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electrophysiology-template.xml
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electrophysiology-template.xml
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<?xml version="1.0" encoding="UTF-8"?>
<?xml-stylesheet type="text/xsl" href="#odml_local_style"?>
<!DOCTYPE odML [ <!ATTLIST xsl:stylesheet id ID #REQUIRED> ]>
<odML version="1.1">
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</style><body><header><h1><a class="white" href="https://templates.g-node.org/templates.xml">odML metadata document</a></h1></header><div class="navWrapper"><navigationContainer><div id="navigationContainer"><hr class="fatline" /><p><h2>Document info</h2><b>Author: </b><xsl:if test="author"><xsl:value-of select="author"/></xsl:if><br/><b>Date: </b><xsl:if test="date"><xsl:value-of select="date"/></xsl:if><br/><b>Version: </b><xsl:if test="version"><xsl:value-of select="version"/></xsl:if><br/><b>Repository: </b><xsl:if test="repository"><xsl:value-of select="repository"/></xsl:if><br/></p><hr class="fatline" /><h2>Structure</h2><font size ="-1" ><xsl:if test="section"><xsl:for-each select="section"><xsl:call-template name="sectionTemplate"><xsl:with-param name="navigation">1</xsl:with-param><xsl:with-param name="anchorBase">Sec</xsl:with-param><xsl:with-param name="url" select="$repository"/></xsl:call-template></xsl:for-each></xsl:if></font><br/></div><div id="contentContainer"><hr class="fatline" /><h2>Content</h2><xsl:if test="section"><xsl:for-each select="section"><xsl:call-template name="sectionTemplate"><xsl:with-param name="navigation">0</xsl:with-param><xsl:with-param name="anchorBase">Sec</xsl:with-param><xsl:with-param name="url" select="$repository"/></xsl:call-template></xsl:for-each></xsl:if></div></navigationContainer></div></body></html></xsl:template><xsl:template name="sectionTemplate" match="section"><xsl:param name="navigation"/><xsl:param name="anchorBase"/><xsl:param name="url"/><xsl:variable name="anchorName" select="concat($anchorBase,position())"/><xsl:variable name="repository"><xsl:choose><xsl:when test="repository"><xsl:value-of select ="repository"/></xsl:when><xsl:otherwise><xsl:value-of select ="$url"/></xsl:otherwise></xsl:choose></xsl:variable><xsl:choose><xsl:when test="$navigation = 1"><ol class="nested"><font size="normal"><a href="#{$anchorName}"><xsl:value-of select="name"/> (type: <xsl:value-of select="type"/>)</a></font><xsl:if test="section"><xsl:for-each select="section"><xsl:call-template name="sectionTemplate"><xsl:with-param name="navigation" select="$navigation"/><xsl:with-param name="anchorBase" select="concat($anchorName,'SubSec')"/><xsl:with-param name="url" select="$repository"/></xsl:call-template></xsl:for-each></xsl:if></ol></xsl:when><xsl:otherwise><a name="{$anchorName}"><h3><xsl:value-of select="name"/> Section</h3></a><p><b>Type: </b><xsl:value-of select="type"/><br/><xsl:choose><xsl:when test ="repository"><b>Repository: </b><xsl:value-of select="repository"/><br/></xsl:when><xsl:otherwise><b>Repository: </b><xsl:value-of select="$repository"/><br/></xsl:otherwise></xsl:choose><b>Link: </b><xsl:if test="link"><xsl:value-of select="link"/></xsl:if><br/><b>Include:</b><xsl:if test="include"><font color="red"><xsl:value-of select="include"/></font></xsl:if><br/><b>Definition: </b><xsl:if test="definition"><xsl:value-of select="definition"/></xsl:if><br/></p><xsl:if test="property"><table border="1" rules="rows" width="100%"><font size="-1"><tr bgcolor="#336699" align="left" valign="middle"><th><font size="+1" color="white"><b>Name</b></font></th><th><font size="+1" color="white"><b>Value</b></font></th><th><font size="+1" color="white"><b>Unit</b></font></th><th><font