Investigation into Indexing XML Data Techniques

The rapid development of XML technology improves the WWW, since the XML data has many advantages and has become a common technology for transferring data cross the internet. Therefore, the objective of this research is to investigate and study the XML indexing techniques in terms of their structures. The main goal of this investigation is to identify the main limitations of these techniques and any other open issues. Furthermore, this research considers most common XML indexing techniques and performs a comparison between them. Subsequently, this work makes an argument to find out these limitations. To conclude, the main problem of all the XML indexing techniques is the trade-off between the size and the efficiency of the indexes. So, all the indexes become large in order to perform well, and none of them is suitable for all users’ requirements. However, each one of these techniques has some advantages in somehow

Optimizing cursor movement in holistic twig joins

Holistic twig join algorithms represent the state of the art for evaluating path expressions in XML queries. Using inverted in-dexes on XML elements, holistic twig joins move a set of index cursors in a coordinated way to quickly ¯nd structural matches. Because each cursor move can trigger I/O, the performance of a holistic twig join is largely determined by how many cursor moves it makes, yet, surprisingly, existing join algorithms have not been optimized along these lines. In this paper, we describe TwigOptimal, a new holistic twig join algorithm with optimal cur-sor movement. We sketch the proof of TwigOptimal's optimality, and describe how TwigOptimal can use information in the return clause of XQuery to boost its performance. Finally, experimen-tal results are presented, showing TwigOptimal's superiority over existing holistic twig join algorithms

Approximating expressive queries on graph-modeled data: The GeX approach

We present the GeX (Graph-eXplorer) approach for the approximate matching of complex queries on graph-modeled data. GeX generalizes existing approaches and provides for a highly expressive graph-based query language that supports queries ranging from keyword-based to structured ones. The GeX query answering model gracefully blends label approximation with structural relaxation, under the primary objective of delivering meaningfully approximated results only. GeX implements ad-hoc data structures that are exploited by a top-k retrieval algorithm which enhances the approximate matching of complex queries. An extensive experimental evaluation on real world datasets demonstrates the efficiency of the GeX query answering

Semantics and efficient evaluation of partial tree-pattern queries on XML

Current applications export and exchange XML data on the web. Usually, XML data are queried using keyword queries or using the standard structured query language XQuery the core of which consists of the navigational query language XPath. In this context, one major challenge is the querying of the data when the structure of the data sources is complex or not fully known to the user. Another challenge is the integration of multiple data sources that export data with structural differences and irregularities. In this dissertation, a query language for XML called Partial Tree-Pattern Query (PTPQ) language is considered. PTPQs generalize and strictly contain Tree-Pattern Queries (TPQs) and can express a broad structural fragment of XPath. Because of their expressive power and flexibility, they are useful for querying XML documents the structure of which is complex or not fully known to the user, and for integrating XML data sources with different structures. The dissertation focuses on three issues. The first one is the design of efficient non-main-memory evaluation methods for PTPQs. The second one is the assignment of semantics to PTPQs so that they return meaningful answers. The third one is the development of techniques for answering TPQs using materialized views. Non-main-memory XML query evaluation can be done in two modes (which also define two evaluation models). In the first mode, data is preprocessed and indexes, called inverted lists, are built for it. In the second mode, data are unindexed and arrives continuously in the form of a stream. Existing algorithms cannot be used directly or indirectly to efficiently compute PTPQs in either mode. Initially, the problem of efficiently evaluating partial path queries in the inverted lists model has been addressed. Partial path queries form a subclass of PTPQs which is not contained in the class of TPQs. Three novel algorithms for evaluating partial path queries including a holistic one have been designed. The analytical and experimental results show that the holistic algorithm outperforms the other two. These results have been extended into holistic and non-holistic approaches for PTPQs in the inverted lists model. The experiments show again the superiority of the holistic approach. The dissertation has also addressed the problem of evaluating PTPQs in the streaming model, and two original efficient streaming algorithms for PTPQs have been designed. Compared to the only known streaming algorithm that supports an extension of TPQs, the experimental results show that the proposed algorithms perform better by orders of magnitude while consuming a much smaller fraction of memory space. An original approach for assigning semantics to PTPQs has also been devised. The novel semantics seamlessly applies to keyword queries and to queries with structural restrictions. In contrast to previous approaches that operate locally on data, the proposed approach operates globally on structural summaries of data to extract tree patterns. Compared to previous approaches, an experimental evaluation shows that our approach has a perfect recall both for XML documents with complete and with incomplete data. It also shows better precision compared to approaches with similar recall. Finally, the dissertation has addressed the problem of answering XML queries using exclusively materialized views. An original approach for materializing views in the context of the inverted lists model has been suggested. Necessary and sufficient conditions have been provided for tree-pattern query answerability in terms of view-to-query homomorphisms. A time and space efficient algorithm was designed for deciding query answerability and a technique for computing queries over view materializations using stack- based holistic algorithms was developed. Further, optimizations were developed which (a) minimize the storage space and avoid redundancy by materializing views as bitmaps, and (b) optimize the evaluation of the queries over the views by applying bitwise operations on view materializations. The experimental results show that the proposed approach obtains largely higher hit rates than previous approaches, speeds up significantly the evaluation of queries without using views, and scales very smoothly in terms of storage space and computational overhead

