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 datetime 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!) http://portal.g-node.org/odml/terminologies/v1.0/recording/recording.xml#recording:Start ResponsiblePerson person 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. http://portal.g-node.org/odml/terminologies/v1.0/project/project.xml#project:PrincipleInvestigator ExperimentalContext text The name of the project, study or wider investigation of which the 'experiment' is a part (if appropriate). http://portal.g-node.org/odml/terminologies/v1.0/project/project.xml#project:Description ElectrophysiologyType string The type of electrophysiology recording reported as 'extra cellular' or 'intra cellular'. http://portal.g-node.org/odml/terminologies/v1.0/experiment/experiment.xml#experiment:Type

carmen_mini/study_subject StudySubject http://portal.g-node.org/odml/terminologies/v1.0/subject/subject.xml#subject Genus string The genus classification of the study subject according to the NCBI taxonomy classification. http://portal.g-node.org/odml/terminologies/v1.0/subject/subject.xml#subject:Genus Species string The species classification of the study subject according to the NCBI taxonomy classification. http://portal.g-node.org/odml/terminologies/v1.0/subject/subject.xml#subject:Species Strain string The strain, genetic variation classification of the study subject, if appropriate. Note this is not the cell line. http://portal.g-node.org/odml/terminologies/v1.0/subject/subject.xml#subject:Strain CellLine string The identifier for the immortalized cell line, if appropriate. http://portal.g-node.org/odml/terminologies/v1.0/subject/subject.xml#subject:CellLine GeneticCharacteristics string The genotype of the study stubject. Genetics characteristics include polymorphisms, disease alleles and haplotypes. http://portal.g-node.org/odml/terminologies/v1.0/subject/subject.xml#subject:Comment GeneticVariation string The genetic modification introduced in addition to strain, if appropriate. http://portal.g-node.org/odml/terminologies/v1.0/subject/subject.xml#subject:Comment DeseaseState string The name of the pathology diagnosed in the subject. The disease state is 'normal' if no disease state has been diagnosed. http://portal.g-node.org/odml/terminologies/v1.0/subject/subject.xml#subject:HealthStatus ClinicalInformation string A link, summary or reference to additional clinical information, if appropriate. http://portal.g-node.org/odml/terminologies/v1.0/subject/subject.xml#subject:Comment Sex string The sex of the subject, in terms of either male, female or hermaphrodite. http://portal.g-node.org/odml/terminologies/v1.0/subject/subject.xml#subject:Gender Age string The time period elapsed since an identifiable point in the life cycle of an organism. If a developmental stage is specified the indentifiable point would be the beginning of that stage. Otherwise the identifiable point must be specifies. For example, 2 hours post surgery. http://portal.g-node.org/odml/terminologies/v1.0/subject/subject.xml#subject:Age DevelopmentalStage string The developmental stage of the of the study subect's life cycle. http://portal.g-node.org/odml/terminologies/v1.0/subject/subject.xml#subject:DevelopmentalStage SubjectLabel string If the subject has been chemically labeled or stained; state the label name. http://portal.g-node.org/odml/terminologies/v1.0/subject/subject.xml#subject:Label SubjectIdentifier string The type and value of the identifier assigned to the subject. http://portal.g-node.org/odml/terminologies/v1.0/subject/subject.xml#subject:Identifier SubjectIdentifierType string 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. http://portal.g-node.org/odml/terminologies/v1.0/subject/subject.xml#subject:Comment SubjectIdentifierValue string The unique string which corresponds to the identifier type. TODO! How does this relate to the Identifier ? http://portal.g-node.org/odml/terminologies/v1.0/subject/subject.xml#subject:Identifier AssociatedSubjectDetails string The organisation (e.g vendor) or individual responsible for the subject. http://portal.g-node.org/odml/terminologies/v1.0/subject/subject.xml#subject:Comment PreparationProtocol string The surgical procedure or the preparation protocol implemented to obtain the specific sample for recording. http://portal.g-node.org/odml/terminologies/v1.0/preparation/preparation.xml#preparation:Description PreparationDate date 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 http://portal.g-node.org/odml/terminologies/v1.0/preparation/preparation.xml#preparation:Date

