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 ontologys 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
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)
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)
External Links
Catrgories