Document ID: EPA-HQ-OPP-2003-0302-0014
Agency: epa
Document Type: Supporting & Related Material
Title: 
Posted Date: 2003-10-07T04:00Z

1
Minimum
Information
About
a
Microarray
Experiment
 
MIAME
for
Toxicogenomics
(
MIAME/
Tox)

DRAFT
 
Based
on
MIAME
1.1
(
February
12,
2003)

Background:
MIAME
and
MIAME/
Tox
The
MIAME/
Tox
document
is
based
on
the
MIAME
1.1
document[
1]
produced
by
the
MGED
(
microarray
gene
expression
database)
Society[
2].
The
goal
of
MIAME
(
minimum
information
about
microarray
experiment)[
3]
is
to
outline
the
minimum
information
required
to
interpret
unambiguously
and
potentially
reproduce
and
verify
an
array
based
gene
expression
monitoring
experiment.
Although
details
for
particular
experiments
may
be
different,
MIAME
aims
to
define
the
core
that
is
common
to
most
experiments.
MIAME
is
not
a
formal
specification,
but
a
set
of
guidelines.
More
information
about
the
MIAME
rationale
can
be
found
in
`
Minimum
information
about
a
microarray
experiment
(
MIAME)
 
toward
standards
for
microarray
data',
A.
Brazma,
et
al.,
Nature
Genetics,
vol
29
(
December
2001),
pp
365
­
371)[
3].
Although
MIAME
concentrates
on
information
content
and
should
not
be
confused
with
a
data
format,
it
also
tries
to
provide
a
conceptual
structure
for
microarray
experiment
descriptions.
Similarly,
MIAME/
Tox
seeks
to
provide
such
a
conceptual
structure
in
the
context
of
toxicogenomics.

In
addition
to
MIAME,
a
standard
microarray
data
model
and
exchange
format
MAGE)[
4],
which
is
able
to
capture
information
specified
by
MIAME,
has
been
submitted
by
EBI
(
for
MGED))
and
Rosetta
Biosoftware)[
5]
and
recently
became
an
Adopted
Specification
of
the
OMG
standards
group[
6]
(
see
http://
www.
mged.
org/
mage).
Many
organizations,
(
including
Agilent,
Affymetrix),
and
Iobion),
have
contributed
ideas
to
MAGE.
MAGE
collectively
refers
to
the
MAGE­
OM
(
object
model)
and
MAGE­
ML[
7]
(
markup
language)
derived
from
the
model.
MAGE­
OM
is
able
to
capture
information
specified
by
MIAME
and
will
be
the
standard
microarray
data
model,
while
MAGE­
ML
is
the
standard
exchange
format.

The
response
of
the
microarray
community
to
MIAME
has
been
very
favourable
and
many
instrument
manufacturers,
software
developers,
and
international
databases
have
moved
to
adapt
their
systems
to
capture
and
manage
MIAMEcompliant
data.
Links
to
software
tools
supporting
the
MIAME
information
capture
and
management
are
available
from
http://
www.
mged.
org/
miame.

An
open
letter
has
been
sent
to
the
main
scientific
journals
by
the
MGED
Society
and
published
by
Nature
[
8],
Science,
The
Lancet
and
Bioinformatics
[
9].
The
letter
includes
a
guide
to
authors,
editors
and
reviewers
of
microarray
gene
expression
papers.
The
guidelines,
based
on
the
MIAME
document,
aim
to
help
authors
to
meet
the
requirements.
They
also
guide
editors
or
reviewers
in
their
evaluation
of
2
whether
or
not
a
manuscript
provides
as
much
information
as
necessary
for
others
to
replicate
and
interpret
the
analysis
presented.
Finally,
the
letter
suggests
that
journals
should
require
submission
of
data
to
either
of
the
two
public
repositories:
ArrayExpress
[
10]
and
GEO
[
11].
The
Nature
group,
The
Lancet,
Cell,
EMBO
and
Toxicology
Pathology
have
responded
accordingly,
by
requiring
an
accession
number
to
be
supplied
at
or
before
acceptance
of
publication.

