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The overall architecture of a process flow for building Knowledge databases (BxKnowledgetm )  is illustrated in the following diagram. The  tables below describe each base infrastructure Task, each  task that extends the infrastructure and each Icon in the illustration.


This illustration conveys the tasks for building and growing Knowledge databases. The tasks in blue (left side) form a fundamental process flow for building base Knowledge databases, while the tasks in yellow (right side) illustrate on-going extension activities to them. They are also integrated with the BxArraytm  Process Flow and linked to external data and information. The links to external databases can be done through URLs (Uniform Resource Locators), files and through OLAP (On-Line Analytical Processing) methods for creating metadata from disparate data sources. Since these databases can become quite large the design allows them to be distributed across multiple hardware servers.

Table describing process flow tasks for the base infrastructure of Knowledge Databases.

Tasks for Base Knowledge Databases Description
Download Genomic/Proteomic/Clinical Data Available information for directly supporting experimental results interpretation and data mining is downloaded. Scripts and custom applications  provide  automatic extraction.
Mine Journals & Publications Data that is not contained in directly accessible databases needs to be manually extracted and put into electronic form for data entry.
Define Control Vocabulary Each type of data needs to have a standard set of names, tags and/or units to facilitate complex queries.
Add Calculated & Reference Data Depending upon the type of experiments and data mining needs, the knowledge databases may need to be augmented with specific types of calculated and/or reference data such as disease types, translational modifications, DNA Binding proteins, SNPs, ...
Filter/Curate Data Extensive checks are made to ensure data is consistent, regularized and uses control vocabulary  before adding to the database.
Design Database First, the database needs to be designed in such a way to encapsulate scientific relationships -- such as a gene is part of a Chromosome and contains a location and has an expression value under certain conditions and codes for a protein. Second the database has to be designed for the type of integration and data mining. The design for a database containing gene data  with  microarray data is different from one without microarray data.
Load Database Once the database is designed and built, then scripts or applications routinely load the information into the knowledge database.

Back to Top of Page     Extension Task Table    Icon Table

Table describing process flow tasks for extending infrastructure of Knowledge Databases.

Tasks for Extending Knowledge Databases Description
Add Links to Internal Experimental Data This represents the seamless integration of the Microarray Process Process Flow Laboratory Information Management System (LIMS) Data that are used in analysis and interpretation of results and report generation.
Add Expression Data Expression data from DNA, SNP, Protein, antibody and other arrays can be added to the knowledge database directly or accessed via links to BxArray(tm) databases.
Add Links to External Data Data that is not explicitly incorporated into the local Knowledge databases can be accessed via links to the external databases. An effective method of linking disparate data sources is by creating metadata using OLAP (On-Line Analytical Processing).
Data Mining Applications The results of data mining applications, such as reference disease biomarkers can be added to the Knowledge databases.
Add Related Experimental Data Different types of experiments such as 2D gels can be used to validate microarray experiments. This type of data can be added to the Knowledge databases.
Update/Annotate A general purpose utility for manually or automatically updating and annotating any data that is stored in the Knowledge databases.

Back to Top of Page   Base Task Table    Icon Table


Table describing process flow Icons.

Process Flow Icons Description
This represents the collection of relational knowledge databases created using BxKnowledgetm Process Flow.
This represents disparate data that resides at external locations and is accessed via links contained in the Knowledge databases.
This represents the reports that are created from primarily from data mining applications using results and the Knowledge databases.


Back to Top of Page    Base Task Table    Extension Task Table



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Last modified: December 22, 2014