PAZAR Documentation
Data formats » PAZAR XML format

PAZAR XML format

Overview

To ease the insertion of data into the database, we have designed an XML exchange format (What is XML?) that can be used to format already existing datasets. The PAZAR Document Type Definition (DTD) is now available as well as a documentation explaining its use. Here are some examples to help you understand the XML format:

  • Example 1 — an interaction between a TF and an upstream binding site, and a set of mutations that affect this interaction
  • Example 2 — a SELEX experiment with an heterodimer transcription factor and the matrix built from the sequences
  • Example 3 — a gene reporter assay and the influence of co-expression with a transcription factor

Note: the XML examples above may be displayed as blank pages in certain web browsers, such as Safari. In these cases, the example files can be opened in a text editor and viewed on the user's computer after being downloaded and saved.

Step-by-step guide

Our step-by-step documentation is meant to help users write a backbone PAZAR XML file containing their data. It does not include all the possibilities and details available through the Document Type Definition, but is a good starting point to understand its structure.

  • Step 1 — getting started
  • Step 2 — capturing the regulatory sequence and (or) TF basic information
  • Step 3 — capturing the evidence Linking a sequence to a TF or to a specific expression

XML validator

Just upload your XML file below and Click on the "Validate" button to check its validity against PAZAR DTD.