Although
details
for
particular
toxicogenomic
experiments
as
published
in
the
literature
may
be
different,
MIAME/
Tox,
like
MIAMI,
aims
to
define
the
core
that
is
common
to
most
toxicogenomic
experiments.
Here,
for
MIAME/
Tox,
the
original
MIAME
1.1
document
has
been
adapted
and
extended
to
fulfill
the
need
of
toxicogenomics
data
capture
and
exchange.
Like
MIAME,
MIAME/
Tox
is
not
a
formal
specification,
but
a
set
of
guidelines.
MIAME/
Tox
supports
a
number
of
different
objectives,
for
example:
linking
data
within
a
study,
and
linking
several
studies
from
one
institution
and
exchanging
toxicogenomics
datasets
among
public
databases.
In
fact,
the
major
objective
of
MIAME/
Tox
is
to
guide
the
development
of
toxicogenomics
databases
and
data
management
software.
Efforts
to
build
international
public
toxicogenomics
databases
are
underway
at
the
National
Center
for
Toxicogenomics
[
12]
National
Institute
of
Environmental
Health
Sciences,
USA
and
at
the
EMBL
European
Bioinformatics
Institute
(
EBI)
[
13],
UK
in
conjunction
with
the
International
Life
Sciences
Institute's
Health
and
Environmental
Sciences
Institute
(
ILSI
HESI)
[
14],
USA.
This
document
addresses
this
objective
by
outlining
the
minimum
information
required
to
interpret
unambiguously
and
potentially
reproduce
and
verify
array­
based
toxicogenomic
experiments.

Toxicogenomics
domains
Following
the
MIAME
rationale,
sufficient
and
structured
information
should
be
recorded
for
toxicogenomics
experiments,
to
correctly
interpret
and
replicate
the
experiments
or
retrieve
and
analyse
the
data.
Minimum
information
to
be
recorded
about
toxicogenomics
experiments
is
defined
in
subsequent
sections
and
should
include
the
following
data
domains:

(
1)
Experimental
design
parameters,
animal
husbandry
information
or
cell
line
and
culture
information,
exposure
parameters,
dosing
regimen,
dose
groups,
and
in­
life
observations.
(
2)
Microarray
data,
specifying
the
number
and
details
of
replicate
array
bioassays
associated
with
particular
samples,
and
including
PCR
transcript
analysis
if
available.
(
3)
Numerical
biological
endpoint
data,
including
necropsy
weights
or
cell
counts
and
doubling
times,
clinical
chemistry
and
enzyme
assays,
hematology,
urinalysis,
other.
(
4)
Textual
endpoint
information
such
as
gross
observations,
pathology
and
microscopy
findings.
3
The
institute
and
animal
number,
study
number
and
dates
are
sufficient
identifiers
to
link
data
domains
from
in­
life
studies.
In
vitro
experiments
will
establish
a
similar
unique
identifier
for
cultures
within
a
study.
Linking
microarray
data
to
biological
endpoint
data
will
be
through
the
individual
biological
material
assay
number
following
MIAME
conventions
for
microarray
standard
sample
extracts.

It
should
be
noted
that
MIAME
only
covers
array­
based
gene
expression
experiments.
A
Proteomics
Standards
Initiative
(
PSI)
[
15],
that
aims
to
define
community
standards
for
data
representation
in
proteomics
to
facilitate
data
comparison,
exchange
and
verification
is
in
a
developmental
stage.
At
the
present
time,
no
metabonomics
standards
initiative
is
known.
Therefore,
this
MIAME/
Tox
document
presently
outlines
the
requirements
for
array­
based
toxicogenomic
experiments
with
the
expectation
that
proteomics
and
metabonomics
standards
will
be
introduced
very
soon.

The
MIAME/
Tox
Ontologies
and
Controlled
Vocabularies
The
MGED
Society
is
developing
ontology
to
provide
standard
terms
for
the
annotation
of
microarray
experiments.
The
MGED
Ontology
[
16,
17]
is
intended
for
the
use
of
investigators
in
annotating
their
microarray
experiments
and
for
software
and
database
developers.
These
terms
will
enable
structured
queries
of
elements
of
the
experiments
and
allow
unambiguous
description
of
how
the
experiment
was
performed.
A
core
MGED
Ontology
will
be
established
by
Sept.
2003,
and
will
remain
unchanged
to
facilitate
software
applications
development.
However,
as
new
applications
of
microarray
technology
arise,
requiring
new
descriptive
terms,
a
second
layer
of
ontology
will
be
built.
The
MGED
Ontology
also
participates
in
the
global
open
biological
ontologies
effort
(
GOBO)
[
18]
that
collects
freely
available
ontologies
for
use
within
the
genomics
and
proteomics
domains.
Therefore,
the
MGED
Ontology
will
only
include
reference
to
available
free
resources.

