PepcDB | Data Preparation

Last updated September 1, 2010

1.  Retrieve required data items from your local database or laboratory management system (LIMS).

The following are the core blocks of information that should be included into the PepcDB data file:

• A list of protein sequences or targets selected for structure determination and/or functional characterization by your laboratory. Each protein sequence should be associated with the data items, including protein name, source organism, and reference to external databases such as Uniprot, Genbank, PFAM, etc.


• All experimental protocols used in production or functional studies of proteins deposited to PepcDB.


• Contact information of the personnel who performed the experiments, including name, laboratory affiliation, and e-mail address.


• All experimental trials should be deposited to PepcDB. This includes both successful and failed experiments. The experimental trials may represent:
  • analytical or large scale trials
  • cloning of a target sequence into different plasmid vectors
  • expression of a target protein in different expression systems
  • different purification pipelines
  • various crystallization or NMR conditions


• Every experimental trial should be associated with a status history showing the dates when the experiment was initiated and completed.

2.  Assemble your data into XML format according to the PepcDB schema specifications. To help you to assemble your data into the PepcDB data file, the following documents are provided:

• Detailed description of the PepcDB content
• PepcDB depositor FAQ

• PepcDB XML schema specification
• PepcDB schema text format
• PepcDB schema diagram

• Download an example of an annotated data file (schema version: pepcDB-v9.1.xsd).
• Download an example of an annotated data file (schema version: pepcDB-v9.2.2.xsd).

3.  If you have any questions regarding PepcDB data deposition, please contact: target-help@sbkb.org