odml-terminologies/v1.1/terminologies.xml

<?xml version="1.0" encoding="UTF-8"?>
<?xml-stylesheet type="text/xsl" href="https://terminologies.g-node.org/_resources/odmlTerminologiesIndex.xsl" xmlns:odml="http://www.g-node.org/odml"?>
<odML version="1.1">

  <section>
    <type>analysis</type>
    <name>Analysis</name>
    <definition>Sections of the Analysis type can be used to describe analyses.</definition>
    <include>https://terminologies.g-node.org/v1.1/analysis/analysis.xml</include>
  </section>

  <section>
    <type>analysis/power_spectrum</type>
    <name>PowerSpectrum</name>
    <definition>Properties of this section define the way a power spectrum was calculated.</definition>
    <include>https://terminologies.g-node.org/v1.1/analysis/power_spectrum.xml</include>
  </section>

  <section>
    <type>analysis/psth</type>
    <name>PSTH</name>
    <definition>An Analysis-type section to describe a PSTH.</definition>
    <include>https://terminologies.g-node.org/v1.1/analysis/psth.xml</include>
  </section>

  <section>
    <type>blackrock</type>
    <name>Blackrock</name>
    <definition>Information on the Cerebus^TM data acquisition system</definition>
    <include>https://terminologies.g-node.org/v1.1/blackrock/blackrock.xml</include>
  </section>

  <section>
    <type>carmen_mini</type>
    <name>CarmenMini</name>
    <definition>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.
    </definition>
    <include>https://terminologies.g-node.org/v1.1/carmenMini/carmen_mini.xml</include>
  </section>

  <section>
    <type>cell</type>
    <name>Cell</name>
    <definition>Specification of the recorded cell. A cell definition should be a subsection of the
      <a href="../subject/subject.xml">Subject</a>
      section.
    </definition>
    <include>https://terminologies.g-node.org/v1.1/cell/cell.xml</include>
  </section>

  <section>
    <type>dataset</type>
    <name>Dataset</name>
    <definition>Names (URLs) and times of recorded data files. Datasets are obtained during a Recording and may belong
      to different Experiments. Related sections that can be used as subsections, parent sections, or siblings are
      Stimulus, HardwareSettings, and Experiment.
    </definition>
    <include>https://terminologies.g-node.org/v1.1/dataset/dataset.xml</include>
  </section>

  <section>
    <type>data_reference</type>
    <name>DataCite</name>
    <definition>A published dataset referenced by a DOI and registered with DataCite. The referenced dataset will contain either the odML file itself or the data the odML is annotating.</definition>
    <include>https://terminologies.g-node.org/v1.1/datareference/datacite.xml</include>
  </section>

  <section>
    <type>data_reference</type>
    <name>DataDOI</name>
    <definition>A published dataset referenced by a DOI. The referenced dataset will contain either the odML file itself or the data the odML is annotating.</definition>
    <include>https://terminologies.g-node.org/v1.1/datareference/datadoi.xml</include>
  </section>

  <section>
    <type>data_reference</type>
    <name>DataURI</name>
    <definition>A published dataset referenced by a URI. The referenced dataset will contain either the odML file itself or the data the odML is annotating.</definition>
    <include>https://terminologies.g-node.org/v1.1/datareference/datauri.xml</include>
  </section>

  <section>
    <type>data_reference</type>
    <name>DataURL</name>
    <definition>A published dataset referenced by a URL. The referenced dataset will contain either the odML file itself or the data the odML is annotating.</definition>
    <include>https://terminologies.g-node.org/v1.1/datareference/dataurl.xml</include>
  </section>

  <section>
    <type>data_reference/description</type>
    <name>DataReferenceDescription</name>
    <definition>Description of a data reference. This Section is defined to be used as a subsection of the 'DataReference' type sections.</definition>
    <include>https://terminologies.g-node.org/v1.1/datareference/referencedescription.xml</include>
  </section>

  <section>
    <type>electrode</type>
    <name>Electrode</name>
    <definition>Properties to describe an electrode.</definition>
    <include>https://terminologies.g-node.org/v1.1/electrode/electrode.xml</include>
  </section>

  <section>
    <type>event</type>
    <name>Event</name>
    <definition>Section for short annotations that are taken during an experiment to describe certain events.
    </definition>
    <include>https://terminologies.g-node.org/v1.1/event/event.xml</include>
  </section>

  <section>
    <type>event_list</type>
    <name>EventList</name>
    <definition>Section for grouping short annotations that are taken during
      an experiment, preparation etc...
    </definition>
    <include>https://terminologies.g-node.org/v1.1/collection/event_list.xml</include>
  </section>