Toxicogenomics
applications
require
specific,
common
terminologies
that
need
to
be
identified
and
subsequently
integrated
within
the
MGED
Ontology.
MIAME/
Tox
content
areas
for
gene
expression
experiment
descriptions
include
sections
that
will
be
provided
in
a
free
text
format,
along
with
information
that
are
recommended
to
be
provided
by
maximum
use
of
controlled
vocabularies
or
external
ontologies
(
such
as
species
taxonomy,
cell
types,
anatomy
terms,
histopathology,
toxicology,
and
chemical
compound
nomenclature).
The
use
of
controlled
vocabularies
is
needed
to
enable
database
queries
and
automated
data
analysis.

Since
few
controlled
vocabularies
have
been
fully
developed,
MIAME/
Tox
encourages
the
users,
if
necessary,
to
provide
their
own
qualifiers
and
values
identifying
the
source
of
the
terminology.
This
is
achieved
through
the
use
of
(
qualifier,
value,
source)

triplets,
for
instance,

(
qualifier:
`
cell
type',
value:
`
epithelial',
source:
`
Gray's
anatomy,
38th
ed.').
4
This
is
recommended
instead
or
in
addition
to
free
text
format
descriptions
wherever
possible
and
will
allow
the
community
to
build
a
knowledge
base
of
the
most
useful
controlled
vocabularies
for
describing
microarray
experiments.

The
MIAME/
Tox
structure
Overview
Microarrays
are
often
manufactured
independently
of
particular
experiments
and
their
design
description
can
be
given
separately.
Therefore,
as
with
MIAME,
MIAME/
Tox
has
two
major
sections.

 
Array
design
description;
 
Gene
expression
experiment
description.

The
first
section
remains
identical
to
the
MIAME
1.1
document,
and
the
second
section
is
extended
to
fulfill
the
need
of
this
toxicogenomics­
specific
application
of
MIAME.
The
two
components
of
MIAME/
Tox
are
discussed
in
further
detail
below.

Array
design
description
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).
Following
terminology
used
in
MAGE,
we
distinguish
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,
exon,
or
splice­
variant.
The
details
that
should
be
given
for
each
of
them
are
described
below.

1)
Array
related
information
 
array
design
name
 
platform
type:
in
situ
synthesized,
spotted
or
other
 
surface
and
coating
specification
 
physical
dimensions
of
array
support
(
e.
g.
of
slide)
 
number
of
features
on
the
array
 
availability
(
e.
g.,
for
commercial
arrays)
or
production
protocol
for
custom
made
arrays
2a)
For
each
reporter
type
 
the
type
of
the
reporter:
synthetic
oligo­
nucleotides,
PCR
products,
plasmids,
colonies,
other
 
single
or
double
stranded
2b)
For
each
reporter
5
 
sequence
or
PCR
primer
information:
 
sequence
or
a
reference
sequence
(
e.
g.,
for
oligonucleotides),
if
known
 
sequence
accession
number
in
DDBJ/
EMBL/
GenBank,
if
exists
 
primer
pair
information,
if
relevant
 
approximate
lengths
if
exact
sequence
not
known
 
clone
information,
if
relevant
(
clone
ID,
clone
provider,
date,
availability)
 
element
generation
protocol
that
includes
sufficient
information
to
reproduce
the
element
for
custom­
made
arrays
that
are
not
generally
available
3a)
For
each
feature
type
 
dimensions
 
attachment
(
covalent/
ionic/
other)
 
technology
used
to
generate
the
feature
3b)
For
each
feature
 
which
reporter
and
the
location
on
the
array
4)
For
each
composite
sequence
 
which
reporters
it
contains
 
the
reference
sequence
 
gene
name
and
links
to
appropriate
databases
(
e.
g.,
SWISS­
PROT,
or
organism
specific
databases),
if
known
and
relevant
5)
Control
elements
on
the
array
 
position
of
the
feature
(
the
abstract
coordinate
on
the
array)
 
control
type
(
spiking,
normalization,
negative,
positive)
 
control
qualifier
(
endogenous,
exogenous)

For
each
array
that
is
not
generally
available
(
e.
g.,
commercially
available),
the
provided
information
should
be
sufficient
to
reproduce
the
array
and
all
its
design
features.

Experiment
description
By
experiment
MIAME
refers
to
a
set
of
one
or
more
hybridizations
that
are
in
some
way
related
(
e.
g.,
related
to
the
same
publication
or
the
same
study).
The
minimum
information
for
a
toxicogenomic
experiment
includes
a
description
of
the
following
five
parts.

