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There are a lot of controversies and challenges facing biochemical research. As a result, several efforts and resources have been dedicated to this field to try and put together theories, facts, theorems, utilities, and facilities all under one self-contained database (Bader et al, 2009). Scientists and institutions have and are still coming up with their own versions of such databases. This is as a result of need to store and represent information regarding bimolecular interactions, molecular complexes, and pathways all in computer readable form. Several databases have been created including; Bimolecular Interaction Network Database (BIND), System for the Analysis of Biomechanical Pathways (SABIO-RK), among others. BIND and SABIO-RK are among the advanced ones hence the need to analyze them as follows;
Data is entered into BIND manually or using automatic methods which may require web-based systems. BIND stores full descriptions of bimolecular interactions, pathways and molecular complexes in data models which make them readable from computers. These models come in differing versions but the construction and development of 2.0 data model which is the latest efficient have enabled researchers to incorporate virtually all features described by molecular mechanisms. The model shows such as interactions between molecules containing proteins and nucleic acids where their chemical responses and photochemical activations leading to conformational transformations are shown (UnixWare, 2002).
Joseph (2009) states that BIND translates proteomic data published as English texts in journals and other publications like PubMed to mineable data forms. The model provides a detailed data specification, data mining facilities and data accessibility through visualization toots. Data is specified as written notations using Abstract Syntax Notation. (A.S.N.) notational language derived from US National Centre for Biotechnology Information (USNCBI). It represents data in three-dimensional structures of biological sequences in Publication the same way USNCBI ASN standards do.
BIND model is undergoing modifications and updates to make the maps and 3-D structures use recent technologies such as; Common Object Remote Brokerage Architecture.6 (CORBA) and Extreme Modeling Language. (XML.) since the data represented in ASN can be easily converted o suit these technologies.
BIND is one of the most common biomolecular database created for several reasons attributing its strength; first, BIND helps in understanding and comprehending complicated cell signaling networks which are known to facilitate cellular processes from their development to becoming diseases. Secondly, BIND uses ASN data specifications which adopt standards from known bodies such as USNCBI and International Union of Pure and Applied Chemistry (IUPAC) making it a formal database understood by almost all scientists. It is also known to respond positively to fit into new upcoming technologies such as CORBA and XML making it a both a maintainable and updatable database (Bader et al, 2001).
Fourthly, BIND is object-relational scheme written in NCBI software Toolkit making it portable from one system to another including their web server. Its data manager has been tested to be compatible and runs in different operating systems such as Windows NT, Linux, HP-UX among others. BIND is also described to an openly-developed system; it released to public domain together with its source code in correspondence to GNU, the general public license after the developers have totally tested Application Program Interface (API). Finally C codes have been used to design BIND to function in a distributed manner.
However BIND provides indispensable source of data, it has been criticized for few downfalls; BIND data model is very difficult to understand and develop. The BIND developers give users a right through general public license to distribute and make changes on the software source codes. This makes its integrity to be questioned regarding the consistency of the versions. Data entry requires that be entered using we-based systems making its use expensive and unavailable (Lane Librarian, 2006).
BIND like any other biological database is a library of biological sciences information relies on scientific experiments and published literature solely as the source of its data. It is converted to computable analysis. The research information is obtained fro proteomics, genomics and other sources like metabolomics and phylogenetics. Unlike these, BIND some programming features which have to adhere to standards such as XML. Finally, BIND gives the user opportunity to distribute and modify unlike other databases administered by the developer alone (Bader et al, 2001).