Table descriptions


Table: deposition
       Holds general information for all deposited structures
Column:
       dep_set_id   - Structure deposition identifier              
                    - String, not null, primary key
       pdb_id       - PDB identifier
                    - String   
       initial_deposition_date - The date of initial deposition
                               - date                 
       annotator_initials - The initials of the annotator processing this entry
                          - String 
       deposit_site - The site where the file was deposited
                    - String
       process_site - The site where the file was prodcessed
                    - String
       status_code  - Code for status of file
                    - String
       author_release_status_code - The release status authorized by the depositor
                                  - String
       title        - A title for the entry
                    - String
       author_list  - A list of audit authors
                    - String seperated by comma
       exp_method   - The method used in the experiment
                    - String
       status_code_exp - status of structure factor or NMR constraints file
                       - String
       SG_center    - The initials of Structural Genomics Projects
                    - String
      

Table: wf_class_dict
       Holds all work flow classe definitions defined in the XML file
Column:
       wf_class_id   - Workflow class identifier
                     - String, not null, primary key
       wf_class_name - Workflow class name    
                     - String  not null
       title       - Title of a workflow
                   - String
       author      - Owner of the class 
                   - String
       version     - Version
                   - String


table: wf_instance
       holds data of actual running workflow insctances.
column:
       ordinal     - Ordinal numbers          
                   - Integer, not null, auto_increment, primary key
       wf_inst_id  - Workflow class identifier
                   - String, not null, key
       wf_class_id - Workflow class identifier
                   - String, not null, key
       dep_set_id  - Deposition identifier
                   - String
       owner       - The user who launch the instance
                   - String
       inst_status - Status of the instance
                   - String
       status_timestamp - The time stamp of the status 
                        - Datetime



Table: wf_task
       A child of workflow instance. It holds data for a particular Workflow task
Column:
       ordinal     - Ordinal numbers
                   - int not null auto_increment primary key,
       wf_task_id  - Workflow task identifier
                   - String, not null,
       wf_inst_id  - Workflow class identifier
                   - String(10)  not null,
       wf_class_id - Workflow class identifier
                   - String, not null,
       dep_set_id  - Deposition identifier        
                   - String, not null,
       task_name   - The name of a workflow task
                   - String
       task_status - Status of the task
                   - String, not null,
       status_timestamp - Time stamp when the status is set/updated
                        - Datetime
       task_type   - Type of a task
                   - String



Table: wf_reference
       Information between instances, tasks that are not in other tables
Column:
       dep_set_id  - Deposition identifier
                   - String, not null, key
       wf_inst_id  - Workflow class identifier
                   - String, key
       wf_task_id  - Task identifier         
                   - String, key
       wf_class_id - Workflow class identifier         
                   - String, key
       hash_id     - Hash key about reference of an instance/task
                   - String, not null, key
       value       - Hash value         
                   - String


Table: da_users
       User information for logging in
Column:
       user_name - User name for logging in
                 - String, not null, primary key
       password  - Password 
                 - String, not null
       groupname - Group code in table da_group
                 - String, not null
       email     - Email address
                 - String, not null
       initials  - Assigned initials for annotators
                 - String
       first_name  - The annotator's or user's first name
                   - String
       last_name   - The annotator's or user's last name
                   - String


 
Table: process_information
       Holds all processing recordes of each deposition
Column:
       dep_set_id    - Deposition identifier
                     - String, not null, part of primary key 
       serial_number - serial number 
                     - Integer, not null, part of primary key 
       process_begin - Time of beginning
                     - Datetime
       process_end   - Time of ending
                     - Datetime     
       remark        - Special remark about the processing
                     - String


Table: da_group 
       Annotation group codes and full names
Column:
       code      - Short name
                 - String NOT NULL, primary key
       groupname - Group of roles
                 - String, NOT NULL
       site      - Geographic site     
                 - String, NOT NULL
       main_page - ?
                 - String


Table: site
       Name of annotation sites 
Column:
       code         - Short name for an annotation site
                    - String, NOT NULL, primary key
       verbose_name - Full name
                    - String
 


