Glossary of Terms

Attribute

An attribute is some class of data that is known about an object. For example, attributes of protein objects include "length", "definition", "sequence", "comments", etc.

Definition

Definitions are human-readable names given to objects contained in the database. 'Definition' is an attribute of every object in the Biozon database. As Biozon incorporates data from a variety of sources, different sources that describe the same object might provide slightly different definitions. For example, "Mitochondrial inheritance component MDM10" and "mdm10p [Saccharomyces cerevisiae]" may be two definitions given to the same protein by two different sources. Therefore, when displaying the profile of a particular object, Biozon decides on one representative definition to display. However, all definitions are considered when searching for a particular object, and all definitions are accessible by viewing the appropriate descriptor documents associated with a given object.

Descriptor

Descriptors are documents that contain data that describe some object in the Biozon database. They contain a number of attributes and values that pertain to the object being described. The type and composition of the descriptors is dependent upon their source and meaning. Examples of descriptors include the Swiss-Prot descriptor and a GO term.

Document

A fundamental unit of data in the Biozon database that contains a number of attributes and associated values. Documents always given a type classification based on their content and meaning.

Object

Objects are documents that define a physical entity (such as a Protein), set of physical entities (such as a Protein Family), or a physical concept (such as an interaction). In the Biozon database, they are the fundamental building blocks of all stored knowledge.

Profile

A profile is a page that displays summary info for a particular object in the Biozon database. Typically, they display the object's type (i.e. protein, structure, etc), its definition, and various quick summary items of interest for that object. Additionally, provide access to visualizations, descriptors that describe that object, related objects, and any other relevant information. Here is an example of a profile page.

Relation

A relation is a fundamental unit of data that indicates that two documents are related somehow. Relations are given a type classification that refines that relationship and and indicates how the documents are related.

Result Set

A result set is a list of objects that are displayed on screen as the results of a search or the result of following a link in a profile page that represents a set (of two or more elements) of related objects of a given type. Result sets typically by default display a reasonable subset of all possible results with navigation controls that allow the manipulation of the number of results shown as well as stepping through the results frame-by-frame. Each result has some sort of identifier or short description indicating what it is, as well as a link to that its profile.

Type

Every element of data in the Biozon database is classified based on its meaning. This classification exists in the form of a hierarchy. A 'type' is a node in such classification hierarchy, and all types have a "is a" relationship with their parent types. There are two such hierarchies, one for documents, and one for relations. Examples of document types include "objects", "interactions", and "Proteins". Examples of relation types include "description" and "membership".

Visualization

An application, image, or other medium that provides some method of possibly interactive visualization of data.

Also see