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@@ -0,0 +1,383 @@
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+<?xml version="1.0" encoding="UTF-8"?>
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+<?xml-stylesheet type="text/xsl" href="odmlDocument.xsl"?>
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+<odML version="1.1">
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+ <id>8c5c5847-d361-4816-93b4-0e7c212931cf</id>
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+ <version>0.1</version>
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+ <author>Jeff Teeters</author>
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+ <date>2020-02-10</date>
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+ <section>
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+ <id>d269e4ee-a1f7-4790-996c-794f748850d4</id>
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+ <type>Experiment</type>
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+ <name>Experiment</name>
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+ <definition>Metadata about the experiment session</definition>
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+ <property>
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+ <id>fbcbefa8-7b1e-4701-a149-e06e92d46c76</id>
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+ <name>species</name>
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+ <value>Mus musculus</value>
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+ <definition>Species. Examples: Mus musculus, Rattus norvegicus</definition>
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+ <type>string</type>
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+ </property>
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+ <property>
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+ <id>b2ac3dde-cf55-42b7-9634-8c2fbef9382c</id>
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+ <name>animalStrain</name>
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+ <value>pl56</value>
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+ <definition>One of: 012569, kj18, JAX stock number, GENSAT ID, other</definition>
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+ <type>string</type>
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+ </property>
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+ <property>
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+ <id>24b87e0c-92fd-4001-bcc8-978f6b45a3a9</id>
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+ <name>animalGeneCopy</name>
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+ <value>1</value>
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+ <definition>0, 1 or 2; 0: homozygous ko; 1: het transgene; 2: homo transgene</definition>
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+ <type>int</type>
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+ </property>
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+ <property>
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+ <id>cb6704d9-223e-4e80-8314-f57c730a79c2</id>
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+ <name>animalGeneModification</name>
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+ <value>tlx-cre</value>
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+ <definition>Examples: PV-ires-Cre, rosa-Cag-lsl-ChR2-YFP, sim1-cre; describe genomic modification</definition>
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+ <type>string</type>
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+ </property>
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+ <property>
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+ <id>3c55be31-6a26-4c7e-a746-532cdce8c3d1</id>
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+ <name>animalSource</name>
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+ <value>GENSAT</value>
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+ <definition>Examples: JAX, GENSAT, investigator name; or other source of the animal</definition>
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+ <type>string</type>
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+ </property>
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+ <property>
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+ <id>e62160fb-500b-4e4b-8590-ff42dea2d3a6</id>
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+ <name>animalGeneticBackground</name>
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+ <value>unidentified</value>
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+ <definition>Example: unidentified; describe breeding history</definition>
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+ <type>string</type>
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+ </property>
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+ <property>
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+ <id>eff278f3-9d1c-45cb-b369-750799d222a5</id>
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+ <name>animalID</name>
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+ <value>anm00221977</value>
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+ <definition>Example: anm0032456; unique animal identifier</definition>
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+ <type>string</type>
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+ </property>
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+ <property>
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+ <id>ff022607-6334-4b9b-bb3b-c2ebed748d99</id>
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+ <name>sex</name>
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+ <value>m</value>
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+ <definition>sex of mouse (m,f)</definition>
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+ <type>string</type>
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+ </property>
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+ <property>
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+ <id>db99aded-e083-4b4c-987f-494891eaad24</id>
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+ <name>dateOfBirth</name>
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+ <value>not recorded</value>
