tcrdb.xml

<?xml version="1.0" encoding="UTF-8"?>
<!-- 

 * Copyright (c) 2015 LabKey Corporation
 *
 * Licensed under the Apache License, Version 2.0 (the "License");
 * you may not use this file except in compliance with the License.
 * You may obtain a copy of the License at
 *
 *     http://www.apache.org/licenses/LICENSE-2.0
 *
 * Unless required by applicable law or agreed to in writing, software
 * distributed under the License is distributed on an "AS IS" BASIS,
 * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 * See the License for the specific language governing permissions and
 * limitations under the License.

 -->
<tables xsi:schemaLocation="http://labkey.org/data/xml ..\..\..\..\schemas\tableInfo.xsd" xmlns="http://labkey.org/data/xml" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
    <table tableName="mixcr_libraries" tableDbType="TABLE" useColumnOrder="true">
        <javaCustomizer class="org.labkey.ldk.query.DefaultTableCustomizer" />
        <tableTitle>MiXCR Libraries</tableTitle>
        <columns>
            <column columnName="rowid">
                <columnTitle>Row Id</columnTitle>
            </column>
            <column columnName="label">

            </column>
            <column columnName="libraryName">
                <columnTitle>Library Name</columnTitle>
            </column>
            <column columnName="species">

            </column>
            <column columnName="additionalParams">
                <columnTitle>Additional Params</columnTitle>
                <description>A semi-colon delimited list of additional command line arguments to pass to mixcr align</description>
            </column>
            <column columnName="libraryId">
                <columnTitle>Reference Genome</columnTitle>
                <nullable>true</nullable>
                <fk>
                    <fkDbSchema>sequenceanalysis</fkDbSchema>
                    <fkTable>reference_libraries</fkTable>
                    <fkColumnName>rowid</fkColumnName>
                </fk>
            </column>
            <column columnName="dateDisabled">
                <columnTitle>Date Disabled</columnTitle>
            </column>
            <column columnName="container">
                <isHidden>true</isHidden>
            </column>
            <column columnName="createdby">
                <isHidden>true</isHidden>
            </column>
            <column columnName="created">
                <isUserEditable>false</isUserEditable>
                <shownInInsertView>false</shownInInsertView>
                <shownInUpdateView>false</shownInUpdateView>
                <nullable>true</nullable>
                <scale>29</scale>
                <isHidden>true</isHidden>
            </column>
            <column columnName="modifiedby">
                <isHidden>true</isHidden>
            </column>
            <column columnName="modified">
                <isUserEditable>false</isUserEditable>
                <shownInInsertView>false</shownInInsertView>
                <shownInUpdateView>false</shownInUpdateView>
                <nullable>true</nullable>
                <scale>29</scale>
                <isHidden>true</isHidden>
            </column>
        </columns>
        <buttonBarOptions includeStandardButtons="true">
            <includeScript>ldk.context</includeScript>
            <includeScript>/tcrdb/buttons.js</includeScript>
            <item text="More Actions" insertAfter="last" iconCls="ellipsis-h">
                <item text="Create Genome">
                    <onClick>TCRdb.buttons.createMixcrGenome(dataRegionName)</onClick>
                </item>
            </item>
        </buttonBarOptions>
    </table>
    <table tableName="loci" tableDbType="TABLE" useColumnOrder="true">
        <javaCustomizer class="org.labkey.ldk.query.DefaultTableCustomizer" />
        <insertUrl></insertUrl>
        <importUrl></importUrl>
        <updateUrl></updateUrl>
        <columns>
            <column columnName="locus">

            </column>
        </columns>
    </table>

    <table tableName="clone_responses" tableDbType="TABLE" useColumnOrder="true">
        <javaCustomizer class="org.labkey.laboratory.query.LaboratoryTableCustomizer" />
        <tableTitle>TCR Clone Responses</tableTitle>
        <titleColumn>rowid</titleColumn>
        <columns>
            <column columnName="rowid">
                <columnTitle>Row Id</columnTitle>
                <isHidden>true</isHidden>
            </column>
            <column columnName="cdna_id">
                <columnTitle>cDNA ID</columnTitle>
                <fk>
                    <fkDbSchema>singlecell</fkDbSchema>
                    <fkTable>cdna_libraries</fkTable>
                    <fkColumnName>rowid</fkColumnName>
                </fk>
            </column>
            <column columnName="nostimid">
                <columnTitle>No Stim / Control cDNA ID</columnTitle>
                <fk>
                    <fkDbSchema>singlecell</fkDbSchema>
                    <fkTable>cdna_libraries</fkTable>
                    <fkColumnName>rowid</fkColumnName>
                </fk>
            </column>
            <column columnName="chain">
                <columnTitle>Chain</columnTitle>
            </column>
            <column columnName="clonotype">
                <columnTitle>Clonotype</columnTitle>
            </column>
            <column columnName="activationFrequency">
                <columnTitle>Activated Freq</columnTitle>
            </column>
            <column columnName="backgroundFrequency">
                <columnTitle>Background Freq</columnTitle>
            </column>
            <column columnName="vGene">
                <columnTitle>V-Gene</columnTitle>
            </column>
            <column columnName="jGene">
                <columnTitle>J-Gene</columnTitle>
            </column>
            <column columnName="totalCells">
                <columnTitle>Total Cells</columnTitle>
            </column>
            <column columnName="totalCloneSize">
                <columnTitle>Total Clone Size</columnTitle>
            </column>
            <column columnName="fractionCloneActivated">
                <columnTitle>Fraction of Clone Activated</columnTitle>
            </column>
            <column columnName="totalCellsForSample">
                <columnTitle>Total Cells For Sample</columnTitle>
            </column>
            <column columnName="oddsRatio">
                <columnTitle>Enrichment (Odds Ratio)</columnTitle>
            </column>
            <column columnName="enrichmentFDR">
                <columnTitle>Enrichment (FDR)</columnTitle>
            </column>
            <column columnName="comments">

