|
|
Description |
MAML
Data format |
When
applicable |
Dependencies |
Allowed
values |
|
Experimental Design
Concepts |
Overview of the
experimental study. |
|
|
|
|
|
Author, laboratory,
and links |
Submitter and
laborarory name of the MIAME. Also any associated URLs |
contact |
Always |
Referenced by
creation_info |
Contact element attribute
list |
|
Contact information |
Name, address, phone,
FAX, email of person to contact. May be different from submitter |
contact |
Always |
Referenced by
experiment_set? |
Contact element
attribute list |
|
Experiment type |
The general kind of
problem that the experiments are designed to address. |
Experiment_set
attributes: type and other_type. Handle more than
one? |
Always |
Should be consistent
with experimental factors. |
experiment_set: type = time_course,
dose_response, single_hybridisation, disease_vs_normal, tissue_comparison,
other (treated_vs_untreated, shock, gene_knock-out, gene_knock-in) |
|
Experimental factors |
Factor(s) that is
varied between experiments. May be same as experiment type but need not be. |
Experimental_factors |
Always |
Referenced by
experiment_design which in turn is referenced by experiment_set |
One or more text
terms. time, dose, genetic
variation, response to treatment or compound, severity, location MGED controlled
vocab? |
|
Platforms used |
The type(s) of
array(s) used. |
possibly contained
in array_definition: description |
Always |
Should be consistent
with Array Design concepts. |
In-house, commercial; filter array (macroarray, membranes), lithographic oligo microarray (Affymetrix), cDNA microarray (attached to glass slides; 2-color fluorescence), oligo array (attached to slide after synthesis; 2-color fluorescence) MGED controlled vocab? |
|
Single or multiple hybridisations |
Establish whether
relationships between hybridisations are needed. Note that one 2-color array
experiment is a single hybridisation. |
Inferred from
hybridisation_list |
Always |
Should be consistent
with experiment type. I.e., not single if type = time_course or dose_response
|
Single, multiple |
|
Ordered/ unordered (what
if both? Describe separately?) |
The order of the data
from the multiple hybridisations is important. |
Inferred from
experiment_set: type possibly contained
in biology_description |
Multiple
hybridisations |
Must be multiple
hybridisation |
Ordered, unordered |
|
Serial |
The hybridisations
were done using sources sampled at successive regular intervals. |
possibly contained
in biology_description |
Multiple
hybridisations |
Ordered |
Yes, no |
|
Serial type |
The meaning of the
serial nature of the hybridisations. |
Experiment_set
attributes: type and other_type. |
Serial = yes |
Should be consistent
with experiment type. |
Time_course,
dose_response |
|
Grouping |
The hybridisations can
be divided up into meaningful groups |
None |
Multiple
hybridisations |
Unordered (apply to
ordered data?) |
Yes, no |
|
Grouping type |
The meaning of the
groups. |
Experiment_set
attributes: type and other_type. |
Grouping = yes |
Should be consistent
with experiment type. |
treatment, disease,
knock-out, knock-in, shock, multiple tissue comparison, other |
|
Sample and arrays list |
The relationships of
each sample and array to each other. |
Biology_description? |
Always |
Should be consistent
with platforms used; single, multiple hybridisations; ordered/ unordered;
serial; grouping; replicates. The element
hybridization references labelled_extract (the ultimate derived sample).
derived_sample references other derived_samples and primary_sample. |
Each sample and each
array are assigned an (unique) ID. A matrix of IDs should be provided
indicating which sample IDs were used on which array IDs. |
|
Replicates |
Hybridisations done
using the same samples. |
replicate_info |
Multiple
hybridisations |
referenced by the
element: quality |
text description in
replicate_info; experimental_design: quality: has_replicates =
“true” |
|
Peer reviewed
publication |
A publication based on
the experimental study has been accepted in a peer-reviewed journal. |
publication |
When one exists |
experiment_set
references publication and experimental_design: quality |
publication: citation
or dbxref attribute list experimental_design:
quality: peer_reviewed = “true” |
|
Number of replicates |
The number (or range)
of times each sample has been replicated. |
can be put in
replicate_info |
Replicates were done |
Should be consistent
with sample and arrays list. referenced by the
element: quality |
Number of replicates
for each sample or minimum and maximum numbers of sample replicates. |
|
Other quality control
steps |
Other measures taken
to ensure or measure quality. |
quality_info |
When these have been
done |
referenced by the
element: quality |
text description in
quality_info |
|
Qualifier, value,
source (may use more than once) |
Describe any
further information about
the experiment set in a structured manner. |
Parameter (for
qualifier, value) Reference (for source) |
When additional
information is available that would be useful to base queries on. |
Should be consistent
with other values |
Qualifier=
parameter:name Value= parameter:value
Source=
reference:description, dbxref (ontology, dictionary, or controlled vocabulary
that terms were drawn from). |
|
Experiment set
description |
Describe any
further information about
the experiment set in free text.
