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  View Structure:



Model BrainML
Submitter LNI Account
Version Version 5 (2009/11/05)
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


trace_groupingContains a set of links to traces forming a logical group.
container: experimentcontains: link*
inherits: collectionlinks: collection, trace
FieldTypeDescription
(type)short textA short description of the grouping type, e.g. 'analysis' or 'simultaneous' etc..
(id)token
(name)?tokenOptional name for the collection.
(ordered)?booleanOrder of contents may be ignored unless present and set to "true".
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traceSuperclass Trace element. Do not use directly.
container: (none)contains: link*, dataset?, labeled_dataset?, datasetC?, datasetR?, datasetX?, datasetB?
inherits: data_elementlinks: recording_site
FieldTypeDescription
(seq)integerOrder of this Trace relative to others in the same View.
(id)?tokenThis attribute is needed so that others may link to it.
(base)?uriSee http://www.w3.org/TR/xmlbase/ for information about this attribute.
labelshort textShort name/description of a View or Trace.
recording_technique?controlledRecording technique employed in collecting Trace.
data_class?controlledThe nature of the data collected in Trace.
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recording_siteContains information on recording site (location and source).
container: experimentcontains: link*, recording_location, recording_source?, subject_or_preparation?, subject?
inherits: entity_elementlinks: subject_or_preparation, experiment
FieldTypeDescription
(id)?tokenThis attribute is needed so that others may link to it.
(base)?uriSee http://www.w3.org/TR/xmlbase/ for information about this attribute.
identifiershort textShort, unique, human-readable name or code that should be same as any references in published work.
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recording_locationDescription of the various recording locations.
container: recording_sitecontains: receptive_field*, motor_behavior*
inherits: (none)links: (none)
FieldTypeDescription
neural_structure_or_anatomy?controlledKeywords describing brain or body location(s).
cytoarchitectural_area?controlledCytoarchitectonic area recording site was found in (Brodmann scheme).
recording_layer?controlledDescription of the recording layers.
cell_type?controlledDescription of the cell types.
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recording_sourceSuperclass for recording sources; do not use directly.
container: recording_sitecontains: ANY
inherits: (none)links: (none)
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subject_or_preparationBase entity for describing the subject or preparation in an experiment. Different models will extend this depending on what descriptors they require.
container: recording_sitecontains: link*
inherits: entity_elementlinks: (none)
FieldTypeDescription
(id)?tokenThis attribute is needed so that others may link to it.
(base)?uriSee http://www.w3.org/TR/xmlbase/ for information about this attribute.
identifiershort textShort, unique, human-readable name or code that should be same as any references in published work.
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experimentHolds 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_elementlinks: (none)
FieldTypeDescription
(id)?tokenThis attribute is needed so that others may link to it.
(base)?uriSee http://www.w3.org/TR/xmlbase/ for information about this attribute.
labelshort textShort name/description of a View or Trace.
annotationlong textParagraph-length description of Experiment.
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submitterA person who signed in and submitted data.
container: experimentcontains: link*
inherits: person_fulllinks: experiment
FieldTypeDescription
(id)?tokenThis attribute is needed so that others may link to it.
(base)?uriSee http://www.w3.org/TR/xmlbase/ for information about this attribute.
initials?short textInitials of name (use instead of first/middle).
first?short textFirst given name.
middle?short textSecond and subsequent given names.
prelast?short textPrefix such as "van" or "von der".
lastshort textSurname.
lineage?short textSuffixes such as "Jr.", "III".
emailshort textEmail address.
phoneshort textPhone number, including international dialing codes.
institutionshort textInstitution or company where researcher works.
homepage?short textHome page of researcher, lab, or institution.
usernametokenAccount name (for submitters of data submissions).
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contributorA person contributing to a data submission.
container: experimentcontains: link*
inherits: personlinks: experiment
FieldTypeDescription
(id)?tokenThis attribute is needed so that others may link to it.
