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Cg im moldef work in progress 2 #3159

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Cg im moldef work in progress 2 #3159

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814181b
changing representation.resolvable to a reference to DocumentReferenc…
khalifa-aly Sep 3, 2024
61af56a
changing representation.resolvable to a reference to DocumentReferenc…
khalifa-aly Sep 3, 2024
9fd66f9
adding simple sequence examples for literal "A" as DNA and Amino Acid…
khalifa-aly Sep 4, 2024
9202dba
adding sequence examples for resolvable element
khalifa-aly Sep 4, 2024
a344ff3
QA edit: renaming Document Reference examples
khalifa-aly Sep 5, 2024
ab0013c
Code system and valueset moleculardefinition encoding
khalifa-aly Sep 5, 2024
e0c5d35
QA renaming the encoding code system to iupac-nucleotide
khalifa-aly Sep 5, 2024
66de666
QA renaming the encoding code system to iupac-nucleotide
khalifa-aly Sep 5, 2024
9b69014
QA removing duplicate description
khalifa-aly Sep 5, 2024
fd267fe
QA edits
khalifa-aly Sep 5, 2024
97c3ff5
Allele literal example
khalifa-aly Sep 5, 2024
ceb6b15
More allele examples and supporting resource instances
khalifa-aly Sep 5, 2024
d187990
QA edit
khalifa-aly Sep 6, 2024
a52f0ff
QA edit
khalifa-aly Sep 6, 2024
72ee0d8
Variation examples for CYP2C19 in various formats, e.g., VRS, SPDI, a…
khalifa-aly Sep 19, 2024
7a1e291
AlleleSliced Example: HLA00381
khalifa-aly Sep 19, 2024
5084894
QA edits
khalifa-aly Sep 19, 2024
c2b3376
updating the example list to include a new set of examples
khalifa-aly Sep 19, 2024
a345098
more descriptive titles and descriptions
khalifa-aly Sep 20, 2024
3099aaa
Adding DocRef examples of genetic files that Support Molecular Defini…
khalifa-aly Sep 20, 2024
caec71d
QA edit, adjusting file names
khalifa-aly Sep 20, 2024
5eadf05
QA edit, adjusting file names
khalifa-aly Sep 20, 2024
583b390
QA edit, adjusting file names
khalifa-aly Sep 20, 2024
06e1890
QA edit, element order and extra spaces
khalifa-aly Sep 20, 2024
2fa947c
Merge pull request #3165 from HL7/master
khalifa-aly Sep 20, 2024
225749e
Merge branch 'master' into cg-im-moldef_work_in_progress_2
sirkyp Oct 11, 2024
a8f1edb
extracted sequence examples of CYP2C19
khalifa-aly Oct 11, 2024
de65a8a
Merge remote-tracking branch 'origin/cg-im-moldef_work_in_progress_2'…
khalifa-aly Oct 11, 2024
53ec8f8
Concatenated example of CYP2C19
khalifa-aly Oct 11, 2024
014d841
Repeated examples for FMR1
khalifa-aly Oct 11, 2024
d396dcd
examples of repeated sequence that was edited by referenced and conta…
khalifa-aly Oct 11, 2024
4d7a1e8
Example list update
khalifa-aly Oct 15, 2024
253aef6
Removing Autogenerated Text
khalifa-aly Oct 16, 2024
3dbc3b3
Merge branch 'master' into cg-im-moldef_work_in_progress_2
sirkyp Oct 17, 2024
a52557d
QA edit, adding genotype concept
khalifa-aly Oct 29, 2024
52ee0ce
Merge remote-tracking branch 'origin/cg-im-moldef_work_in_progress_2'…
khalifa-aly Oct 29, 2024
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26 changes: 26 additions & 0 deletions source/documentreference/documentreference-example-genomicfile-af1961831-url.xml
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<?xml version="1.0" encoding="UTF-8"?>