size="+1" color="white"><b>Type</b></font></th><th><font size="+1" color="white"><b>Uncertainty</b></font></th><th><font size="+1" color="white"><b>Definition</b></font></th><th><font size="+1" color="white"><b>Dependency</b></font></th><th><font size="+1" color="white"><b>Dependency Value</b></font></th></tr><xsl:for-each select="property"><xsl:variable name="anchor"><xsl:value-of select ="name"/></xsl:variable><tr><td width="15%"><a name="{$anchor}"/><p><xsl:value-of select="name"/></p></td><td width="10%"><p><xsl:value-of select="value"/></p></td><td width="5%"><p><xsl:value-of select="unit"/><br/></p></td><td width="5%"><p><xsl:value-of select="type"/></p></td><td width="5%"><p><xsl:value-of select="uncertainty"/><br/></p></td><td width="22.5%"><p><xsl:value-of select="definition"/></p></td><td width="5%"><p><xsl:value-of select="dependency"/></p></td><td width="5%"><p><xsl:value-of select="dependencyValue"/></p></td></tr></xsl:for-each></font></table></xsl:if><a href="#top"><tiny>top</tiny></a><hr class="thinline" /><xsl:if test="section"><xsl:for-each select="section"><xsl:call-template name="sectionTemplate"><xsl:with-param name="navigation" select="$navigation"/><xsl:with-param name="anchorBase" select="concat($anchorName,'SubSec')"/><xsl:with-param name="url" select="$repository"/></xsl:call-template></xsl:for-each></xsl:if></xsl:otherwise></xsl:choose></xsl:template>
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<id>5c4adfd1-62f9-4265-90bc-6bdb822a8065</id>
<version>1.0</version>
<author>Reema Gupta</author>
<section>
<id>ec31c7fa-d38e-424f-af03-ec762d2c3e30</id>
<type>n.s.</type>
<name>electrophysiology</name>
<definition>Electrophysiology-template template schema generated by the CEDAR Template Editor 2.6.56</definition>
<section>
<id>e5149164-5a40-422e-9efa-fcd0b33b512c</id>
<type>n.s.</type>
<name>in2pb-header</name>
<definition>Header to be used for metadata templates created for In2PB projects.</definition>
<property>
<id>2c06a292-7651-44a1-adc1-3fd4203b1da6</id>
<name>in2pb-header</name>
<value></value>
<definition>Header to be used for metadata templates created for In2PB projects.</definition>
</property>
</section>
<section>
<id>e5b52bb8-4097-48b5-8cb3-f43e375f65b4</id>
<type>n.s.</type>
<name>electrophysiology-header</name>
<definition>Header with instructions for the electrophysiology metadata.</definition>
<property>
<id>3c62092a-52c9-4bde-91b0-66c1bd08a4a2</id>
<name>electrophysiology-header</name>
<value></value>
<definition>Header with instructions for the electrophysiology metadata.</definition>
</property>
</section>
<section>
<id>78de3107-989b-47cd-9ba4-3666fcdfd7ab</id>
<type>n.s.</type>
<name>probe-element</name>
<definition>Probes are physical devices used for recording the electrophysiological data. They can be permanently implanted (chronic recordings) or inserted just for the recording (acute recordings).</definition>
<property>
<id>1403b374-63f4-4235-ac14-a39b41d4afd2</id>
<name>probeID</name>
<value></value>
<definition>Unique identifier for each electrophysiological recording probe that is referenced in the dataset.</definition>
</property>
<property>
<id>daecb2aa-c0cd-4929-9d80-239160c33339</id>
<name>probeType</name>
<value></value>
<definition>Type of probe used – Utah array, laminar, single tetrode, etc.</definition>
</property>
<property>
<id>07657286-1e1d-407d-834f-663a6f0ccce4</id>
<name>probeX</name>
<value></value>
<definition>Probe position along the global coordinate system x-axis.</definition>
</property>
<property>
<id>b30a2a51-7209-44e3-b2ef-78f67ad4508f</id>
<name>probeY</name>
<value></value>
<definition>Probe position along the global coordinate system y-axis.</definition>
</property>
<property>
<id>5e27819c-13ab-4a74-add9-35d0cc938b47</id>
<name>probeZ</name>