(base)?uriSee http://www.w3.org/TR/xmlbase/ for information about this attribute.
initials?short textInitials of name (use instead of first/middle).
first?short textFirst given name.
middle?short textSecond and subsequent given names.
prelast?short textPrefix such as "van" or "von der".
lastshort textSurname.
lineage?short textSuffixes such as "Jr.", "III".
email?short textEmail address.
phone?short textPhone number, including international dialing codes.
institution?short textInstitution or company where researcher works.
homepage?short textHome page of researcher, lab, or institution.
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protocolExperimental protocol.
container: experimentcontains: link*, stimulus_nudge*
inherits: method_elementlinks: experiment
FieldTypeDescription
(id)?tokenThis attribute is needed so that others may link to it.
(base)?uriSee http://www.w3.org/TR/xmlbase/ for information about this attribute.
preparationcontrolledPreparation type used in this Protocol.
descriptionlong textShort verbal description of Protocol.
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stimulus_nudgeHolds details on subject preparation and response elicitation.
container: protocolcontains: (none)
inherits: (none)links: (none)
FieldTypeDescription
effectorcontrolledThe agent effecting one aspect of the Protocol.
patterncontrolledThe manner in which an agent acts to effect one aspect of the Protocol.
locationcontrolledThe locus at which an agent acts to effect one aspect of the Protocol.
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viewSuperclass View element. Do not use directly, but any View defined should declare itself in a substitution group with this.
container: experimentcontains: link*
inherits: data_elementlinks: recording_site
FieldTypeDescription
(seq)integerOrdering position of this View within its containing experiment.
(id)?tokenThis attribute is needed so that others may link to it.
(base)?uriSee http://www.w3.org/TR/xmlbase/ for information about this attribute.
number_of_trials?integerNumber of trials contributing to View or Histogram's data.
labelshort textShort name/description of a View or Trace.
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x_y_viewView for containing X-Y (2-dimensional plot) data. Traces share common X- and Y-axis units.
container: experimentcontains: link*, x_y_trace+
inherits: viewlinks: recording_site
FieldTypeDescription
(seq)integerOrdering position of this View within its containing experiment.
(id)?tokenThis attribute is needed so that others may link to it.
(base)?uriSee http://www.w3.org/TR/xmlbase/ for information about this attribute.
number_of_trials?integerNumber of trials contributing to View or Histogram's data.
labelshort textShort name/description of a View or Trace.
horizontal_axis_unitsunitUnit of measure for horizontal axis (often a temporal unit).
horizontal_axis_labelshort textShort, informative label for horizontal axis.
vertical_axis_unitsunitUnit of measure for vertical axis (dependent variable).
vertical_axis_labelshort textShort, informative label for vertical axis.
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x_y_traceBivariate 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_viewcontains: link*, dataset?, labeled_dataset?, datasetC?, datasetR?, datasetX?, datasetB?
inherits: tracelinks: recording_site
FieldTypeDescription
(seq)integerOrder of this Trace relative to others in the same View.
(id)?tokenThis attribute is needed so that others may link to it.
(base)?uriSee http://www.w3.org/TR/xmlbase/ for information about this attribute.
labelshort textShort name/description of a View or Trace.
recording_technique?controlledRecording technique employed in collecting Trace.
data_class?controlledThe nature of the data collected in Trace.
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histogram_viewView for containing histogram data.
container: experimentcontains: link*, histogram_trace+, histogram_prebin_trace*, histogram_raw_trace*
inherits: viewlinks: recording_site
FieldTypeDescription
(seq)integerOrdering position of this View within its containing experiment.
(id)?tokenThis attribute is needed so that others may link to it.
(base)?uriSee http://www.w3.org/TR/xmlbase/ for information about this attribute.
number_of_trials?integerNumber of trials contributing to View or Histogram's data.
labelshort textShort name/description of a View or Trace.
horizontal_axis_unitsunitUnit of measure for horizontal axis (often a temporal unit).
horizontal_axis_labelshort textShort, informative label for horizontal axis.
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histogram_traceSuperclass for histogram traces.
container: histogram_viewcontains: link*, dataset?, labeled_dataset?, datasetC?, datasetR?, datasetX?, datasetB?
inherits: tracelinks: recording_site
FieldTypeDescription
(seq)integerOrder of this Trace relative to others in the same View.
