BrainML Model Repository

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View Structure:

Model	BrainML
Submitter	LNI Account
Version	Version 5 (2010/05/23)
Namespace	urn:bml/brainml.org:internal/BrainML/5
Comments	Moved elements that are related to computational analysis to Analysis model schema. The following elements and their components have been moved: analysis_input, analysis_output, and algorithm.
View	Structure Vocabulary (with IDs)

BrainML Model: "brainml"
This is a tabular description of the entities and fields making up the "brainml" data model. Regular expression notation is used to indicate quantities -- i.e., '?' following a term means 0 or 1 occurrence, '*' means 0 or more occurrences, '+' means 1 or more occurrences, and no following character means exactly 1 occurrence. Fields with names in (parentheses) are attributes in the XML; all others are subelements with text content. The term "ANY" under 'Contains:' means an element can contain any other element as content. This description is also available in XML format.
This schema specifies basic common elements that most BrainML schemas are expected to use and inherit from. Nothing is specific to a particular field of neuroscience. Included are: View and Trace definitions Basic recording site definitions Basic protocol definition Experiment definition
Depends on models: BrainMetaL, AnimalSubject
Index of Entities
condition
contributor
event_list_trace
experiment
histogram_prebin_trace
histogram_raw_trace
histogram_trace
histogram_view
piecewise_series_trace
protocol
recording_location
recording_site
recording_source
signal_channel
spike_train_trace
stimulus_nudge
subject_or_preparation
submitter
time_series_trace
time_series_view
time_trace
trace
trace_grouping
view
x_y_trace
x_y_view

trace_grouping Contains a set of links to traces forming a logical group.
container: experiment contains: link*
inherits: collection links: collection, trace
Field Type Description
(type) short text A short description of the grouping type, e.g. 'analysis' or 'simultaneous' etc..
(id) token
(name)? token Optional name for the collection.
(ordered)? boolean Order of contents may be ignored unless present and set to "true".
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trace Superclass Trace element. Do not use directly.
container: (none) contains: link*, dataset?, labeled_dataset?, datasetC?, datasetR?, datasetX?, datasetB?
inherits: data_element links: recording_site
Field Type Description
(seq) integer Order of this Trace relative to others in the same View.
(id)? token This attribute is needed so that others may link to it.
(base)? uri See http://www.w3.org/TR/xmlbase/ for information about this attribute.
label short text Short name/description of a View or Trace.
recording_technique? controlled Recording technique employed in collecting Trace.
data_class? controlled The nature of the data collected in Trace.
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recording_site Contains information on recording site (location and source).
container: experiment contains: link*, recording_location, recording_source?, subject_or_preparation?, subject?
inherits: entity_element links: subject_or_preparation, experiment
Field Type Description
(id)? token This attribute is needed so that others may link to it.
(base)? uri See http://www.w3.org/TR/xmlbase/ for information about this attribute.
identifier short text Short, unique, human-readable name or code that should be same as any references in published work.
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recording_location Description of the various recording locations.
container: recording_site contains: receptive_field*, motor_behavior*
inherits: (none) links: (none)
Field Type Description
neural_structure_or_anatomy? controlled Keywords describing brain or body location(s).
cytoarchitectural_area? controlled Cytoarchitectonic area recording site was found in (Brodmann scheme).
recording_layer? controlled Description of the recording layers.
cell_type? controlled Description of the cell types.
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recording_source Superclass for recording sources; do not use directly.
container: recording_site contains: ANY
inherits: (none) links: (none)
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subject_or_preparation Base entity for describing the subject or preparation in an experiment. Different models will extend this depending on what descriptors they require.
container: recording_site contains: link*
inherits: entity_element links: (none)
Field Type Description
(id)? token This attribute is needed so that others may link to it.
(base)? uri See http://www.w3.org/TR/xmlbase/ for information about this attribute.
identifier short text Short, unique, human-readable name or code that should be same as any references in published work.
