Repository navigation
Update define-xml branch - #163
Merged
Merged
Conversation
Update of the README.md with technical info #75
… by SoA Workbench.
… by SoA Workbench.
Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>
Fix/100, 98, 78
Three-layer LinkML model for the CDISC 360i lab data flow, making the lab Data Transfer Agreement a typed, validatable contract traceable from USDM upstream to SDTM-LB downstream, joined on the BiomedicalConcept hub. - Agreement layer: DataTransferAgreement and friends (types the DTA app JSON) - Semantic layer: BiomedicalConcept / DatasetSpecialization, anchored to a vendored, re-derivable CDISC COSMoS specialization (HGBBLD / C64848) - Instance layer: nested Transmission payload; the three LAB Tx unit blocks (PLR*/CVU*/SIU*) normalized into one Result keyed by unitSystem - CURIE prefixes declared (ncit -> NCIt PURL, labtx -> LAB Tx Model v2.0 wiki); schema id follows the sibling define.yaml convention (https://cdisc.org/...) - Four example instances, all validate cleanly (linkml-validate; lint: 0 errors) - index.html: the browser-only DTA app demo - Licensed MIT to match this repository
Pi add json docs
Add dta2sdtm: Digital DTA logical data model (LinkML)
Fix/descriptor workaround
Rename of protocol directory to NCT01797120
Feature/key sequence
…and missing crf specializations. Narrative content is now added when the USDM is generated for the NCT01797120 study.
Fixed missing BCs, associated properties and CRF specializations
Fixed NoneType errors in build_vlm_lookup
test suite for create_define_json
Rebuilds the model against the DTA MVP Inventory, which the workstream confirmed as the DTA User Requirements. Added (agreement layer): - TestSpecification — the agreed test table: per-test vendor and standard codes, method, specimen, LOINC, data type, units, blinding. Fills the gap between concept scope (BcSelection) and file mechanics (TransferRequirements), where the agreement previously said nothing about which tests actually arrive. - TransferDataset / TransferVariable — the declared file structure. Replaced (instance layer): - TransferRecord (60 flat variables) replaces the nested LAB v2 graph (Subject > Collection > Specimen > Panel > LabTestResult > Result). This is a change of transfer vocabulary, not just shape: the removed graph modelled LAB v2 variables, TransferRecord models SDTM-shaped columns plus vendor passthrough. The two share essentially only STUDYID. Agreement <-> instance, modelled rather than asserted: - file level: Transmission.dta_version_ref names the DTA version fulfilled - test level: natural-key join on (test_panel_name + data_provider_test_code), falling back to data_provider_test_name. No surrogate key — no real transfer file carries one, and tests are not always coded. Design rule — permissive payload, strict agreement. Enums bind on the agreement side where the sponsor controls values; vendor-populated payload slots stay strings so a conformant-but-unanticipated file is not rejected at ingest. UnitEnum and LbTestCdEnum become documented reference vocabularies bound to no slot, because real transfers carry values outside any fixed subset. Project-defined slots (transfer_structure_version, dta_version_ref) say so in their annotations. Nothing is presented as CDISC terminology unless it is. BREAKING: instances valid against v0.1.0's nested Transmission will not validate against v0.2.0. All four bundled examples are updated accordingly. Verified: schema compiles; all five examples validate.
Latest JSON from SoA Workbench v1.6.0
processes latest USDM files
Feature/cdisc base url
feat(dta2sdtm): DTA logical data model v0.2.0
…ialization updated for RANDOMIZATION activity. New amendment entity created in the USDM JSON.
…ialization updated for RANDOMIZATION activity. New amendment entity created in the USDM JSON.
Update to the JSON files
Feature/crf generation
This branch was successfully deployed
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
9 participants
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
No description provided.