Macromolecular Structure Database group
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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”