Relational databases are not well suited for representing and processing hierarchical data. Clever schemes are required to represent trees in the flat format of the relational model, as well as answering queries such as retrieving all nodes in a sub-tree, all nodes at a particular level and the nodes on the path from a node to one of its descendants. Some areas where hierarchical data needs to be stored and processed include XML data warehousing, organization chart in automation systems, bioinformatics and pyramidal games that require hierarchical data representation. In this book, a new method (Arya) is proposed to represent hierarchical data structures in relational database systems so that queries proved on trees can be executed efficiently. This method reshapes hierarchical data structures to non-hierarchical graphs using extra pointers to be accessed directly from each node to its ancestors. The cost for the gained performance is only a small increase in the space required for the representation of the original tree, which is significantly less than the used space by other methods.
With the advent of Big Data, data integration is very important topic in the heterogeneous bioinformatics landscape. This book starts off with the current state of biological pathway databases in general, and in particular, plant pathway databases. We explore different models to interface with the various stakeholders of biological data repositories. We discuss the potential use of XML as a repository for information integration, downstream processing, and data. Having explored different alternatives, we build up our own comprehensive knowledge repository for plant metabolic networks. A public website was built to make information available for ad-hoc users. In addition, a dedicated API (MetNetAPI: is provided to accommodate bioinformaticians and software developers who wish to build advanced applications on top of the warehouse. Integrated databases are only useful when they can be synchronized with their respective external sources. We've created a framework for a systematic approach to integration. This work thus provides a roadmap to current and future biological database projects
The term markup means a detailed instruction, usually written on a manuscript to be typeset, concerning style of type, makeup of pages, and the like . Markups basically implements the idea of typesetting, i.e. designing fonts for characters and arranging them in some order . The descendants of various text markups include development of markup languages such GML, SGML, HTML and XML. This book intends to target students, scientists, researchers who which to use markups in handling their biological data. The first focus in on Chemical Markup Language (CML), a language for representing chemical data. This is followed by explicit information on Bioinformatics Sequence Markup Language (BSML), used for storing an handling sequence-based biological data. The last section of the book deals with handling Systems Biology data by introducing and explaining Systems Biology Markup Language (SBML).
This book constitutes the refereed proceedings of the 8th International Conference on Language and Automata Theory and Applications, LATA 2014, held in Madrid, Spain in March 2014.The 45 revised full papers presented together with 4 invited talks were carefully reviewed and selected from 116 submissions. The papers cover the following topics: algebraic language theory, algorithms on automata and words, automata and logic, automata for system analysis and program verification, automata, concurrency and Petri nets, automatic structures, combinatorics on words, computability, computational complexity, descriptional complexity, DNA and other models of bio-inspired computing, foundations of finite state technology, foundations of XML, grammars (Chomsky hierarchy, contextual, unification, categorial, etc.), grammatical inference and algorithmic learning, graphs and graph transformation, language varieties and semigroups, parsing, patterns, quantum, chemical and optical computing, semantics, string and combinatorial issues in computational biology and bioinformatics, string processing algorithms, symbolic dynamics, term rewriting, transducers, trees, tree languages and tree automata, weighted automata.
This book constitutes the refereed proceedings of the 9th International Conference on Language and Automata Theory and Applications, LATA 2015, held in Nice, France in March 2015. The 53 revised full papers presented together with 5 invited talks were carefully reviewed and selected from 115 submissions. The papers cover the following topics: algebraic language theory, algorithms for semi-structured data mining, algorithms on automata and words, automata and logic, automata for system analysis and program verification, automata networks, concurrency and Petri nets, automatic structures, cellular automata, codes, combinatorics on words, computational complexity, data and image compression, descriptional complexity, digital libraries and document engineering, foundations of finite state technology, foundations of XML, fuzzy and rough languages, grammatical inference and algorithmic learning, graphs and graph transformation, language varieties and semigroups, parallel and regulated rewriting, parsing, patterns, string and combinatorial issues in computational biology and bioinformatics, string processing algorithms, symbolic dynamics, term rewriting, transducers, trees, tree languages and tree automata, weighted automata.