Metadata & Data Documentation

Documents the PhD data architecture by defining the core variable registry, source tables, join logic, Mplus-ready four-character aliases, and stream-specific use of data for reproducible obstetric HIV analysis.

Keywords

PhDDesk

Focus

Structured metadata and data documentation for reproducible obstetric HIV phenotype modeling, longitudinal inference, and dynamic prediction.

Overview

This documentation stream formalizes the data architecture that supports the PhD analytical program after the Proposal Abstract stage. The objective is to move from conceptual aims to an explicit variable registry, join-key strategy, and analytical-use map so that each downstream model is tied to a documented data object rather than an informal extraction workflow.

The current metadata build is organized around six linked assets:

1. The source eCRF data dictionary for the pregnancy cohort.
2. A complete variable shortlist spanning social, clinical, treatment, and outcome domains.
3. A core analytical shortlist restricted to variables with direct methodological use across the PhD aims.
4. An aim-linked use map that records why each retained variable is needed and where it enters the statistical pipeline.
5. A synthetic ADaM contract that fixes the prototype analysis datasets and model-input files before live data are linked.
6. A shortlist-to-ADaM derivation map that shows how the prototype social-risk indicators are constructed from retained baseline source fields.

The current core registry has already been mapped to the three main data-analytic streams that follow the methodological audit. The same variable does not have a single static role across the dissertation; some variables act as baseline confounders in one stream, time-varying predictors in another, and endpoint-support variables in the translational prediction stage. The prototype data layer now also records where a derived analysis variable begins, rather than allowing it to appear only inside downstream model code.

Documentation Design

The metadata layer is being built around three principles:

1. Variable provenance must be explicit. Every retained field should be traceable to its source table, join key, and intended analytical role.
2. Aim-specific use must be documented. The registry should show whether a variable is used for phenotype construction, confounding control, trajectory modeling, endpoint definition, or dynamic prediction support.
3. Missingness and timing cannot be treated as afterthoughts. Because the cohort contains irregular visit schedules and partial biomarker capture, the documentation needs to record missing-data burden and temporal anchors as part of the analysis design.
4. Derived variables must be traceable to retained source fields. The prototype ADaM layer should expose the derivation logic for social-risk indicators and other constructed variables instead of hiding them inside analysis scripts.

Mplus Naming Layer

The current metadata build now includes a provisional Mplus naming layer for core variables. These aliases are designed to be short, syntax-friendly, and easier to manage in model scripts while still retaining a CDISC-style domain logic.

The current naming proposal follows four rules:

1. All analysis names are uppercase.
2. Each suggested alias is limited to a maximum of 4 characters.
3. The first two characters identify the source-domain family.
4. The last two characters summarize the variable concept and remain provisional until the analysis dataset structure is finalized.

Current Documentation Scope
Documentation asset	Current role
db_ecrf_data_dictionary.csv	Source-level variable definitions and field naming reference.
maternal_health_variable_shortlist.csv	Broad candidate registry for maternal-health analysis planning.
maternal_health_variable_shortlist_core.csv	Core analytical variable set for the PhD program.
maternal_health_core_use_by_objective.qmd	Aim-linked documentation of variable use and methodological justification.

Analytical Coverage
Research stream	Core variables	Scope
Social Risk Phenotypes and the Maternal Burden of Obstetric HIV: A Causal Mixture Modeling Approach	27	Baseline social structure, reproductive history, STI context, and treatment covariates used for latent social-risk phenotyping and causal mixture modeling.
Multivariate Maternal Risk Phenotyping: Handling Time-Unstructuredness in Growth Mixture Models	17	Physiological and HIV-related markers used to characterize multivariate maternal risk trajectories under irregular follow-up.
Multidimensional Latent Burden and Translational Stratification: A Dynamic Prediction Framework	62	Outcome, timing, biomarker, follow-up, and support variables used for severe maternal outcome definition and dynamic prediction.