(id)?tokenThis attribute is needed so that others may link to it.
(base)?uriSee http://www.w3.org/TR/xmlbase/ for information about this attribute.
labelshort textShort name/description of a View or Trace.
recording_technique?controlledRecording technique employed in collecting Trace.
data_class?controlledThe nature of the data collected in Trace.
number_of_trialsintegerNumber of trials contributing to View or Histogram's data.
vertical_axis_labelshort textShort, informative label for vertical axis.
vertical_axis_typecontrolledType of units reflected by bar height: 'probability', 'percentage', 'Hz', or 'count'.
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histogram_prebin_tracePrebinned 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_viewcontains: link*, dataset?, labeled_dataset?, datasetC?, datasetR?, datasetX?, datasetB?
inherits: histogram_tracelinks: recording_site
FieldTypeDescription
(seq)integerOrder of this Trace relative to others in the same View.
(id)?tokenThis attribute is needed so that others may link to it.
(base)?uriSee http://www.w3.org/TR/xmlbase/ for information about this attribute.
labelshort textShort name/description of a View or Trace.
recording_technique?controlledRecording technique employed in collecting Trace.
data_class?controlledThe nature of the data collected in Trace.
number_of_trialsintegerNumber of trials contributing to View or Histogram's data.
vertical_axis_labelshort textShort, informative label for vertical axis.
vertical_axis_typecontrolledType of units reflected by bar height: 'probability', 'percentage', 'Hz', or 'count'.
bin_startfloating pointFirst bin center for Histogram (in H-axis units).
bin_widthfloating pointWidth of bin in Histogram (in H-axis units).
number_of_bins?integerNumber of bins in Histogram.
min_max_are_rangesbooleanWhether 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_traceRaw 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_viewcontains: link*, dataset?, labeled_dataset?, datasetC?, datasetR?, datasetX?, datasetB?
inherits: histogram_tracelinks: recording_site
FieldTypeDescription
(seq)integerOrder of this Trace relative to others in the same View.
(id)?tokenThis attribute is needed so that others may link to it.
(base)?uriSee http://www.w3.org/TR/xmlbase/ for information about this attribute.
labelshort textShort name/description of a View or Trace.
recording_technique?controlledRecording technique employed in collecting Trace.
data_class?controlledThe nature of the data collected in Trace.
number_of_trialsintegerNumber of trials contributing to View or Histogram's data.
vertical_axis_labelshort textShort, informative label for vertical axis.
vertical_axis_typecontrolledType of units reflected by bar height: 'probability', 'percentage', 'Hz', or 'count'.
min_value?floating pointMinimum h-axis value in raw histogram.
max_value?floating pointmaximum h-axis value in a raw histogram.
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time_series_viewView for containing time-series data.
container: experimentcontains: link*, time_trace+, event_list_trace*, time_series_trace*, spike_train_trace*, piecewise_series_trace*
inherits: viewlinks: recording_site
FieldTypeDescription
(seq)integerOrdering position of this View within its containing experiment.
(id)?tokenThis attribute is needed so that others may link to it.
(base)?uriSee http://www.w3.org/TR/xmlbase/ for information about this attribute.
number_of_trials?integerNumber of trials contributing to View or Histogram's data.
labelshort textShort name/description of a View or Trace.
horizontal_axis_unitsunitUnit of measure for horizontal axis (often a temporal unit).
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time_traceSuperclass with common elements of all traces valid in time series view.
container: time_series_viewcontains: link*, dataset?, labeled_dataset?, datasetC?, datasetR?, datasetX?, datasetB?
inherits: tracelinks: recording_site
FieldTypeDescription
(seq)integerOrder of this Trace relative to others in the same View.
(id)?tokenThis attribute is needed so that others may link to it.
(base)?uriSee http://www.w3.org/TR/xmlbase/ for information about this attribute.
labelshort textShort name/description of a View or Trace.
recording_technique?controlledRecording technique employed in collecting Trace.
data_class?controlledThe nature of the data collected in Trace.
t_startfloating pointRecording start time for Trace.
