EMBL-EBI Dimitris Dimitropoulos MSD-mine

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

EMBL-EBI Characteristics  Classical systems give list of entries for visualisation  MSD-mine returns detailed records, homogenised and ready for analysis  Allows arbitrary queries on the more than  100 entities (tables)  organised in 9 sections (or marts)  restrictions and results for 2000 attributes  combine entities based on 450 relations  Operability safeguards  Reject long queries (10 mins) and overload of results (1000 rows)

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

EMBL-EBI Filter build page  Areas on the page  Entity area (E): select entities and relations  Restriction area (R): set or view the restrictions  Filter area (F): view the nodes of the filter  Description area (D): context sensitive documentation

EMBL-EBI MSDSD marts  MSDSD is organised in sections (marts)  Each mart is a set of entities that may start a filter

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

EMBL-EBI Combine entities  Using one of its relations  Relations are organised per mart  Understand cardinality  User may choose the new entity as the working node and follow its relations

EMBL-EBI MSD preferences  User may set preferences to specify MSDSD shortcuts for filters  All assemblies – Representative assembly – Assymetric unit  All models – Representative model  One chain per sequence  All entries – SCOP or DALI entries – Custom set

EMBL-EBI Execute query  View-Navigate results  Load all records  Set result based constraints  View details  Navigate relation links  Export in Text-XML-Script

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

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

EMBL-EBI First Example  Find the entries with resolution < 1.2  Select the “Structure” mart and  Choose the Entry table  Set the restriction on resolution  Browse the results

EMBL-EBI Filter Expressions  Find the entries with resolution < 1.2 and are related to HEMOGLOBIN  Add the main restriction on the resolution and  Add a sub-expression where the logical operator is “Or”  And the title contains the word “HEMO” or “HAEMO” or “GLOBIN”

EMBL-EBI A simple distribution chart  Find the distribution of assembly types  Use the “Assembly” table from the “Structure” mart  Execute the query  Go to the analysis page for the “Assembly type” attribute

EMBL-EBI Relation and external links  Find entries related to “cell death” and follow their GO (gene ontology) mappings and the links to the external GO service  Use the “Entry” table where the title contains the word “death”  Follow the GO mappings for a particular entry  Follow the links to the GO database

EMBL-EBI A more complex example  Find the active site contacts of helices that are part of beta- alpha-beta motifs  Examine their linearity  Select “Motif” as the starting point and combine with “Helix” and “Residue Contacts”  Add a restriction  View results and statistics for the helix linearity  Focus (drill) on an area of interest

EMBL-EBI Saving results and exporting  Find the binding sites of “kinked” residues  Build the query by combining “Residue”, “Helix” and “Site” tables  Save the results on a local file  Export the results  in XML  TAB delimited  as a script

EMBL-EBI Preferences and 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 representative set  For our own custom representative set

EMBL-EBI Custom filters and results  Find the percentage of residues that interact in helix interactions, of helices with similar size  Use the “Helix interaction” table  Add a custom “normalised interaction factor” result item  Add a custom restriction “one helix is at most double in size than the other”  View the distribution of the “interaction factor”