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experiment Holds an entire submission.
container: (none) contains: link*, submitter*, contributor+, author*, citation*, protocol, recording_site+, view+, trace_grouping*, x_y_view*, histogram_view*, time_series_view*
inherits: data_element links: (none)
Field Type Description
(id)? token This attribute is needed so that others may link to it.
(base)? uri See http://www.w3.org/TR/xmlbase/ for information about this attribute.
label short text Short name/description of a View or Trace.
annotation long text Paragraph-length description of Experiment.
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submitter A person who signed in and submitted data.
container: experiment contains: link*
inherits: person_full links: experiment
Field Type Description
(id)? token This attribute is needed so that others may link to it.
(base)? uri See http://www.w3.org/TR/xmlbase/ for information about this attribute.
initials? short text Initials of name (use instead of first/middle).
first? short text First given name.
middle? short text Second and subsequent given names.
prelast? short text Prefix such as "van" or "von der".
last short text Surname.
lineage? short text Suffixes such as "Jr.", "III".
email short text Email address.
phone short text Phone number, including international dialing codes.
institution short text Institution or company where researcher works.
homepage? short text Home page of researcher, lab, or institution.
username token Account name (for submitters of data submissions).
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contributor A person contributing to a data submission.
container: experiment contains: link*
inherits: person links: experiment
Field Type Description
(id)? token This attribute is needed so that others may link to it.
(base)? uri See http://www.w3.org/TR/xmlbase/ for information about this attribute.
initials? short text Initials of name (use instead of first/middle).
first? short text First given name.
middle? short text Second and subsequent given names.
prelast? short text Prefix such as "van" or "von der".
last short text Surname.
lineage? short text Suffixes such as "Jr.", "III".
email? short text Email address.
phone? short text Phone number, including international dialing codes.
institution? short text Institution or company where researcher works.
homepage? short text Home page of researcher, lab, or institution.
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protocol Experimental protocol.
container: experiment contains: link*, stimulus_nudge*
inherits: method_element links: experiment
Field Type Description
(id)? token This attribute is needed so that others may link to it.
(base)? uri See http://www.w3.org/TR/xmlbase/ for information about this attribute.
preparation controlled Preparation type used in this Protocol.
description long text Short verbal description of Protocol.
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stimulus_nudge Holds details on subject preparation and response elicitation.
container: protocol contains: (none)
inherits: (none) links: (none)
Field Type Description
effector controlled The agent effecting one aspect of the Protocol.
pattern controlled The manner in which an agent acts to effect one aspect of the Protocol.
location controlled The locus at which an agent acts to effect one aspect of the Protocol.
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view Superclass View element. Do not use directly, but any View defined should declare itself in a substitution group with this.
container: experiment contains: link*
inherits: data_element links: recording_site
Field Type Description
(seq) integer Ordering position of this View within its containing experiment.
(id)? token This attribute is needed so that others may link to it.
(base)? uri See http://www.w3.org/TR/xmlbase/ for information about this attribute.
number_of_trials? integer Number of trials contributing to View or Histogram's data.
label short text Short name/description of a View or Trace.
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x_y_view View for containing X-Y (2-dimensional plot) data. Traces share common X- and Y-axis units.
container: experiment contains: link*, x_y_trace+
inherits: view links: recording_site
Field Type Description
(seq) integer Ordering position of this View within its containing experiment.
(id)? token This attribute is needed so that others may link to it.
(base)? uri See http://www.w3.org/TR/xmlbase/ for information about this attribute.
number_of_trials? integer Number of trials contributing to View or Histogram's data.
label short text Short name/description of a View or Trace.
horizontal_axis_units unit Unit of measure for horizontal axis (often a temporal unit).
horizontal_axis_label short text Short, informative label for horizontal axis.
vertical_axis_units unit Unit of measure for vertical axis (dependent variable).
vertical_axis_label short text Short, informative label for vertical axis.
