Databases

How to communicate with a database:

SQL, Structured Query Language

Communication among websites:

HTML - is a Markup language, that was designed to display data and focus on how data looks

XML, extensible Markup language, was designed to describe data and focus on what data is. XML uses Document Type Definition (DTD) or an XML schema to describe the data. XML was desigend to carry data, and is not a replacement for HTML.

Representing programs:

UML, unified modeling language, is a standard way to specify, construct and document systems that use object-oriented code. It is in itself a language that generates diagrams that are designed to let developers and customers view a software system from a different perspective and in varying degrees of abstraction.

Standardization of bioinformatics databases:

Design and implementation of microarray gene expression markup language (MAGE-ML)
Meaningful exchange of microarray data is currently difficult because it is rare that published data provide sufficient information depth or are even in the same format from one publication to another. Only when data can be easily exchanged will the entire biological community be able to derive the full benefit from such microarray studies.

Results

To this end we have developed three key ingredients towards standardizing the storage and exchange of microarray data. First, we have created a minimal information for the annotation of a microarray experiment (MIAME)-compliant conceptualization of microarray experiments modeled using the unified modeling language (UML) named MAGE-OM (microarray gene expression object model). Second, we have translated MAGE-OM into an XML-based data format, MAGE-ML, to facilitate the exchange of data. Third, some of us are now using MAGE (or its progenitors) in data production settings. Finally, we have developed a freely available software tool kit (MAGE-STK) that eases the integration of MAGE-ML into end users' systems. http://www.mged.org/

Data warehouses

GUS