            </column>
            <column columnName="container">
                <isHidden>true</isHidden>
            </column>
            <column columnName="createdby">
                <isHidden>true</isHidden>
            </column>
            <column columnName="created">
                <isUserEditable>false</isUserEditable>
                <shownInInsertView>false</shownInInsertView>
                <shownInUpdateView>false</shownInUpdateView>
                <nullable>true</nullable>
                <scale>29</scale>
                <isHidden>true</isHidden>
            </column>
            <column columnName="modifiedby">
                <isHidden>true</isHidden>
            </column>
            <column columnName="modified">
                <isUserEditable>false</isUserEditable>
                <shownInInsertView>false</shownInInsertView>
                <shownInUpdateView>false</shownInUpdateView>
                <nullable>true</nullable>
                <scale>29</scale>
                <isHidden>true</isHidden>
            </column>
        </columns>
    </table>
    <table tableName="clones" tableDbType="TABLE" useColumnOrder="true">
        <javaCustomizer class="org.labkey.laboratory.query.LaboratoryTableCustomizer" />
        <tableTitle>TCR Clones</tableTitle>
        <titleColumn>rowid</titleColumn>
        <columns>
            <column columnName="rowid">
                <columnTitle>Row Id</columnTitle>
                <isHidden>true</isHidden>
            </column>
            <column columnName="cloneName">
                <columnTitle>Clone Name</columnTitle>
                <nullable>false</nullable>
            </column>
            <column columnName="displayName">
                <columnTitle>Clone Display Name</columnTitle>
                <nullable>true</nullable>
                <description>This can be used to group multiple related clones, such as permutations of the same original clone</description>
            </column>
            <column columnName="chain">
                <columnTitle>Chain/Locus</columnTitle>
                <nullable>false</nullable>
            </column>
            <column columnName="cdr3">
                <columnTitle>CDR3</columnTitle>
                <nullable>false</nullable>
            </column>
            <column columnName="vGene">
                <columnTitle>V-Gene</columnTitle>
                <fk>
                    <fkDbSchema>tcrdb</fkDbSchema>
                    <fkTable>tcr_sequences</fkTable>
                    <fkColumnName>name</fkColumnName>
                    <fkDisplayColumnName useRawValue="true"/>
                </fk>
            </column>
            <column columnName="dGene">
                <columnTitle>D-Gene</columnTitle>
            </column>
            <column columnName="jGene">
                <columnTitle>J-Gene</columnTitle>
                <fk>
                    <fkDbSchema>tcrdb</fkDbSchema>
                    <fkTable>tcr_sequences</fkTable>
                    <fkColumnName>name</fkColumnName>
                    <fkDisplayColumnName useRawValue="true"/>
                </fk>
            </column>
            <column columnName="cGene">
                <columnTitle>Constant Gene</columnTitle>
                <fk>
                    <fkDbSchema>tcrdb</fkDbSchema>
                    <fkTable>tcr_sequences</fkTable>
                    <fkColumnName>name</fkColumnName>
                    <fkDisplayColumnName useRawValue="true"/>
                </fk>
            </column>
            <column columnName="status">
                <columnTitle>Status</columnTitle>
            </column>
            <column columnName="comments">

            </column>
            <column columnName="synthesized">
                <columnTitle>Synthesized?</columnTitle>
            </column>
            <column columnName="animals">
                <columnTitle>Animals With Clone</columnTitle>
            </column>
            <column columnName="responses">
                <columnTitle>Responses With Clone</columnTitle>
            </column>
            <column columnName="container">
                <isHidden>true</isHidden>
            </column>
            <column columnName="createdby">
                <isHidden>true</isHidden>
            </column>
            <column columnName="created">
                <isUserEditable>false</isUserEditable>
                <shownInInsertView>false</shownInInsertView>
                <shownInUpdateView>false</shownInUpdateView>
                <isHidden>true</isHidden>
            </column>
            <column columnName="modifiedby">
                <isHidden>true</isHidden>
            </column>
            <column columnName="modified">
                <isUserEditable>false</isUserEditable>
                <shownInInsertView>false</shownInInsertView>
                <shownInUpdateView>false</shownInUpdateView>
                <isHidden>true</isHidden>
            </column>
        </columns>
    </table>