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x_y_trace Bivariate trace consisting of a list of x- and y-values. Dataset 'dimensions' should have two values, the first indicating the number of data points in the trace (or *), the second indicating the size of each tuple. This should be 2 for plain (x,y) pairs, 3 for (x, y, y-error), 4 for (x, y, y-error, x-error). To use asymmetrical error bars, set second dimension to 6 and use the format (x, y, +y-error, -y-error, +x-error, -x-error).
container: x_y_view contains: link*, dataset?, labeled_dataset?, datasetC?, datasetR?, datasetX?, datasetB?
inherits: trace links: recording_site
Field Type Description
(seq) integer Order of this Trace relative to others in the same View.
(id)? token This attribute is needed so that others may link to it.
(base)? uri See http://www.w3.org/TR/xmlbase/ for information about this attribute.
label short text Short name/description of a View or Trace.
recording_technique? controlled Recording technique employed in collecting Trace.
data_class? controlled The nature of the data collected in Trace.
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histogram_view View for containing histogram data.
container: experiment contains: link*, histogram_trace+, histogram_prebin_trace*, histogram_raw_trace*
inherits: view links: recording_site
Field Type Description
(seq) integer Ordering position of this View within its containing experiment.
(id)? token This attribute is needed so that others may link to it.
(base)? uri See http://www.w3.org/TR/xmlbase/ for information about this attribute.
number_of_trials? integer Number of trials contributing to View or Histogram's data.
label short text Short name/description of a View or Trace.
horizontal_axis_units unit Unit of measure for horizontal axis (often a temporal unit).
horizontal_axis_label short text Short, informative label for horizontal axis.
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histogram_trace Superclass for histogram traces.
container: histogram_view contains: link*, dataset?, labeled_dataset?, datasetC?, datasetR?, datasetX?, datasetB?
inherits: trace links: recording_site
Field Type Description
(seq) integer Order of this Trace relative to others in the same View.
(id)? token This attribute is needed so that others may link to it.
(base)? uri See http://www.w3.org/TR/xmlbase/ for information about this attribute.
label short text Short name/description of a View or Trace.
recording_technique? controlled Recording technique employed in collecting Trace.
data_class? controlled The nature of the data collected in Trace.
number_of_trials integer Number of trials contributing to View or Histogram's data.
vertical_axis_label short text Short, informative label for vertical axis.
vertical_axis_type controlled Type of units reflected by bar height: 'probability', 'percentage', 'Hz', or 'count'.
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histogram_prebin_trace Prebinned histogram trace. Dataset 'dimensions' should have two values, the first indicating the number of data points in the trace (or *), the second indicating the size of each tuple, either 1 (value), 2 (value, +/- error), or 3 (value, + error, - error).
container: histogram_view contains: link*, dataset?, labeled_dataset?, datasetC?, datasetR?, datasetX?, datasetB?
inherits: histogram_trace links: recording_site
Field Type Description
(seq) integer Order of this Trace relative to others in the same View.
(id)? token This attribute is needed so that others may link to it.
(base)? uri See http://www.w3.org/TR/xmlbase/ for information about this attribute.
label short text Short name/description of a View or Trace.
recording_technique? controlled Recording technique employed in collecting Trace.
data_class? controlled The nature of the data collected in Trace.
number_of_trials integer Number of trials contributing to View or Histogram's data.
vertical_axis_label short text Short, informative label for vertical axis.
vertical_axis_type controlled Type of units reflected by bar height: 'probability', 'percentage', 'Hz', or 'count'.
bin_start floating point First bin center for Histogram (in H-axis units).
bin_width floating point Width of bin in Histogram (in H-axis units).
number_of_bins? integer Number of bins in Histogram.
min_max_are_ranges boolean Whether or not the first and last bar heights reflect measurement including h-axis values less than min or greater than max.
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histogram_raw_trace Raw histogram trace that the end-consumer selects bin size for. The values provided here are raw values (e.g., the list of times after a marker that spikes occurred). The binning process counts up the numbers of values within each range.
container: histogram_view contains: link*, dataset?, labeled_dataset?, datasetC?, datasetR?, datasetX?, datasetB?
inherits: histogram_trace links: recording_site
Field Type Description
(seq) integer Order of this Trace relative to others in the same View.