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+ <definition>Format: yyyymmdd (international standard notation)</definition>
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+ <type>string</type>
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+ </property>
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+ <property>
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+ <id>288e7de3-058b-4a4c-8239-9acba888c3c1</id>
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+ <name>dateOfExperiment</name>
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+ <value>20140115</value>
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+ <definition>Format: yyyymmdd (international standard notation)</definition>
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+ <type>string</type>
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+ </property>
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+ <property>
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+ <id>008d808b-85fc-4fe1-9593-d6a641d5591d</id>
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+ <name>timeOfExperiment</name>
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+ <value>114656</value>
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+ <definition>Format: hhmmss (international standard notation)</definition>
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+ <type>string</type>
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+ </property>
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+ <property>
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+ <id>52f84e9b-ab04-44ee-af0d-1513074d25e0</id>
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+ <name>experimenters</name>
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+ <value>Nuo Li</value>
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+ <definition>names of experimenters</definition>
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+ <type>string</type>
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+ </property>
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+ <property>
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+ <id>458d6701-6164-4198-b43c-80e1aec8023f</id>
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+ <name>citation</name>
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+ <value>**PMID currently not avaliable</value>
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+ <definition>PMID</definition>
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+ <type>string</type>
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+ </property>
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+ <property>
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+ <id>c5dcf340-92bb-456f-9136-63149b2ee1d1</id>
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+ <name>whiskerConfig</name>
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+ <value>full</value>
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+ <definition>Description of the state of the whiskers during the experiment. Examples: full/ C row/ C2</definition>
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+ <type>string</type>
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+ </property>
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+ <property>
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+ <id>714f7ab6-b796-4a38-8ae0-cbfb38d829ce</id>
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+ <name>weightBefore</name>
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+ <value></value>
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+ <definition>Weight of subject at the beginning of the experiment, in grams; Example: 20</definition>
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+ </property>
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+ <property>
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+ <id>da31d652-727d-44db-8ca6-f14084eba49f</id>
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+ <name>da31d652-727d-44db-8ca6-f14084eba49f</name>
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+ <value></value>
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+ <definition>Weight of subject at the end of the experiment, in grams; Example: 21</definition>
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+ </property>
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+ <property>
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+ <id>61cf3645-7b8e-48ba-878c-e89911e62da6</id>
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+ <name>experimentType</name>
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+ <value>[behavior,extracellular,photostim]</value>
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+ <definition>Specifies the types of experiments, not exclusive; see detailed decription below. Is one of: behavior/extracellular/wholeCell/calciumImaging/photostim.</definition>
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+ <type>string</type>
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+ </property>
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+ <property>
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+ <id>455e83c9-61f5-46f8-9e15-bd3b03df82ad</id>
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+ <name>455e83c9-61f5-46f8-9e15-bd3b03df82ad</name>
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+ <value>Paxinos</value>
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+ <definition>Specifies reference atlast for anatomical locations; Example: Allen Reference Atlas</definition>
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+ <type>string</type>
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+ </property>
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+ </section>
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+ <section>
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+ <id>8c129122-3b31-46da-91a9-a4b8ba0f4eb5</id>
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+ <type>Surgerical procedures</type>
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+ <name>Surgerical_procedures</name>
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+ <definition>Procedures used for the surgery</definition>
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+ <section>
