyclic Joins. Bibliographic Notes. Exercises. Notes on Practical Languages. SQL: The Structured Query Language. Query-by-Example and Microsoft Access. Confronting the Real World. Bibliographic Notes. Exercises. C. CONSTRAINTS. Functional and Join Dependency. Motivation. Functional and Key Dependencies. join and Multivalued Dependencies. The Chase. Bibliographic Notes. Exercises. Inclusion Dependency. Inclusion Dependency in Isolation. Finite versus Infinite Implication. Nonaxiomatizability of fd's + ind's. Restricted Kinds of Inclusion Dependency. Bibliographic Notes. Exercises. A Larger Perspective. A Unifying Framework. The Chase revisited. Axiomatization. An Algebraic Perspective. Bibliographic Notes. Exercises. Design and Dependencies. Semantic Data Models. Normal Forms. Universal Relation Assumption. Bibliographic Notes. Exercises. D. DATALOG AND RECURSION. Datalog. Syntax of Datalog. Model-Theoretic Semantics. Fixpoint Semantics. Proof-Theoretic Approach. Static Program Analysis. Bibliographic Notes. Exercises. Evaluation of Datalog. Seminaive Evaluation. Top-Down Techniques. Magic. Two Improvements. Bibliographic Notes. Exercises. Recursion and Negation. Algebra + While. Calculus + Fixpoint. Datalog with Negation. Equivalence. Recursion in Practical Language. Bibliographic Notes. Exercises. Negation in Datalog. The Basic Problem. Stratified Semantics. Well-Founded Semantics. Expressive Power. Negation as Failure of Brief. Bibliographic Notes. Exercises. E. EXPRESSIVENESS AND COMPLEXITY. Sizing up Languages. Queries. Complexity of Queries. Languages and Complexity. Bibliographic Notes. Exercises. First Order, Fixpoint and While. Complexity of First-Order Queries. Expressiveness of First-Order Queries. Fixpoint and While Queries. The Impact of Order. Bibliographic Notes. Exercises. Highly Expressive Languages. While(N)-while with Arithmetic. While(new)-while with New Values. While(uty)-An Untyped Extension of while. Bibliographic Notes. Exercises. F. FINALE. Incomplete Information. Warm-Up. Weak Representation Systems. Conditional Tables. The Complexity of Nulls. Other Approaches. Bibliographic Notes. Exercises. Complex Values. Complex Value Databases. The Algebra. The Caculas. Examples. Equivalence Theorems. Fixpoint and Deduction. Expressive Power and Complexity. A Practicle Query Language for Complex Values. Bibliographic Notes. Exercises. Object Databases. Informal Presentation. Formal Definition of an OODB Model. Languages for OODB Queries. Languages for Methods. Further Issues for OODB's. Bibliographic Notes. Exercises. Dynamic Aspects. Updated Languages. Transactional Schemas. Updating Views and Deductive Databases. Active Databases. Temporal Databases and Constraints. Bibliographic Notes. Exercises. Bibliography. Symbol Index. Index. 0201537710T04062001

The recent advent of DNA sequencing technologies facilitates the use of genome sequencing data that provide means for more informative and precise classification and identification of members of the Bacteria and Archaea. Because the current species definition is based on the comparison of genome sequences between type and other strains in a given species, building a genome database with correct taxonomic information is of paramount need to enhance our efforts in exploring prokaryotic diversity and discovering novel species as well as for routine identifications. Here we introduce an integrated database, called EzBioCloud, that holds the taxonomic hierarchy of the Bacteria and Archaea, which is represented by quality-controlled 16S rRNA gene and genome sequences. Whole-genome assemblies in the NCBI Assembly Database were screened for low quality and subjected to a composite identification bioinformatics pipeline that employs gene-based searches followed by the calculation of average nucleotide identity. As a result, the database is made of 61 700 species/phylotypes, including 13 132 with validly published names, and 62 362 whole-genome assemblies that were identified taxonomically at the genus, species and subspecies levels. Genomic properties, such as genome size and DNA G+C content, and the occurrence in human microbiome data were calculated for each genus or higher taxa. This united database of taxonomy, 16S rRNA gene and genome sequences, with accompanying bioinformatics tools, should accelerate genome-based classification and identification of members of the Bacteria and Archaea. The database and related search tools are available at www.ezbiocloud.net/.

The MIT-BIH Arrhythmia Database was the first generally available set of standard test material for evaluation of arrhythmia detectors, and it has been used for that purpose as well as for basic research into cardiac dynamics at about 500 sites worldwide since 1980. It has lived a far longer life than any of its creators ever expected. Together with the American Heart Association Database, it played an interesting role in stimulating manufacturers of arrhythmia analyzers to compete on the basis of objectively measurable performance, and much of the current appreciation of the value of common databases, both for basic research and for medical device development and evaluation, can be attributed to this experience. In this article, we briefly review the history of the database, describe its contents, discuss what we have learned about database design and construction, and take a look at some of the later projects that have been stimulated by both the successes and the limitations of the MIT-BIH Arrhythmia Database.