carmen_mini/recording_location RecordingLocation LocationStructure string The anatomical part or structure of the subject under investigation or recorded from. For example brain or cell culture. http://portal.g-node.org/odml/terminologies/v1.0/cell/cell.xml#cell:Structure BrainArea string 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). http://portal.g-node.org/odml/terminologies/v1.0/cell/cell.xml#cell:BrainArea SliceThickness float mm The thickness of the recording slice in milimeters. http://portal.g-node.org/odml/terminologies/v1.0/preparation/preparation.xml#preparation:SliceThickness SliceOrientation string 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). http://portal.g-node.org/odml/terminologies/v1.0/preparation/preparation.xml#preparationSliceOrientation CellType string 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. http://portal.g-node.org/odml/terminologies/v1.0/cell/cell.xml#cell:CellType TargetCellType string 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 ConfirmedCellType string 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.

carmen_mini/task Task Protocol string A description of the task protocol undertaken by the subject. http://portal.g-node.org/odml/terminologies/v1.0/experiment/bahavior.xml#experiment/behavior:Description SensoryConditions string The sensory conditions during the task protocol. Equipment string The Model Name, Model Number and Manufacturer for equipment used in the task protocol. Recording string If the task is recorded state how and what data types are being recorded.

carmen_mini/stimulus Stimulus Protocol string A description of the stimulus protocol undertaken by the subject. http://portal.g-node.org/odml/terminologies/v1.0/stimulus/stimulus.xml#stimulus:Description SensoryConditions string The sensory conditions during the stimulus protocol. Solutions string Description of the solutions used in terms of name, components with concentrations,(if appropriate). Equipment string 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 Recording string If the stimulus is recorded state how and what data types are being recorded.

carmen_mini/behavioural_event BehaviouralEvent Event string A description of the behavioural event observed. Equipment string The equipment use to record the behavioural event, if recorded in terms of The Model Name, Model Number and Manufacturer. BehaviouralEventRecording string The type of recording of the behavioural event, the file format and the format encoding.

carmen_mini/recording Recording Protocol string A description of the recording protocol. Conditions string The subject conditions during the recording. Invivo or invitro preparation If invivo was it anesthetised or awake? If awake what was the stimulus condition. ContainingDevice string Containing device temperature of the subject or sample (for example, a bath): Include temperature if appropriate. Solutions string Description of the solutions used in terms of name, components with concentrations,(if appropriate). http://portal.g-node.org/odml/terminologies/v1.0/preparation/preparation.xml#preparation:BathSolution SolutionFlowSpeed string The flow speed of the solution described in (ref x.x) in terms of ml/min. http://portal.g-node.org/odml/terminologies/v1.0/preparation/preparation.xml#preparation:SolutionFlowSpeed Electrode string The type of electrode and the Model Name, Model Number and Manufacturer for specialised equipment. ElectrodeConfiguration string 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). http://portal.g-node.org/odml/terminologies/v1.0/electrode/electrode.xml#electrode:Configuration ElectrodeImpedance string The electrode range or impedance of the electrode. http://portal.g-node.org/odml/terminologies/v1.0/electrode/electrode.xml#electrode:Impedance Amplifier string The Model Name, Model Number and Manufacturer of the amplifier. Filter string The Model Name, Model Number and Manufacturer of the filter. FilterSettings string The settings or the parameters of the filter. Recorder string The Model Name, Model Number and Manufacturer of the recorder.

carmen_mini/timeseries_data TimeSeriesData DataFormat string The name of the data format of the time series data and specific encoding. For example, ASCII or binary encoding. SamplingRate string The sampling rate of the recording. http://portal.g-node.org/odml/terminologies/v1.0/hardware/daq.xml#hardware/daq:AISampleRate FileLocation URL 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). http://portal.g-node.org/odml/terminologies/v1.0/dataset/dataset.xml#dataset:FileURL