<DocumentReference xmlns="http://hl7.org/fhir">
<id value="example-genomicfile-af1961831-url"/>
<identifier>
<system value="http://www.somesystemabc.net/identifiers/files"/>
<value value="11111"/>
</identifier>
<status value="current"/>
<docStatus value="preliminary"/>
<description value="Homo sapiens MHC class I antigen (HLA-B) gene"/>
<securityLabel>
<coding>
<system value="http://terminology.hl7.org/CodeSystem/v3-Confidentiality"/>
<code value="R"/>
<display value="Restricted"/>
</coding>
</securityLabel>
<content>
<attachment>
<contentType value="text/html"/>
<url value="https://www.ebi.ac.uk/ena/browser/api/fasta/AF196183.1"/>
<title value="Homo sapiens MHC class I antigen (HLA-B) gene"/>
</attachment>
</content>
</DocumentReference>
27 changes: 27 additions & 0 deletions source/documentreference/documentreference-example-genomicfile-cyp2c19-accession.xml
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<?xml version="1.0" encoding="UTF-8"?>

<DocumentReference xmlns="http://hl7.org/fhir">
<id value="example-genomicfile-cyp2c19-accession"/>

<identifier>
<system value="https://www.ncbi.nlm.nih.gov/nuccore"/>
<value value="NG_008384.3"/>
</identifier>
<status value="current"/>
<docStatus value="preliminary"/>
<description value="CYP2C19 gene sequence"/>
<securityLabel>
<coding>
<system value="http://terminology.hl7.org/CodeSystem/v3-Confidentiality"/>
<code value="R"/>
<display value="Restricted"/>
</coding>
</securityLabel>
<content>
<attachment>
<contentType value="text/html"/>
<url value="https://www.ncbi.nlm.nih.gov/nuccore/NG_008384"/>
<title value="Homo sapiens cytochrome P450 family 2 subfamily C member 19 (CYP2C19), RefSeqGene (LRG_584) on chromosome 10"/>
</attachment>
</content>
</DocumentReference>
28 changes: 28 additions & 0 deletions source/documentreference/documentreference-example-genomicfile-cyp2c19-attached.xml
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26 changes: 26 additions & 0 deletions source/documentreference/documentreference-example-genomicfile-cyp2c19-url.xml
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<?xml version="1.0" encoding="UTF-8"?>

<DocumentReference xmlns="http://hl7.org/fhir">
<id value="example-genomicfile-cyp2c19-url"/>
<identifier>
<system value="http://www.somesystemabc.net/identifiers/files"/>
<value value="11111"/>
</identifier>
<status value="current"/>
<docStatus value="preliminary"/>
<description value="CYP2C19 gene sequence"/>
<securityLabel>
<coding>
<system value="http://terminology.hl7.org/CodeSystem/v3-Confidentiality"/>
<code value="R"/>
<display value="Restricted"/>
</coding>
</securityLabel>
<content>
<attachment>
<contentType value="text/html"/>
<url value="https://www.ncbi.nlm.nih.gov/nuccore/NG_008384"/>
<title value="Homo sapiens cytochrome P450 family 2 subfamily C member 19 (CYP2C19), RefSeqGene (LRG_584) on chromosome 10"/>
</attachment>
</content>
</DocumentReference>
27 changes: 27 additions & 0 deletions source/documentreference/documentreference-example-genomicfile-hla00001.xml
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<?xml version="1.0" encoding="UTF-8"?>

<DocumentReference xmlns="http://hl7.org/fhir">
<id value="example-genomicfile-hla00001"/>

<identifier>
<system value="http://www.somesystemabc.net/identifiers/files"/>
<value value="11111"/>
</identifier>
<status value="current"/>
<docStatus value="preliminary"/>
<description value="A sample Document Reference instance representing HLA00001."/>
<securityLabel>
<coding>
<system value="http://terminology.hl7.org/CodeSystem/v3-Confidentiality"/>
<code value="R"/>
<display value="Restricted"/>
</coding>
</securityLabel>
<content>
<attachment>
<contentType value="text/html"/>
<url value="https://www.ebi.ac.uk/Tools/dbfetch/dbfetch?db=imgthla;id=HLA00001;format=fasta;style=raw"/>
<title value="HLA00001"/>
</attachment>
</content>
</DocumentReference>
27 changes: 27 additions & 0 deletions source/documentreference/documentreference-example-genomicfile-mw7162561.xml
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<?xml version="1.0" encoding="UTF-8"?>