<value></value>
<definition>Probe position along the global coordinate system z-axis.</definition>
</property>
<property>
<id>4fe3c6a2-2335-47a8-aada-633a00439fb1</id>
<name>probeManufacturer</name>
<value></value>
<definition>Manufacturer of the probe system, eg., ‘opnephys’,’blackrock’, etc.</definition>
</property>
<property>
<id>630c8db7-3def-4987-8f2f-579efa7cb1e0</id>
<name>probeDeviceSerialNumber</name>
<value></value>
<definition>Manufacturer provided serial number of the probe.</definition>
</property>
<property>
<id>e324e266-b7a3-453b-b7a7-4804011ddd07</id>
<name>electrodeCount</name>
<value></value>
<definition>Number of miscellaneous analog electrodes for auxiliary signals (e.g. 2)</definition>
</property>
<property>
<id>c30969cf-27aa-4d0a-936a-6e81bbd817fd</id>
<name>probeWidth</name>
<value></value>
<definition>Physical width of the probe in mm, e.g. 5. This dimension corresponds to the x’ axis of the Euler transformation defined by alpha, beta and gamma rotations values below.</definition>
</property>
<property>
<id>544aa23c-1458-49fe-bdd0-204a2b560b9e</id>
<name>probeHeight</name>
<value></value>
<definition>Physical width of the probe in mm, e.g. 5. This dimension corresponds to the y’ axis of the Euler transformation defined by alpha, beta and gamma rotations values below.</definition>
</property>
<property>
<id>419ce921-c25c-401a-8f5a-872d1b25526f</id>
<name>probeDepth</name>
<value></value>
<definition>Physical depth of the probe in mm, e.g. 0.3. This dimension should be omitted or set to 0 for two-dimensional (shank-type) probes. This dimension corresponds to the z’ axis of the Euler transformation defined by alpha, beta and gamma rotations values below.</definition>
</property>
<property>
<id>ec58ff18-0271-48da-b600-87cd3906e6d9</id>
<name>probeAlphaRotation</name>
<value></value>
<definition>Euler angle in degree to match probe extension dimensions (width, height, depth) to global x, y, z coordinates</definition>
</property>
<property>
<id>9a5762fd-6219-4eda-927c-2966dd43aa2a</id>
<name>probeBetaRotation</name>
<value></value>
<definition>Euler angle in degree to match probe extension dimensions (width, height, depth) to global x, y, z coordinates.</definition>
</property>
<property>
<id>104c3cde-877d-4470-9079-b9ed9b66c15d</id>
<name>probeGammaRotation</name>
<value></value>
<definition>Euler angle in degree to match probe extension dimensions (width, height, depth) to global x, y, z coordinates.</definition>
</property>
<property>
<id>62da7e0f-cddb-4bfd-af3e-466292816143</id>
<name>probeCoordinateReferencePoint</name>
<value></value>
<definition>Point of the probe that is described by the probe coordinates and on which the alpha, beta and gamma rotations are applied</definition>
</property>
<property>
<id>6f4c71db-ce6a-4e3d-8410-269433dd82d9</id>
<name>probeHemisphere</name>
<value></value>
<definition>Brain hemisphere where probe was located in.</definition>
</property>
<property>
<id>3e2ea94e-bcfd-4231-9af7-b75678240af6</id>
<name>associatedBrainRegion</name>
<value></value>
<definition>Textual indication of the location of the probe in the brain.</definition>
</property>
<property>
<id>e3215aef-000e-4032-9589-39b0a4ab2f42</id>
<name>associatedBrainRegionID</name>
<value></value>
<definition>Identifier of the associated brain region based on BIRNLEX ontology.</definition>
</property>
<property>
<id>27c8a160-2d3a-4bc4-b5d8-a5ca8d93b3a2</id>
<name>associatedBrainRegionQualityType</name>
<value></value>
<definition>The method used to identify the associated brain region (estimated|proof) depending on anatomical pictures proofing the location or indirect estimation of the location.</definition>
</property>
<property>
<id>3957994c-8cb4-4630-a674-1449bc864599</id>
