PepcDB: Depositor FAQ

Last updated 10/05/2006

This page contains answeres to many frequently asked questions. If this page does not address your concern, please contact us at target-help@deposit.rcsb.org

Frequently Asked Questions

• What is PepcDB?
• What is the difference between PepcDB and TargetDB?
• What is deposited to the PepcDB?
• What protocols should be deposited to PepcDB?
• How many details should I provide in the protocol description?
• How do I document small modifications to a standard protocol?
• How are multiple experimental trials documented in PepcDB?
• How is target experimental progress documented in PepcDB?
• Should I deposit failed experimental trials into PepcDB?
• What contact information should be deposited to PepcDB?
• What data format is used to submit to PepcDB?
• Where can I find PepcDB schema and documentation?
• How do I submit data to PepcDB?
• Should data deposited to PepcDB be consistent with data in TargetDB?

What is PepcDB?

PepcDB is the Protein Expression Purification Crystallization Database. It is designed to document every step of the protein production pipeline, including reference and contact information.

What is the difference between PepcDB and TargetDB?

TargetDB, a target registration database, provides information on the progress and status of targets selected for structure determination. PepcDB extends the content of TargetDB with status history, stop conditions, reusable text protocols and contact information.

What is deposited to PepcDB?

PepcDB contains the following data:

• Protein sequences selected for structure determination.
• Experimental protocols describing each step in protein production.
• Target experimental status history.
• Lists of multiple experimental trials, including successful and unsuccessful experimental trials.
• Small modifications to standard protocols associated with specific experimental trials.
• Contact information related to a target or experimental trial.

What protocols should be deposited to PepcDB?

Separate protocols should be provided for each step of protein production:

1. Selection:        Example
2. Growth:           Example
3. PCR:               Example
4. Cloning:          Example
5. Expression:     Example
6. Purification:     Example
7. Crystallization: Example
8. NMR:               Example

The Protocol List contains the details about each experimental step in protein production. Each experimental step should be represented as a distinct entry in this list. The granularity of protocol description should be consistent with the list of experimental steps defined in Trial Protocol type. For example, a separate entry in the protocol list should be provided for "cloning" and should not be combined with the description of other steps such as expression, purification, etc. Descriptions within the protocol list can divide experimental steps into a number of substeps. Each step/substep in the protocol list is assigned a protocol identifier, a protocol name, a brief description, and the associated detailed description of the experimental protocol. The protocol identifier is referenced when describing the specific set of procedures used in a particular experimental trial. It is important that this section contains the detailed protocols corresponding to each of the experimental steps in all of the trials described in the project data file.

How many details should I provide in the protocol description?

Protocols should provide a detailed description of the experimental procedure. The level of experimental detail should be similar to the "Material Methods" section in a scientific journal such as the Journal of Biological Chemistry.

How do I document small modifications to a standard protocol?

Small changes introduced to a standard protocol associated with specific experimental trials should be documented in the Trial Protocol Details. This may represent modifications to the cloning vector, crystallization buffer, a change in expression temperature, etc. The small experimental changes should be deposited as a separate data item with reference to the main protocols.

How are multiple experimental trials documented in PepcDB?

All experimental trials should be deposited into PepcDB and documented in the trial list. The trial list should include:

• analytical and large scale experimental trials.
• successful and failed trials.

How is target experimental progress documented in PepcDB?

Experimental progress is documented for each trial associated with a target entry. It is represented in the Status History List.

• Ordering of experimental steps

  The list of steps in the status history list and their associated start and stop dates should be ordered chronologically by start date. The date information provided in this section should reflect the logical ordering of experimental steps and should provide a real measure of the time required to complete each step. Making all of the dates in the status history list the same is discouraged unless this level of productivity was actually achieved.

• Experimental steps in status history

  The trial status history list should include all experimental steps required to reach the current trial status. For example, if the last trial status is "purified", the status history list should also include "selected", "cloned", "expressed", and also "soluble" if expression resulted in soluble protein.

• Current status and status history consistency

  The trial current status should reference the last successful step in the status history list.

Should I deposit failed experimental trials into PepcDB?

Experimental trials which were terminated due to technical or other reasons should be deposited to PepcDB along with successful trials. This data should be documented in Trial Stop Details. The experimental step at which work was terminated and the explanation for the termination should be also provided. The former should correspond to one of the specified termination conditions.

What contact information should be deposited to PepcDB?

The Contact Information List should include names of the laboratories, groups, or individual researchers within the SG center that contributed to the protein's production. The list should also include the detailed address and e-mail address of a person who was in charge of the experiment.

Both the target contact ID and the trial contact ID should only reference contact information specified in the contact information list.

Which format is used to submit data to the PepcDB?

Target data are submitted to PepcDB in XML format.

Where can I find PepcDB schema and documentation?

To view and download PepcDB schema, please follow this link. PepcDB documentation can be viewed here.

How do I submit data to PepcDB?

PepcDB XML data files can be submitted on-line using the XML Validation Tool located at the PepcDB data entry and validation site.

Should data deposited to PepcDB be consistent with TargetDB?

Any target data provided to PepcDB should be consistent with data provided to TargetDB. Specifically, target ID, target experimental status, and target protein sequence should be the same in both databases. The TargetDB/PepcDB annotators can identify inconsistencies in data provided to both databases, but it is not possible to resolve these differences. TargetDB targets that are not deposited to PepcDB are automatically migrated to PepcDB.