(id)? token This attribute is needed so that others may link to it.
(base)? uri See http://www.w3.org/TR/xmlbase/ for information about this attribute.
label short text Short name/description of a View or Trace.
recording_technique? controlled Recording technique employed in collecting Trace.
data_class? controlled The nature of the data collected in Trace.
number_of_trials integer Number of trials contributing to View or Histogram's data.
vertical_axis_label short text Short, informative label for vertical axis.
vertical_axis_type controlled Type of units reflected by bar height: 'probability', 'percentage', 'Hz', or 'count'.
min_value? floating point Minimum h-axis value in raw histogram.
max_value? floating point maximum h-axis value in a raw histogram.
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time_series_view View for containing time-series data.
container: experiment contains: link*, time_trace+, event_list_trace*, time_series_trace*, spike_train_trace*, piecewise_series_trace*
inherits: view links: recording_site
Field Type Description
(seq) integer Ordering position of this View within its containing experiment.
(id)? token This attribute is needed so that others may link to it.
(base)? uri See http://www.w3.org/TR/xmlbase/ for information about this attribute.
number_of_trials? integer Number of trials contributing to View or Histogram's data.
label short text Short name/description of a View or Trace.
horizontal_axis_units unit Unit of measure for horizontal axis (often a temporal unit).
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time_trace Superclass with common elements of all traces valid in time series view.
container: time_series_view contains: link*, dataset?, labeled_dataset?, datasetC?, datasetR?, datasetX?, datasetB?
inherits: trace links: recording_site
Field Type Description
(seq) integer Order of this Trace relative to others in the same View.
(id)? token This attribute is needed so that others may link to it.
(base)? uri See http://www.w3.org/TR/xmlbase/ for information about this attribute.
label short text Short name/description of a View or Trace.
recording_technique? controlled Recording technique employed in collecting Trace.
data_class? controlled The nature of the data collected in Trace.
t_start floating point Recording start time for Trace.
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event_list_trace Trace consisting of a list of event times and describing labels. These labels may be either strings, integers, or decimal values. Data should be contained in a 'labeled_dataset' element, whose first child is a decimal type dataset, and whose second child is a dataset of any type.
container: time_series_view contains: link*, dataset?, labeled_dataset?, datasetC?, datasetR?, datasetX?, datasetB?
inherits: time_trace links: trace, recording_site
Field Type Description
(seq) integer Order of this Trace relative to others in the same View.
(id)? token This attribute is needed so that others may link to it.
(base)? uri See http://www.w3.org/TR/xmlbase/ for information about this attribute.
label short text Short name/description of a View or Trace.
recording_technique? controlled Recording technique employed in collecting Trace.
data_class? controlled The nature of the data collected in Trace.
t_start floating point Recording start time for Trace.
t_end floating point Recording end time for Trace.
stimulus boolean Indication of whether Trace represents stimulus signal or neuron response.
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time_series_trace Trace consisting of a regularly-sampled list of data values.
container: time_series_view contains: link*, dataset?, labeled_dataset?, datasetC?, datasetR?, datasetX?, datasetB?
inherits: time_trace links: recording_site
Field Type Description
(seq) integer Order of this Trace relative to others in the same View.
(id)? token This attribute is needed so that others may link to it.
(base)? uri See http://www.w3.org/TR/xmlbase/ for information about this attribute.
label short text Short name/description of a View or Trace.
recording_technique? controlled Recording technique employed in collecting Trace.
data_class? controlled The nature of the data collected in Trace.
t_start floating point Recording start time for Trace.
t_rate floating point Trace sampling rate, in units of horizontal axis.
stimulus boolean Indication of whether Trace represents stimulus signal or neuron response.
vertical_axis_units unit Unit of measure for vertical axis (dependent variable).
