Transcript Macromolecular Structure Database group

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MSD-mine
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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
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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
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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
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Filter build page
 Page areas
Entities
(entities and
relations)
Restrictions
Filter
(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 to expand
& use
Click for
documentation
Use in your
query
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Define Restrictions
 Select the attribute
 Choose the operator
 Type in the value or
select one from a
sample list
 Add the new
restriction
value
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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
analysis
All/Representative
assembly
Asymmetric unit
All/Representative model
One chain per sequence
All entries
SCOP or DALI entries
Custom 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 betaalpha-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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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
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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”