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Add phenopacket extraction template #484

Merged
merged 67 commits into from
Dec 13, 2024
Merged

Add phenopacket extraction template #484

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e95b5e7
First iteration - Phenopacket class
caufieldjh Nov 21, 2024
8878997
Add Family and Cohort classes
caufieldjh Nov 21, 2024
2f51ef1
Add classes from core/base
caufieldjh Nov 21, 2024
7485441
Adapt Biosample class from linkml-phenopackets
caufieldjh Nov 22, 2024
c1eca0a
Adapt Disease class from linkml-phenopackets
caufieldjh Nov 22, 2024
50b49f4
Add more prefixes
caufieldjh Nov 22, 2024
dbf0a87
Adapt Interpretation classes and enums from linkml-phenopackets
caufieldjh Nov 22, 2024
334964b
Adapt Individual classes and enums from linkml-phenopackets
caufieldjh Nov 22, 2024
2bfc1da
Adapt Measurement classes from linkml-phenopackets
caufieldjh Nov 22, 2024
1796bba
Adapt Medical_Action classes and enums from linkml-phenopackets
caufieldjh Nov 22, 2024
ac0b19c
Adapt Meta_Data classes from linkml-phenopackets
caufieldjh Nov 22, 2024
a6ffe21
Add Pedigree classes and enum from linkml-phenopackets
caufieldjh Nov 23, 2024
8d003c9
Add Phenotypic_feature classes from linkml-phenopackets
caufieldjh Nov 23, 2024
bb4de7a
Cleanup
caufieldjh Nov 23, 2024
d8a2246
Restrict to single patients for now
caufieldjh Nov 23, 2024
27ec952
Skip id fields to be grounded or assigned after grounding
caufieldjh Nov 23, 2024
fa08ffe
Fix spacing on Evidence class
caufieldjh Nov 23, 2024
6c37c26
Fix issues with assigning prompt examples
caufieldjh Nov 23, 2024
94c404c
Add vrsatile from linkml-phenopackets
caufieldjh Nov 23, 2024
3586aad
Add vrs from linkml-phenopackets
caufieldjh Nov 23, 2024
e483d06
Add missing VariationSet
caufieldjh Nov 23, 2024
5639234
Add initial python phenopackets
caufieldjh Nov 23, 2024
73c2c9d
Extra simple template for testing
caufieldjh Dec 3, 2024
b855560
Improvements to Individual class
caufieldjh Dec 4, 2024
0d0bdf6
Improvements to PhenotypicFeature class
caufieldjh Dec 4, 2024
ac63394
Expand prompts in main class
caufieldjh Dec 5, 2024
875645c
Linting n' formatting
caufieldjh Dec 5, 2024
7998d3d
Template updates
caufieldjh Dec 9, 2024
f6312e1
Back to minimal working state
caufieldjh Dec 11, 2024
77649bc
Minimal functional version for multiple subjects
caufieldjh Dec 11, 2024
91a3bad
Update prompts in Individual class
caufieldjh Dec 11, 2024
4479238
Expand Measurement and Procedure classes
caufieldjh Dec 11, 2024
d3a185a
Expand Biosample class
caufieldjh Dec 12, 2024
5add454
Prompt tuning to avoid empty values
caufieldjh Dec 12, 2024
2831651
Merge remote-tracking branch 'origin' into 482-add-phenopacket-extrac…
caufieldjh Dec 12, 2024
bc475f1
More adjustments to avoid NAs
caufieldjh Dec 12, 2024
f76119f
Expand Interpretation class and child classes
caufieldjh Dec 12, 2024
b67a211
Expand Disease class
caufieldjh Dec 13, 2024
83ea889
A fix for the Interpretation class diagnosis slot
caufieldjh Dec 13, 2024
9cad9f2
Expand MedicalAction class
caufieldjh Dec 13, 2024
d41fc31
Update the PhenotypicFeature class
caufieldjh Dec 13, 2024
94b89b6
Expand the Evidence class
caufieldjh Dec 13, 2024
e10d467
Comments
caufieldjh Dec 13, 2024
f5e168b
Comments and cleanup
caufieldjh Dec 13, 2024
48e73c4
Fix for empty metadata
caufieldjh Dec 13, 2024
d802678
Set up grounding for phenotypes
caufieldjh Dec 13, 2024
f0fe649
Add more grounding classes
caufieldjh Dec 13, 2024
f4d15c8
Tweaks for the Measurement class
caufieldjh Dec 13, 2024
e33e146
Tweaks and grounding for the Quantity class
caufieldjh Dec 13, 2024
3c6c43f
Expand ReferenceRange class
caufieldjh Dec 13, 2024
88ef3a4
Expand the TypedQuantity class
caufieldjh Dec 13, 2024
edcbe97
Add DescriptiveClass for grounding
caufieldjh Dec 13, 2024
fd444d9
Updates and grounding for MedicalAction
caufieldjh Dec 13, 2024
d92b14e
Tweaks to RadiationTherapy
caufieldjh Dec 13, 2024
c39a29e
Expand the Treatment class
caufieldjh Dec 13, 2024
7ca24ee
Grounding in the Disease class
caufieldjh Dec 13, 2024
9d7fc9b
Add GenderClass for grounding
caufieldjh Dec 13, 2024
56d572c
Grounding in VitalStatus
caufieldjh Dec 13, 2024
196bed6
Grounding for TherapeuticRegimen
caufieldjh Dec 13, 2024
bdd4150
More grounding for PhenotypicFeature
caufieldjh Dec 13, 2024
6f2b5d0
Add grounding for genetic variants
caufieldjh Dec 13, 2024
1bbf16e
Grounding for Biosample class
caufieldjh Dec 13, 2024
986731d
Grounding for tumor progression
caufieldjh Dec 13, 2024
ddc1dfa
Updates for RadiationTherapy class
caufieldjh Dec 13, 2024
fe68424
Minor prompt tuning
caufieldjh Dec 13, 2024
a62741f
More annotators
caufieldjh Dec 13, 2024
4792b15
A fix for assigning ids to Individuals
caufieldjh Dec 13, 2024
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