Much of the complexity within cells arises from functional and regulatory interactions among proteins. The core of these interactions is increasingly known, but novel interactions continue to be discovered, and the information remains scattered across different database resources, experimental modalities and levels of mechanistic detail. The STRING database (https://string-db.org/) systematically collects and integrates protein-protein interactions-both physical interactions as well as functional associations. The data originate from a number of sources: automated text mining of the scientific literature, computational interaction predictions from co-expression, conserved genomic context, databases of interaction experiments and known complexes/pathways from curated sources. All of these interactions are critically assessed, scored, and subsequently automatically transferred to less well-studied organisms using hierarchical orthology information. The data can be accessed via the website, but also programmatically and via bulk downloads. The most recent developments in STRING (version 12.0) are: (i) it is now possible to create, browse and analyze a full interaction network for any novel genome of interest, by submitting its complement of encoded proteins, (ii) the co-expression channel now uses variational auto-encoders to predict interactions, and it covers two new sources, single-cell RNA-seq and experimental proteomics data and (iii) the confidence in each experimentally derived interaction is now estimated based on the detection method used, and communicated to the user in the web-interface. Furthermore, STRING continues to enhance its facilities for functional enrichment analysis, which are now fully available also for user-submitted genomes.

In addition to maintaining the GenBank(R) nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides data analysis and retrieval resources for the data in GenBank and other biological data made available through NCBI's website. NCBI resources include Entrez, PubMed, PubMed Central, LocusLink, the NCBI Taxonomy Browser, BLAST, BLAST Link (BLink), Electronic PCR, OrfFinder, Spidey, RefSeq, UniGene, HomoloGene, ProtEST, dbMHC, dbSNP, Cancer Chromosome Aberration Project (CCAP), Entrez Genomes and related tools, the Map Viewer, Model Maker, Evidence Viewer, Clusters of Orthologous Groups (COGs) database, Retroviral Genotyping Tools, SARS Coronavirus Resource, SAGEmap, Gene Expression Omnibus (GEO), Online Mendelian Inheritance in Man (OMIM), the Molecular Modeling Database (MMDB), the Conserved Domain Database (CDD) and the Conserved Domain Architecture Retrieval Tool (CDART). Augmenting many of the web applications are custom implementations of the BLAST program optimized to search specialized data sets. All of the resources can be accessed through the NCBI home page at: http://www.ncbi.nlm.nih.gov.

BACKGROUND: Functional annotation of differentially expressed genes is a necessary and critical step in the analysis of microarray data. The distributed nature of biological knowledge frequently requires researchers to navigate through numerous web-accessible databases gathering information one gene at a time. A more judicious approach is to provide query-based access to an integrated database that disseminates biologically rich information across large datasets and displays graphic summaries of functional information. RESULTS: Database for Annotation, Visualization, and Integrated Discovery (DAVID; http://www.david.niaid.nih.gov) addresses this need via four web-based analysis modules: 1) Annotation Tool - rapidly appends descriptive data from several public databases to lists of genes; 2) GoCharts - assigns genes to Gene Ontology functional categories based on user selected classifications and term specificity level; 3) KeggCharts - assigns genes to KEGG metabolic processes and enables users to view genes in the context of biochemical pathway maps; and 4) DomainCharts - groups genes according to PFAM conserved protein domains. CONCLUSIONS: Analysis results and graphical displays remain dynamically linked to primary data and external data repositories, thereby furnishing in-depth as well as broad-based data coverage. The functionality provided by DAVID accelerates the analysis of genome-scale datasets by facilitating the transition from data collection to biological meaning.

PlantCARE is a database of plant cis-acting regulatory elements, enhancers and repressors. Regulatory elements are represented by positional matrices, consensus sequences and individual sites on particular promoter sequences. Links to the EMBL, TRANSFAC and MEDLINE databases are provided when available. Data about the transcription sites are extracted mainly from the literature, supplemented with an increasing number of in silico predicted data. Apart from a general description for specific transcription factor sites, levels of confidence for the experimental evidence, functional information and the position on the promoter are given as well. New features have been implemented to search for plant cis-acting regulatory elements in a query sequence. Furthermore, links are now provided to a new clustering and motif search method to investigate clusters of co-expressed genes. New regulatory elements can be sent automatically and will be added to the database after curation. The PlantCARE relational database is available via the World Wide Web at http://sphinx.rug.ac.be:8080/PlantCARE/.