<name>referenceAtlas</name>
<value></value>
<definition>Reference atlas used for associated brain region</definition>
</property>
<property>
<id>a097e576-eeaf-4765-ba39-b140e26637c6</id>
<name>probeMaterial</name>
<value></value>
<definition>A textual description of the base material of the probe.</definition>
</property>
</section>
<section>
<id>de75deeb-2d08-4103-858f-bc2fbaaecd39</id>
<type>n.s.</type>
<name>electrode-element</name>
<definition>Electrodes describe the points of electrodes to the tissue used for recording electrophysiological signals.</definition>
<property>
<id>51c06e4f-9401-49c8-8f47-6203149ab6d4</id>
<name>electrodeID</name>
<value></value>
<definition>Unique identifier for the electrode, to match and be referenced in channel description.</definition>
</property>
<property>
<id>697b9a09-a536-42e3-800f-046fd28e5be2</id>
<name>electrodeProbeID</name>
<value></value>
<definition>Identifier to specify which shank of the probe the electrode is present. Alternatively, electrode probe identifier could be used here.</definition>
</property>
<property>
<id>dea45413-b5da-467a-b8dc-e109b9267fa1</id>
<name>shankID</name>
<value></value>
<definition>Id to specify which shank of the probe the electrode is on. This is useful for spike sorting when the electrodes are on a multi-shank probe.</definition>
</property>
<property>
<id>0be02611-7297-43ab-a13a-7ba4bb03c17b</id>
<name>electrodeHemisphere</name>
<value></value>
<definition>Brain hemisphere where the electrode was located.</definition>
</property>
<property>
<id>2aa88314-adfc-4bf0-8b50-08d8a3e6218e</id>
<name>electrodeX</name>
<value></value>
<definition>Recorded position along the local x-axis relative to the probe origin and rotation.</definition>
</property>
<property>
<id>01cd6af5-a79f-4270-8e36-00637b57fab2</id>
<name>electrodeY</name>
<value></value>
<definition>Recorded position along the local y-axis relative to the probe origin and rotation.</definition>
</property>
<property>
<id>4b573a3e-fab8-4845-8f52-ac657bb4dc56</id>
<name>electrodeZ</name>
<value></value>
<definition>Recorded position along the local z-axis relative to the probe origin and rotation.</definition>
</property>
<property>
<id>9bdbd8a9-b57c-4283-b0a9-98a98a7b466a</id>
<name>electrodeImpedance</name>
<value></value>
<definition>Impedance of the electrode or pipette (pipette_resistance). This can be a single value or a list of two values indicating a value range. It must be in kOhm</definition>
</property>
<property>
<id>7707799d-788a-41e3-b946-3d357b18dc1b</id>
<name>electrodeSize</name>
<value></value>
<definition>Size of the electrode, e.g. non-insulated surface area or length of non-insulated cable.</definition>
</property>
<property>
<id>15c26f75-b35e-4190-8a83-4b4a07f67f6e</id>
<name>electrodeShape</name>
<value></value>
<definition>Description of the shape of the electrode, e.g. square, circle, etc.</definition>
</property>
<property>
<id>809c47c1-ed8b-4503-be72-95f07e0b2c84</id>
<name>electrodeMaterial</name>
<value></value>
<definition>Material of the electrode surface.</definition>
</property>
<property>
<id>c91da254-1166-475a-8ff0-20e184e69bde</id>
<name>electrodeLocation</name>
<value></value>
<definition>Textual indication of the location of the electrode (e.g. cortical layer 3, ca1, etc)</definition>
</property>
<property>
<id>2bb11e21-114a-4e5e-8fe0-b2de83aa1d18</id>
<name>electrodeInsulationMaterial</name>
<value></value>
<definition>Material used for insulation around the electrode.</definition>
</property>
</section>
<section>
<id>9877ec91-05f7-49f1-a84f-f3f09d0dd0f3</id>
<type>n.s.</type>
<name>channel-element</name>
<definition>Channels are virtual sources of recorded signals. These might be of neuronal origin (e.g. online filtered LFP signals) or generated by the recording setup (e.g. synchronization signals, behavioral signals, etc).</definition>
