MIARE: Minimum Information About an RNAi Experiment : ControlledVocabulary

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Introduction

A controlled vocabulary is a list of terms whose meanings are specifically defined. The purpose is to improve communication and data searching by ensuring that everyone is using the same term to mean the same thing. This consistency of terms is one of the most important concepts in Minimum Information guidelines where effort is expended to use the same term in annotating an experiment instead of slightly different ones to refer to the same thing.

Ontologies and Controlled Vocabulary

A formal ontology is a controlled vocabulary expressed in an ontology representation language. This language has a grammar for using vocabulary terms to express something meaningful within a specified domain of interest. The grammar contains formal constraints (e.g., specifies what it means to be a well-formed statement, assertion, query, etc.) on how terms in the ontology’s controlled vocabulary can be used together.

Controlled vocabularies per se describe neither the relations amoing entities nor relations among concepts, and consequently cannot support inference process.


Controlled Vocabulary in MIARE

The MIARE Reporting guidelines contains a number of reporting requirements that should be defined using a Controlled Vocabulary.

Experimental Description
• Type of silencing RNA reagent (CV)
• Keywords (CV)
• Target Organism genus and species (CV) NCBI Taxonomy

Experimental Design
• Description of replicates (CV)
• Assays being conducted (CV)

Bio-source Properties
• Organism genus and species (CV) NCBI Taxonomy
• Contact details for sample
• Where descriptors are relevant to the particular sample include
o Animal/plant strain or line (CV)
o Sex (CV) MGED-Ontology
o Age (CV) MGED-Ontology
o Development stage (CV) MGED-Ontology
o Organism part (tissue) (CV)MGED-Ontology
o Cell Type(CV) Cell Type Ontology
o Cell Line(CV) MGED-Ontology
o Genetic Variation (CV) MGED-Ontology
o Individual Genetic Characteristics MGED-Ontology
o Disease state (CV) MGED-Ontology

• Sepration Technique (CV) MGED-Ontology

Pretreatment
• Treatment type (CV)
• Compound (CV) MGED-Ontology

Assay Plate Description
• Assay plate type (CV)
• Assay plate layout (for each position specify the following)
o Reagent group and control type (CV)

Silencing RNA Reagent
• silencing RNA reagent (CV)
• Modifications to silencing RNA reagent (CV)

Delivery
• Delivery Type(CV)
o Delivery reagent type (CV)

Post treatment
• Treatment type (CV)
• Compound (CV)

Assay
• Instrument
o Type of readout (CV)
Data Analysis
• Normalisation method (CV) OECD
• Scoring method (CV) OECD
• Quality controls steps (CV)


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