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Cg im molseq work in progress 2 #2963

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Cg im molseq work in progress 2 #2963

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3beed19
Updating the structure definition to reflect the new design of the Mo…
khalifa-aly Aug 30, 2023
2c3ddf5
removing MolSeq from the patient compartment
khalifa-aly Aug 30, 2023
8d6dafb
updating the search params to reflect the new design, i.e., definitional
khalifa-aly Aug 30, 2023
404dff9
updating the example list
khalifa-aly Aug 30, 2023
d996e43
building the new example
khalifa-aly Aug 30, 2023
a0649ba
deleting the focus example
khalifa-aly Aug 30, 2023
f4547d3
updating the notes to reflect the new MolSeq modeling based on CG IM …
khalifa-aly Aug 30, 2023
50e2ac6
deleting the complex variant example
khalifa-aly Aug 30, 2023
f805632
deleting the sequence block examples
khalifa-aly Aug 30, 2023
f9b2250
deleting the TPMT examples
khalifa-aly Aug 30, 2023
98384e4
deleting the fusion and ordinal examples
khalifa-aly Aug 30, 2023
eda57aa
deleting the pgx examples
khalifa-aly Aug 30, 2023
e53425d
deleting the breast cancer example
khalifa-aly Aug 30, 2023
0cdec20
deleting genetic examples 3-5
khalifa-aly Aug 30, 2023
d039f38
deleting invariant tests msq-5 and msq-6
khalifa-aly Aug 30, 2023
e782b7a
Merge pull request #2966 from HL7/master
khalifa-aly Sep 1, 2023
68c4735
moving relative.coordinate to relative.edit.coordinate
khalifa-aly Sep 12, 2023
c820023
commenting out relative.seqRange. TODO be deleted with other commente…
khalifa-aly Sep 12, 2023
020e0da
making relative.startingSee mandatory, i.e., 1..1
khalifa-aly Sep 12, 2023
4549aa4
updating the example to reflect the new change to relative.edit.coord…
khalifa-aly Sep 12, 2023
570d108
Merge branch 'master' into cg-im-molseq-work_in_progress_2
khalifa-aly Oct 9, 2023
cad4166
MolSeq is a definitional resource removing Search Parameter 'subject'
khalifa-aly Oct 9, 2023
5154246
Merge pull request #2988 from HL7/master
khalifa-aly Oct 16, 2023
efcd79d
QA fixes on structuredefinition-MolecularSequence.xml
khalifa-aly Nov 12, 2023
8b6573a
Update compartments.xml
khalifa-aly Aug 9, 2024
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1,817 changes: 911 additions & 906 deletions source/compartments.xml
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116 changes: 58 additions & 58 deletions source/molecularsequence/bundle-MolecularSequence-search-params.xml
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Expand Up @@ -21,64 +21,64 @@
</SearchParameter>
</resource>
</entry>
<entry>
<resource>
<SearchParameter>
<id value="MolecularSequence-subject"/>
<extension url="http://hl7.org/fhir/StructureDefinition/structuredefinition-standards-status">
<valueCode value="trial-use"/>
</extension>
<extension url="http://hl7.org/fhir/build/StructureDefinition/path">
<valueString value="MolecularSequence.subject"/>
</extension>
<url value="http://hl7.org/fhir/build/SearchParameter/MolecularSequence-subject"/>
<description value="The subject that the sequence is about"/>
<code value="subject"/>
<type value="reference"/>
<expression value="MolecularSequence.subject"/>
<processingMode value="normal"/>
</SearchParameter>
</resource>
</entry>
<entry>
<resource>
<SearchParameter>
<id value="MolecularSequence-patient"/>
<extension url="http://hl7.org/fhir/StructureDefinition/structuredefinition-standards-status">
<valueCode value="trial-use"/>
</extension>
<extension url="http://hl7.org/fhir/build/StructureDefinition/path">
<valueString value="MolecularSequence.subject"/>
</extension>
<url value="http://hl7.org/fhir/build/SearchParameter/MolecularSequence-patient"/>
<description value="The subject that the sequence is about"/>
<code value="patient"/>
<type value="reference"/>
<expression value="MolecularSequence.subject.where(resolve() is Patient)"/>
<processingMode value="normal"/>
<target value="Patient"/>
</SearchParameter>
</resource>
</entry>
<entry>
<resource>
<SearchParameter>
<id value="MolecularSequence-focus"/>
<extension url="http://hl7.org/fhir/StructureDefinition/structuredefinition-standards-status">
<valueCode value="trial-use"/>