    <table tableName="stims" tableDbType="TABLE" useColumnOrder="true">
        <javaCustomizer class="org.labkey.laboratory.query.LaboratoryTableCustomizer" />
        <tableTitle>Stim Experiments</tableTitle>
        <titleColumn>rowid</titleColumn>
        <columns>
            <column columnName="rowid">
                <columnTitle>Row Id</columnTitle>
                <isHidden>true</isHidden>
            </column>
            <column columnName="cdna_id">
                <columnTitle>cDNA ID</columnTitle>
                <fk>
                    <fkDbSchema>singlecell</fkDbSchema>
                    <fkTable>cdna_libraries</fkTable>
                    <fkColumnName>rowid</fkColumnName>
                </fk>
            </column>
            <column columnName="controlStimId">
                <columnTitle>No Stim / Control cDNA ID</columnTitle>
                <fk>
                    <fkDbSchema>singlecell</fkDbSchema>
                    <fkTable>cdna_libraries</fkTable>
                    <fkColumnName>rowid</fkColumnName>
                </fk>
            </column>
            <column columnName="quantificationMethod">
                <columnTitle>Quantification Method</columnTitle>
            </column>
            <column columnName="quantification">
                <columnTitle>Quantification</columnTitle>
            </column>
            <column columnName="flowQuantificationMethod">
                <columnTitle>Flow Quantification Method</columnTitle>
            </column>
            <column columnName="flowQuantification">
                <columnTitle>Flow Quantification</columnTitle>
            </column>
            <column columnName="nClones">
                <columnTitle># Clones</columnTitle>
            </column>
            <column columnName="comment">

            </column>
            <column columnName="container">
                <isHidden>true</isHidden>
            </column>
            <column columnName="createdby">
                <isHidden>true</isHidden>
            </column>
            <column columnName="created">
                <isUserEditable>false</isUserEditable>
                <shownInInsertView>false</shownInInsertView>
                <shownInUpdateView>false</shownInUpdateView>
                <nullable>true</nullable>
                <isHidden>true</isHidden>
            </column>
            <column columnName="modifiedby">
                <isHidden>true</isHidden>
            </column>
            <column columnName="modified">
                <isUserEditable>false</isUserEditable>
                <shownInInsertView>false</shownInInsertView>
                <shownInUpdateView>false</shownInUpdateView>
                <nullable>true</nullable>
                <isHidden>true</isHidden>
            </column>
        </columns>
    </table>
    <table tableName="repertoire_stats" tableDbType="TABLE" useColumnOrder="true">
        <javaCustomizer class="org.labkey.laboratory.query.LaboratoryTableCustomizer" />
        <tableTitle>TCR Repertoire Stats</tableTitle>
        <titleColumn>rowid</titleColumn>
        <columns>
            <column columnName="rowid">
                <columnTitle>Row Id</columnTitle>
                <isHidden>true</isHidden>
            </column>
            <column columnName="cdna_id">
                <columnTitle>cDNA ID</columnTitle>
                <fk>
                    <fkDbSchema>singlecell</fkDbSchema>
                    <fkTable>cdna_libraries</fkTable>
                    <fkColumnName>rowid</fkColumnName>
                </fk>
            </column>
            <column columnName="metricName">
                <columnTitle>Metric Name</columnTitle>
            </column>
            <column columnName="value">
                <columnTitle>Value</columnTitle>
            </column>
            <column columnName="qualValue">
                <columnTitle>Qualitative Value</columnTitle>
            </column>
            <column columnName="comment">

            </column>
            <column columnName="container">
                <isHidden>true</isHidden>
            </column>
            <column columnName="createdby">
                <isHidden>true</isHidden>
            </column>
            <column columnName="created">
                <isUserEditable>false</isUserEditable>
                <shownInInsertView>false</shownInInsertView>
                <shownInUpdateView>false</shownInUpdateView>
                <nullable>true</nullable>
                <isHidden>true</isHidden>
            </column>
            <column columnName="modifiedby">
                <isHidden>true</isHidden>
            </column>
            <column columnName="modified">
                <isUserEditable>false</isUserEditable>
                <shownInInsertView>false</shownInInsertView>
                <shownInUpdateView>false</shownInUpdateView>
                <nullable>true</nullable>
                <isHidden>true</isHidden>
            </column>
        </columns>
    </table>
</tables>