1.
Toxicogenomic
experimental
design
2.
Biological
materials
used,
extract
preparation
and
labeling,
toxicological
assays.
3.
Hybridization
procedures
and
parameters
4.
Gene
expression
measurement
data
and
6
5.
Specifications
of
data
processing
Note:
A
potentially
reusable
part
of
the
experiment
description
is
`
laboratory
protocols,'
including
data
processing
methods
(
e.
g.,
normalization).
MIAME
encourages
the
user
to
assign
unique
identifiers
to
all
reusable
parts
of
the
experiment
description
and
to
reference
these
when
the
respective
parts
are
reused
(
indicating
any
deviations).
A
standard
for
the
description
of
protocols,
including
the
data
transformation
protocols
is
being
developed
by
the
MGED
Society
[
19];

MIAME/
Tox
recommends
the
following
details
on
each
of
these
sections.

1.
Toxicogenomic
experimental
design
This
section
is
common
to
all
hybridizations
performed
in
the
toxicogenomic
experiment,
such
as
the
goal,
brief
description,
experimental
factors
tested.
The
following
information
is
included
in
the
experimental
design.

1.1
Authors,
laboratory,
contact
1.2
Type
of
the
experiment
for
instance:
 
Acute,
pre­
chronic
or
chronic
treatment
 
multiple
tissue
comparison
 
temperature
shock
 
biomarker
identification
 
normal
vs.
diseased
comparison
 
treated
vs.
untreated
comparison
 
time
course
 
dose
response
 
effect
of
gene
knock­
out
 
effect
of
gene
knock­
in
(
transgenics)
 
other.

(
Note
that
multiple
types
are
possible,
e.
g.
an
`
acute'
experiment
can
also
be
a
`
dose­
response'
type
if
multiple
doses
of
the
compound
are
tested)

Also,
see
http://
www.
mged.
org/
ontology
1.3
Experimental
factors,
i.
e.
organisms,
parameters
or
conditions
tested,
for
instance,
 
species
 
strain
 
sex
type
7
 
age
and
weight
 
cell
line
 
cell
type
 
developmental
stage
 
disease
state
 
genotype
 
protocol
 
route
of
exposure
 
temperature
 
time
of
treatments
and
observations
 
dose(
s)
in
standard
units
 
genetic
variation
 
response
to
a
treatment
or
compound
 
other.

Also,
see
http://
www.
mged.
org/
ontology
1.4
How
many
hybridizations
in
the
experiment?

1.5
If
a
common
(
standard)
reference
material
used
for
all
hybridizations
1.6
Quality
control
steps
taken:
 
Replicates
done
(
yes/
no),
type
of
replicates,
description
 
biological
 
technical
 
if
pools
of
extracts
(
yes/
no)
were
used
versus
extracts
from
individual
samples,
description
 
whether
dye
swap
is
used
(
only
for
two
channel
platforms)
 
other
(
e.
g.,
polyA
tails,
low
complexity
regions,
unspecific
binding)
 
other.

Also,
see
http://
www.
mged.
org/
ontology
1.7
A
brief
description
of
the
experiment
and
its
goal
and
a
link
to
a
publication
if
one
exists
1.8
Links
(
URL),
citations
2.
Biological
materials
used,
extract
preparation
and
labeling,
toxicological
assays.

By
biological
material
(
sample)
MIAME/
Tox
refers
to
the
material
used
in
toxicological
investigations
and
from
which
the
nucleic
acids
were
extracted
for
subsequent
labelling
and
hybridization,
and
toxicological
assays.
In
this
section
all
8
steps
that
precede
the
hybridization
with
the
array
are
described.
We
can
usually
distinguish
between:

Source
of
the
sample
(
biosource
properties);
Treatments
applied
to
the
samples
(
manipulations);
Toxicological
assessments;
Extract
preparation;
Extract
labelling;
and
Hybridization
controls.

The
use
of
terms
from
the
MGED
Ontology
is
highly
encouraged.

Here
below
we
list
the
most
essential
items
that
are
usually
needed.

2.1
Biosource
properties
 
organism
(
NCBI
taxonomy)
 
sample
source
provider
 
descriptors
relevant
to
the
particular
sample,
such
as
sex
age
weights
development
stage
organism
part
(
tissue)
of
the
organism's
anatomy
from
which
the
biological
material
is
derived
(
if
samples
are
cells)
cell
type
animal/
plant
strain
or
line
genetic
variation
(
e.
g.,
gene
knockout,
transgenic
variation)
individual
genetic
characteristics
(
e.
g.,
disease
alleles,
polymorphisms)
disease
state
or
normal
additional
clinical
information
available
(
link)
an
individual
identifier
(
for
interrelation
of
the
biological
materials
in
the
experiment)

