friday seminar 15 10 2004

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Facilitating Standardization and Exchange of Array Design

ADF MAGE-ML Tool

Pierre Marguerite – Friday Seminar

EBI – Microarray Informatics Team

15 October 2004

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15/10/2004 - Friday Seminar Pierre Marguerite

Microarray Informatics Team2

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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conversiontool

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MAGE-ML (MAGE-OM)Description Biosequence

Array

Array Design DesignElement DesignElement

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MAGE-ML (next)

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ADF (previous)

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Array Design File

adh

adr

adc

Header

contacts

Technical Information

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Array Design File

adr

adc

ReportersFeatures

Feature /Reporter

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Array Design FileComposite

Characteristics

Map to reporters

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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:

1. Header file is a tab-delimited-file2. Item names are correct or can be identified

if an item is not identified, it is skipped.1. All mandatory items are present in the header

• Data/file content checklist1. Correct field value format

Possible value types:"Integer"

• "Free Text"• "Controlled vocabulary"• "MGED ontology term"• "DatabaseEntry"• "Sequence"• "Species"

2. Check single multiple value

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Checking lists (feature reporter)• Feature Reporter file• File/Data structure checklist:

1. Header File is correct (structure and data )2. FeatureReporter file is a tab-delimited-file3. Header item names are correct (unknown items are skipped)4. All mandatory items are present. item cardinalities and dependences are correct.5. Database tags are approved and database accession numbers are correct6. Item order is correct (Optional, do not fail the checking)7. Field dependences are correct

• Data/file content checklist1. FeatureReporter file structure must be correct2. Mandatory Field are present. Field cardinalities and field value multiplicities must be correct.3. 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

4. Duplicate features must not exist5. Duplicate Reporter (equal names) must have the characteristics.

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Checking lists (composite)• CompositeSequence• File/Data structure checklist:

1. Feature Reporter file must be correct (structure and data)2. CompositeSequence file is a tab-delimited-file3. Header item names are correct. (Unknown items are skipped)4. All mandatory items are present. Header item cardinalities and dependences are

correct5. Column order is correct (non mandatory)

• Data/file content checklist1. Composite file structure must be correct2. All mandatory fields are present. Field cardinalities are correct3. Field values are in expected format. Field multiplicity is correct (same as

Feature/Reporter)4. Names in map are reporter or composite sequence names5. 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 / DAML+OIL

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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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friday seminar 15 10 2004

Technology

correct structure

correct mandatory field

file item names

file header item names

correct item order

names names

correct field values

correct duplicate features