<property>
<id>5ca54849-fc32-47fe-87f3-05b4e6e18411</id>
<name>channelID</name>
<value></value>
<definition>Identifier for the channel, to be referenced in the data files.</definition>
</property>
<property>
<id>6d7f1a38-6ece-40b4-8f5f-580fb74804dc</id>
<name>channelType</name>
<value></value>
<definition>Type of the channel, e.g. Neural signal, digital trial events, synchronization pulses, etc</definition>
</property>
<property>
<id>7a9f69c4-b6a9-4ce9-b4c6-f036419fcd06</id>
<name>channelUnit</name>
<value></value>
<definition>Physical unit of the value represented in this channel.</definition>
</property>
<property>
<id>c9210fdc-d92f-40ef-8885-04080f389ff1</id>
<name>samplingFrequency</name>
<value></value>
<definition>Sampling rate of the channel in Hz.</definition>
</property>
<property>
<id>cb324485-80dd-4185-badd-24b3530c1687</id>
<name>channelLabel</name>
<value></value>
<definition>Human readable identifier for non-contact related signal, e.g. Daq internal synchronization signals, behavioral signals, behavioral cues, etc.</definition>
</property>
<property>
<id>a480e30b-0ac6-46cc-858d-3c4a6fb90d1a</id>
<name>channelElectrodeID</name>
<value></value>
<definition>Identifier for the electrode for a electrode based channel. Not applicable for non-contact related signal.</definition>
</property>
<property>
<id>ad505c35-9dae-40fd-9a7d-99727dab4ee1</id>
<name>dataStreamID</name>
<value></value>
<definition>Data stream of the recording the signal.</definition>
</property>
<property>
<id>b63fbfab-5a64-4de9-a5ea-ea46d495e992</id>
<name>channelDescription</name>
<value></value>
<definition>Brief free-text description of the channel, or other information of interest.</definition>
</property>
<property>
<id>2abd7663-3e99-424c-b11c-2d3c7cb82f98</id>
<name>hardwareFilters</name>
<value></value>
<definition>List of hardware filters (amplifiers) applied, details to be referenced from recording setup metadata for electrophysiology.</definition>
</property>
<property>
<id>f3b22bb7-1c43-4863-bf81-c35eab28f043</id>
<name>softwareFilters</name>
<value></value>
<definition>List of temporal software filters applied, details to be referenced from recording setup metadata for electrophysiology.</definition>
</property>
<property>
<id>eb629465-67d7-44af-a8e4-d51da97a035f</id>
<name>notchFilters</name>
<value></value>
<definition>List of notch filters applied, e.g. low_frequency, high_frequency, etc.</definition>
</property>
<property>
<id>405c7372-6cda-471d-89ac-239bf8595a67</id>
<name>channelStatus</name>
<value></value>
<definition>Data quality observed on the channel (good/bad). A channel is considered bad if its data quality is compromised by excessive noise. Description of noise type SHOULD be provided in channelStatusDescription.</definition>
</property>
<property>
<id>f8a60533-2294-484b-9a3a-97564d1c7292</id>
<name>channelStatusDescription</name>
<value></value>
<definition>Freeform text description of noise or artifact affecting data quality on the channel.</definition>
</property>
<property>
<id>5dd2e7ca-b9f1-4914-bc04-2ddb087c62ee</id>
<name>channelGain</name>
<value></value>
<definition>Amplification factor applied from signal detection at the contact to the signal stored in the data file in dB.</definition>
</property>
<property>
<id>356364c8-4298-4a17-9ef3-8d37cb9a5b95</id>
<name>channelTimeOffset</name>
<value></value>
<definition>Time shift between signal of this channel to the reference channel.</definition>
</property>
<property>
<id>9c61b407-2933-4b14-95de-8b37bf41b1b4</id>
<name>channelTimeReference</name>
<value></value>
<definition>Reference channel used for time alignment of signals.</definition>
