A Data Transformation System for Biological Data Sources

Scientific data of importance to biologists in the Human Genome Project resides not only in conventional databases, but in structured files maintained in a number of different formats (e.g. ASN.1 and ACE) as well a.s sequence analysis packages (e.g. BLAST and FASTA). These formats and packages contain a number of data types not found in conventional databases, such as lists and variants, and may be deeply nested. We present in this paper techniques for querying and transforming such data, and illustrate their use in a prototype system developed in conjunction with the Human Genome Center for Chromosome 22. We also describe optimizations performed by the system, a crucial issue for bulk data

Segmenting and labeling query sequences in a multidatabase environment

When gathering information from multiple independent data sources, users will generally pose a sequence of queries to each source, combine (union) or cross-reference (join) the results in order to obtain the information they need. Furthermore, when gathering information, there is a fair bit of trial and error involved, where queries are recursively refined according to the results of a previous query in the sequence. From the point of view of an outside observer, the aim of such a sequence of queries may not be immediately obvious. We investigate the problem of isolating and characterizing subsequences representing coherent information retrieval goals out of a sequence of queries sent by a user to different data sources over a period of time. The problem has two sub-problems: segmenting the sequence into subsequences, each representing a discrete goal; and labeling each query in these subsequences according to how they contribute to the goal. We propose a method in which a discriminative probabilistic model (a Conditional Random Field) is trained with pre-labeled sequences. We have tested the accuracy with which such a model can infer labels and segmentation on novel sequences. Results show that the approach is very accurate (> 95% accuracy) when there are no spurious queries in the sequence and moderately accurate even in the presence of substantial noise (∼70% accuracy when 15% of queries in the sequence are spurious). © 2011 Springer-Verlag

Software architecture style for interoperable databases

We propose a layered and component based software architecture style which supports interoperability in multiple databases (DB). The architectural style's building blocks and its constraints are described and the deployment of two design patterns outlined. Components placed in our architectural layers exhibit a linear topology and request/reply processing style. The constraints include communications between components which are not in the adjacent architectural layers and extension of the intuitive many : one bindings between components towards many : many. We comment on similarities with mediation architectures and outline some implementation issues

Myriad: Design and implementation of a federated database prototype

This paper describes our experiences in the design and implementation of Myriad, and in the project management. Special emphasis is given to discussing design alternatives and their impact on Myriad. This paper also presents the software engineering principles and the project management techniques we used in developing Myriad and the lessons we learned. We believe these lessons would be useful for practitioners who wish to develop a similar syste

Toward Self-Organising Service Communities

This paper discusses a framework in which catalog service communities are built, linked for interaction, and constantly monitored and adapted over time. A catalog service community (represented as a peer node in a peer-to-peer network) in our system can be viewed as domain specific data integration mediators representing the domain knowledge and the registry information. The query routing among communities is performed to identify a set of data sources that are relevant to answering a given query. The system monitors the interactions between the communities to discover patterns that may lead to restructuring of the network (e.g., irrelevant peers removed, new relationships created, etc.)

A comparative study of transaction management services in multidatabase heterogeneous systems

Multidatabases are being actively researched as a relatively new area in which many aspects are not yet fully understood. This area of transaction management in multidatabase systems still has many unresolved problems. The problem areas which this dissertation addresses are classification of multidatabase systems, global concurrency control, correctness criterion in a multidatabase environment, global deadlock detection, atomic commitment and crash recovery. A core group of research addressing these problems was identified and studied. The dissertation contributes to the multidatabase transaction management topic by introducing an alternative classification method for such multiple database systems; assessing existing research into transaction management schemes and based on this assessment, proposes a transaction processing model founded on the optimal properties of transaction management identified during the course of this research.ComputingM. Sc. (Computer Science

A cooperative framework for molecular biology database integration using image object selection.

The theme and the concept of 'Molecular Biology Database Integration’ and the problems associated with this concept initiated the idea for this Ph.D research. The available technologies facilitate to analyse the data independently and discretely but it fails to integrate the data resources for more meaningful information. This along with the integration issues created the scope for this Ph.D research. The research has reviewed the 'database interoperability' problems and it has suggested a framework for integrating the molecular biology databases. The framework has proposed to develop a cooperative environment to share information on the basis of common purpose for the molecular biology databases. The research has also reviewed other implementation and interoperability issues for laboratory based, dedicated and target specific database. The research has addressed the following issues: - diversity of molecular biology databases schemas, schema constructs and schema implementation -multi-database query using image object keying -database integration technologies using context graph - automated navigation among these databases This thesis has introduced a new approach for database implementation. It has introduced an interoperable component database concept to initiate multidatabase query on gene mutation data. A number of data models have been proposed for gene mutation data which is the basis for integrating the target specific component database to be integrated with the federated information system. The proposed data models are: data models for genetic trait analysis, classification of gene mutation data, pathological lesion data and laboratory data. The main feature of this component database is non-overlapping attributes and it will follow non-redundant integration approach as explained in the thesis. This will be achieved by storing attributes which will not have the union or intersection of any attributes that exist in public domain molecular biology databases. Unlike data warehousing technique, this feature is quite unique and novel. The component database will be integrated with other biological data sources for sharing information in a cooperative environment. This/involves developing new tools. The thesis explains the role of these new tools which are: meta data extractor, mapping linker, query generator and result interpreter. These tools are used for a transparent integration without creating any global schema of the participating databases. The thesis has also established the concept of image object keying for multidatabase query and it has proposed a relevant algorithm for matching protein spot in gel electrophoresis image. An object spot in gel electrophoresis image will initiate the query when it is selected by the user. It matches the selected spot with other similar spots in other resource databases. This image object keying method is an alternative to conventional multidatabase query which requires writing complex SQL scripts. This method also resolve the semantic conflicts that exist among molecular biology databases. The research has proposed a new framework based on the context of the web data for interactions with different biological data resources. A formal description of the resource context is described in the thesis. The implementation of the context into Resource Document Framework (RDF) will be able to increase the interoperability by providing the description of the resources and the navigation plan for accessing the web based databases. A higher level construct is developed (has, provide and access) to implement the context into RDF for web interactions. The interactions within the resources are achieved by utilising an integration domain to extract the required information with a single instance and without writing any query scripts. The integration domain allows to navigate and to execute the query plan within the resource databases. An extractor module collects elements from different target webs and unify them as a whole object in a single page. The proposed framework is tested to find specific information e.g., information on Alzheimer's disease, from public domain biology resources, such as, Protein Data Bank, Genome Data Bank, Online Mendalian Inheritance in Man and local database. Finally, the thesis proposes further propositions and plans for future work