SequencingLab

SequencingLab is designed to be a container resource holding results from a sequencing lab performed for a patient. It contains raw genetic files generated from a lab as well as meta data necessary for meaningful usage of those files. This includes the type of sample used in sequencing, species of the organism from which the sample is gathered, and many others. Expected usages of the resource include documentation of sequencing for clinical use and research using NGS.

List of Extension Elements

  • species - Species of the target in a sequencing lab; e.g. code of Mycobacterium tuberculosis
  • sampleType - Type of the sample used in sequencing lab; possible values: germline | somatic | prenatal
  • sampleSource - Specific source of the sample used in sequencing lab; e.g. code of saliva
  • assembly - Reference genome used for aligning reads from the sequencing lab; e.g. GRCh37
  • file - File generated from the lab

Extension Definition

<Profile xmlns="http://hl7.org/fhir">
    <contained>
        <ValueSet id="valueset-assembly">
            <name value="assembly"/>
            <status value="draft"/>
            <define>
                <system value="http://genomics.smartplatforms.org/dictionary"/>
                <caseSensitive value="1"/>
                <concept>
                    <code value="GRCh37"/>
                    <abstract value="0"/>
                </concept>
                <concept>
                    <code value="GRCh38"/>
                    <abstract value="0"/>
                </concept>
                <!--NOTE: this is an incomplete list of genomes-->
            </define>
        </ValueSet>
        <ValueSet id="valueset-valuetype">
            <name value="assembly"/>
            <status value="draft"/>
            <define>
                <system value="http://genomics.smartplatforms.org/dictionary"/>
                <caseSensitive value="0"/>
                <concept>
                    <code value="germline"/>
                    <abstract value="0"/>
                </concept>
                <concept>
                    <code value="somatic"/>
                    <abstract value="0"/>
                </concept>
                <concept>
                    <code value="prenatal"/>
                    <abstract value="0"/>
                </concept>
            </define>
        </ValueSet>
    </contained>
    <text>
        <status value="generated"/>
        <div>
            <h1>Sequencing Lab</h1>
            <p>This is an extension to Observation resource, supporting storing results from a sequencing lab</p>
        </div>
    </text>
    <status vlaue="draft"/>
    <extensionDefn>
        <code value="species"/>
        <display value="Species of the sample used in this sequencing lab"/>
        <contextType value="Observation"/>
        <context value="Obervation"/>
        <definition>
            <short value="Species of sample"/>
            <formal value="Species of the sample used in this sequencing lab"/>
            <min value="1"/>
            <max value="1"/>
            <type>
                <code value="CodeableConcept"/>
            </type>
        </definition>
    </etensionDefn>
    <extensionDefn>
        <code value="sampleType"/>
        <display value="Type of the sample used in this sequencing lab"/>
        <contextType value="Observation"/>
        <context value="Observation"/>
        <definition>
            <short value="Sample type"/>
            <formal value"Type of the sample used in this sequencing lab"/>
            <min value="1"/>
            <max value="1"/>
            <type>
                <code value="code"/>
            </type>
            <binding>
                <name value="SampleType"/>
                <ixExtensible value="1"/>
                <conformance value="required"/>
                <description value="List of acceptable values of sample types in sequencing lab"/>
                <referenceValueSet>
                    <reference value="#valueset-sampletype"/>
                </referenceValueSet>
            </binding>
        </definition>
    </etensionDefn>
    <extensionDefn>
        <code value="sampleSource"/>
        <display value="Source of the sample used in this sequencing lab"/>
        <contextType value="Observation"/>
        <context value="Observation"/>
        <definition>
            <short value="Sample source"/>
            <formal value"Ontological representation of the source of the sample used in this sequencing lab"/>
            <min value="0"/>
            <max value="1"/>
            <type>
                <code value="CodeableConcept"/>
            </type>
        </definition>
    </etensionDefn>
    <extensionDefn>
        <code value="assembly"/>
        <display value="Assembly chosen for alignment of the sequences generated in this sequencing lab"/>
        <contextType value="Observation"/>
        <context value="Observation"/>
        <definition>
            <short value="Assembly for alignment"/>
            <formal value="Assembly chosen for alignment of the sequences generated in this sequencing lab"/>
            <min value="0"/>
            <max value="1"/>
            <type>
                <code value="code"/>
            </type>
            <binding>
                <name value="Assembly"/>
                <ixExtensible value="1"/>
                <conformance value="required"/>
                <description value="List of acceptable values of assembly in sequencing lab"/>
                <referenceValueSet>
                    <reference value="#valueset-assembly"/>
                </referenceValueSet>
            </binding>
        </definition>
    </extensionDefn>
    <extensionDefn>
        <code value="file"/>
        <display value="Result files of the sequencing lab"/>
        <contextType value="Observation"/>
        <context value="Observation"/>
        <definition>
            <short value="Result file of the sequencing lab"/>
            <formal value="Genetic file resulted from the sequencing lab"/>
            <min value="0"/>
            <max value="*"/>
            <type>
                <code value="Attachment"/>
            </type>
        </definition>
    </extensionDefn>
</Profile>