TargetTrack | Data Deposition Guidelines

Last updated: October 31, 2013

The TargetTrack database is updated weekly on Fridays.

All groups interested in enabling biomedical research are encouraged to deposit their data to TargetTrack. Note that once a target is deposited to TargetTrack, it is considered public domain and cannot be removed from the database.

How should I provide my data?

1. XML data file

TargetTrack primarily accepts XML files. The current schema version is targetTrack-v1.4.1 (released April 2013) 

Update (10/31/2013) Full user documentation of the current TargetTrack schema is available: TargetTrack User Documentation 

The TargetTrack User Documentation contains the following sections:

  • Extensions in Target Definition describes how to define complex targets in TargetTrack. Examples using the new nomenclature defined in the TargetTrack schema are provided. The examples listed show how we can model a complex target either as a series of sequences OR as a series of references to existing targets. This allows depositors to decide exactly how they want to model a complex target.
  • Summary of Schema Changes details all the changes that were made from PepcDB to TargetTrack, as well as changes made between TargetTrack schema versions.
  • TargetTrack Data Definitions defines all TargetTrack schema elements, with supporting examples.

Update (10/31/2013) In addition, there are multiple supporting documentation files of the schema listed here: 

Schema Documentation (HTML) XML Schema (v1.4.1)
Schema Documentation (PDF) Short XML example
All Enumeration Options (XLS) Schema Diagram (JPG)

 

2. Spreadsheet

Update (05/29/12) A spreadsheet can also be used if your target list is shorter. We recommend that if you have 50 targets or more, you may want to consider a LIMS system as manual entry with this spreadsheet may prove laborious.

To deposit targets by spreadsheet, download the following three files and follow the TargetTrack Spreadsheet Instructions document.

How detailed should my protocols be?

There are free text elements where you insert the entire protocol into your data file, and reference them for each experimental step. Please review our Protocol Style Guide to learn how best to describe your protocols.

Can I test my TargetTrack XML file?

It is important to validate your XML datafiles to make sure there are no errors. There are two ways to use the validation software:

  • Online: Use the TargetTrack Deposition Tool. If you do not wish your test file to be included in the next TargetTrack database update, include the word "testing" along with your site name in the "Enter Center Name" box.
  • Local Installation: A standalone package of the validation tool is also available for download. This package is limited to Linux/Unix operating systems.

TargetTrack files tested using the online tool will not be used for database deposition until you notify us that they are ready for use.

I'm ready! How do I deposit my TargetTrack file?

TargetTrack is updated every Friday, so please time your depositions accordingly:


Support for this resource is provided by the Protein Structure Initiative:Biology program at NIGMS.

Questions and comments? target-help@sbkb.org