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spike_train_trace Trace consisting of a list of event times at which spikes occurred.
container: time_series_view contains: link*, dataset?, labeled_dataset?, datasetC?, datasetR?, datasetX?, datasetB?
inherits: time_trace links: recording_site
Field Type Description
(seq) integer Order of this Trace relative to others in the same View.
(id)? token This attribute is needed so that others may link to it.
(base)? uri See http://www.w3.org/TR/xmlbase/ for information about this attribute.
label short text Short name/description of a View or Trace.
recording_technique? controlled Recording technique employed in collecting Trace.
data_class? controlled The nature of the data collected in Trace.
t_start floating point Recording start time for Trace.
t_end floating point Recording end time for Trace.
stimulus? boolean Indication of whether Trace represents stimulus signal or neuron response.
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piecewise_series_trace The piecewise_series trace is a time series in which flat or linear sections are encoded compactly. The data consists of a list of segments. Each segment starts with a type code and a duration. Type code may be 1, indicating a constant-value segment, 2, indicating a linear segment, 3, indicating a normal (fully-specified) segment, or 4, indicating an empty segment (gap). The duration is an integer count indicating the number of samples specified by this segment. For constant-value segments, the next number is the constant value to be held for this segment. For linear segments, the next number is the final value this segment reaches at the end of its duration. The values before it are to be interpolated linearly starting from the value of the series just before the linear segment begins. (A linear segment cannot begin a piecewise series -- use a length-0 constant-value segment to indicate the starting value if needed.) For type 3 segments, the next duration numbers are the actual samples for this segment. For type 4 segments, there are no numbers following the duration. Instead, the time series is understood to have no values (not been recorded) for the given duration.
container: time_series_view contains: link*, dataset?, labeled_dataset?, datasetC?, datasetR?, datasetX?, datasetB?
inherits: time_series_trace links: recording_site
Field Type Description
(seq) integer Order of this Trace relative to others in the same View.
(id)? token This attribute is needed so that others may link to it.
(base)? uri See http://www.w3.org/TR/xmlbase/ for information about this attribute.
label short text Short name/description of a View or Trace.
recording_technique? controlled Recording technique employed in collecting Trace.
data_class? controlled The nature of the data collected in Trace.
t_start floating point Recording start time for Trace.
t_rate floating point Trace sampling rate, in units of horizontal axis.
stimulus boolean Indication of whether Trace represents stimulus signal or neuron response.
vertical_axis_units unit Unit of measure for vertical axis (dependent variable).
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signal_channel Represents a channel containing a data stream recorded from some source, such as a neuron, or a stimulus variable.
container: (none) contains: (none)
inherits: (none) links: (none)
Field Type Description
(id) token Unique identifier for the channel.
(seq) integer Sequence number for the channel, out of its group.
(name) token Short, precise, descriptive name for the channel.
(units) token Units for the channel's values. Note this is not controlled in the way units generally are in BrainML (based on the BrainMetaL 'unit' type), but a plain string.
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condition Experimental condition. This is a generic structure for holding information about the conditions under which data is collected that is not otherwise represented in the data model. This provides a dimension of flexibility to allow recording of information not anticipated at the time of data model construction, however it is generally best to avoid use of this facility when possible because it prevents standardization on descriptors used. This makes data more difficult to search for and link to data in other databases.
container: (none) contains: link*
inherits: method_element links: (none)
Field Type Description
(name) short text A short descriptive name of what this condition represents.
(type) token Data type for this condition's value: either 'numeric' or 'text'.
(value) short text Value for the experimental condition. Should follow 'type'.
(units)? token For numeric condition values that represent measured quantities, specify the units. Note this is not controlled in the way units generally are in BrainML (based on the BrainMetaL 'unit' type), but a plain string.
(id)? token This attribute is needed so that others may link to it.
(base)? uri See http://www.w3.org/TR/xmlbase/ for information about this attribute.
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Weill Medical College of Cornell University