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Home : Workgroups : MIAME : MIAME MAGE-OM : MIAME Glossary

MIAME concepts are listed in alphabetical order and definitions are provided.

Age

The time period elapsed since an identifiable point in the life cycle of an organism. (If a developmental stage is specified, the identifiable point would be the beginning of that stage. Otherwise the identifiable point must be specified such as planting)

[MGED Ontology Definition]

Amount of nucleic acid labeled

The amount of nucleic acid labeled

Amplification method

The method used to amplify the nucleic acid extracted

Array design

The layout or conceptual description of array that can be implemented as one or more physical arrays. The array design specification consists of the description of the common features of the array as the whole, and the description of each array design elements (e.g., each spot). MIAME distinguishes between three levels of array design elements: feature (the location on the array), reporter (the nucleotide sequence present in a particular location on the array), and composite sequence (a set of reporters used collectively to measure an expression of a particular gene)

Array design name

Given name for the array design, that helps to identify a design between others (e.g: EMBL yeast 12K ver1.1)

Array dimensions

The physical dimension of the array support (e.g. of slide)

Array related information

Description of the array as the whole

Attachment

How the element (reporter) sequences are physically attached to the array (e.g. covalent, ionic)

Author, laboratory, and contact

Person(s) and organization (s) names and details (address, phone, FAX, email, URL)

Biomaterial manipulation

Information on the treatment applied to the biomaterial

Bio-source properties

Information on the source of the sample

Cell line

The identifier for the immortalized cell line if one was used to derive the BioMaterial [MGED Ontology Definition]

Cell type

Cell type used in the experiment if non mixed. If mixed the targeted cell type should be used [MGED Ontology Definition]

Clone information

For each reporter, the identity of the clone along with information on the clone provider, the date obtained, and availability

Common reference

A hybridization to which all the other hybridisations have been compared

Composite sequence information

The set of reporters contained in the composite sequence. The nucleotide sequence information for each composite element: number of oligonucleotides, oligonucleotide sequences (if given), and the reference sequence accession number (from relevant databases)

Composite sequence related information

Information on the set of reporters used collectively to measure an expression of a particular gene

Compound

A drug, solvent, chemical, etc., that can be measured [MGED Ontology Definition]

Contact details for sample

The resource (e.g, company, hospital, geographical location) used to obtain or purchase the BioMaterial and the type of specimen [MGED Ontology Definition]

Control elements position

The position of the control features on the array

Control elements related information

Array elements that have an expected value and/or are used for normalization

Control type

The type of control used for the normalization and their qualifier

Data processing protocol

Documentation of the set of steps taken to process the data, including: the normalization strategy and the algorithm used to allow comparison of all data

Developmental stage

The developmental stage of the organism's life cycle during which the BioMaterial was extracted [MGED Ontology Definition]

Disease state

The name of the pathology diagnosed in the organism from which the BioMaterial was derived. The disease state is normal if no disease has been diagnosed [MGED Ontology Definition]

Element dimensions

The physical dimensions of each features

Experiment description

Free text description of the experiment and link to an electronic publication in a peer-reviewed journal

Experiment design

Experiment is a lang=EN-US set of one or more hybridizations that are in some way related (e.g., related to the same publication MIAME distinguishes between lang=EN-US : the experiment design (the design, purpose common to all hybridisations performed in the experiment), the sample used (sample characteristics, the extract preparation and the labeling), the hybridisation (procedures and parameters) and the data (measurements and specifications)

Experiment type (s)

A controlled vocabulary that classify an experiment

Experimental design

Design and purpose common to all hybridisations performed in the experiment

Experimental factor (s)

Parameter (s) or condition (s) tested in the experiment

Extraction method

The protocol used to extract nucleic acids from the sample

Features related information

Information on the location of the reporters on the array

Final gene expression table (s)

Derived measurement value summarizing related elements and replicates, providing the type of reliability indicator used

Gene name

The gene represented at each composite sequence: name and links to appropriate databases (e.g. SWISS-PTOR or organism specific database)

Genetic variation

The genetic modification introduced into the organism from which the BioMaterial was derived. Examples of genetic variation include specification of a transgene or the gene knocked-out [MGED Ontology Definition]

Growth conditions

A description of the isolated environment used to grow organisms or parts of the organism [MGED Ontology Definition]

Hybridization protocol

Documentation of the set of steps taken in the hybridization, including: solution (e.g. concentration of solutes); blocking agent and concentration used; wash procedure; quantity of labelled target used; time; concentration; volume, temperature, and description of the hybridization instruments

Hybridizationextract preparation

Information on the extract preparation for each extract prepared from the sample

Hybridizations

Procedures and parameters for each hybridization

Image analysis and quantitation.

