Sample of the ebi database

This is not the true Relational database. This contains some extracts of the database and lacks all NMR and many tables. It is an outline of the types of information that can be loaded and checked and stored in the database. The starting point for taking the database is the designer 2000 file not these individual example sql files that are given here solely as an illustration of some of the details.

These files can be populated by the EBI and not only include the pdb hetgroups and standard groups (and modified standard groups) but also data from the NCI list

The xray reference data files can be extended as required.

  • 1. Parameters reference data
  • 2. Topology reference data
  • 3. Xray reference data

    This starts and entry

  • 4. An entry

    This is per dataset and illustrates some of the detail that is filled in as an entry is filled in

  • 5. Xray Exp data sets

  • 6. HKL data
  • 7. MAD data
  • 8. MIR data
  • 9. REFINE data
  • 10. NCS data
  • 11. Coordinates
  • 12. Properties

  • 13. admin at ebi
  • 14. list of ebi db tables

    The search database is very different and is a simplified data warehouse and not all types of searches are carried out through the realtional tables as the deposition database is the archive. For example sequence searches are not carried out on the db tables nor are topological searches. For particular types of data external binary indexed files are used for the application. nauty style connectivity graphs are stored in a binary file, and distance matrix for site etc are stored separetely. As other ebi databases are ready links are to be made into the sws/embl seq databases and the ensemble project as well as metabolic pathways.

    For ccp4/gui to run say an mlphare script and get an output of see mlphare.txt for a fuller output then say the data in : 

    loop_
_phasing_MIR_der_site.der_id
_phasing_MIR_der_site.id
_phasing_MIR_der_site.atom_type_symbol
_phasing_MIR_der_site.fract_x
_phasing_MIR_der_site.fract_y
_phasing_MIR_der_site.fract_z
_phasing_MIR_der_site.B_iso
_phasing_MIR_der_site.ebi_Occupancy_iso
_phasing_MIR_der_site.ebi_occupancy_iso_esd
Pb(OAc)2       1      PB     0.640     0.765     0.069  10.000   1.843   0.020
Pb(OAc)2       2      PB     0.637     0.469     0.018  10.000   1.776   0.020
AuI3           3      AU     0.542     0.990     0.169  10.000   1.907   0.035
AuI3           4      AU     0.561     0.014     0.141  10.000   1.719   0.034
AuI3           5      AU     0.551     1.001     0.155  10.000   2.473   0.035
KHgI3          6      HG     0.550     0.989     0.151  15.000   2.833   0.043

    This can be loaded in an oracle database by using perldb or even more simpler using ccp4/gui written sql scripts to use sqlplus @load_xxxx into a table like 

    
CREATE TABLE DEP_DER_SITE (
   SITE_ID            VARCHAR2(8)  NOT NULL,
   DMD_DMD_ID         NUMBER(10,0) NOT NULL,
   DDS2_ID            NUMBER(10,0) NOT NULL,
   ELEMENT            VARCHAR2(2)  NOT NULL,
   OCCUPANCY_ISO      NUMBER(8,0)      NULL,
   OCCUPANCY_ISO_ESD  NUMBER(8,0)      NULL,
   OCCUPANCY_ANOM     NUMBER(8,0)      NULL,
   OCCUPANCY_ANOM_ESD NUMBER(8,0)      NULL,
   B_ISO              NUMBER(8,0)      NULL,
   B_ISO_ESD          NUMBER(8,0)      NULL,
   CARTN_X            NUMBER(8,0)      NULL,
   CARTN_X_ESD        NUMBER(8,0)      NULL,
   CARTN_Y            NUMBER(8,0)      NULL,
   CARTN_Y_ESD        NUMBER(8,0)      NULL,
   CARTN_Z            NUMBER(8,0)      NULL,
   CARTN_Z_ESD        NUMBER(8,0)      NULL,
   DETAILS            VARCHAR2(80)     NULL)

    is a simple task

    The derivative information can be saved in other tables such as per derivative: 

    CREATE TABLE DEP_MIR_DER (
         DDS_DDS_ID          NUMBER(10,0) NOT NULL,
         DERIVATIVE_ID       NUMBER(38)   NOT NULL,
         DPL_DPL_ID          NUMBER(10,0) NOT NULL,
         DMD_ID              NUMBER(10,0) NOT NULL,
         NUM_OF_SITES        NUMBER(38)       NULL,
         NUM_ANOMALOUS       NUMBER(38)       NULL,
         NUM_CENTRIC         NUMBER(38)       NULL,
         NUM_ACENTRIC        NUMBER(38)       NULL,
         POWER_CENTRIC       NUMBER(8,0)      NULL,
         POWER_ACENTRIC      NUMBER(8,0)      NULL,
         RCULLIS_ACENTRIC    NUMBER(8,0)      NULL,
         RCULLIS_ANOMALOUS   NUMBER(8,0)      NULL,
         RCULLIS_CENTRIC     NUMBER(8,0)      NULL,
         D_RES_HIGH          NUMBER(8,0)      NULL,
         D_RES_LOW           NUMBER(8,0)      NULL,
         REFLNS_CRITERIA     VARCHAR2(80)     NULL,
         DETAILS             VARCHAR2(1000)   NULL)

while dataset info would be kept in table DEP_DATA_SET    
see 
  •         5.  Xray Exp data sets