  <section>
    <type>experiment</type>
    <name>Experiment</name>
    <definition>Specification of an experiment. The Experiment is part of a Project and the recorded data for a specific
      Experiment are found in Datasets. Possible subsections are, for example, Dataset and Stimulus.
    </definition>
    <include>https://terminologies.g-node.org/v1.1/experiment/experiment.xml</include>
  </section>

  <section>
    <type>experiment/behavior</type>
    <name>Behavior</name>
    <definition>Properties for describing an behavioural experiment.</definition>
    <include>https://terminologies.g-node.org/v1.1/experiment/behavior.xml</include>
  </section>

  <section>
    <type>experiment/electrophysiology</type>
    <name>Electrophysiology</name>
    <definition>Properties for describing an electrophysiological experiment.</definition>
    <include>https://terminologies.g-node.org/v1.1/experiment/electrophysiology.xml</include>
  </section>

  <section>
    <type>experiment/imaging</type>
    <name>Imaging</name>
    <definition>Properties for describing an imaging experiment ranging from conventional light microscpoy to fMRI.
    </definition>
    <include>https://terminologies.g-node.org/v1.1/experiment/imaging.xml</include>
  </section>

  <section>
    <type>experiment/psychophysics</type>
    <name>Psychophysics</name>
    <definition>Properties for describing an psychophysical experiment.</definition>
    <include>https://terminologies.g-node.org/v1.1/experiment/psychophysics.xml</include>
  </section>

  <section>
    <type>hardware_properties</type>
    <name>HardwareProperties</name>
    <include>https://terminologies.g-node.org/v1.1/collection/hardware_properties.xml</include>
  </section>

  <section>
    <type>hardware_settings</type>
    <name>HardwareSettings</name>
    <definition>The used values of variable properties of hardware
      components. There are two sections for describing hardware
      components: the "HardwareProperties" and the "HardwareSettings"
      section. While the HardwareProperties describe the fixed
      properties of the hardware that can not be changed, the
      HardwareSettings section describes the actual, adjustable,
      parameters of the hardware that may change with each recording
      or dataset. For example, the sample rate of an data-acquisition
      board or the settings of a filter. In each of these two sections
      there are subsections for each device that correspond to the
      class of the device like data-acquisition, amplifier, etc. Some
      properties are common for any type.
    </definition>
    <include>https://terminologies.g-node.org/v1.1/collection/hardware_settings.xml</include>
  </section>

  <section>
    <type>hardware</type>
    <name>Hardware</name>
    <definition>Fixed properties of hardware components used in the
      experimental setup. There are two sections for describing
      hardware components: the "HardwareProperties" and the
      "HardwareSettings" section. While the HardwareProperties
      describe the fixed properties of the hardware that can not be
      changed, the HardwareSettings section describes the actual,
      adjustable, parameters of the hardware that may change with each
      recording or dataset. For example, the sample rate of an
      data-acquisition board or the settings of a filter. In each of
      these two sections there are subsections for each device that
      correspond to the class of the device like data-acquisition,
      amplifier, etc. Some properties are common for any
      type.
    </definition>
    <include>https://terminologies.g-node.org/v1.1/hardware/hardware.xml</include>
  </section>

  <section>
    <type>hardware/amplifier</type>
    <name>Amplifier</name>
    <definition>The amplifier section defines elements that can be used to describe amplifier properties and settings.
    </definition>
    <include>https://terminologies.g-node.org/v1.1/hardware/amplifier.xml</include>
  </section>

  <section>
    <type>hardware/attenuator</type>
    <name>Attenuator</name>
    <definition>Settings of the data acquisition system. most settings refer to individual channels the channel
      number should be given after the property name like DAQ. AISampleRate0 for the sampling rate of the analog
      input channel 0.
    </definition>
    <include>https://terminologies.g-node.org/v1.1/hardware/attenuator.xml</include>
  </section>

  <section>
    <type>hardware/camera_objective</type>
    <name>CameraObjective</name>
    <definition>This section contains properties that describe a camera objective.</definition>
    <include>https://terminologies.g-node.org/v1.1/hardware/camera_objective.xml</include>
  </section>

  <section>
    <type>hardware/daq</type>
    <name>DataAcquisition</name>
    <definition>The hardware section describes the settings of the used hardware. There should be one hardware section
      for each hardware item that was used.
    </definition>
    <include>https://terminologies.g-node.org/v1.1/hardware/daq.xml</include>
  </section>

