RAD and MIAME Express Web Annotation Forms

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RAD and MIAME ExpressWeb Annotation Forms

• Angel Pizarro
• Center for Bioinformatics, CBIL
• University of Pennsylvania

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Annotation Needs

• In order to collect all the necessary
  experimental info from the bench-investigator,
  need
• user-friendly interfaces
• use of ontologies
• known terms with a defined meaning
• minimize free text
• queries can be generated using CV terms

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• 1.1 Basic Features common to all pages in
  MIAMExpress

Bear in mind for navigating MIAMExpress
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The Help Page
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• 1.2. Specific features common to the branching
  Forms

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• 2.2 Select a submission type from the main hub

• Remember the quick links to the helpnotes.

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• 2.3.1 Protocol Submission Form

• The form is divided in 6 sections corresponding
  to 6 basic protocols of a microarray experiment

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• 2.3.1 Protocol Submission Form

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• 2.3.2 Work case Submitting an Extraction Protocol

http//www.ebi.ac.uk/miamexpress/
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GUS (Genomics Unified Schema)

• RAD is part of GUS
• http//www.gusdb.org/
• This platform maximizes the utility of stored
  data by warehousing them in a schema that
  integrates the genome, transcriptome, gene
  regulation and networks, ontologies and
  controlled vocabularies, gene expression
• Relational schema, Perl object layer, plug-ins
• Source code available through a CVS repository
  hosted by the Sanger Institute
• Generate MAGE-ML to enable easy deposition into
  ArrayExpress (MAGEstk)

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RAD uses MIAME/MAGE
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RAD web-forms for Annotationhttps//www.cbil.upe
nn.edu/RAD/forms/php/

• General Architecture
• Module based
• Written in php
• Data input accomplished by Perl object layer
• Front-end data integrity checked by JavaScript
• Exploit the RAD ontologies, which comprises the
  OWG efforts, e.g.
• Study Design Study Design Type, Study Factor
  Type
• Biomaterials material type, biosource type,
  strain, cell line, dev. stage, organism part,
• Exploit data privacy and project/group separation
  present in RAD
• Cover all parts of the MIAME checklist
• Allow to enter very specific details of the
  experiments

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Logical Flow
Login
New User Registration
Data Preferences (Group, Project)
Study
Misc
From Assay to Quantification
Study Design
Biomaterials (samples, treatments)
Module I
Module II
Module III
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Flexible entry points

• There are dependencies between forms.
• However access to all forms is opened at all
  times. This allows
• Choice of depth-first or breadth-first annotation
  according to which best optimizes batching for
  the data at hand.
• Entering of info at different times, without
  having to fill it all in in the same session.

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Batching

• Enabled whenever possible
• One form currently not batched is the Assay
  one. Could be batched if the common fields are
  always the same for expected data
• There are various combinations in which the forms
  can be used so to batch the information. The
  optimal combination for a given dataset will
  depend on the particular kind of information
  available for that dataset.

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From Assay to Quantification RAD3 Tables
Assay
Array
AssayParam
Acquisition
AcquisitionParam
RelatedAcquisition
RelatedQuantification
Quantification
QuantificationParam
is parent of
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Study Design RAD3 Tables
StudyAssay
StudyDesignAssay
Assay
StudyDesignType
StudyFactorValue
OntologyEntry
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MGED Ontology
Can add terms
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BioMaterial RAD3 Tables
BioMaterialMeasurement
OntologyEntry
BioMaterialCharacteristic
Treatment
BioMaterialImp
LabelMethod
LabeledExtract
BioSample
BioSource
AssayLEX
AssayBioMaterial
Assay
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MGED Ontology
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MGED Ontology
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An Example BioMaterial
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Help

• By clicking on ? next to each field in each
  form, a window with usage for that field pops-up.
  This queries GUS.App.FormHelp
• Windows displaying descriptions of protocols
  already in RAD can be opened upon clicking a
  button.
• Windows displaying definitions for certain MGED
  ontology entries can be opened upon clicking a
  button.
• A general tutorial with sample annotation is
  under development.

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Benefits of Annotation
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Benefits (2)
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Benefits (3)
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Export to MAGE
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MIAMExpress Team

• The Microarray Team _at_ EBI
• Alvis Brazma Ugis Sarkans
• Developers
• Mohamad Shojatalab Niran Abeygunawardena.
  Sergio Contrino
• Curators
• Helen Parkinson Susanna Sansone Ele Holloway
  Gaurab Mukherjee. Philippe Rocca-Serra

http//www.ebi.ac.uk/miamexpress/
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RAD WebForms Group

• Elisabetta Manduchi
• Greg Grant
• Junmin Liu
• Trish Whetzel
• Hongxian He
• Matt Mailman
• Chris Stoeckert

http//www.gusdb.org