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event_list_traceTrace 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_viewcontains: link*, dataset?, labeled_dataset?, datasetC?, datasetR?, datasetX?, datasetB?
inherits: time_tracelinks: trace, recording_site
FieldTypeDescription
(seq)integerOrder of this Trace relative to others in the same View.
(id)?tokenThis attribute is needed so that others may link to it.
(base)?uriSee http://www.w3.org/TR/xmlbase/ for information about this attribute.
labelshort textShort name/description of a View or Trace.
recording_technique?controlledRecording technique employed in collecting Trace.
data_class?controlledThe nature of the data collected in Trace.
t_startfloating pointRecording start time for Trace.
t_endfloating pointRecording end time for Trace.
stimulusbooleanIndication of whether Trace represents stimulus signal or neuron response.
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time_series_traceTrace consisting of a regularly-sampled list of data values.
container: time_series_viewcontains: link*, dataset?, labeled_dataset?, datasetC?, datasetR?, datasetX?, datasetB?
inherits: time_tracelinks: recording_site
FieldTypeDescription
(seq)integerOrder of this Trace relative to others in the same View.
(id)?tokenThis attribute is needed so that others may link to it.
(base)?uriSee http://www.w3.org/TR/xmlbase/ for information about this attribute.
labelshort textShort name/description of a View or Trace.
recording_technique?controlledRecording technique employed in collecting Trace.
data_class?controlledThe nature of the data collected in Trace.
t_startfloating pointRecording start time for Trace.
t_ratefloating pointTrace sampling rate, in units of horizontal axis.
stimulusbooleanIndication of whether Trace represents stimulus signal or neuron response.
vertical_axis_unitsunitUnit of measure for vertical axis (dependent variable).
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spike_train_traceTrace consisting of a list of event times at which spikes occurred.
container: time_series_viewcontains: link*, dataset?, labeled_dataset?, datasetC?, datasetR?, datasetX?, datasetB?
inherits: time_tracelinks: recording_site
FieldTypeDescription
(seq)integerOrder of this Trace relative to others in the same View.
(id)?tokenThis attribute is needed so that others may link to it.
(base)?uriSee http://www.w3.org/TR/xmlbase/ for information about this attribute.
labelshort textShort name/description of a View or Trace.
recording_technique?controlledRecording technique employed in collecting Trace.
data_class?controlledThe nature of the data collected in Trace.
t_startfloating pointRecording start time for Trace.
t_endfloating pointRecording end time for Trace.
stimulus?booleanIndication of whether Trace represents stimulus signal or neuron response.
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piecewise_series_traceThe 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_viewcontains: link*, dataset?, labeled_dataset?, datasetC?, datasetR?, datasetX?, datasetB?
inherits: time_series_tracelinks: recording_site
FieldTypeDescription
(seq)integerOrder of this Trace relative to others in the same View.
(id)?tokenThis attribute is needed so that others may link to it.
(base)?uriSee http://www.w3.org/TR/xmlbase/ for information about this attribute.
labelshort textShort name/description of a View or Trace.
recording_technique?controlledRecording technique employed in collecting Trace.
data_class?controlledThe nature of the data collected in Trace.
t_startfloating pointRecording start time for Trace.
t_ratefloating pointTrace sampling rate, in units of horizontal axis.
stimulusbooleanIndication of whether Trace represents stimulus signal or neuron response.
vertical_axis_unitsunitUnit of measure for vertical axis (dependent variable).
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signal_channelRepresents 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)
FieldTypeDescription
(id)tokenUnique identifier for the channel.
(seq)integerSequence number for the channel, out of its group.
(name)tokenShort, precise, descriptive name for the channel.
(units)tokenUnits 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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conditionExperimental 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_elementlinks: (none)
FieldTypeDescription
(name)short textA short descriptive name of what this condition represents.
(type)tokenData type for this condition's value: either 'numeric' or 'text'.
(value)short textValue for the experimental condition. Should follow 'type'.
(units)?tokenFor 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)?tokenThis attribute is needed so that others may link to it.
(base)?uriSee http://www.w3.org/TR/xmlbase/ for information about this attribute.
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