<DocumentReference xmlns="http://hl7.org/fhir">
<id value="example-genomicfile-mw7162561"/>

<identifier>
<system value="http://www.somesystemabc.net/identifiers/files"/>
<value value="11111"/>
</identifier>
<status value="current"/>
<docStatus value="preliminary"/>
<description value="A sample Document Reference instance representing Homo sapiens isolate 7 BRCA1 (BRCA1) gene, exon 10 and partial cds."/>
<securityLabel>
<coding>
<system value="http://terminology.hl7.org/CodeSystem/v3-Confidentiality"/>
<code value="R"/>
<display value="Restricted"/>
</coding>
</securityLabel>
<content>
<attachment>
<contentType value="text/html"/>
<url value="https://www.ncbi.nlm.nih.gov/nuccore/MW716256.1?report=fasta"/>
<title value="Homo sapiens isolate 7 BRCA1 (BRCA1) gene, exon 10 and partial cds"/>
</attachment>
</content>
</DocumentReference>
26 changes: 26 additions & 0 deletions source/documentreference/documentreference-example-genomicfile-ng0083843.xml
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<?xml version="1.0" encoding="UTF-8"?>

<DocumentReference xmlns="http://hl7.org/fhir">
<id value="example-genomicfile-ng0083843"/>
<identifier>
<system value="http://www.somesystemabc.net/identifiers/files"/>
<value value="11111"/>
</identifier>
<status value="current"/>
<docStatus value="preliminary"/>
<description value="A sample Document Reference instance representing Homo sapiens cytochrome P450 family 2 subfamily C member 19 (CYP2C19), RefSeqGene (LRG_584) on chromosome 10."/>
<securityLabel>
<coding>
<system value="http://terminology.hl7.org/CodeSystem/v3-Confidentiality"/>
<code value="R"/>
<display value="Restricted"/>
</coding>
</securityLabel>
<content>
<attachment>
<contentType value="text/html"/>
<url value="https://www.ncbi.nlm.nih.gov/nuccore/NG_008384.3?report=fasta"/>
<title value="Homo sapiens cytochrome P450 family 2 subfamily C member 19 (CYP2C19), RefSeqGene (LRG_584) on chromosome 10"/>
</attachment>
</content>
</DocumentReference>
27 changes: 27 additions & 0 deletions source/documentreference/documentreference-example-genomicfile-nm0002513.xml
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<?xml version="1.0" encoding="UTF-8"?>

<DocumentReference xmlns="http://hl7.org/fhir">
<id value="example-genomicfile-nm0002513"/>

<identifier>
<system value="http://www.somesystemabc.net/identifiers/files"/>
<value value="11111"/>
</identifier>
<status value="current"/>
<docStatus value="preliminary"/>
<description value="A sample Document Reference instance representing Homo sapiens mutS homolog 2 (MSH2), transcript variant 1, mRNA."/>
<securityLabel>
<coding>
<system value="http://terminology.hl7.org/CodeSystem/v3-Confidentiality"/>
<code value="R"/>
<display value="Restricted"/>
</coding>
</securityLabel>
<content>
<attachment>
<contentType value="text/html"/>
<url value="https://www.ncbi.nlm.nih.gov/nuccore/NM_000251.3?report=fasta"/>
<title value="Homo sapiens mutS homolog 2 (MSH2), transcript variant 1, mRNA"/>
</attachment>
</content>
</DocumentReference>
27 changes: 27 additions & 0 deletions source/documentreference/documentreference-example-genomicfile-nm0007694.xml
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<?xml version="1.0" encoding="UTF-8"?>

<DocumentReference xmlns="http://hl7.org/fhir">
<id value="example-genomicfile-nm0007694"/>

