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A Survey on Bioinformatics Data and Service Integration Using Ontology and Declarative Workflow Query Language
| Content Provider | Semantic Scholar |
|---|---|
| Author | Ahmed, Emdad |
| Copyright Year | 2007 |
| Abstract | Formulating and executing queries over distributed, autonomous and heterogeneous resources is an important topic within e-science in general and bioinformatics in particular. The advent of the Internet and the Web and their subsequent ubiquity have brought forth opportunities to connect biological information sources across all types of boundaries. Examples of such information sources include databases, XML documents, and other unstructured sources. Uniformly querying those information sources has been extensively investigated. We survey the current research on the fundamental problems to efficiently process and optimize queries over Web Data integration systems. Bioinformatics domain has been chosen to illustrate the query processing capabilities over the heterogeneous information sources. We surveyed different approaches to data integration such as warehouse, mediator-based and navigational. The complex biological data stored in bioinformatics databases often require the addition of knowledge to specify and constrain the values held in the database. One way of capturing knowledge within bioinformatics applications and databases is the use of ontologies. The ontology is also central to the query processing and reconciliation of heterogeneities. For efficient query processing, we advocate for the selection of relevant information sources; the use of meta data as well as to use source constraints. We propose that current data integration approaches should be enhanced by ontological knowledge and ISA relationships and inter-ontology mappings in ontologies should be explored. Electronically available data on the Web is exploding at an ever increasing pace. Much of this data is unstructured, which makes searching hard and traditional database querying impossible. Many Web documents, however, contain an abundance of recognizable constants that together describe the essence of a documents content. For these kinds of data-rich, multiple-record documents (e.g. advertisements, movie reviews, weather reports, travel information, sports summaries, financial statements etc) we can apply a conceptual-modeling approach to extract and structure data automatically. we can automatically produce a database scheme and recognizers for constants and keywords, and then invoke routines to recognize and extract data from unstructured web documents and structure it according to the generated database scheme, which can later be used in declarative ad hoc query. The transition of the World Wide Web from a paradigm of static Web pages to one of dynamic Web services provides new and exciting opportunities for bioinformatics with respect to data dissemination,transformation, and integration. Integration of data and service from heterogeneous sources demand significant advances in middleware system, which we plan to implement. |
| File Format | PDF HTM / HTML |
| Alternate Webpage(s) | http://paris.cs.wayne.edu/~ay2703/research/publications/MyPhDQualifying.pdf |
| Language | English |
| Access Restriction | Open |
| Content Type | Text |
| Resource Type | Article |