</extension>
<extension url="http://hl7.org/fhir/build/StructureDefinition/path">
<valueString value="MolecularSequence.focus"/>
</extension>
<url value="http://hl7.org/fhir/build/SearchParameter/MolecularSequence-focus"/>
<description value="What the molecular sequence is about, when it is not about the subject of record"/>
<code value="focus"/>
<type value="reference"/>
<expression value="MolecularSequence.focus"/>
<processingMode value="normal"/>
</SearchParameter>
</resource>
</entry>
<!-- <entry>
<resource>
<SearchParameter>
<id value="MolecularSequence-subject"/>
<extension url="http://hl7.org/fhir/StructureDefinition/structuredefinition-standards-status">
<valueCode value="trial-use"/>
</extension>
<extension url="http://hl7.org/fhir/build/StructureDefinition/path">
<valueString value="MolecularSequence.subject"/>
</extension>
<url value="http://hl7.org/fhir/build/SearchParameter/MolecularSequence-subject"/>
<description value="The subject that the sequence is about"/>
<code value="subject"/>
<type value="reference"/>
<expression value="MolecularSequence.subject"/>
<processingMode value="normal"/>
</SearchParameter>
</resource>
</entry>-->
<!-- <entry>
<resource>
<SearchParameter>
<id value="MolecularSequence-patient"/>
<extension url="http://hl7.org/fhir/StructureDefinition/structuredefinition-standards-status">
<valueCode value="trial-use"/>
</extension>
<extension url="http://hl7.org/fhir/build/StructureDefinition/path">
<valueString value="MolecularSequence.subject"/>
</extension>
<url value="http://hl7.org/fhir/build/SearchParameter/MolecularSequence-patient"/>
<description value="The subject that the sequence is about"/>
<code value="patient"/>
<type value="reference"/>
<expression value="MolecularSequence.subject.where(resolve() is Patient)"/>
<processingMode value="normal"/>
<target value="Patient"/>
</SearchParameter>
</resource>
</entry>-->
<!-- <entry>
<resource>
<SearchParameter>
<id value="MolecularSequence-focus"/>
<extension url="http://hl7.org/fhir/StructureDefinition/structuredefinition-standards-status">
<valueCode value="trial-use"/>
</extension>
<extension url="http://hl7.org/fhir/build/StructureDefinition/path">
<valueString value="MolecularSequence.focus"/>
</extension>
<url value="http://hl7.org/fhir/build/SearchParameter/MolecularSequence-focus"/>
<description value="What the molecular sequence is about, when it is not about the subject of record"/>
<code value="focus"/>
<type value="reference"/>
<expression value="MolecularSequence.focus"/>
<processingMode value="normal"/>
</SearchParameter>
</resource>
</entry>-->
<entry>
<resource>
<SearchParameter>
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17 changes: 0 additions & 17 deletions source/molecularsequence/invariant-tests/msq-5.f1.fail.json
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24 changes: 0 additions & 24 deletions source/molecularsequence/invariant-tests/msq-5.p1.pass.json
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25 changes: 0 additions & 25 deletions source/molecularsequence/invariant-tests/msq-6.f1.fail.json
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15 changes: 0 additions & 15 deletions source/molecularsequence/invariant-tests/msq-6.p1.pass.json
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4 changes: 2 additions & 2 deletions source/molecularsequence/list-MolecularSequence-examples.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -30,7 +30,7 @@
</item>
</entry>
-->
<entry>
<!--<entry>
<extension url="http://hl7.org/fhir/build/StructureDefinition/description">
<valueString value="Example of representing complex variants in MolecularSequence resource"/>
</extension>
Expand Down Expand Up @@ -161,5 +161,5 @@
<reference value="MolecularSequence/molecularsequence-focus-example"/>
<display value="Example of focus (the mother was sequenced) versus subject (a child is the patient of record)"/>
</item>
</entry>
</entry>-->
</List>
121 changes: 114 additions & 7 deletions source/molecularsequence/molecularsequence-example.xml
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Expand Up @@ -2,12 +2,119 @@
<MolecularSequence xmlns="http://hl7.org/fhir">
<id value="example"/>
<type value="dna"/>
