EMBL-EBI MSD-mine
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MSD-mine overview
Web application for online data analysis and miningFor 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
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Characteristics
Not overview visualisation of hits from predefined queries
Online analysis of homogenised data
Arbitrary queries on100 entities (tables) in 9 sections (marts)restrictions and results for 2000 attributescombine entities based on 450 relations
Operability safeguardsReject long queries and overload of results
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Exploring MSDSD
Explores and explains MSDSDWith context sensitive help and descriptionsWith links to MSDSD documentation
Helps to understand the structure of MSDSD
Helps learning query writing in SQL for advanced custom queries
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Filter build page
Page areasEntities
(entities and relations)
RestrictionsFilter
(entities joined)
Description (context sensitive)
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MSDSD marts
MSDSD is organised in sections (marts)
A mart is a closely related set of tables
Click for documentationClick to expand
& use
Use in your query
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Define Restrictions
Select the attribute
value
Choose the operator
Type in the value or select one from a sample list
Add the new restriction
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Combine entities
Using one of its relations
Relations are organised per mart
Understand cardinality
Choose the the working node and follow its relations
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MSDSD preferences
Constraint shortcuts
Important for correct analysisAll/Representative
assemblyAsymmetric unitAll/Representative modelOne chain per sequenceAll entries SCOP or DALI entriesCustom set of entries
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Execute query
View-Navigate results
Load all records
Result based constraints
View details
Relation links
Export: Text-XML-script
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Data analysis
Complete or Sample
Range or Value
Fully customisable
Context sensitive chart
Data drill operations
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Analysis over a base attribute
Choose base attribute
Choose grouping operation for analysis attribute
Options and data-drill operations supported
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Basic example
Find the entries with resolution < 1.2 Select the “Structure”
mart Choose the Entry table Set restriction on
resolution Browse the
results
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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”
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Simple distribution chart
Find the distribution of assembly types Use table “Assembly” Execute the query Analysis for the attribute
“Assembly type”
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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
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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
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Binding sites of “kinked” residues
Combining “Residue”, “Helix” and “Site”
Save the results on a local file
Export the resultsin XMLTextas a script
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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
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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”