  <section>
    <type>hardware/eyetracker</type>
    <name>Eyetracker</name>
    <definition>Properties of an eyetracker.</definition>
    <include>https://terminologies.g-node.org/v1.1/hardware/eyetracker.xml</include>
  </section>

  <section>
    <type>hardware/filter</type>
    <name>Filter</name>
    <definition>Properties a filter modul for analog signal conditioning.</definition>
    <include>https://terminologies.g-node.org/v1.1/hardware/filter.xml</include>
  </section>

  <section>
    <type>hardware/filter_set</type>
    <name>Filterset</name>
    <definition>The FilterSet or also FilterCube used in a microscope.</definition>
    <include>https://terminologies.g-node.org/v1.1/hardware/filter_set.xml</include>
  </section>

  <section>
    <type>hardware/iaq</type>
    <name>ImageAcquisition</name>
    <definition>Properties to define an Image acquisition device. This can be a framegrabber, a camera etc.</definition>
    <include>https://terminologies.g-node.org/v1.1/hardware/iaq.xml</include>
  </section>

  <section>
    <type>hardware/microscope</type>
    <name>Microscope</name>
    <definition>The Microscope section describes the properties of the used microscope.</definition>
    <include>https://terminologies.g-node.org/v1.1/hardware/microscope.xml</include>
  </section>

  <section>
    <type>hardware/microscope_objective</type>
    <name>MicroscopeObjective</name>
    <definition>This section contains properties that describe the objective used in a microscope.</definition>
    <include>https://terminologies.g-node.org/v1.1/hardware/microscope_objective.xml</include>
  </section>

  <section>
    <type>hardware/scanner</type>
    <name>Scanner</name>
    <definition>The Scanner used to scan microscope images.</definition>
    <include>https://terminologies.g-node.org/v1.1/hardware/scanner.xml</include>
  </section>

  <section>
    <type>hardware/stimulus_isolator</type>
    <name>StimulusIsolator</name>
    <definition>Properties of a stimulus Isolator device.</definition>
    <include>https://terminologies.g-node.org/v1.1/hardware/stimulus_isolator.xml</include>
  </section>

  <section>
    <type>license</type>
    <name>License</name>
    <definition>This section contains keywords to a data or software license.</definition>
    <include>https://terminologies.g-node.org/v1.1/license/license.xml</include>
  </section>

  <section>
    <type>model/lif</type>
    <name>Leaky integrate and fire</name>
    <definition>Section to describe a leaky integrate and fire neuron model.</definition>
    <include>https://terminologies.g-node.org/v1.1/model/lif.xml</include>
  </section>

  <section>
    <type>model/multi_compartment</type>
    <name>Multi compartment model</name>
    <definition>Section to describe a biophysical model that consists of a number of compartments.</definition>
    <include>https://terminologies.g-node.org/v1.1/model/multi_compartment.xml</include>
  </section>

  <section>
    <type>model/pif</type>
    <name>perfect integrate and fire</name>
    <definition>Section to describe a perfect integrate and fire model.</definition>
    <include>https://terminologies.g-node.org/v1.1/model/pif.xml</include>
  </section>

  <section>
    <type>model/single_compartment</type>
    <name>One compartment model</name>
    <definition>Section to describe a biophysical model that consists of a single compartment.</definition>
    <include>https://terminologies.g-node.org/v1.1/model/single_compartment.xml</include>
  </section>

  <section>
    <type>person</type>
    <name>Person</name>
    <definition>Information about a person. E.g. as Experimenter, Author, etc.</definition>
    <include>https://terminologies.g-node.org/v1.1/person/person.xml</include>
  </section>

  <section>
    <type>preparation</type>
    <name>Preparation</name>
    <definition>Description of the preparation procedure.</definition>
    <include>https://terminologies.g-node.org/v1.1/preparation/preparation.xml</include>
  </section>

  <section>
    <type>project</type>
    <name>Project</name>
    <definition>Information about the project.</definition>
    <include>https://terminologies.g-node.org/v1.1/project/project.xml</include>
  </section>

  <section>
    <type>protocol</type>
    <name>protocol</name>
    <definition>Information about the experimental protocol.</definition>
    <include>https://terminologies.g-node.org/v1.1/protocol/protocol.xml</include>
  </section>

  <section>
    <type>questionnaire/question</type>
    <name>Question</name>
    <definition>Description of a question if a questionnaire.</definition>
    <include>https://terminologies.g-node.org/v1.1/questionnaire/question.xml</include>
  </section>

