Searches

Biozon data is searchable through three modes. The first, and easiest, is a "quick search" that searches through the definitions of all data objects currently in the Biozon database. The second, more useful mode is the "simple" search. This is the method of choice if you are interested in a very specific entity (with a specific accession number or definition). The third, and most powerful, is the "complex search", which allows searches that involve multiple data types.

Quick Search

In this mode Biozon searches definitions of all known data objects in the database for the given search string. The search string you provide contains a list of words that you would like the object's definition (or perhaps words that you would like excluded. The quick search reads your search string in a similar fashion to standard web search engines, and most of the same rules still apply. For example, phrases are represented by "quotes around the phrase", excludes words are preceded by a hyphen (-excluded -word), and there is an implicit 'and' around every bare word. You may explicitly use the words 'and' and 'or' to represent logical ANDs and ORs when building the phrase

Once a phrase has been entered, pressing the Go button will execute the query. Of every data type that matches the query, a result set will appear containing only the first 10 matches. Navigating a result set for a particular matching object type (i.e. changing the number of hits shown, displaying further matches, etc) will cause the result sets for all other types to disappear.

Simple Searches

Simple search is a type-specific search that looks for all entities of a certain type (e.g. protein sequences) that match a specific keyword or gene name, for example. Clicking on the icon that corresponds to the desired data type in the Biozon homepage, will take you to a form that displays all attributes that are associated with this data type and were indexed in Biozon. These attributes are collected from multiple sources. Thus, a user can search, for example, Genbank accession numbers and GO terms using the same form. The attributes are generally divided into four categories: identifiers (accession numbers, gene names, etc), descriptions (definition, keywords, GO terms, etc), physical properties (such as length, or resolution) and taxonomy.

If you are interested in a specific entity with a specific accession number (e.g a protein structure with PDB accession code 1CTF), type the accession code in the corresponding text-box in the form.

Complex Searches

Complex searches are more focused and far-reaching than quick search or simple search. To start, complex searches are oriented around a single return type (e.g. "I am looking for all proteins that are involved in known interactions and have a solved structure"), but queries can involve many different types and their relationships with each other. Creating such queries involves specifying search constraints on various known attributes of each type (if there are any), as well as on how to relate them to one another (e.g. "I am looking for the structure of a protein that is involved in a particular interaction...")

Because of their flexibility and power of expression, much attention was spent on creating a suitable interface in which to frame such queries. More details on its use and how transform an idea into a complex query can be found in Creating Complex Queries. You can also view a short demo

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