For
recommendations
on
controlled
vocabularies
that
can
be
used
see
http://
www.
mged.
org/
ontology
2.2
Sample
manipulations:
laboratory
protocols
and
relevant
parameters,
such
as:
 
facilities
details
 
animal
husbandry
and
housing
details
 
cell
culture
conditions
 
growth
conditions
(
passage
level
and
frequency)
 
metabolic
competency
of
cell
strains
 
treatment
(
stressor),
in
vivo,
in
vitro
9
 
treatment
type
(
e.
g.,
compound,
small
molecule,
heat
shock,
cold
shock,
food
deprivation,
diet)
 
treatment
compound
name
and
grade
formulation,
including
manufacturer
 
type
of
compound
(
e.
g.
chemical,
drug
or
solvent)
 
CASRN,
chemical
structure/
molecular
formula
 
vehicle
for
chemical
treatment
 
exposure
method
(
route
of
administration,
e.
g.
oral,
gavage,
mucolar,
medium,
intraperitoneal,
intramuscular,
intravenous,
topical)
 
duration
 
dose
(
and
unit)
 
separation
technique,
for
tissues
or
cells
from
a
heterogeneous
sample
(
e.
g.,
none,
trimming,
microdissection,
FACS)
 
date/
time
at
death
or
at
sacrifice
 
sacrifice
method
For
recommendations
on
controlled
vocabularies
that
can
be
used
see
http://
www.
mged.
org/
ontology
2.3.
Toxicological
assessments:
laboratory
protocols
and
relevant
parameters
measured
and
data
files
e.
g.,

Clinical
observations
 
weight
 
survival
(
yes/
no)
 
signs
(
e.
g.,
general,
behavior)
 
site
of
application
 
lesions
 
color
effects
 
other
Gross
necropsy
examination
 
organs
and
tissues
examination
list
 
organs
and
tissues
collection
list
 
organs
and
tissues
weight
list
 
organs
and
tissues
storage
method
and
location
Histopathology
evaluation
 
which
biological
materials
(
control
and
experimental)
 
slide
preparation,
storage
method
and
location
 
topography
(
definite
anatomical
region)
 
system
 
organ
 
sites
 
cell
type(
s)
10
 
morphology(
s)
 
qualifier(
s)
for
the
morphology(
s)

Clinical
pathology
 
hematology
(
e.
g.,
erythrocyte
count,
mean
corpuscular
volume,
hemoglobin)
 
clinical
chemistry
(
e.
g.,
sorbitol
dehydrogenase
(
SDH),
alkaline
phosphatase
(
ALP),
creatine
kinase
(
CK))
 
other
parameters
measured,
e.
g.,
sperm
morphology
and
vaginal
cytology
evaluation
(
SMVCE)
 
estrous
cycle
length
 
micronucleated
erythrocytes
determination
 
functional
observation
battery
 
other.

For
recommendations
on
controlled
vocabularies
to
be
used,
see
http://
www.
mged.
org/
ontology.

Note:
Understanding
the
historical
measures
made
at
a
given
institution
may
help
standardize
data
and
improve
comparisons.
The
medical
community
uses
the
INR
value
(
international
normalized
ratio)
in
some
cases
to
compare
data
from
different
clinical
labs.
This
is
the
ratio
of
experimental
finding
for
the
patient
compared
to
standard
values
obtained
in
the
same
lab.
Microarray
data
are
reported
as
ratios
from
dual
channel
experiments
and
as
intensity
values
from
oligonucleotide
arrays.
Clinical
data
should
be
reported
in
comparable
ways
so
that
patterns
can
be
detected,
e.
g.,
the
clinical
data
may
be
compared
to
historical
values,
or
to
control
values
for
the
particular
study.
In
either
case,
defining
the
standard
for
comparison
is
important.

2.4
Hybridization
extract
preparation
protocol
for
each
extract
prepared
from
the
biological
material,
including
 
extraction
method
 
whether
total
RNA,
mRNA,
or
genomic
DNA
is
extracted
 
amplification
(
RNA
polymerases,
PCR)

2.5
Labeling
protocol
for
each
labeling
prepared
from
the
extract,
including
 
amount
of
nucleic
acids
labeled
 
label
used
(
e.
g.,
A­
Cy3,
G­
Cy5,
33P,
 .)
 
label
incorporation
method
 
Facility
details
(
if
this
part
of
the
experiments
has
been
carried
out
in
facility
different
from
the
sample
treatment
and
toxicological
assessments
steps
above,
e.
g.
consortium,
contracting
out.