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+ <id>a40b99e0-6687-4af6-9fc5-050b1cbc5642</id>
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+ <type>virus</type>
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+ <name>Virus</name>
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+ <definition>viral injection metadata</definition>
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+ <property>
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+ <id>a45e34a4-df04-4fba-b064-b90c327a1c5e</id>
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+ <name>virusSource</name>
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+ <value>Janelia core</value>
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+ <definition>Source of virus. Examples: Upenn, Janelia core, investigator, other</definition>
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+ <type>string</type>
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+ </property>
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+ <property>
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+ <id>451da662-5b2a-472d-9d9c-932675e579b9</id>
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+ <name>virusID</name>
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+ <value>Addgene41015</value>
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+ <definition>Upenn designation; or addgene; Example: AV-9-PV2833</definition>
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+ <type>string</type>
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+ </property>
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+ <property>
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+ <id>4daa7f4e-ae68-42bd-8db7-484c301d3401</id>
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+ <name>virusLotNumber</name>
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+ <value></value>
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+ <definition>virus lot number</definition>
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+ </property>
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+ <property>
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+ <id>1fac4172-7a62-4825-b4ac-d451cc21d246</id>
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+ <name>infectionCoordinates</name>
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+ <value>[[2.5, -1.5, 0.3]","[2.5, -1.5, 0.7]]</value>
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+ <definition>Locations of infection if based on histology or injection (ml, ap, depth) relative to bregma; in millimeters; if multiple injection sites give list of (x,y,z) coordinates.</definition>
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+ <type>string</type>
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+ </property>
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+ <property>
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+ <id>7a33177b-8009-481d-be19-42979635c087</id>
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+ <name>infectionLocation</name>
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+ <value>M2</value>
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+ <definition>location of infection according to atlas. Examples: vS1 C2 barrel</definition>
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+ <type>string</type>
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+ </property>
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+ <property>
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+ <id>f2845552-6e87-495a-9994-b4dd34ae87b6</id>
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+ <name>virusTiter</name>
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+ <value>untitered</value>
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+ <definition>nominal titer</definition>
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+ <type>string</type>
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+ </property>
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+ <property>
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+ <id>7aa2bacb-d893-43de-8a02-3da51b159ff4</id>
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+ <name>injectionVolume</name>
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+ <value>[100,100]</value>
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+ <definition>injection volume, in nL; Examples: 50, 50</definition>
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+ <type>int</type>
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+ </property>
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+ <property>
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+ <id>5bcf48a4-87a3-4d50-937b-c45ab981343f</id>
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+ <name>injectionDate</name>
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+ <value>20130904</value>
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+ <definition>Format: yyyymmdd</definition>
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+ <type>string</type>
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+ </property>
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+ </section>
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+ <property>
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+ <id>9353ebcb-33a9-434f-9113-35d6c2d73ed7</id>
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+ <name>surgicalManipulation</name>
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+ <value>virus injection</value>
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+ <definition>Specifies the types of surgical manipulations. Not exclusive. Examples: Virus injection/fiber implant/window implant/drug injection/electroporation</definition>
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+ <type>string</type>
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+ </property>
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+ </section>
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+ <section>
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+ <id>5c7a3468-336d-4e58-88f8-1d6e1cef2b3f</id>
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+ <type>Extracellular recordings</type>
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+ <name>Extracellular</name>