Each image has a corresponding image quantitation table, where a row represents a array design element and a column to a different quantitation types (e.g. mean or median pixel intensity)

Image analysis output

The complete image analysis output for each image

Image analysis protocol

Documentation of the set of steps taken to quantify the image including: the image analysis software, the algorithm and all the parameters used

In vitro treatment

The manipulation of the cell culture condition for the purposes of generating one of the variables under study and the documentation of the set of steps taken in the treatment

In vivo treatment

The manipulation of the organism for the purposes of generating one of the variables under study and the documentation of the set of steps taken in the treatment

Individual genetic characteristics

The genotype of the individual organism from which the BioMaterial was derived [MGED Ontology Definition]

Individual number

Identifier or number of the individual organism from which the BioMaterial was derived. For patients, the identifier must be approved by Institutional Review Boards (IRB, review and monitor biomedical research involving human subjects) or appropriate body [MGED Ontology Definition]

Label incorporation method

The label incorporation method used

Label used

The name of the label used

Measurements

MIAME distinguishes between three levels of data processing: image (raw data), image analysis and quantitation, gene expression data matrix (normalized and summarized data)

Normalized and summarized data

Several quantitation tables are combined using data processing metrics to obtain the 'final' gene expression measurement table (gene expression data matrix) associated with the experiment

Nucleic acid type

The type of nucleic acid extracted (e.g. total RNA, mRNA)

Number of elements on the array

The number of features on the array

Number of hybridisations

Number of hybridizations performed in the experiment

Organism

The genus and species (and subspecies) of the organism from which the BioMaterial is derived [MGED Ontology Definition]

Organism part

The part or tissue of the organism's anatomy from which the BioMaterial was derived MGED Ontology Definition]

Platform type

The technology type used to place the biological sequence on the array

Production protoco

A description of how the array was manufactured

Provider

The primary contact (manufacturer) for the information on the array design

Qualifier, value, source (may use more than once)

Describe any further information about the array in a structured manner

Quality control steps

Measures taken to ensure or measure quality: replicates (number and description), dye swap (for two channel platforms) or others (unspecific binding, low complexity regions, polyA tails)

Raw data

Each hybridization has at least one image

Relationship between samples and arrays

Relationship between the labelled extract (related to which sample which extract) and arrays (design, batch and serial number) in the experiment

Reporter and location

The arrangement and the system used to specify the location of each features on the array (e.g. grid, row, column, zone)

Reporter approximate length

The approximate length of the reporter's sequence

Reporter generation protocol

A description of how the reporters were generated

Reporter related information

Information on the nucleotide sequence present in a particular location on the array

Reporter sequence information

The nucleotide sequence information for reporter: sequence accession number (from DDBJ/EMBL/GenBank), the sequence itself (if known) or a reference sequences (e.g. for oligonucleotides) and PCR primers pair information (if relevant)

Reporter type

Physical nature of the reporter (e.g. PCR product, synthesized oligonucleotide)

Sample

The biological material from which the nucleic acids have been extracted for subsequent labelling and hybridisation. MIAME distinguishes between: source of the sample (bio-source), its treatment, the extract preparation, and its labeling

Sample labeling

Information on the labeling preparation for each labelled extract

Scanner image file

The TIFF file including header

Scanning protocol

Documentation of the set of steps taken for scanning the array and generating an image including: description of the scanning instruments and the parameter settings

Separation technique

Technique to separate tissues or cells from a heterogenous sample (e.g. trimming, microdissection, FACS)

Sex

Term applied to any organism able to undergo sexual reproduction in order to differentiate the individuals or type involved. Sexual reproduction is defined as the ability to exchange genetic material with the potential of recombinant progeny [MGED Ontology Definition]

Single or double stranded

Whether the reporter sequences are single or double stranded

Spike type and qualifier

The type of spike used (e.g. oligonucleotide, plasmid DNA, transcript) and its qualifier (e.g. concentration, expected ratio, labelling methods)

Spiking control

External controls added to the hybridisation extract (s)

Spiking control feature

Position of the feature (s) on the array expected to hybridise to the spiking control

Strain or line

Animals or plants that have a single ancestral breeding pair or parent as a result of brother x sister or parent x offspring matings

[MGED Ontology Definition]

Surface and coating specification

Type of surface and name for the type of coating used

Targeted cell type

The targeted cell type is the cell of primary interest. The BioMaterial may be derived from a mixed population of cells although only one cell type is of interest [MGED Ontology Definition]

Treatment type

The type of manipulation applied to the BioMaterial for the purposes of generating one of the variables under study [MGED Ontology Definition]

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Last modified: 26 Sep, 2005.                              Contact Us
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