https://terminologies.g-node.org/v1.1/terminologies.xml
1.0
2011-01-21
carmen_mini
Carmen Mini
This is a convenience section that lists the terms of the CARMEN MINI (Gibson et al. Nature Precedings,
2009 Version 0.6) and maps them to the odml "standard" terminologies.
carmen_mini/contact_and_context
ContactAndContext
DateAndTime
The date and time of work initiation in YYYY-MM-DD hh:mm:ss format. (TODO ISO 8601 requires the T
lib has to able to deal with it!)
datetime
ResponsiblePerson
The (stable) primary contact person for this data set; this could be the experimenter, lab head,
line manager etc. Where responsibility rests with an institutional role (e.g. one of a number of duty
officers) rather than a person, give the official name of the role rather than any one person. In all cases
give affiliation and stable contact information, which consists of (i) Name, (ii) Postal address and (iii)
Email address.
person
ExperimentalContext
The name of the project, study or wider investigation of which the 'experiment' is a part (if
appropriate).
text
ElectrophysiologyType
The type of electrophysiology recording reported as 'extra cellular' or 'intra cellular'.
string
carmen_mini/study_subject
StudySubject
Genus
The genus classification of the study subject according to the NCBI taxonomy classification.
string
Species
The species classification of the study subject according to the NCBI taxonomy classification.
string
Strain
The strain, genetic variation classification of the study subject, if appropriate. Note this is not
the cell line.
string
CellLine
The identifier for the immortalized cell line, if appropriate.
string
GeneticCharacteristics
The genotype of the study stubject. Genetics characteristics include polymorphisms, disease alleles
and haplotypes.
string
GeneticVariation
The genetic modification introduced in addition to strain, if appropriate.
string
DeseaseState
The name of the pathology diagnosed in the subject. The disease state is 'normal' if no disease
state has been diagnosed.
string
ClinicalInformation
A link, summary or reference to additional clinical information, if appropriate.
string
Sex
The sex of the subject, in terms of either male, female or hermaphrodite.
string
Age
The time period elapsed since an identifiable point in the life cycle of an organism. If a
developmental stage is specified the identifiable point would be the beginning of that stage. Otherwise the
identifiable point must be specifies. For example, 2 hours post surgery.
string
DevelopmentalStage
The developmental stage of the of the study subject's life cycle.
string
SubjectLabel
If the subject has been chemically labeled or stained; state the label name.
string
SubjectIdentifier
The type and value of the identifier assigned to the subject.
string
SubjectIdentifierType
The type and value of the identifier assigned to the subject. For example, vendor or patient
identifier. For patients, the identifier must be approved by an Institutional Review Board or appropriate
body.
string
SubjectIdentifierValue
The unique string which corresponds to the identifier type. TODO! How does this relate to the
Identifier ?
string
AssociatedSubjectDetails
The organisation (e.g vendor) or individual responsible for the subject.
string
PreparationProtocol
The surgical procedure or the preparation protocol implemented to obtain the specific sample for
recording.
string
PreparationDate
The date the surgical procedure or the preparation protocol was performed to obtain the specific
sample for recording. Given in the ISO:8601 representation. YYYY-MM-DDThh:mm:ss
date
carmen_mini/recording_location
RecordingLocation
LocationStructure
The anatomical part or structure of the subject under investigation or recorded from. For example
brain or cell culture.
string
BrainArea
If the anatomical structure under study from 3.(a) is the brain then state the location. If the
anatomical structure under study is the mammalian brain then state the location using Neuronames.
(http://braininfo.rprc.washington.edu/aboutfolder/aboutbi.html).
string
SliceThickness
The thickness of the recording slice in millimeters.
float
mm
SliceOrientation
State the planes of the slice, in terms of either i) coronal (widthways), ii) saggital (lengthways
parallel to midline) or iii) tangential (lengthways perpendicular to midline).
string
CellType
The cell type of the anatomical structure given in 3.(a) under investigation if non mixed. If mixed
the target cell type should be provided.
string
TargetCellType
The cell type of the anatomical structure given in 3.(a) under investigation if non mixed. If mixed
the target cell type should be provided
string
ConfirmedCellType
The method of coordinate assignment given in 2.3.1. Reported as 'anatomy confirmation', 'estimation'
or chemical label (this includes antibodies and staining). The label used should be reported in section 2.(l).
Additional information such as recordings or image files which also confirm the location can be referenced
here.
string
carmen_mini/task
Task
Protocol
A description of the task protocol undertaken by the subject.
string
SensoryConditions
The sensory conditions during the task protocol.
string
Equipment
The Model Name, Model Number and Manufacturer for equipment used in the task protocol.
string
Recording
If the task is recorded state how and what data types are being recorded.
string
carmen_mini/stimulus
Stimulus
Protocol
A description of the stimulus protocol undertaken by the subject.
string
SensoryConditions
The sensory conditions during the stimulus protocol.
string
Solutions
Description of the solutions used in terms of name, components with concentrations,(if
appropriate).
string
Equipment
The Model Name, Model Number and Manufacturer for specialised equipment used during the stimulus
protocol. If electrode(s) are used then they should be described following the structure presented in ref x.x
string
Recording
If the stimulus is recorded state how and what data types are being recorded.
string
carmen_mini/behavioural_event
BehaviouralEvent
Event
A description of the behavioural event observed.
string
Equipment
The equipment use to record the behavioural event, if recorded in terms of The Model Name, Model
Number and Manufacturer.
string
BehaviouralEventRecording
The type of recording of the behavioural event, the file format and the format encoding.
string
carmen_mini/recording
Recording
Protocol
A description of the recording protocol.
string
Conditions
The subject conditions during the recording. Invivo or invitro preparation If invivo was it
anesthetised or awake? If awake what was the stimulus condition.
string
ContainingDevice
Containing device temperature of the subject or sample (for example, a bath): Include temperature if
appropriate.
string
Solutions
Description of the solutions used in terms of name, components with concentrations,(if
appropriate).
string
SolutionFlowSpeed
The flow speed of the solution described in (ref x.x) in terms of ml/min.
string
Electrode
The type of electrode and the Model Name, Model Number and Manufacturer for specialised equipment.
string
ElectrodeConfiguration
The configuration or arrangement of the electrode. For example, a 2-dimensional array. Also state
the distance between each electrode. If the study uses voltage clamp in a patch configuration, state the
access resistance (the resistance of the cell membrane, which is in series with the electrode resistance).
string
ElectrodeImpedance
The electrode range or impedance of the electrode.
string
Amplifier
The Model Name, Model Number and Manufacturer of the amplifier.
string
Filter
The Model Name, Model Number and Manufacturer of the filter.
string
FilterSettings
The settings or the parameters of the filter.
string
Recorder
The Model Name, Model Number and Manufacturer of the recorder.
string
carmen_mini/timeseries_data
TimeSeriesData
DataFormat
The name of the data format of the time series data and specific encoding. For example, ASCII or
binary encoding.
string
SamplingRate
The sampling rate of the recording.
string
FileLocation
The time series file location should be made available when the experiment is published, for
example, using a Uniform Resource Identifier (URI) or a Digital Object Identifier (DOI). (Note this will be
achieved automatically via submission to the CARMEN system).
URL