  <section>
    <type>questionnaire/questionnaire</type>
    <name>Questionnaire</name>
    <definition>Description of a questionnaire.</definition>
    <include>https://terminologies.g-node.org/v1.1/questionnaire/questionnaire.xml</include>
  </section>

  <section>
    <type>recording</type>
    <name>Recording</name>
    <definition>During a recording session in a Setup Datasets are obtained from Cells and/or a Subject by using various
      stimuli (Stimulus section).
    </definition>
    <include>https://terminologies.g-node.org/v1.1/recording/recording.xml</include>
  </section>

  <section>
    <type>response</type>
    <name>Response</name>
    <definition>General description of an received response (on stimulus).</definition>
    <include>https://terminologies.g-node.org/v1.1/response/response.xml</include>
  </section>

  <section>
    <type>setup</type>
    <name>Setup</name>
    <definition>The experimental setup used in the recordings. By using HardwareProperties as a subsection, a very
      detailed description of the setup can be given.
    </definition>
    <include>https://terminologies.g-node.org/v1.1/setup/setup.xml</include>
  </section>

  <section>
    <type>stimulus</type>
    <name>Stimulus</name>
    <definition>General description of an applied stimulus. This section is basis of various related sections that
      specify more specific stimuli.
    </definition>
    <include>https://terminologies.g-node.org/v1.1/stimulus/stimulus.xml</include>
  </section>

  <section>
    <type>stimulus/dc</type>
    <name>DC</name>
    <definition>Property definitions to describe a DC stimulus meaning a constant stimulus e.g. a constant illumination,
      current etc.
    </definition>
    <include>https://terminologies.g-node.org/v1.1/stimulus/dc.xml</include>
  </section>

  <section>
    <type>stimulus/gabor</type>
    <name>Gabor</name>
    <include>https://terminologies.g-node.org/v1.1/stimulus/gabor.xml</include>
  </section>

  <section>
    <type>stimulus/grating</type>
    <name>Grating</name>
    <definition>Property definitions to describe Gabor stimuli.</definition>
    <include>https://terminologies.g-node.org/v1.1/stimulus/grating.xml</include>
  </section>

  <section>
    <type>stimulus/movie</type>
    <name>Movie</name>
    <definition>Properties to describe a movie (or image sequence) stimulus.</definition>
    <include>https://terminologies.g-node.org/v1.1/stimulus/movie.xml</include>
  </section>

  <section>
    <type>stimulus/pulse</type>
    <name>Pulse</name>
    <definition>Properties to describe a simple pulse stimulus that starts from and returns to a certain baseline.
    </definition>
    <include>https://terminologies.g-node.org/v1.1/stimulus/pulse.xml</include>
  </section>

  <section>
    <type>stimulus/ramp</type>
    <name>Ramp</name>
    <definition>A ramp stimulus may either linearly increase or decrease in amplitude. Starting from a certain start
      amplitude and reaching with a certain slope the destination amplitude.
    </definition>
    <include>https://terminologies.g-node.org/v1.1/stimulus/ramp.xml</include>
  </section>

  <section>
    <type>stimulus/random_dot</type>
    <name>RandomDot</name>
    <definition>Properties to describe a random dot stimulus.</definition>
    <include>https://terminologies.g-node.org/v1.1/stimulus/random_dot.xml</include>
  </section>

  <section>
    <type>stimulus/sawtooth</type>
    <name>Sawtooth</name>
    <include>https://terminologies.g-node.org/v1.1/stimulus/sawtooth.xml</include>
  </section>

  <section>
    <type>stimulus/sine_wave</type>
    <name>Sinewave</name>
    <definition>Sawtooth Properties.</definition>
    <include>https://terminologies.g-node.org/v1.1/stimulus/sine_wave.xml</include>
  </section>

  <section>
    <type>stimulus/square_wave</type>
    <name>Squarewave</name>
    <definition>A squarewave stimulus was presented. Squarewaves modulate with a certain frequency about the intensity
      offset.
    </definition>
    <include>https://terminologies.g-node.org/v1.1/stimulus/square_wave.xml</include>
  </section>

  <section>
    <type>stimulus/white_noise</type>
    <name>Whitenoise</name>
    <definition>Property definitions to describe a white noise stimulus.</definition>
    <include>https://terminologies.g-node.org/v1.1/stimulus/white_noise.xml</include>
  </section>

  <section>
    <type>subject</type>
    <name>Subject</name>
    <definition>The investigated experimental subject (animal or person).
      May contain the Cell and Preparation sections as subsections.
    </definition>
    <include>https://terminologies.g-node.org/v1.1/subject/subject.xml</include>
  </section>

</odML>