|
biology_description; analysis_description |
When additional
information is available. |
Should be consistent
with other experiment_set and experiment_design elements and attributes |
Free text |
|
|
Description |
MAML
Data format |
When
applicable |
Dependencies |
Allowed
values |
|
Array design |
Description of each array used and each array element (spot). |
|
|
|
|
|
Array design name |
Submitter’s name for the array design (e.g., Stanford Human 10K set, lymphochip) |
Array_definition |
Always |
Should not be the same as other submitter’s names unless it is the same array design. Referenced by array_platform. References array_element_list. |
Array_definition attributes: model_name, version |
|
Platform type |
Indicator of whether the array is made by spotting or by in situ synthesis |
None |
Always |
Should be consistent with platforms used |
In situ synthesized, spotted |
|
Provider |
The manufacturer of the array. May be the submitter. |
contact
|
Always. |
Should be consistent with platforms used. Referenced by array_definition. |
Contact element attribute list. |
|
Surface type |
Example types are glass, membrane. |
Array_definition |
When array design is novel (i.e., cannot refer to
manufacturer). |
Should be consistent with platform type Referenced by array_platform. References array_element_list. |
Array_definition attribute: surface_type = glass,
membrane, other.(replaces absorptive, nonabsorptive) |
|
Surface type name |
A descriptive name such as “in-house coated EMBL slides” |
Array_definition |
When array design is novel (i.e., cannot refer to manufacturer). |
Surface type Referenced by array_platform. References array_element_list. |
Array_definition attribute: surface_type_name = brief text |
|
Array dimensions |
The length of each of the array’s two dimensions. |
Array_definition |
When array design is novel (i.e., cannot refer to manufacturer). |
Referenced by array_platform. References array_element_list. |
Array_definition attributes: short_axis_length, long_axis_length |
|
Number of array elements |
The number of
(composite) elements in the array. |
Array_definition |
When array design is novel (i.e., cannot refer to manufacturer). |
Referenced by array_platform. References array_element_list. |
Array_definition attribute: number_of_elements |
|
Reference system |
The arrangement and system used to specify the location for each element on the array. |
Array_element attributes: block, row, column?
|
When array design is novel (i.e., cannot refer to manufacturer). |
Should be consistent with array dimensions and number of array elements. Referenced by array_element_list. |
Type of element arrangement (e.g., grid, row, column) and numbering for each type. |
|
Provider ID |
A unique ID assigned by the manufacturer such as a serial number. |
Array_platform |
Always |
Should be consistent with samples and arrays list. References array_definition. |
Array_platform |
|
Production protocol |
A description of how the array was manufactured. Should include origin of reference system (e.g., upper left). |
Protocol |
When array design is novel (i.e., cannot refer to manufacturer). |
Should be consistent with reference system. Referenced by array_element_list. |
Protocol subelements and attributes. type = “array_printing” Hardware subelements and attributes. Type = “array_printer” |
|
Qualifier,
value, source (may use more than once) |
Describe
any further information
about the array in a structured manner.
|
Parameter
(for qualifier, value) Reference
(for source) |
When
additional information is available that would be useful to base queries on. |
Should be
consistent with other values Referenced
by array_definition. |
Qualifier=
parameter:name Value=
parameter:value Source=
reference:description, dbxref (ontology, dictionary, or controlled vocabulary
that terms were drawn from). |
|
Element position |
Location on the array that can be used to identify the element on an image of the array. |
Array_element |
When array design is novel (i.e., cannot refer to manufacturer). |
Should be consistent with reference system. |
Array_element attributes: block, row, column, x_microns, y_microns |
|
Element type |
Physical nature of the elements. |
Array_element_list |
When array design is novel (i.e., cannot refer to manufacturer). |
Should be consistent with platform type. |
Array_element_list attribute: derivation = empty, pcr, synthesized_oligo, intact_plasmid, colony, other |
|
Element clone information |
For each element, the identity of the clone along with information on the clone provider, the date obtained, and availability. |
Clone |
When elements are obtained from clones and when array design is novel (i.e., cannot refer to manufacturer). |
Should be consistent with element type. Referenced by array_element. |
Clone: db_xref and name attribute (identity); description (provider, date obtained, availability) |
|
Element sequence information |
The nucleotide sequence located at each element. |
Actual_sequence; reference sequence |
When elements are NOT composite and when array design is
novel (i.e., cannot refer to manufacturer) or when additional is available. |
Should be consistent with element type and clone. Referenced by array_element, also by clone and gene. |
actual_sequence and reference sequence subelements and attributes. Specify start and stop if use reference sequence. |
|
Composite element sequence information |
The number of distinct sequences in each composite element and the sequences. |
array_element: type = multiple_sequence |
When elements ARE composite and when array design is novel (i.e., cannot refer to manufacturer). |
Should be consistent with element type. |
inferred from number of actual_sequence and reference_sequences associated with an array_element. |
|
Single or double stranded |
Whether the element sequences are single or double stranded. |
Array_element_list |
When array design is novel (i.e., cannot refer to manufacturer). |
Should be consistent with element type. |
Array_element_list attribute: strandedness = single, double |
|
Element dimensions |
The physical dimensions of each element. |
Array_element_list |
When array design is novel (i.e., cannot refer to manufacturer). |
Should be consistent with array dimensions and number of array elements. |
Array_element_list attribute: diameter_target (implies
circle, why not 2 axes?) |
|
Nucleotide attachment |
How the element sequences are physically attached to the array. |
Array_element_list< |