Medical-Event-Data-Standard meds issues

Medical-Event-Data-Standard / meds

Schema definitions and Python types for Medical Event Data Standard, a standard for medical event data such as EHR and claims data

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If/when we add more cohesive validation utilities, we should also check that time strings for dataset metadata are in the right format.

#49 mmcdermott opened 2 months ago
0
Added new constants for fields, types, and directories. All directory constants are relative to the `MEDS_ROOT` dir.

#48 mmcdermott closed 2 months ago
1
Update to v3.1

#47 EthanSteinberg closed 3 months ago
1
[Proposal] We should somehow integrate with/use/provide Croissant wrappers

#46 mmcdermott opened 3 months ago
0
[Proposal] patient_id -> subject_id rename

#45 EthanSteinberg closed 3 months ago
1
We should provide a MEDS synthetic data generator to help with testing

#44 mmcdermott opened 3 months ago
2
Should MEDS datasets write `_metadata` or `_common_metadata` files?

#43 mmcdermott opened 3 months ago
2
Do we really want to store all the label columns in every task dataframe even when the task will just have one kind of label?

#42 mmcdermott opened 3 months ago
2
How do we encode multi-label or sparse task labels?

#41 mmcdermott opened 3 months ago
0
Should we have a `duration_value` label type for TTE tasks?

#40 mmcdermott opened 3 months ago
0
Proposal for next release: `metadata/codes.parquet` should be guaranteed to have all unique codes (or codes + code modifiers) for the dataset, even if other rows are empty.

#39 mmcdermott closed 3 months ago
1
We should add a `created_at` timestamp to the `dataset.json` metadata file.

#38 mmcdermott closed 3 months ago
0
We should have some utilities to validate and re-cast to the target schema given they exist in functional forms.

#37 mmcdermott opened 3 months ago
7
We need to update documentation and comments here to reflect that `parent_codes` must be formatted in a specific way.

#36 mmcdermott closed 3 months ago
4
Documentation updates

#35 EthanSteinberg closed 3 months ago
8
We should export constants for sentinel field names (patient ID, code, timestamp) and the patient ID type

#34 mmcdermott closed 3 months ago
0
We should try to deduplicate schema definitions between TypedDict and pa schemas

#33 mmcdermott opened 3 months ago
0
MEDS 0.3 Release Candidate

#32 mmcdermott closed 3 months ago
6
MEDS 0.3 Tracker

#31 mmcdermott closed 3 months ago
4
Set up a wiki/read-the-docs as a starting point for using/developing MEDS

#30 rvandewater opened 5 months ago
0
[Question] Including static patient variables in Patient Schema

#29 simonEllershaw closed 5 months ago
1
[Proposal] Collapse properties into the event struct

#28 EthanSteinberg closed 3 months ago
0
MEDS v2 Release

#27 EthanSteinberg closed 6 months ago
0
[Proposal] Should Patient IDs always be integers?

#26 scottfleming opened 6 months ago
3
We need a usage document outlining the kinds of usage MEDS is best aligned to support and in what ways.

#25 mmcdermott opened 7 months ago
0
[Infrastructure] We should have a set of standard performance benchmarks for MEDS to compare schema changes and new technologies for using MEDS

#24 mmcdermott opened 7 months ago
1
How do I retrieve the visit information efficiently in the MEDS?

#23 ChaoPang opened 7 months ago
7
[Proposal] Remove both datetime_value and text_value as they are better handled in properties

#22 EthanSteinberg closed 3 months ago
0
V2 Release Tracker

#21 EthanSteinberg closed 6 months ago
0
[Proposal] Usability: Change from double -> single nesting

#20 Miking98 closed 6 months ago
27
[Proposal] Change `Event.time` => `Event.start_datetime` (required) and `Event.end_datetime` (optional)

#19 Miking98 closed 3 months ago
1
Add non-bool Label value options

#18 Miking98 closed 7 months ago
3
person_concept_id in omop?

#17 zakcay closed 7 months ago
13
[Proposal] Usability: Change `Event.time` => `Event.datetime`

#16 Miking98 closed 3 months ago
6
"Metadata" is used in both code/dataset specific metadata and as custom "measurement metadata" in the core schema. This is a bit confusing.

#15 mmcdermott closed 7 months ago
3
[Proposal] Code Metadata Expansions

#14 mmcdermott opened 9 months ago
2
Re-add static measurements

#13 mmcdermott closed 9 months ago
1
Static Measurements

#12 mmcdermott closed 9 months ago
8
Change mentions of `ESDS` to `MEDS`

#11 scottfleming closed 8 months ago
0
Move logic from __init_.py to schema submodules. Ref #3.

#10 tompollard closed 10 months ago
2
Run tests in the MEDS-ETL repository. Ref #8.

#9 tompollard closed 10 months ago
0
Add MEDS ETL tests to the github workflow?

#8 tompollard closed 10 months ago
1
Add github workflow to publish packages

#7 tompollard closed 7 months ago
1
Add simple github workflow.

#6 tompollard closed 10 months ago
3
Add tests for the three schema (patient_schema, label, dataset_metadata)

#5 tompollard closed 10 months ago
2
Add typing_extensions dependency.

#4 tompollard closed 11 months ago
0
Move logic out of __init__.py

#3 tompollard closed 10 months ago
1
Incorporate changes to be more compatible with OHDSI

#2 EthanSteinberg closed 7 months ago
1
Run MEDS ETLs as part of a testing framework

#1 tompollard closed 10 months ago
0