| 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. |
| 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. |