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+ <definition>Extracellular recordings metadata</definition>
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+ <property>
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+ <id>cac9dae7-0019-4f76-8c41-91262b41b681</id>
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+ <name>recordingCoordinates</name>
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+ <value>[2.5,-1.5,687.0422254603595]</value>
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+ <definition>Location of probe 1 (ml, ap, depth) relative to bregma; in millimeters. This is the center of the tips; for example, the location in a 4-shank electrode will be specified as a point along the tips, but between the two center shanks. Example: P: 1.5; Lat: 3.5; depth</definition>
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+ <type>float</type>
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+ </property>
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+ <property>
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+ <id>5b1a1c7b-1ba7-4054-a007-d2b3296ba707</id>
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+ <name>recordingLocation</name>
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+ <value>M2</value>
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+ <definition>location according to reference atlas or anatomy or ISI; Example: vS1, C2, Paxinos or ISI</definition>
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+ <type>string</type>
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+ </property>
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+ <property>
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+ <id>c2431605-6aac-432b-94f8-60c01b391b37</id>
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+ <name>recordingMarker</name>
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+ <value>stereotaxic</value>
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+ <definition>Examples: DiI, lesion, stereotaxic, ISI</definition>
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+ <type>string</type>
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+ </property>
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+ <property>
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+ <id>70f44ba2-083e-4ab6-bd99-915bf82b84cd</id>
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+ <name>recordingType</name>
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+ <value>accute</value>
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+ <definition>One of: chronic, accute</definition>
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+ <type>string</type>
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+ </property>
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+ <property>
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+ <id>07a08055-1a39-420f-a78f-0063c1a2154f</id>
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+ <name>penetrationN</name>
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+ <value>1</value>
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+ <definition>The nth time to access the tissue. Example: 1</definition>
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+ <type>int</type>
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+ </property>
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+ <property>
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+ <id>2735702c-bed1-499d-aba7-4c0ee306c238</id>
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+ <name>probeSource</name>
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+ <value>neuronexus</value>
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+ <definition>Examples: neuronexus, apig</definition>
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+ <type>string</type>
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+ </property>
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+ <property>
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+ <id>b797fe33-3caa-4fe2-81f3-0934da480289</id>
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+ <name>probeType</name>
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+ <value>A4x8-5mm-100-200-177</value>
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+ <definition>NN part#/ tetrode / Janelia ref</definition>
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+ <type>string</type>
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+ </property>
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+ <property>
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+ <id>7743fea9-b19b-4495-a94e-f05a7ed9e2d8</id>
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+ <name>groundCoordinates</name>
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+ <value>[-5, -1, 1]</value>
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+ <definition>(ml, ap, depth) relative to bregma; in millimeters</definition>
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+ <type>string</type>
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+ </property>
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+ <property>
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+ <id>fe082305-69cb-45ad-adfb-d48c0af031df</id>
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+ <name>referenceCoordinates</name>
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+ <value></value>
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+ <definition>(ml, ap, depth) relative to bregma; in millimeters</definition>
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+ <type>string</type>
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+ </property>
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+ <property>
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+ <id>91fbb84f-adef-4e18-bb41-a84553a24258</id>
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+ <name>siteLocations</name>
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+ <value>[(2.5;-1.2;0.577),(2.5;-1.2;0.477),(2.5;-1.2;0.377),(2.5;-1.2;0.277),(2.5;-1.2;0.177),(2.5;-1.2;0.077),(2.5;-1.2;-0.023),(2.5;-1.2;-0.123),(2.5;-1.4;0.577),(2.5;-1.4;0.477),(2.5;-1.4;0.377),(2.5;-1.4;0.277),(2.5;-1.4;0.177),(2.5;-1.4;0.077),(2.5;-1.4;-0.023),(2.5;-1.4;-0.123),(2.5;-1.6;0.577),(2.5;-1.6;0.477),(2.5;-1.6;0.377),(2.5;-1.6;0.277),(2.5;-1.6;0.177),(2.5;-1.6;0.077),(2.5;-1.6;-0.023),(2.5;-1.6;-0.123),(2.5;-1.8;0.577),(2.5;-1.8;0.477),(2.5;-1.8;0.377),(2.5;-1.8;0.277),(2.5;-1.8;0.177),(2.5;-1.8;0.077),(2.5;-1.8;-0.023),(2.5;-1.8;-0.123)]</value>