<identifier>
<system value="http://www.somesystemabc.net/identifiers/files"/>
<value value="11111"/>
</identifier>
<status value="current"/>
<docStatus value="preliminary"/>
<description value="(CYP2C19), mRNA"/>
<securityLabel>
<coding>
<system value="http://terminology.hl7.org/CodeSystem/v3-Confidentiality"/>
<code value="R"/>
<display value="Restricted"/>
</coding>
</securityLabel>
<content>
<attachment>
<contentType value="text/html"/>
<url value="https://www.ncbi.nlm.nih.gov/nuccore/NM_000769.4?report=fasta"/>
<title value="Homo sapiens cytochrome P450 family 2 subfamily C member 19 (CYP2C19), mRNA"/>
</attachment>
</content>
</DocumentReference>
26 changes: 26 additions & 0 deletions source/documentreference/documentreference-example-genomicfile-nm0020245.xml
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<?xml version="1.0" encoding="UTF-8"?>

<DocumentReference xmlns="http://hl7.org/fhir">
<id value="example-genomicfile-nm0020245"/>
<identifier>
<system value="http://www.somesystemabc.net/identifiers/files"/>
<value value="11111"/>
</identifier>
<status value="current"/>
<docStatus value="preliminary"/>
<description value="A sample Document Reference instance representing Homo sapiens FMRP translational regulator 1 (FMR1), transcript variant ISO1, mRNA."/>
<securityLabel>
<coding>
<system value="http://terminology.hl7.org/CodeSystem/v3-Confidentiality"/>
<code value="R"/>
<display value="Restricted"/>
</coding>
</securityLabel>
<content>
<attachment>
<contentType value="text/html"/>
<url value="https://www.ncbi.nlm.nih.gov/nuccore/NM_002024.5?report=fasta"/>
<title value="Homo sapiens FMRP translational regulator 1 (FMR1), transcript variant ISO1, mRNA"/>
</attachment>
</content>
</DocumentReference>
123 changes: 123 additions & 0 deletions source/documentreference/list-DocumentReference-examples.xml
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Expand Up @@ -112,4 +112,127 @@
<display value="Metadata pointing at a FHIR Document Bundle example"/>
</item>
</entry>

<!-- Below are entries from Clinical Genomics Workgroup to Support Molecular Definition instances-->