2.6
External
controls
added
to
hybridization
extract(
s)
(
spiking
controls)
 
element
on
array
expected
to
hybridize
to
spiking
control
11
 
spike
type
(
e.
g.,
oligonucleotide,
plasmid
DNA,
transcript)
 
spike
qualifier
(
e.
g.,
concentration,
expected
ratio,
labelling
methods
if
different
than
that
of
the
extract)

3.
Hybridization
procedures
and
parameters
Each
hybridization
description
should
include
information
about
which
labelled
extract
(
related
to
which
biological
material,
which
extract)
and
which
array
(
e.
g.,
array
design,
batch
and
serial
number)
has
been
used
in
the
experiment;
and
the
hybridization
protocol,
normally
including:
 
the
solution
(
e.
g.,
concentration
of
solutes)
 
blocking
agent
 
wash
procedure
 
quantity
of
labeled
target
used
 
time,
concentration,
volume,
temperature
 
description
of
the
hybridization
instruments
4.
Measurement
data
and
specifications
of
data
processing
We
distinguish
between
three
levels
of
data
processing
 
raw
data
(
images),
image
quantitations
and
gene
expression
data
matrix.
Each
hybridization
has
at
least
one
image,
each
image
has
a
corresponding
image
quantitation
table,
where
a
row
represents
an
array
design
element
and
a
column
to
a
different
quantitation
types,
such
as
mean
or
median
pixel
intensity.
Several
quantitation
tables
can
be
combined
using
data
processing
metrics
to
obtain
the
`
final'
gene
expression
measurement
table
associated
with
the
experiment.
12
1)
Raw
data
description
should
include
 
for
each
scan
laboratory
protocol
for
scanning,
including
scanning
hardware
and
software,
scan
parameters,
including
laser
power,
spatial
resolution,
pixel
space,
PMT
voltage;
 
scanned
images;
It
should
be
noted
that
MGED
does
not
have
consensus
whether
the
provision
of
images
is
a
part
of
MIAME.

2)
Image
analysis
and
quantitation
 
image
analysis
software
specification
and
version,
availability,
and
the
description
or
identification
of
the
algorithm
and
all
the
parameters
used
 
for
each
image
the
complete
image
analysis
output
(
of
the
particular
image
analysis
software)

3)
Normalized
and
summarized
data
 
gene
expression
data
matrix
data
processing
protocol,
including
normalization
algorithm
(
for
detailed
recommendations,
see
http://
www.
mged.
org/
normalization)
gene
expression
data
table(
s)
derived
from
the
experiment
as
the
whole,
derived
measurement
value
summarizing
related
elements
and
replicates
as
used
by
the
author
(
this
may
constitute
replicates
of
the
element
on
the
same
or
different
arrays
or
hybridizations,
as
well
as
different
elements
related
to
the
same
entity
e.
g.,
gene)
providing
a
reliability
indicator
for
each
data
point
(
e.
g.,
standard
deviation)
is
encouraged.
Note
that
toxicology
data
may
also
be
normalized
to
signal­,
fold­
change
ratios
to
facilitate
comparison
to
similarly­
expressed
microarray
data
(
especially
when
2­
fluor
labelling
has
been
used).

This
ends
the
experiment
description.

MIAME/
Tox
is
continuously
developing
in
accordance
with
our
understanding
of
microarray
technology
and
its
applications
to
toxicology.
Please
join
the
MIAME/
Tox
discussion
list
(
mged­
toxico@
lists.
sourceforge.
net,
to
subscribe:
http://
lists.
sourceforge.
net/
lists/
listinfo/
mged­
toxico)
and
contribute
with
your
ideas
and
comments.
13
References
[
1]
MIAME
1.1:
http://
www.
mged.
org/
Workgroups/
MIAME/
miame_
1.1.
html
[
2]
MGED
Society:
http://
www.
mged.
org
[
3]
Brazma
A
et
al.
(
2001).
Minimum
information
about
a
microarray
experiment
(
MIAME)
­
toward
standards
for
microarray
data.
Nature
Genetics,
29,
365­
371.
[
4]
MAGE
Adopted
Specification:
http://
www.
omg.
org/
techprocess/
meetings/
schedule/
Gene_
Expression_
RFP.
html
[
5]
Rosetta
Biosoftware:
http://
www.
rosettabio.
com/
home.
html
[
6]
OMG:
http://
www.
omg.
org
[
7]
Spellman
PT
et
al.
(
2002).
Design
and
implementation
of
microarray
gene
expression
markup
language
(
MAGE­
ML).
Genome
Biology,
3(
9),
research
0046.1­
0046.9.
[
8]
Microarray
standards
at
last.
Nature
2002
419:
323.
[
9]
Ball
CA
et
al.
(
2002).
An
open
letter
to
the
scientific
journals.
Science,
298(
5593):
539.
Bioinformatics,
18(
11):
1409.
The
Lancet,
360:
1019.
[
10]
Brazma
A
et
al.
(
2003)
ArrayExpress
 