From the Publisher: For over 25 years, C. J. Date's An Introduction to Database Systems has been the authoritative resource for readers interested in gaining insight into and understanding of the principles of database systems. This revision continues to provide a solid grounding in the foundations of database technology and to provide some ideas as to how the field is likely to develop in the future.. Readers of this book will gain a strong working knowledge of the overall structure, concepts, and objectives of database systems and will become familiar with the theoretical principles underlying the construction of such systems.

The explosion of image data on the Internet has the potential to foster more sophisticated and robust models and algorithms to index, retrieve, organize and interact with images and multimedia data. But exactly how such data can be harnessed and organized remains a critical problem. We introduce here a new database called “ImageNet”, a large-scale ontology of images built upon the backbone of the WordNet structure. ImageNet aims to populate the majority of the 80,000 synsets of WordNet with an average of 500–1000 clean and full resolution images. This will result in tens of millions of annotated images organized by the semantic hierarchy of WordNet. This paper offers a detailed analysis of ImageNet in its current state: 12 subtrees with 5247 synsets and 3.2 million images in total. We show that ImageNet is much larger in scale and diversity and much more accurate than the current image datasets. Constructing such a large-scale database is a challenging task. We describe the data collection scheme with Amazon Mechanical Turk. Lastly, we illustrate the usefulness of ImageNet through three simple applications in object recognition, image classification and automatic object clustering. We hope that the scale, accuracy, diversity and hierarchical structure of ImageNet can offer unparalleled opportunities to researchers in the computer vision community and beyond.

A system-wide understanding of cellular function requires knowledge of all functional interactions between the expressed proteins. The STRING database aims to collect and integrate this information, by consolidating known and predicted protein-protein association data for a large number of organisms. The associations in STRING include direct (physical) interactions, as well as indirect (functional) interactions, as long as both are specific and biologically meaningful. Apart from collecting and reassessing available experimental data on protein-protein interactions, and importing known pathways and protein complexes from curated databases, interaction predictions are derived from the following sources: (i) systematic co-expression analysis, (ii) detection of shared selective signals across genomes, (iii) automated text-mining of the scientific literature and (iv) computational transfer of interaction knowledge between organisms based on gene orthology. In the latest version 10.5 of STRING, the biggest changes are concerned with data dissemination: the web frontend has been completely redesigned to reduce dependency on outdated browser technologies, and the database can now also be queried from inside the popular Cytoscape software framework. Further improvements include automated background analysis of user inputs for functional enrichments, and streamlined download options. The STRING resource is available online, at http://string-db.org/.

The RefSeq project at the National Center for Biotechnology Information (NCBI) maintains and curates a publicly available database of annotated genomic, transcript, and protein sequence records (http://www.ncbi.nlm.nih.gov/refseq/). The RefSeq project leverages the data submitted to the International Nucleotide Sequence Database Collaboration (INSDC) against a combination of computation, manual curation, and collaboration to produce a standard set of stable, non-redundant reference sequences. The RefSeq project augments these reference sequences with current knowledge including publications, functional features and informative nomenclature. The database currently represents sequences from more than 55,000 organisms (>4800 viruses, >40,000 prokaryotes and >10,000 eukaryotes; RefSeq release 71), ranging from a single record to complete genomes. This paper summarizes the current status of the viral, prokaryotic, and eukaryotic branches of the RefSeq project, reports on improvements to data access and details efforts to further expand the taxonomic representation of the collection. We also highlight diverse functional curation initiatives that support multiple uses of RefSeq data including taxonomic validation, genome annotation, comparative genomics, and clinical testing. We summarize our approach to utilizing available RNA-Seq and other data types in our manual curation process for vertebrate, plant, and other species, and describe a new direction for prokaryotic genomes and protein name management.

The Carbohydrate-Active Enzyme (CAZy) database is a knowledge-based resource specialized in the enzymes that build and breakdown complex carbohydrates and glycoconjugates. As of September 2008, the database describes the present knowledge on 113 glycoside hydrolase, 91 glycosyltransferase, 19 polysaccharide lyase, 15 carbohydrate esterase and 52 carbohydrate-binding module families. These families are created based on experimentally characterized proteins and are populated by sequences from public databases with significant similarity. Protein biochemical information is continuously curated based on the available literature and structural information. Over 6400 proteins have assigned EC numbers and 700 proteins have a PDB structure. The classification (i) reflects the structural features of these enzymes better than their sole substrate specificity, (ii) helps to reveal the evolutionary relationships between these enzymes and (iii) provides a convenient framework to understand mechanistic properties. This resource has been available for over 10 years to the scientific community, contributing to information dissemination and providing a transversal nomenclature to glycobiologists. More recently, this resource has been used to improve the quality of functional predictions of a number genome projects by providing expert annotation. The CAZy resource resides at URL: http://www.cazy.org/.

