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Cg im moldef work in progress 2 #3159

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merged 139 commits into from
Feb 21, 2025
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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
13e0522
Adding Sequence and document reference to Homo sapiens chromosome 10,…
khalifa-aly Oct 30, 2024
4c55396
Adding allele and variation example instance of PgX-var-1011 and 1012
khalifa-aly Oct 30, 2024
6525d39
Adding variation example instance of PgX-var-1013, 1014 and 1015
khalifa-aly Oct 31, 2024
f86b79c
Adding variation example instance of PgX-var-1016, 1017 and 1018
khalifa-aly Oct 31, 2024
63e5925
Merge pull request #3207 from HL7/master
khalifa-aly Nov 1, 2024
a875909
Adding variation example instance of PgX-var-1019 and 1020
khalifa-aly Nov 1, 2024
aa61540
Merge remote-tracking branch 'origin/cg-im-moldef_work_in_progress_2'…
khalifa-aly Nov 1, 2024
022f34e
Adding NC_000010.10 to the example list
khalifa-aly Nov 4, 2024
63da36f
Adding Pgx-var-1021
khalifa-aly Nov 4, 2024
c379acf
QA edit, adjusting display name
khalifa-aly Nov 4, 2024
4ed10cb
Adding new examples to the list
khalifa-aly Nov 4, 2024
0aea287
QA edits
khalifa-aly Nov 4, 2024
ffaad3e
Merge pull request #3240 from HL7/master
khalifa-aly Nov 25, 2024
ab39be4
adding the coordinateSystem to the location element
khalifa-aly Dec 3, 2024
c9d8837
updating the allele examples according to the newly added coordinateS…
khalifa-aly Dec 3, 2024
1fa8c39
updating the haplotype example according to the newly added coordinat…
khalifa-aly Dec 3, 2024
37b0c66
updating the CYP2C19 Variation examples according to the newly added …
khalifa-aly Dec 3, 2024
99cc500
updating the PgX Variation examples according to the newly added coor…
khalifa-aly Dec 3, 2024
58637a7
Adding the Description element to the resource as a markdown
khalifa-aly Dec 11, 2024
9c177c5
Adding the topology element to the resource as a codeable concept
khalifa-aly Dec 11, 2024
ef1e176
renaming the type element to moleculeType and make it a codeable concept
khalifa-aly Dec 11, 2024
3f2c554
Adding another type element and make it a codeable concept 0..* to de…
khalifa-aly Dec 11, 2024
9ffb0c0
QA edit
khalifa-aly Dec 11, 2024
7f6be25
updating the moleculeType element within example instances
khalifa-aly Dec 11, 2024
0f7f23d
updating the moleculeType element within example instances
khalifa-aly Dec 11, 2024
a676efc
updating the moleculeType element within example instances
khalifa-aly Dec 11, 2024
b405f85
updating the moleculeType element within example instances
khalifa-aly Dec 11, 2024
c1f22e3
updating the moleculeType element within example instances
khalifa-aly Dec 11, 2024
81880f3
updating the moleculeType element within example instances
khalifa-aly Dec 11, 2024
d505cbe
updating the moleculeType element within example instances
khalifa-aly Dec 11, 2024
74c60e0
updating the allele profile to reflect the rename moleculeType element
khalifa-aly Dec 11, 2024
b6862c2
updating the alleleSliced profile to reflect the rename moleculeType …
khalifa-aly Dec 11, 2024
6e00eab
updating the genotype profile to reflect the rename moleculeType element
khalifa-aly Dec 11, 2024
fc974d5
updating the haplotype profile to reflect the rename of moleculeType …
khalifa-aly Dec 11, 2024
8acd69e
updating the sequence profile to reflect the rename of moleculeType e…
khalifa-aly Dec 11, 2024
41676d5
updating the variation profile to reflect the rename of moleculeType …
khalifa-aly Dec 11, 2024
ef7ccbd
updating the search params to reflect the rename of moleculeType element
khalifa-aly Dec 11, 2024
749b35d
updating moleculeType element to codeable concept within examples
khalifa-aly Dec 11, 2024
1584155
updating moleculeType element to codeable concept within examples
khalifa-aly Dec 11, 2024
53118d6
updating moleculeType element to codeable concept within examples
khalifa-aly Dec 11, 2024
748f7b3
updating moleculeType element to codeable concept within examples
khalifa-aly Dec 11, 2024
a535981
updating moleculeType element to codeable concept within examples
khalifa-aly Dec 11, 2024
55a2293
updating moleculeType element to codeable concept within examples
khalifa-aly Dec 11, 2024
0fcb8f4
updating moleculeType element to codeable concept within examples
khalifa-aly Dec 11, 2024
3ad3fdd
updating moleculeType element to codeable concept within examples
khalifa-aly Dec 11, 2024
8236992
updating moleculeType element to codeable concept within examples
khalifa-aly Dec 11, 2024
6318a8d
updating moleculeType element to codeable concept within examples
khalifa-aly Dec 11, 2024
5f4adc1
updating moleculeType element to codeable concept within examples
khalifa-aly Dec 11, 2024
319cc5c
updating moleculeType element to codeable concept within examples
