1. EMBL-EBI MSD-mine

2. EMBL-EBI MSD-mine overview  Web application for online data analysis and mining For the advanced MSDSD researcher Interactive ad-hoc queries Exploitation of integrated knowledge Analysis, charts and Data drill  Combining of information with multiple joins  Generic but customised for the MSDSD

3. EMBL-EBI Characteristics  Not overview visualisation of hits from predefined queries  Online analysis of homogenised data  Arbitrary queries on 100 entities (tables) in 9 sections (marts) restrictions and results for 2000 attributes combine entities based on 450 relations  Operability safeguards Reject long queries and overload of results

4. EMBL-EBI Exploring MSDSD  Explores and explains MSDSD With context sensitive help and descriptions With links to MSDSD documentation  Helps to understand the structure of MSDSD  Helps learning query writing in SQL for advanced custom queries

5. EMBL-EBI Filter build page  Page areas Entities (entities and relations) Restrictions Filter (entities joined) Description (context sensitive)

6. EMBL-EBI MSDSD marts  MSDSD is organised in sections (marts)  A mart is a closely related set of tables Click for documentation Click to expand & use Use in your query

7. EMBL-EBI Define Restrictions Select the attribute value Choose the operator Type in the value or select one from a sample list Add the new restriction

8. EMBL-EBI Combine entities Using one of its relations Relations are organised per mart Understand cardinality Choose the the working node and follow its relations

9. EMBL-EBI MSDSD preferences  Constraint shortcuts  Important for correct analysis All/Representative assembly Asymmetric unit All/Representative model One chain per sequence All entries SCOP or DALI entries Custom set of entries

10. EMBL-EBI Execute query View-Navigate results Load all records Result based constraints View details Relation links Export: Text-XML-script

11. EMBL-EBI Data analysis Complete or Sample Range or Value Fully customisable Context sensitive chart Data drill operations

12. EMBL-EBI Analysis over a base attribute Choose base attribute Choose grouping operation for analysis attribute Options and data-drill operations supported

13. EMBL-EBI Basic example  Find the entries with resolution < 1.2 Select the “Structure” mart Choose the Entry table Set restriction on resolution Browse the results

14. EMBL-EBI Filter Expressions  Entries with resolution<1.2 related to HEMOGLOBIN Add restriction on resolution “Or” sub-expression Title contains the word “HEMO” or “HAEMO” or “GLOBIN”

15. EMBL-EBI Simple distribution chart  Find the distribution of assembly types Use table “Assembly” Execute the query Analysis for the attribute “Assembly type”

16. EMBL-EBI Relations - external links  Entries related to “cell death” follow their GO mappings “Entries” where title contains the word “death” GO mappings for an entry Links to GO database

17. EMBL-EBI A more complex example  Linearity of helices that are part of beta- alpha-beta motifs and have active site contacts Start with “Motif” table Combine with “Helix” and “Residue Contacts” Add a restriction View results and statistics for the helix linearity Focus (drill) on an area of interest

18. EMBL-EBI Saving results and exporting  Binding sites of “kinked” residues  Combining “Residue”, “Helix” and “Site”  Save the results on a local file  Export the results in XML Text as a script

19. EMBL-EBI Preferences - representative sets  Find the distribution of number of crystals in experiments  Use the “XRay-data” table  View the distribution of number of crystals For the whole PDB For the DALI set For a custom representative set

20. EMBL-EBI Custom filters and results  Percentage of residues that interact in helix interactions, of helices of similar size “Helix interaction” table Custom “normalised interaction factor” result item Custom restriction “one helix is at most double in size than the other” View the distribution of the “interaction factor”