a
Public
Repository
for
Microarray
Gene
Expression
Data
at
the
EBI
(
2003).
Nucleic
Acids
Res
31
(
1):
68­
71.
[
11]
Edgar
R
et
al.
(
2002)
Gene
Expression
Omnibus:
NCBI
gene
expression
and
hybridization
array
data
repository.
Nucleic
Acids
Research,
30(
1),
207­
210.
[
12]
NIEHS
NCT:
http://
www.
niehs.
nih.
gov/
nct/
[
13]
EMBL
EBI
Microarray
Informatics:
http://
www.
ebi.
ac.
uk/
microarray/
index.
html
[
14]
ILSI
HESI:
http://
hesi.
ilsi.
org/
[
15]
The
Proteomics
Standards
Initiative
(
PSI):
http://
psidev.
sourceforge.
net/
[
16]
Stoeckert
CJ
et
al.
(
2002).
Microarray
databases:
standards
and
ontologies.
Nature
Genetics,
32
Suppl:
469­
73.
[
17]
MGED
Society
­
Ontology:
http://
www.
mged.
org/
ontology
[
18]
GOBO:
http://
www.
geneontology.
org/
doc/
gobo.
html
[
19]
MGED
Society
­
Normalization:
http://
www.
mged.
org/
normalisation
14
MIAME/
Tox
Glossary
MIAME/
Tox
requirements
are
listed
in
alphabetical
order
and
definitions
are
provided.

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).
There
are
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
and
version
for
the
array
design,
that
helps
to
identify
a
design
between
others
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)

Biological
material
(
sample)
The
source
material,
on
which
the
toxicological
investigations
have
been
carried
out
and
from
which
the
nucleic
acids
have
been
extracted
for
subsequent
labelling
and
hybridization,
and
toxicological
assays.

Biosource
properties
Information
on
the
source
of
the
biological
material
(
e.
g.
organism,
sample
provider,
sex,
age,
weights
or
cell
type,
cell
line)

Clinical
observation
Clinical
pathology
Examination
of
body
tissues
and
fluids
derived
from
the
sample
by
chemical,
physical,
microbiological
and
immunological,
methods
Clone
information
For
each
reporter,
the
identity
of
the
clone
along
with
information
on
the
clone
provider,
the
date
obtained,
and
availability
Common
(
standard)
reference
material
Composite
sequence
The
set
of
reporters
used
collectively
to
measure
an
expression
of
a
particular
gene,
exon,
or
splicevariant
Control
elements
(
array)
Array
elements
that
have
an
expected
value
and/
or
are
used
for
normalization
Control
qualifier
(
array)
Terms
used
to
further
define
a
control
element
(
e.
g.
endogenous,
exogenous)

Control
type
(
array)
The
type
of
control
used
for
the
normalization
(
e.
g.
spiking,
normalization,
negative,
positive)

Dimensions
(
feature)
The
physical
dimensions
of
each
features
15
Element
(
array)
There
are
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)

Element
generation
protocol
A
description
of
how
the
reporters
were
generated
Experiment
A
set
of
one
or
more
hybridizations
that
are
in
some
way
related
(
e.
g.,
related
to
the
same
publication
or
study).

Experimental
factor
Parameter
or
condition
tested
in
the
experiment
(
e.
g.
route
of
exposure,
temperature,
time,
dose)

Extraction
method
Documentation
of
the
set
of
steps
taken
to
extract
nucleic
acids
from
the
biological
material
Feature
(
array)
A
specific
instance
of
a
reporter
located
on
an
array,
commonly
referred
to
as
a
spot.

Final
gene
expression
table
(
s)
Derived
measurement
value
summarizing
related
elements
and
replicates,
providing
the
type
of
reliability
indicator
used
Gross
necropsy
examination
Post­
mortem
examination
of
the
organs
and
body
tissue
to
determine
cause
of
death
or
pathological
condition
Hybridization
The
process
of
treating
an
array
with
one
or
more
labelled
extracts
under
a
specified
set
of
conditions
Hybridization
extract
preparation
Information
on
the
extract
preparation
for
each
extract
prepared
from
the
sample,
the
type
of
extract
(
e.
g.

total
RNA,
mRNA)
and
the
amplification
method
used
(
e.
g.
RNA
polymerases,
PCR)