<subject>
<reference value="Patient/example"/>
</subject>
<!-- <subject>
<reference value="Patient/example"/>
</subject>-->
<!-- <formatted>
<contentType value="application/json"/>
<url value="http://grch37.rest.ensembl.org/ga4gh/variants/3:rs1333049?content-type=application/json"/>
<title value="GA4GH API"/>
</formatted>-->
<literal>
<sequenceValue value="ATGAACAGACAAGTAAAAGACATGACAGYGATACTTTCCCAGAGCTGAAGTTAACAAATGCACCTGGTTC
TTTTACTAAGTGTTCAAATACCAGTGAACTTAAAGAATTTGTCAATCCTAGCCTTCCAAGAGAAGAAAAA
GAAGAGAAACTAGAAACAGTTAAAGTGTCTAATAATGCTGAAGACCCCAAAGATCTCATGTTAAGTGGAG
AAAGGGTTTTGCAAACTGAAAGATCTGTAGAGAGTAGCAGTATTTCAYTGGTACCTGGTACTGATTATGG
CACTCAGGAAAGTATCTCGTTACTGGAAGTTAGCACTCTAGGGAAGGCAAAAACAGAACCAAATAAATGT
GTGAGTCAGTGTGCAGCATTTGAAAACCCCAAGGGACTAATTCATGGTTGTTCCAAAGATAATAGAAATG
ACACAGAAGGCTTTAAGTATCCATTGGGACATGAAGTTAACCACAGTCGGGAAACAAGCATAGAAATGGA
AGAAAGTGAACTTGATGCTCAGTATTTGCAGAATACATTCAAGGTTTCAAAGCGCCAGTCATTTGCTCYG
TTTTCAAATCCAGGAAATGCAGAAGAGGAATGTGCAACATTCTCTGCCCACTCTGGGTCCTTAAAGAAAC
AAAGTCCAAAAGTCACTTTTGAATGTGAACAAAAGGAAGAAAATCAAGGAAAGAATGAGTCTAATATCAA
GCCTGTACAGACAGTTAATATCACTGCAGGCTTTCCTGTGGTTGGTCAGAAAGA"/>
<!-- <encoding>
<coding>
<system value="http://terminology.hl7.org/CodeSystem/..."/>
<code value=""/>
<display value=""/>
</coding>
<text value=""/>
</encoding>-->
</literal>
<formatted>
<contentType value="application/json"/>
<url value="http://grch37.rest.ensembl.org/ga4gh/variants/3:rs1333049?content-type=application/json"/>
<title value="GA4GH API"/>
<contentType value="text/html"/>
<url value="https://www.ncbi.nlm.nih.gov/nuccore/MW716256.1?report=fasta"/>
</formatted>
</MolecularSequence>
<relative>
<startingSequence>
<reference value="MolecularSequence/StartingSequenceExample"/>
<type value="MolecularSequence"/>
<display value="Starting Sequence Resource"/>
</startingSequence>
<edit>
<coordinateSystem>
<coding>
<system value="http://loinc.org"/>
<code value="LA30100-4"/>
<display value="0-based interval counting"/>
</coding>
<text value="0-based interval counting"/>
</coordinateSystem>
<start value="0"/>
<end value="725"/>
<replacementSequence>
<reference value="MolecularSequence/ReplacementSequenceExample"/>
<type value="MolecularSequence"/>
<display value="Replacement Sequence Resource"/>
</replacementSequence>
<replacedSequence>
<reference value="MolecularSequence/ReplacedSequenceExample"/>
<type value="MolecularSequence"/>
<display value="Replaced Sequence Resource"/>
</replacedSequence>
</edit>
</relative>
<extracted>
<startingSequence>
<reference value="MolecularSequence/StartingSequenceExample"/>
<type value="MolecularSequence"/>
<display value="Starting Sequence Resource"/>
</startingSequence>
<start value="0"/>
<end value="745"/>
<coordinateSystem>
<coding>
<system value="http://loinc.org"/>
<code value="LA30100-4"/>
<display value="0-based interval counting"/>
</coding>
<text value="0-based interval counting"/>
</coordinateSystem>
<reverseComplement value="false"/>
</extracted>
<!-- <repeated>
<sequenceMotif>
<reference value="MolecularSequence/SequenceMotifExample"/>
<type value="MolecularSequence"/>
<display value="Sequence Motif Resource"/>
</sequenceMotif>
<copyCount value="5"/>
</repeated>-->
<concatenated>
<sequenceElement>
<sequence>
<reference value="MolecularSequence/Sequence0ConcatenatedExample"/>
<type value="MolecularSequence"/>
<display value="Sequence-of index 0-Resource for concatenated sequence example"/>
</sequence>
<ordinalIndex value="0"/>
</sequenceElement>
<sequenceElement>
<sequence>
<reference value="MolecularSequence/Sequence1ConcatenatedExample"/>
<type value="MolecularSequence"/>
<display value="Sequence-of index 1-Resource for concatenated sequence example"/>
</sequence>
<ordinalIndex value="1"/>
</sequenceElement>
<sequenceElement>
<sequence>
<reference value="MolecularSequence/Sequence2ConcatenatedExample"/>
<type value="MolecularSequence"/>
<display value="Sequence-of index 2-Resource for concatenated sequence example"/>
</sequence>
<ordinalIndex value="2"/>
</sequenceElement>
</concatenated>

</MolecularSequence>
37 changes: 0 additions & 37 deletions source/molecularsequence/molecularsequence-focus-example.xml
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