Table: sgcenters 
       Initials and names of Structural Genomics Projects
Column:
       code         - Initials of a structual genomics project
                    - String, NOT NULL, primary key
       verbose_name - Full name of a structual genomics project
                    - String, NOT NULL
  


Table: database_PDB_obs_spr 
       Holds entries that are obsolete or superseded
Column: 
       dep_set_id     - Deposition identifier
                      - String, not null, part of primary key 
       id             - other id 
                      - String
       date           - Obsolete or superseded date
                      - datetime
       pdb_id         - Old PDB ID
                      - String
       replace_pdb_id - replaced PDB ID
                      - String, not null, part of primary key 



Table: database_related
       Holds other database related infomation
Column: 
       dep_set_id   - Deposition identifier
                    - String, not null, part of primary key
       db_name      - The name of related database
                    - String, not null, part of primary key
       details      - More information
                    - String
       content_type - Type e.g. split
                    - String
       db_id        - Related database id
                    - String, not null, part of primary key
 


Table: database_ref
       Hold all related database references.
Column:
       dep_set_id    - Deposition identifier
                     - String, not null, part of primary key
       database_name - The database name of any other site
                     - String, not null, part of primary key
       database_code - Database identifier
                     - String, not null
 


Table: author_corrections
       Holds records of author's correction sent after deposition
Column:
       ordinal       - Ordinal numbers
                     - Integer, not null, auto_increment, primary key
       dep_set_id    - Deposition identifier
                     - String, not null, key
       content       - Content about corrections
                     - String, not null
       sending_date  - Date sending new corrections
                     - date
       remark        - Other information
                     - String
 


Table: dep_with_problems
       Holds records that have problem during deposition
Column:
       ordinal    - Ordinal numbers
                  - Integer, not null, auto_increment, primary key
       dep_set_id - Deposition identifier
                  - String, not null, key
       type       - type of problems or errors
                  - String, not null
       detail     - Details about problem/error
                  - String



Table: release_request
       Holding the entries that author request for release
Column:
       dep_set_id   - Deposition identifier
                    - String, not null, key
       citation     - Citation in the journal
                    - String
       release_date - Requested release date          
                    - date
       PubMed_id    - The PubMed identifier
                    - Integer




Table: contact_author
       Holds depositor's contact information
Column:
       dep_set_id        - Deposition identifier
                         - String, not null, part of primary key
       name_salutation   - The salutation of the author, e.g. Dr., Mr.
                         - String
       name_first        - The first name of the author
                         - String, not null, part of primary key
       name_last         - The last name of the author
                         - String, not null, part of primary key
       name_mi           - The middle initial(s) of the author
                         - String
       role              - The role of this author in the project
                         - String, not null
       email             - The email address
                         - String, not null
       address_1         - The mailing address of the author (line 1 of 3)
                         - String, not null
       address_2         - The mailing address of the author (line 2 of 3)
                         - String
       address_3         - The mailing address of the author (line 3 of 3)
                         - String
       city              - The city in the mailing address
                         - String, not null
       state_province    - The state or province in the mailing address
                         - String
       postal_code       - The zip code in the mailing address
                         - String, not null
       country           - The country in the mailing address
                         - String, not null
       phone             - The phone number
                         - String
       fax               - The fax number
                         - String
       organization_type - The organization type to which the author is affiliated
                         - String, not null



Table: status
       The definitions for the processing status code used in PDB
Column:
       code         - Status code ('REL','HOLD',...)
                    - String, primary key

       verbose_name - The meaning of the Status code
                    - String



Table: django_session
       Hold session information generated from the user interface
Column:
       session_key  - Session Key
                    - String, primary key
       session_data - session data
                    - Text
       expire_date  - Expiration date
                    - Datetime



Table: manager_site
       Hold site information of the work flow manager
Column:
       id            - unique identifier
                     - String, not null, primary key
       code          - Site code
                     - String
       display_name  - Full name of a site
                     - String