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
Image
analysis
and
quantitation
Each
image
has
a
corresponding
image
analysis
output
from
the
particular
image
analysis
software.
In
an
image
quantitation
table
a
row
represents
a
array
design
element
and
a
column
correspond
to
a
different
quantitation
types
(
e.
g.
mean
or
median
pixel
intensity).
This
has
an
associated
image
analysis
protocol,

the
set
of
steps
taken
to
quantify
the
image
including:
the
image
analysis
software,
the
algorithm
and
all
the
parameters
used
Label
incorporation
method
The
method
used
to
incorporate
the
label
into
the
extracts
Label
used
The
type
of
the
label
used
(
e.
g.
A­
Cy3,
G­
Cy5,
33P)

Location
(
feature)
The
abstract
coordinate
of
each
features
on
the
array
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.
This
has
an
associated
data
processing
protocol,
including
normalization
algorithm
and
a
reliability
indicator
for
each
data
point
(
e.
g.,
standard
deviation).
Toxicology
data
may
also
be
normalized
to
signal­,
fold­

change
ratios
to
facilitate
comparison
to
similarly­
expressed
microarray
data
especially
for
two
channel
16
experiments
Numerical
biological
endpoint
data
Biological
endpoint
with
quantitative
measurements
(
e.
g.
clinical
pathology)

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

Platform
type
(
array)
The
technology
type
used
to
place
the
biological
sequence
on
the
array
Position
(
control
elements)
The
abstract
coordinate
of
each
the
control
features
on
the
array
Primer
information
For
each
reporter,
PCR
primers
pair
sequence
and
length
Production
protocol
(
array)
A
description
of
how
the
custom
made
array
was
manufactured
Qualifier,
value,
source
Describe
any
further
information
about
the
array
or
an
experiment
in
a
structured
manner
Quality
control
steps
Measures
taken
to
ensure
or
measure
quality,
e.
g.,
dye
swap
(
for
two
channel
platforms),
biological
replicate
(
samples
taken
from
more
than
one
organism),
technical
replicate
(
same
biological
material
hybridized
to
more
than
one
array).

Raw
data
Each
hybridization
has
at
least
one
image
and
associated
laboratory
protocol
for
scanning,
hardware
and
software,
scan
parameters
(
including
laser
power,
spatial
resolution,
pixel
space
and
PMT
voltage)

Reference
sequence
(
reporter)
The
sequence
from
which
the
reporter
(
e.
g.
oligo­
nucleotides)
have
been
derived
Reporter
The
nucleotide
sequence
present
in
a
feature.
The
same
reporter
can
be
also
used
at
multiple
features
to
generate
replicate
measurements.

Reporter
type
Physical
nature
of
the
reporter
(
e.
g.
PCR
product,
synthesized
oligo­
nucleotide,
plasmids,
colonies)

Scanner
image
file
The
TIFF
file
including
header
Sequence
information
(
reporter)
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

Single
or
double
stranded
(
reporter)
Whether
the
reporter
sequences
are
single
(
oligo­
nucleotide)
or
double
stranded
(
e.
g.
PCR
product)

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
(
hybridization)
External
controls
added
to
the
hybridization
extract
(
s)

Spiking
control
element
(
array)
Position
of
the
feature
(
s)
on
the
array
expected
to
hybridize
to
the
spiking
control
Surface
and
coating
specification
(
array)
Type
of
surface
and
name
for
the
type
of
coating
used
Textual
biological
endpoint
data
Biological
endpoint
with
nominal
measurements
(
e.
g.
clinical
observations
and
gross
necropsy
examination)

Toxicogenomics
experiment
description
MIAME/
Tox
distinguishes
between:
the
toxicogenomic
experiment
design
(
the
design,
purpose
common
to
all
hybridizations
performed
in
the
experiment
and
the
parameters),
the
biological
material
used
(
biological
material
characteristics,
the
extract
preparation
and
the
labelling
and
the
toxicological
assays),

the
hybridization
(
procedures
and
parameters)
and
the
gene
expression
data
(
measurements
and
17
specifications)

Toxicogenomics
experimental
design
Design
and
purpose
common
to
all
hybridizations
performed
in
the
experiment,
including
a
brief
description,
person(
s),
organization
(
s)
names
and
details,
type
of
the
experiment,
experimental
factors,

number
of
hybridizations,
quality
controls
and
link
to
a
publication.

Toxicological
assessments
Process
designed
to
determine
factors
contributing
to
the
possible
adverse
effects
of
a
treatment,

including
laboratory
protocols,
relevant
parameters
measured
and
data
files
for
numerical
biological
endpoint
and
textual
biological
endpoint
data
Type
of
experiment
A
controlled
vocabulary
that
classify
an
experiment
(
e.
g.
acute,
pre­
chronic,
chronic)