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