</property>
<property>
<id>fbb21c10-efec-4e28-971b-da3dc8e45e9b</id>
<name>channelReference</name>
<value></value>
<definition>Contact used as physical reference, e.g. contact identifier, physical location (subdural, chamber screw).</definition>
</property>
<property>
<id>afc73fcc-8f79-4d11-9277-5e04277ffa23</id>
<name>channelGround</name>
<value></value>
<definition>Information on the ground, e.g. Chamber screw, head post, ear clip, etc</definition>
</property>
</section>
<section>
<id>c9973e1f-bdf5-4ad3-a38c-dd26f8e55cc7</id>
<type>n.s.</type>
<name>acquisiton-system-element</name>
<definition>Information about the hardware and software of the data acquisition system.</definition>
<property>
<id>0866418e-f2cf-4b77-919f-44886e1b85ae</id>
<name>powerLineFrequency</name>
<value></value>
<definition>Frequency (in Hz) of the power line at the setup location.</definition>
</property>
<property>
<id>dc41b4d6-e430-4e49-a9de-d28b4bd71e7d</id>
<name>manufacturer</name>
<value></value>
<definition>Manufacturer of the acquisition system (e.g. "OpenEphys”, “Alphaomega",”Blackrock”)</definition>
</property>
<property>
<id>3e0bd70b-624b-4b2a-b9dc-42f1203b900d</id>
<name>manufacturerModelName</name>
<value></value>
<definition>Name of the data acquisition system used.</definition>
</property>
<property>
<id>30cd431b-052f-4b21-a57c-7bd4b9830810</id>
<name>manufacturerModelVersion</name>
<value></value>
<definition>Version of the data acquisition system.</definition>
</property>
<property>
<id>e052a4aa-0509-4bc1-bf2f-1b17807a19e5</id>
<name>recordingSetupCustomName</name>
<value></value>
<definition>Custom name of the data acquisition system.</definition>
</property>
<property>
<id>c8b08893-ec8a-47eb-a9ba-4ce35b9f1bde</id>
<name>institutionName</name>
<value></value>
<definition>The name of the institution where data is recorded.</definition>
</property>
<property>
<id>138e3ec3-df53-46d9-acae-da32fd021bb9</id>
<name>institutionAddress</name>
<value></value>
<definition>The address of the institution where data is recorded.</definition>
</property>
<property>
<id>54f56495-4df0-4a6c-9011-aa1f136e2bfe</id>
<name>samplingFrequency</name>
<value></value>
<definition>Internal (maximum) sampling frequency of the recording in Hz.</definition>
</property>
<property>
<id>46421c38-7beb-4d60-9a35-1f004db75c23</id>
<name>serialNumbers</name>
<value></value>
<definition>The serial number of the components of the setup, recommended to add serial numbers and versions of ALL components constituting the setup.</definition>
</property>
<property>
<id>2175d40b-2789-4852-beca-a7886134f524</id>
<name>usesSoftwareSuite</name>
<value></value>
<definition>Software suite used for data acquisition.</definition>
</property>
<property>
<id>9a84586b-3fa6-4f61-9293-3dac50ca6a13</id>
<name>softwareVersions</name>
<value></value>
<definition>Version of the acquisition softwares.</definition>
</property>
<property>
<id>1957df1c-630e-43be-9ba1-5c3e58da29bc</id>
<name>systemCreator</name>
<value></value>
<definition>Name of the person(s) who set up the system.</definition>
</property>
<property>
<id>de2a682c-3409-40fd-bb27-0a827aaeac67</id>
<name>systemMaintainer</name>
<value></value>
<definition>Name of the person(s) who maintains the system.</definition>
</property>
</section>
<section>
<id>e6c348ff-90a5-4665-958a-a7241b057d1b</id>
<type>n.s.</type>
<name>free-text-field</name>
<definition>A free text element to allow the user to provide any additional information.</definition>
</section>
<property>
<id>297372a2-60ad-4856-9140-38001a9fb756</id>
<name>free-text-field</name>
<value></value>
<definition>A free text element to allow the user to provide any additional information.</definition>
</property>
</section>
</odML>