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MIAME, ArrayExpress and the data submission tool
MIAMExpress
Helen ParkinsonMicroarray Informatics Team
European Bioinformatics Institute
Bio-ontologies workshop, 5 December,2001
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Talk Structure
MIAME Ontologies in a database context Datasubmission tool - MIAMExpress
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Standards in a database context
Data input,avoiding free text Data curation,ontology building Data query (web interface) Data exchange (via MAGE-ML) Linking to external databases for
sequence, samples, and cluster annotations
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General MIAME principles
Recorded info should be sufficient to interpret and replicate the experiment
Information should be structured so that querying and automated data analysis and mining are feasible
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MIAME – Minimum Information About a Microarray Experiment
PublicationExternal links
6 parts of a microarray experiment
www.mged.org
Hybridisation ArrayGene
(e.g., EMBL)Sample
Source(e.g., Taxonomy)
Data
Experiment
Normalisation
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Use case scenariosReturn a summary of all experiments that use a specified type of biosource (primary source).
Group the experiments according to treatment.
Return a summary of all experiments done examining effects of a specified treatment
Group the experiments according to biosource.
Return a summary of all experiments measuring the expression of a specified gene.
Indicate when experiments confirm results, provide new information, or conflict.
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Why do we need an ontologyfor the database
To perform structured queries To ensure data is described accurately
and consistently To avoid problems with free text
searching To avoid excessive curation workload
in future
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organism (NCBI taxonomy)cell source - provider cell type (if derived from primary sources (s))sexagegrowth conditionsdevelopment stageorganism part (tissue)animal/plant strain or linegenetic variation (e.g., gene knockout, transgenic variation)individualindividual genetic characteristics (e.g., disease alleles, polymorphisms)disease state or normaltarget cell typecell line and source (if applicable)in vivo treatments (organism or individual treatments)in vitro treatments (cell culture conditions)treatment type (e.g., small molecule, heat shock, cold shock, food deprivation)compoundis additional clinical information available (link)separation technique (e.g., none, trimming, microdissection, FACS)
laboratory protocol for sample treatment……
MIAME Section on Sample Source and Treatment
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What sort of annotation do we see?
Free text (free text is bad) complex sentence construction
No references, no defintions, synonyms Incomplete annotation e.g. “control” Inconsistent use of terms e.g. experiment,
probe, target…… Publication references to websites with
supplementary pdf’s
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Excerpts from a (good) Sample Descriptioncourtesy of M. Hoffman, S. Schmidtke, Lion BioSciences
Organism: Mus musculus [ NCBI taxonomy browser ]Cell source: in-house bred mice (contact: [email protected]) Sex: female [ MGED ]Age: 3 - 4 weeks after birth [ MGED ]Growth conditions: normal
controlled environment20 - 22 oC average temperaturehoused in cages according to EU legislationspecified pathogen free conditions (SPF)14 hours light cycle10 hours dark cycle
[Developmental stage]: stage 28 (juvenile (young) mice)) [ GXD "Mouse Anatomical Dictionary" ]Organism part: thymus [ GXD "Mouse Anatomical Dictionary" ]Strain or line: C57BL/6 [International Committee on Standardized Genetic Nomenclature for Mice]Genetic Variation: Inbr (J) 150. Origin: substrains 6 and 10 were separated prior to 1937. This substrain is now probably the most widely used of all inbred strains. Substrain 6 and 10 differ at the H9, Igh2 and Lv loci. Maint. by J,N, Ola. [International Committee on Standardized Genetic Nomenclature for Mice ]Treatment: in vivo [MGED] [intraperitoneal] injection of [dexamethasone] into mice, 10 microgram per 25 g bodyweight of the mouseCompound: drug [MGED] synthetic [glucocorticoid] [dexamethasone], dissolved in PBS
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ArrayExpress DatabaseMAGE-OM Model
Curation Database
User Login
Array Submission
Protocol Sub.
Experiment submission
MIAMExpress
Query Interface for Public Data
Analysis ToolsExpression Profiler
Large ScaleSubmissionsMAGE-ML
format
Submitter LIMS
Browse Arrays
Browse Protocols
Browse Protocols
Data File ExportExternal
Applications
Browse Arrays
External Databases,
EMBL, Ontology Resources…
etc
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MGED/ ArrayExpress
Ontology
Production Curation Tool/Browser Public Browser
LIMSMIAMExpress
External Ontologies
MAGE-ML Data checking
ontologies
LIMS
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Introduction to MIAMExpressa tool for datasubmisson
The submission tool is simpler implementation of the ArrayExpress model in Mysql
Faster, easier to update, cheap Short term solution to the problem of data
submission in a non XML format Must be granular enough to be useful And not be too time consuming to complete
a submission
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MIAMExpress Based on MIAME concepts and
questionnaire Experiment, Array, Protocol submissions CV wherever possible Future versions organism specific pages and
related linked ontologies Allow user driven ontology development Will be developed according to user needs Will also need to be an update tool
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Login
Pending/New Experiment
Sample1 Sample2 Sample3 Samplen Sample protocol
Hybridisations Hyb protocol
Array1 Array2 Array3 Arrayn Scanning protocol
Data1 Data2 Data3 Datan Image analysis protocol
Combined Experiment Data Transformation protocol
Submit Final free text comment
Create account
Extracts 1…nExtracts 1…n Extracts 1…n Extracts 1…n
E1 E2 En E1 E2 En E1 E2 En E1 E2 En
Extraction protocol
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Design Considerations
Speed and ease of use, scalability Need to browse existing protocols and array
designs in ArrayExpress Requirement for curator control over
submissions Submissions tracking Future use as a LIMS Flexibility
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Problems with tool design Granularity Including ontology information in a
usable format Length of submission time Getting lost within the pages Users don’t start to submit till they have
a proof Conforming to MAGE-OM
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Features of MIAMExpress Creates a user login account instead of on-
the-fly submissions so sessions can be saved Allows existing protocols to be copied and
saved and linked to more than one hyb/expt Forms the basis of a LIMS using the
ArrayExpress model Will be available as a stand alone tool for
local installation Is open source and free Will be supported by curation staff and
developers
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Expected Users
Users with limited local bioinformatics support
Users of bought in arrays without LIMS Small scale users with self made
arrays who will need to provide a description
Array Submissions are expected from manufacturers (MAGE-ML format)
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MIAMExpress v2.0KeyLargoExpress?
Dynamic Species specific Browsable ontologies including MGED QVS removed Less free text,more controlled vocabularies Pretty up the front end Curation staff interface
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Acknowledgments Microarray Informatics Team Industry Support team, EBI MGED Chris Stoeckert, U. Penn. Ontology builders everywhere Liz Ford
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Demo Version of MIAMExpress
Coming soon to www.ebi.ac.uk.microarray
Beta tester recuitment