Solving the intractable problem: optimal performance for worst case scenarios in XML twig pattern matching

In the history of databases, eXtensible Markup Language (XML) has been thought of as the standard format to store and exchange semi-structured data. With the advent of IoT, XML technologies can play an important role in addressing the issue of processing a massive amount of data generated from heterogeneous devices. As the number and complexity of such datasets increases there is a need for algorithms which are able to index and retrieve XML data efficiently even for complex queries. In this context twig pattern matching , finding all occurrences of a twig pattern query (TPQ), is a core operation in XML query processing. Until now holistic joins have been considered the state-of-the-art TPQ processing algorithms, but they fail to guarantee an optimal evaluation except at the expense of excessive storage costs which limit their scope in large datasets. In this article, we introduce a new approach which significantly outperforms earlier methods in terms of both the size of the intermediate storage and query running time. The approach presented here uses Child Prime Labels (Alsubai & North, 2018) to improve the filtering phase of bottom-up twig matching algorithms and a novel algorithm which avoids the use of stacks, thus improving TPQs processing efficiency. Several experiments were conducted on common benchmarks such as DBLP, XMark and TreeBank datasets to study the performance of the new approach. Multiple analyses on a range of twig pattern queries are presented to demonstrate the statistical significance of the improvements

Efficient evaluation of generalized path pattern queries on XML data

Finding the occurrences of structural patterns in XML data is a key operation in XML query processing. Existing algorithms for this operation focus almost exclusively on path-patterns or tree-patterns. Requirements in flexible querying of XML data have motivated recently the introduction of query languages that allow a partial specification of path-patterns in a query. In this paper, we focus on the efficient evaluation of partial path queries, a generalization of path pattern queries. Our approach explicitly deals with repeated labels (that is, multiple occurrences of the same label in a query). We show that partial path queries can be represented as rooted dags for which a topological ordering of the nodes exists. We present three algorithms for the efficient evaluation of these queries under the indexed streaming evaluation model. The first one exploits a structural summary of data to generate a set of path-patterns that together are equivalent to a partial path query. To evaluate these path-patterns, we extend PathStack so that it can work on path-patterns with repeated labels. The second one extracts a spanning tree from the query dag, uses a stack-based algorithm to find the matches of the root-to-leaf paths in the tree, and merge-joins the matches to compute the answer. Finally, the third one exploits multiple pointers of stack entries and a topological ordering of the query dag to apply a stack-based holistic technique. An analysis of the algorithms and extensive experimental evaluation shows that the holistic algorithm outperforms the other ones

AMMO-Prot: amine system project 3D-model finder

BACKGROUND: Amines are biogenic amino acid derivatives, which play pleiotropic and very important yet complex roles in animal physiology. For many other relevant biomolecules, biochemical and molecular data are being accumulated, which need to be integrated in order to be effective in the advance of biological knowledge in the field. For this purpose, a multidisciplinary group has started an ontology-based system named the Amine System Project (ASP) for which amine-related information is the validation bench. RESULTS: In this paper, we describe the Ontology-Based Mediator developed in the Amine System Project (http://asp.uma.es) using the infrastructure of Semantic Directories, and how this system has been used to solve a case related to amine metabolism-related protein structures. CONCLUSIONS: This infrastructure is used to publish and manage not only ontologies and their relationships, but also metadata relating to the resources committed with the ontologies. The system developed is available at http://asp.uma.es/WebMediator

Child Prime Label Approaches to Evaluate XML Structured Queries

The adoption of the eXtensible Markup Language (XML) as the standard format to store and exchange semi-structure data has been gaining momentum. The growing number of XML documents leads to the need for appropriate XML querying algorithms which are able to retrieve XML data efficiently. Due to the importance of twig pattern matching in XML retrieval systems, finding all matching occurrences of a tree pattern query in an XML document is often considered as a specific task for XML databases as well as a core operation in XML query processing. This thesis presents a design and implementation of a new indexing technique, called the Child Prime Label (CPL) which exploits the property of prime numbers to identify Parent-Child (P-C) edges in twig pattern queries (TPQs) during query evaluation. The CPL approach can be incorporated efficiently within the existing labelling schemes. The major contributions of this thesis can be seen as a set of novel twig matching algorithms which apply the CPL approach and focus on reducing the overhead of storing useless elements and performing unnecessary computations during the output enumeration. The research presented here is the first to provide an efficient and general solution for TPQs containing ordering constraints and positional predicates specified by the XML query languages. To evaluate the CPL approaches, the holistic model was implemented as an experimental prototype in which the approaches proposed are compared against state-of-the-art holistic twig algorithms. Extensive performance studies on various real-world and artificial datasets were conducted to demonstrate the significant improvement of the CPL approaches over the previous indexing and querying methods. The experimental results demonstrate the validity and improvements of the new algorithms over other related methods on common various subclasses of TPQs. Moreover, the scalability tests reveal that the new algorithms are more suitable for processing large XML datasets