Facilitating Standardization and Exchange of Array Design

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Facilitating Standardization and Exchange of
Array Design

• ADF MAGE-ML Tool

Pierre Marguerite Friday Seminar
15 October 2004
EBI Microarray Informatics Team
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ADF MAGE-ML Tool

• Application
• stand-alone
• plateform independant
• Supports
• Simple/Complex microarray layout
• Differents microarray applications
• gene_expression
• snp_detection
• comparative_genomic_hybridization
• binding_site_identification
• Others (minimal)
• Respects Good practices

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conversion tool
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MAGE-ML (MAGE-OM)
Array
Description
Biosequence
DesignElement
Array Design
DesignElement
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MAGE-ML (next)
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ADF (previous)
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Array Design File
adc
adr
contacts
adh
Header
Technical Information
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Array Design File
Reporters
Features
adc
adr
Feature /Reporter
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Array Design File
Composite
Map to reporters
Characteristics
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ADF version differences

• 3 parts (files) instead of 1
• As Workbook or text files
• No Reporter Identifier item
• No Reporter Group role item
• New Chromosome item
• New Chromosome_band item
• New Species item

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• 2 mandatory steps
• Validation
• Conversion

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Validation

• File format validation
• File content validation
• Validation of controlled vocabulary
• MGED ontology terms
• Approved Databases (Tags, Accession numbers)
• Automatic curation (when possible)

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Validation

• two levels of checking
• Relaxed
• Strict
• two execution modes
• A complete mode
• A step-by-step mode
• Error Log for correction

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Checking lists (header)

• File/Data structure checklist
• Header file is a tab-delimited-file
• Item names are correct or can be identified
• if an item is not identified, it is skipped.
• All mandatory items are present in the header
• Data/file content checklist
• Correct field value format
• Possible value types
• "Integer"
• "Free Text"
• "Controlled vocabulary"
• "MGED ontology term"
• "DatabaseEntry"
• "Sequence"
• "Species"
• Check single multiple value

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Checking lists (feature reporter)

• Feature Reporter file
• File/Data structure checklist
• Header File is correct (structure and data )
• FeatureReporter file is a tab-delimited-file
• Header item names are correct (unknown items are
  skipped)
• All mandatory items are present. item
  cardinalities and dependences are correct.
• Database tags are approved and database
  accession numbers are correct
• Item order is correct (Optional, do not fail the
  checking)
• Field dependences are correct
• Data/file content checklist
• FeatureReporter file structure must be correct
• Mandatory Field are present. Field cardinalities
  and field value multiplicities must be correct.
• Field values are in a mandatory format
• Database tags are approved by ArrayExpress and
  are supplied in lower caseand between square
  brackets
• Database ID are correct
• Ontology terms are correct (MGED ontology)
• Sequences are correct following the associated
  polymer type (DNA, RNA, protein)
• Integer field values are correct
• Duplicate features must not exist

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Checking lists (composite)

• CompositeSequence
• File/Data structure checklist
• Feature Reporter file must be correct (structure
  and data)
• CompositeSequence file is a tab-delimited-file
• Header item names are correct. (Unknown items
  are skipped)
• All mandatory items are present. Header item
  cardinalities and dependences are correct
• Column order is correct (non mandatory)
• Data/file content checklist
• Composite file structure must be correct
• All mandatory fields are present. Field
  cardinalities are correct
• Field values are in expected format. Field
  multiplicity is correct (same as
  Feature/Reporter)
• Names in map are reporter or composite sequence
  names
• No duplicate CompositeSequences (same names)

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Checking lists

• Header item names are correct
• All mandatory items are present
• All mandatory fields are present.
• No Duplicate features
• Duplicate Reporter (equal names) must have the
  characteristics.
• No duplicate CompositeSequences (same names)
• Names in map are reporter or composite sequence
  names

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MGED Ontology / DAMLOIL
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Approved Databases
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User modes
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Implementation - technical choices

• -MAGE-stk
• JaxB
• Configuration (default parameters)

Performance 4000 features 10 minutes
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Installer - izpack
http//www.izforge.com/izpack/
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http//www.ebi.ac.uk/adf
http//www.ebi.ac.uk/adf/
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