A Molecular Biology Database Digest

Computational Biology or Bioinformatics has been defined as the application of mathematical and Computer Science methods to solving problems in Molecular Biology that require large scale data, computation, and analysis [18]. As expected, Molecular Biology databases play an essential role in Computational Biology research and development. This paper introduces into current Molecular Biology databases, stressing data modeling, data acquisition, data retrieval, and the integration of Molecular Biology data from different sources. This paper is primarily intended for an audience of computer scientists with a limited background in Biology

UML Class Diagram or Entity Relationship Diagram : An Object Relational Impedance Mismatch

It is now nearly 30 years since Peter Chen’s watershed paper “The Entity-Relationship Model –towards a Unified View of Data”. [1] The entity relationship model and variations and extensions to ithave been taught in colleges and universities for many years. In his original paper Peter Chen looked at converting his new ER model to the then existing data structure diagrams for the Network model. In recent years there has been a tendency to use a Unified Modelling Language (UML) class diagram forconceptual modeling for relational databases, and several popular course text books use UMLnotation to some degree [2] [3]. However Object and Relational technology are based on different paradigms. In the paper we argue that the UML class diagram is more of a logical model (implementation specific). ER Diagrams on theother hand, are at a conceptual level of database design dealing with the main items and their relationships and not with implementation specific detail. UML focuses on OOAD (Object Oriented Analysis and Design) and is navigational and program dependent whereas the relational model is set based and exhibits data independence. The ER model provides a well-established set of mapping rules for mapping to a relational model. In this paper we look specifically at the areas which can cause problems for the novice databasedesigner due to this conceptual mismatch of two different paradigms. Firstly, transferring the mapping of a weak entity from an Entity Relationship model to UML and secondly the representation of structural constraints between objects. We look at the mixture of notations which students mistakenly use when modeling. This is often the result of different notations being used on different courses throughout their degree. Several of the popular text books at the moment use either a variation of ER,UML, or both for teaching database modeling. At the moment if a student picks up a text book they could be faced with either; one of the many ER variations, UML, UML and a variation of ER both covered separately, or UML and ER merged together. We regard this problem as a conceptual impedance mismatch. This problem is documented in [21] who have produced a catalogue of impedance mismatch problems between object-relational and relational paradigms. We regard the problems of using UML class diagrams for relational database design as a conceptual impedance mismatch as the Entity Relationship model does not have the structures in the model to deal with Object Oriented concepts Keywords: EERD, UML Class Diagram, Relational Database Design, Structural Constraints, relational and object database impedance mismatch. The ER model was originally put forward by Chen [1] and subsequently extensions have been added to add further semantics to the original model; mainly the concepts of specialisation, generalisation and aggregation. In this paper we refer to an Entity-Relationship model (ER) as the basic model and an extended or enhanced entity-relationship model (EER) as a model which includes the extra concepts. The ER and EER models are also often used to aid communication between the designer and the user at the requirements analysis stage. In this paper when we use the term “conceptual model” we mean a model that is not implementation specific.ISBN: 978-84-616-3847-5 3594Peer reviewe

From local laboratory data to public domain database in search of indirect association of diseases: AJAX based gene data search engine.

This paper presents an extensible schema for capturing laboratory gene variance data with its meta-data properties in a semi-structured environment. This paper also focuses on the issues of creating a local and task specific component database which is a subset of global data resources. An XML based genetic disorder component database schema is developed with adequate flexibilities to facilitate searching of gene mutation data. A web based search engine is developed that allows researchers to query a set of gene parameters obtained from local XML schema and subsequently allow them to automatically establish a link with the public domain gene databases. The application applies AJAX (Asynchronous Javascript and XML), a cutting-edge web technology, to carry out the gene data searching function

Potentially Polluting Marine Sites GeoDB: An S-100 Geospatial Database as an Effective Contribution to the Protection of the Marine Environment

Potentially Polluting Marine Sites (PPMS) are objects on, or areas of, the seabed that may release pollution in the future. A rationale for, and design of, a geospatial database to inventory and manipu-late PPMS is presented. Built as an S-100 Product Specification, it is specified through human-readable UML diagrams and implemented through machine-readable GML files, and includes auxiliary information such as pollution-control resources and potentially vulnerable sites in order to support analyses of the core data. The design and some aspects of implementation are presented, along with metadata requirements and structure, and a perspective on potential uses of the database