PepcDB/TargetDB Discussion Topics

[forumadmin]

We are planning to introduce modifications to PepcDB schema outlined below. Your suggestions/comments are very much appreciated.

To view modified PepcDB diagram please go here: http://pdb-linux-5.rutgers.edu:9080/pepcdb/schema/pepcDB-v9.2.2.jpg

To view PepcDB schema in XML format please go here:
http://pdb-linux-5.rutgers.edu:9080/pepcdb/schema/pepcDB-v9.2.2.xsd


Please note that all new data elements are optional.

1.Data element <psiProgram> is replaced by <projectList>. This element was introduced to identify targets that might belong to several different SG projects or project stages for example PSI-1 and PSI-2

2.New element <targetCategoryList> is added at the target level. This item is introduced to identify targets that are classified in specific category. Currently two category codes are proposed such as “biomedical” and “community nominated”.

3.Element <status> is introduced to target level to identify current status of a target.

4.Element <targetStopDetails> is introduced to target level to describe details for stopping work on a target.

5. Reference to protocol Id is introduced into <statusHistoryList> to identify analytical and preparative experimental scales, or cloning into propagation vs expression vectors.

6.Element <trailMeasurementList> is introduced to capture measurements associated with an experimental trial such as metal content, stoichiometry, posttranslational modification, molecular weight, pI, et.

7. New protocol type “gene synthesis” is included into the current protocol type list. This is to distinguish targets derived from synthetic, codon-optimized DNA.

8. Additional enumeration code, "insert", is included into <sequenceType>. We anticipate to replace sequence type 'clone' with 'insert' in the future in order to reach consistency in terminology with Material Depository: PlasmID.