■ Data mining and knowledge discovery in databases have been attracting a significant amount of research, industry, and media attention of late. What is all the excitement about? This article provides an overview of this emerging field, clarifying how data mining and knowledge discovery in databases are related both to each other and to related fields, such as machine learning, statistics, and databases. The article mentions particular real-world applications, specific data-mining techniques, challenges involved in real-world applications of knowledge discovery, and current and future research directions in the field. Across a wide variety of fields, data are

This book is an introduction to the design and implementation of concurrency control and recovery mechanisms for transaction management in centralized and distributed database systems. Concurrency control and recovery have become increasingly important as businesses rely more and more heavily on their on-line data processing activities. For high performance, the system must maximize concurrency by multiprogramming transactions. But this can lead to interference between queries and updates, which concurrency control mechanisms must avoid. In addition, a satisfactory recovery system is necessary to ensure that inevitable transaction and database system failures do not corrupt the database.

Clustering algorithms are attractive for the task of class iden-tification in spatial databases. However, the application to large spatial databases rises the following requirements for clustering algorithms: minimal requirements of domain knowledge to determine the input parameters, discovery of clusters with arbitrary shape and good efficiency on large da-tabases. The well-known clustering algorithms offer no solu-tion to the combination of these requirements. In this paper, we present the new clustering algorithm DBSCAN relying on a density-based notion of clusters which is designed to dis-cover clusters of arbitrary shape. DBSCAN requires only one input parameter and supports the user in determining an ap-propriate value for it. We performed an experimental evalua-tion of the effectiveness and efficiency of DBSCAN using synthetic data and real data of the SEQUOIA 2000 bench-mark. The results of our experiments demonstrate that (1) DBSCAN is significantly more effective in discovering clus-ters of arbitrary shape than the well-known algorithm CLAR-ANS, and that (2) DBSCAN outperforms CLARANS by factor of more than 100 in terms of efficiency.

The Human Metabolome Database (HMDB) is currently the most complete and comprehensive curated collection of human metabolite and human metabolism data in the world. It contains records for more than 2180 endogenous metabolites with information gathered from thousands of books, journal articles and electronic databases. In addition to its comprehensive literature-derived data, the HMDB also contains an extensive collection of experimental metabolite concentration data compiled from hundreds of mass spectra (MS) and Nuclear Magnetic resonance (NMR) metabolomic analyses performed on urine, blood and cerebrospinal fluid samples. This is further supplemented with thousands of NMR and MS spectra collected on purified, reference metabolites. Each metabolite entry in the HMDB contains an average of 90 separate data fields including a comprehensive compound description, names and synonyms, structural information, physico-chemical data, reference NMR and MS spectra, biofluid concentrations, disease associations, pathway information, enzyme data, gene sequence data, SNP and mutation data as well as extensive links to images, references and other public databases. Extensive searching, relational querying and data browsing tools are also provided. The HMDB is designed to address the broad needs of biochemists, clinical chemists, physicians, medical geneticists, nutritionists and members of the metabolomics community. The HMDB is available at: www.hmdb.ca.

We are given a large database of customer transactions. Each transaction consists of items purchased by a customer in a visit. We present an efficient algorithm that generates all significant association rules between items in the database. The algorithm incorporates buffer management and novel estimation and pruning techniques. We also present results of applying this algorithm to sales data obtained from a large retailing company, which shows the effectiveness of the algorithm.

Part 1 The lexical database: nouns in WordNet, George A. Miller modifiers in WordNet, Katherine J. Miller a semantic network of English verbs, Christiane Fellbaum design and implementation of the WordNet lexical database and searching software, Randee I. Tengi. Part 2: automated discovery of WordNet relations, Marti A. Hearst representing verb alterations in WordNet, Karen T. Kohl et al the formalization of WordNet by methods of relational concept analysis, Uta E. Priss. Part 3 Applications of WordNet: building semantic concordances, Shari Landes et al performance and confidence in a semantic annotation task, Christiane Fellbaum et al WordNet and class-based probabilities, Philip Resnik combining local context and WordNet similarity for word sense identification, Claudia Leacock and Martin Chodorow using WordNet for text retrieval, Ellen M. Voorhees lexical chains as representations of context for the detection and correction of malapropisms, Graeme Hirst and David St-Onge temporal indexing through lexical chaining, Reem Al-Halimi and Rick Kazman COLOR-X - using knowledge from WordNet for conceptual modelling, J.F.M. Burg and R.P. van de Riet knowledge processing on an extended WordNet, Sanda M. Harabagiu and Dan I Moldovan appendix - obtaining and using WordNet.