|
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]
|