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+ <definition>array of locations, one per site (ml, ap, depth); in micrometers</definition>
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+ <type>3-tuple</type>
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+ </property>
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+ <property>
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+ <id>3717d030-7163-474a-ac4a-80c2cae489fa</id>
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+ <name>extracellularDataType</name>
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+ <value>[sorted spike times,spike waveform snipets,spike band voltage traces]</value>
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+ <definition>Either: sorted spike times, spike waveform snipets, spike band voltage traces, local field potential</definition>
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+ <type>string</type>
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+ </property>
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+ <property>
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+ <id>994832ae-fbac-4aa2-a0cd-fc879777cab0</id>
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+ <name>cellType</name>
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+ <value>[pyramidal,interneuron,pyramidal tract neuron,corpus callosal projection neuron]</value>
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+ <definition>Array of cell types; Example: pyramidal, PT neuron</definition>
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+ <type>string</type>
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+ </property>
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+ <property>
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+ <id>bd6a264f-1ef3-4bec-a714-a18d2d9acf72</id>
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+ <name>identificationMethod</name>
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+ <value>[waveform shape,waveform shape,ChR tagging and collision test,ChR tagging and collision test]</value>
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+ <definition>Example: waveform shape, ChR tagging</definition>
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+ <type>string</type>
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+ </property>
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+ <property>
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+ <id>f7539e1a-1046-4fa8-adac-9ffb4552f9d1</id>
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+ <name>amplifierRolloff</name>
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+ <value></value>
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+ <definition>rolloff frequency of the recording system, kHz</definition>
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+ </property>
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+ <property>
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+ <id>9391b7b7-6ac0-4855-b082-b611966114e9</id>
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+ <name>spikeSorting</name>
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+ <value>manual</value>
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+ <definition>algorithm or manual; for algorithm, provide citation of the original method paper</definition>
|
|
|
+ <type>string</type>
|
|
|
+ </property>
|
|
|
+ <property>
|
|
|
+ <id>21f2a41a-9f50-469f-a4c1-1976a279a131</id>
|
|
|
+ <name>ADunit</name>
|
|
|
+ <value>14 bits</value>
|
|
|
+ <definition>Describe the AD unit; example: '14 bits'</definition>
|
|
|
+ <type>string</type>
|
|
|
+ </property>
|
|
|
+ </section>
|
|
|
+ <section>
|
|
|
+ <id>b64450ca-875e-40d7-b16d-4490723b2efb</id>
|
|
|
+ <type>Photostim</type>
|
|
|
+ <name>Photostim</name>
|
|
|
+ <definition>Photostimulation metadata</definition>
|
|
|
+ <property>
|
|
|
+ <id>fb2dde7c-2c79-48b7-a97a-cbe7464cc7e3</id>
|
|
|
+ <name>photostimWavelength</name>
|
|
|
+ <value>473</value>
|
|
|
+ <definition>photostimulation wavelength in nanometers</definition>
|
|
|
+ <type>int</type>
|
|
|
+ </property>
|
|
|
+ <property>
|
|
|
+ <id>095c96bb-56dd-42e5-8ee7-d9fd2891f54b</id>
|
|
|
+ <name>stimulationMethod</name>
|
|
|
+ <value>[clear skull,craniotomy]</value>
|
|
|
+ <definition>specifies the types of photostimulation experiment, not exclusive. Examples: clear skull, craniotomy, glass window, optica fiber, 2P excitation</definition>
|
|
|
+ <type>string</type>
|
|
|
+ </property>
|
|
|
+ <property>
|
|
|
+ <id>ac183231-f064-47a7-9647-fa2f4df3fd82</id>
|
|
|
+ <name>photostimCoordinates</name>
|
|
|
+ <value>[(2.5;1.5;0),(2.5;-1.5;0)]</value>
|
|
|
+ <definition>x,y,z; laser focal location or fiber tip location; (ml, ap, depth) relative to bregma; in millimeters</definition>
|
|
|
+ <type>3-tuple</type>
|
|
|
+ </property>
|
|
|
+ <property>
|
|
|
+ <id>8ba62818-93cf-4423-988e-21b02675aaf1</id>
|
|
|
+ <name>photostimLocation</name>
|
|
|
+ <value>[ALM,ALM]</value>
|
|
|
+ <definition>Example: ALM</definition>
|
|
|
+ <type>string</type>
|
|
|
+ </property>
|
|
|
+ <property>
|
|
|
+ <id>3e4b7974-1ee2-4343-983d-e31e6dece2b9</id>
|
|
|
+ <name>identificationMethod</name>
|
|
|
+ <value>[stereotaxic coordinate,stereotaxic coordinate]</value>
|
|
|
+ <definition>Example: histology</definition>
|
|
|
+ <type>string</type>
|
|
|
+ </property>
|
|
|
+ </section>
|
|
|
+ <section>
|
|
|
+ <id>881eaec9-ee79-48df-945c-517e80ce60b0</id>
|
|
|
+ <type>Behavior</type>
|
|
|
+ <name>Behavior</name>
|
|
|
+ <definition>Behavior metadata</definition>
|
|
|
+ <property>
|
|
|
+ <id>69c4c885-0d2f-4056-8680-836450fd0d27</id>
|
|
|
+ <name>task_keyword</name>
|
|
|
+ <value>[detection,discrimination,lick Left lick Right,delay,somatosensory,motor,response,reward]</value>
|
|
|
+ <definition>One of: detection, discrimination, go nogo, lick Left lick Right, delay, somatosensory, motor, response, reward</definition>
|
|
|
+ <type>string</type>
|
|
|
+ </property>
|
|
|
+ </section>
|
|
|
+</odML>
|