<entry>
<extension url="http://hl7.org/fhir/build/StructureDefinition/description">
<valueString value="A Genomic Data File representing Homo sapiens MHC class I antigen (HLA-B) gene"/>
</extension>
<extension url="http://hl7.org/fhir/build/StructureDefinition/title">
<valueString value="documentreference-example-genomicfile-af1961831-url"/>
</extension>
<item>
<reference value="DocumentReference/example-genomicfile-af1961831-url"/>
<display value="A Genomic Data File representing Homo sapiens MHC class I antigen (HLA-B) gene"/>
</item>
</entry>
<entry>
<extension url="http://hl7.org/fhir/build/StructureDefinition/description">
<valueString value="A Genomic Data File representing CYP2C19 gene sequence"/>
</extension>
<extension url="http://hl7.org/fhir/build/StructureDefinition/title">
<valueString value="documentreference-example-genomicfile-cyp2c19-accession"/>
</extension>
<item>
<reference value="DocumentReference/example-genomicfile-cyp2c19-accession"/>
<display value="A Genomic Data File representing CYP2C19 gene sequence"/>
</item>
</entry>
<entry>
<extension url="http://hl7.org/fhir/build/StructureDefinition/description">
<valueString value="A Genomic Data File representing Homo sapiens cytochrome P450 family 2 subfamily C member 19 (CYP2C19), RefSeqGene (LRG_584) on chromosome 10"/>
</extension>
<extension url="http://hl7.org/fhir/build/StructureDefinition/title">
<valueString value="documentreference-example-genomicfile-cyp2c19-attached"/>
</extension>
<item>
<reference value="DocumentReference/example-genomicfile-cyp2c19-attached"/>
<display value="A Genomic Data File representing Homo sapiens cytochrome P450 family 2 subfamily C member 19 (CYP2C19), RefSeqGene (LRG_584) on chromosome 10"/>
</item>
</entry>
<entry>
<extension url="http://hl7.org/fhir/build/StructureDefinition/description">
<valueString value="A Genomic Data File representing CYP2C19 gene sequence through URL"/>
</extension>
<extension url="http://hl7.org/fhir/build/StructureDefinition/title">
<valueString value="documentreference-example-genomicfile-cyp2c19-url"/>
</extension>
<item>
<reference value="DocumentReference/example-genomicfile-cyp2c19-url"/>
<display value="A Genomic Data File representing CYP2C19 gene sequence through URL"/>
</item>
</entry>
<entry>
<extension url="http://hl7.org/fhir/build/StructureDefinition/description">
<valueString value="A Genomic Data File representing HLA00001 through URL"/>
</extension>
<extension url="http://hl7.org/fhir/build/StructureDefinition/title">
<valueString value="documentreference-example-genomicfile-hla00001"/>
</extension>
<item>
<reference value="DocumentReference/example-genomicfile-hla00001"/>
<display value="A Genomic Data File representing HLA00001 through URL"/>
</item>
</entry>
<entry>
<extension url="http://hl7.org/fhir/build/StructureDefinition/description">
<valueString value="A Genomic Data File representing Homo sapiens isolate 7 BRCA1 (BRCA1) gene, exon 10 and partial cds"/>
</extension>
<extension url="http://hl7.org/fhir/build/StructureDefinition/title">
<valueString value="documentreference-example-genomicfile-mw7162561"/>
</extension>
<item>
<reference value="DocumentReference/example-genomicfile-mw7162561"/>
<display value="A Genomic Data File representing Homo sapiens isolate 7 BRCA1 (BRCA1) gene, exon 10 and partial cds"/>
</item>
</entry>
<entry>
<extension url="http://hl7.org/fhir/build/StructureDefinition/description">
<valueString value="A Genomic Data File representing Homo sapiens cytochrome P450 family 2 subfamily C member 19 (CYP2C19), RefSeqGene (LRG_584) on chromosome 10"/>
</extension>
<extension url="http://hl7.org/fhir/build/StructureDefinition/title">
<valueString value="documentreference-example-genomicfile-ng0083843"/>
</extension>
<item>
<reference value="DocumentReference/example-genomicfile-ng0083843"/>
<display value="A Genomic Data File representing Homo sapiens cytochrome P450 family 2 subfamily C member 19 (CYP2C19)"/>
</item>
</entry>
<entry>
<extension url="http://hl7.org/fhir/build/StructureDefinition/description">
<valueString value="A Genomic Data File representing Homo sapiens mutS homolog 2 (MSH2), transcript variant 1, mRNA"/>
</extension>
<extension url="http://hl7.org/fhir/build/StructureDefinition/title">
<valueString value="documentreference-example-genomicfile-nm0002513"/>
</extension>
<item>
<reference value="DocumentReference/example-genomicfile-nm0002513"/>
<display value="A Genomic Data File representing Homo sapiens mutS homolog 2 (MSH2)"/>
</item>
</entry>
<entry>
<extension url="http://hl7.org/fhir/build/StructureDefinition/description">
<valueString value="A Genomic Data File representing Homo sapiens cytochrome P450 family 2 subfamily C member 19 (CYP2C19), mRNA"/>
</extension>
<extension url="http://hl7.org/fhir/build/StructureDefinition/title">
<valueString value="documentreference-example-genomicfile-nm0007694"/>
</extension>
<item>
<reference value="DocumentReference/example-genomicfile-nm0007694"/>
<display value="A Genomic Data File representing Homo sapiens cytochrome P450 family 2 subfamily C member 19 (CYP2C19), mRNA"/>
</item>
</entry>
<entry>
<extension url="http://hl7.org/fhir/build/StructureDefinition/description">
<valueString value="A Genomic Data File representing Homo sapiens FMRP translational regulator 1 (FMR1), transcript variant ISO1, mRNA"/>
</extension>
<extension url="http://hl7.org/fhir/build/StructureDefinition/title">
<valueString value="documentreference-example-genomicfile-nm0020245"/>
</extension>
<item>
<reference value="DocumentReference/example-genomicfile-nm0020245"/>
<display value="A Genomic Data File representing Homo sapiens FMRP translational regulator 1 (FMR1)"/>
</item>
</entry>
</List>
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