khalifa-aly Dec 11, 2024
74b5437
updating moleculeType element to codeable concept within examples
khalifa-aly Dec 11, 2024
7b5f0c4
updating moleculeType element to codeable concept within examples
khalifa-aly Dec 11, 2024
c1c142a
updating representation.extracted to reflect the new coordinate inter…
khalifa-aly Dec 19, 2024
366edc5
updating representation.relative to reflect the new coordinate interv…
khalifa-aly Dec 19, 2024
fc4b35c
updating end and start elements to be of integer datatype 1..1
khalifa-aly Dec 19, 2024
ad03158
updating the example to reflect the new coordinate interval structure
khalifa-aly Dec 19, 2024
78eabef
updating the example to reflect the new coordinate interval structure
khalifa-aly Dec 19, 2024
9e58c15
updating the example to reflect the new coordinate interval structure
khalifa-aly Dec 19, 2024
d5390d8
updating the example to reflect the new coordinate interval structure
khalifa-aly Dec 19, 2024
e0c5f19
updating the example to reflect the new coordinate interval structure
khalifa-aly Dec 19, 2024
e8ed3a5
updating the example to reflect the new coordinate interval structure
khalifa-aly Dec 19, 2024
a9c3088
QA edit, start and end element names
khalifa-aly Dec 19, 2024
175cadc
comment for deleting commented out lines later
khalifa-aly Dec 19, 2024
ef983dc
Merge branch 'master' into cg-im-moldef_work_in_progress_2
khalifa-aly Dec 20, 2024
2697c8c
Merge pull request #3256 from HL7/master
khalifa-aly Jan 7, 2025
b5183c5
removing un-necessary element
khalifa-aly Jan 7, 2025
9faf63b
removing un-necessary element
khalifa-aly Jan 7, 2025
f64f70e
Merge branch 'master' into cg-im-moldef_work_in_progress_2
sirkyp Jan 27, 2025
df11216
Documentation updates
sirkyp Jan 28, 2025
dde543f
Update moleculardefinition-notes.xml
sirkyp Jan 28, 2025
a58ad9a
Add more structure to the examples page.
sirkyp Jan 28, 2025
e77f163
New CS and VS (molec type), tweaks to existing, add bindings
sirkyp Jan 31, 2025
7d9142f
Some CS/VS fixes for moleculetype
sirkyp Feb 4, 2025
dc8e712
New CS/VS (normalization, orientation), new bindings, updated encodin…
sirkyp Feb 4, 2025
b320cc6
removing conformance to allele profile
khalifa-aly Feb 10, 2025
59cdaa9
removing conformance to allele profile
khalifa-aly Feb 10, 2025
82030e6
removing conformance to allele profile
khalifa-aly Feb 10, 2025
7a778f3
removing conformance to genotype profile
khalifa-aly Feb 10, 2025
3d7eb39
removing conformance to haplotype profile
khalifa-aly Feb 10, 2025
74f0b26
removing conformance to variation profile
khalifa-aly Feb 10, 2025
9393c4a
removing conformance to variation profile
khalifa-aly Feb 10, 2025
c410b7d
removing conformance to variation profile
khalifa-aly Feb 10, 2025
4cb3cfe
removing conformance to sequence profile
khalifa-aly Feb 10, 2025
97ec057
removing conformance to sequence profile
khalifa-aly Feb 10, 2025
7e74a4a
Merge pull request #3289 from HL7/master
khalifa-aly Feb 10, 2025
a831f9a
Ease binding strengths
sirkyp Feb 10, 2025
ad6a6ad
removing profiles
khalifa-aly Feb 12, 2025
5877cc4
Merge branch 'master' into cg-im-moldef_work_in_progress_2
khalifa-aly Feb 17, 2025
781589c
Merge branch 'master' into cg-im-moldef_work_in_progress_2
khalifa-aly Feb 18, 2025
dddc361
removing Coding System from the focus CC elements
khalifa-aly Feb 18, 2025
74f1410
deleting valueSets: encoding, focus, moleculeType, normalization, and…
khalifa-aly Feb 18, 2025
359fdf7
deleting Code Systems: encoding, focus, moleculeType, normalization, …
khalifa-aly Feb 18, 2025
f6df76d
removing Coding System from the focus CC elements
khalifa-aly Feb 18, 2025
4823752
removing code system from focus and encoding elements
khalifa-aly Feb 18, 2025
ddbb6e6
removing code system from focus and encoding elements
khalifa-aly Feb 18, 2025
c7ac02b
removing Code System bindings of: moleculeType, orientation, focus, e…
khalifa-aly Feb 18, 2025
8781dac
Merge remote-tracking branch 'refs/remotes/origin/master' into cg-im-…
patrick-werner Feb 19, 2025
8e12f97
Merge branch 'master' into cg-im-moldef_work_in_progress_2
khalifa-aly Feb 19, 2025
c1d8372
fixed moleculetype SP MolecularDefinition
patrick-werner Feb 19, 2025
6cc5cc5
Fix some search params
sirkyp Feb 19, 2025
310cdee
New examples
sirkyp Feb 20, 2025
108078d
Updates and fixes to newest contained example
sirkyp Feb 20, 2025
499f1ef
Merge branch 'master' into cg-im-moldef_work_in_progress_2
lmckenzi Feb 20, 2025
8fc9d36
updating PharmVar coding elements
khalifa-aly Feb 20, 2025
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QA edit
khalifa-aly committed Sep 6, 2024
commit d187990205397c224c0210aa0e1540767c379fb3
Original file line number Diff line number Diff line change
@@ -24,6 +24,9 @@
<startQuantity>
<value value="1016"/>
</startQuantity>
<endQuantity>
<value value="1016"/>
</endQuantity>
</coordinateInterval>
</sequenceLocation>
</location>