EMBL-EBI

MSD-mine

EMBL-EBI

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

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 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”