Preliminary Mplus Alias Scheme
Item	Current rule
Naming style	CDISC-style uppercase alias suggestion
Maximum length	4 characters
Structure	2-character source-domain prefix + 2-character analysis suffix
Intended use	Mplus-ready short names for modeling datasets and syntax files
Status	Provisional naming layer to be refined with the evolving analysis data model

Synthetic ADaM Contract
Variable	Label	Role	Source anchor	Notes
ADLB
BMI_ANT	Antenatal BMI	biomarker	bmi	Longitudinal anthropometry.
CD4_CNT	CD4 count	biomarker	cd4_count	Longitudinal immune marker.
DAYS_SINCE_ANC1	Days since first ANC	time_var	visit chronology	Clinical timescale.
GEST_DAYS_CORRECTED	Corrected gestational age (days)	time_var	edddt / last_menstrual_period	Gold-standard gestational timescale.
HGB_LVL	Hemoglobin	biomarker	haemoglobin	Longitudinal hematology marker.
LOG_VL	Log viral load	biomarker	viral_load	Longitudinal HIV biomarker.
ADSL
BASE_AGE	Maternal age at enrollment	baseline_covariate	age	Baseline demographic covariate.
BASE_BMI	Baseline BMI	baseline_covariate	bmi	Baseline physiologic covariate.
CD4_BASE	Baseline CD4 count	baseline_covariate	cd4_count	Baseline HIV disease activity marker.
ECON	Economic strain indicator	derived_social_indicator	highest_education + number_of_rooms + work_status	Derived from shortlisted fields: highest_education, number_of_rooms, work_status.
ECTV	Time-varying material strain signal	derived_social_indicator	use_family_planning	Derived from shortlisted fields: use_family_planning.
EST_GA_AT_ANC1	Estimated gestational age at first ANC (days)	timing_anchor	est_gestational_age_wks	Clinical timeline anchor.
GRAVIDITY	Prior pregnancies	baseline_covariate	total_number_pregnancies	Baseline reproductive history.
HOUS	Housing constraint indicator	derived_social_indicator	kind_of_toilet + number_of_rooms + people_sleep_in_room + tap_water	Derived from shortlisted fields: kind_of_toilet, number_of_rooms, people_sleep_in_room, tap_water.
MOM_ID	Analysis mother identifier	subject_key	usubjid	Anchored to maternal_health_variable_shortlist_core.csv
PART	Partner-context risk indicator	derived_social_indicator	marital_status + partner_hiv_status + partner_other_sexual_relations	Derived from shortlisted fields: marital_status, partner_hiv_status, partner_other_sexual_relations.
PRTV	Time-varying partner-context signal	derived_social_indicator	partner_other_sexual_relations	Derived from shortlisted fields: partner_other_sexual_relations.
SITE_COMPLEX	Facility complexity	design_covariate	siteid/sitenm	Ordinal site complexity proxy.
SITE_COUNTRY	Country	design_covariate	country	Site-level context.
SITE_ID	Site identifier	design_covariate	siteid	Primary clustering variable for multilevel mixture models.
SITE_VL_SUPP	Site-level viral suppression rate	design_covariate	siteid	Continuous contextual covariate.
SOC_RISK_CLASS	Synthetic latent social risk class	simulation_latent_truth	Derived	Used only for synthetic data generation and fallback prediction.
TRNS	Transport barrier indicator	derived_social_indicator	travel_time_to_clinic	Derived from shortlisted fields: travel_time_to_clinic.
ADSL_RAW
highest_education	Your highest level of education	shortlist_source_field	highest_education	Shortlisted baseline source retained in the synthetic prototype (SOCDEM).
kind_of_toilet	What kind of toilet do you have	shortlist_source_field	kind_of_toilet	Shortlisted baseline source retained in the synthetic prototype (SOCDEM).
marital_status	Marital status	shortlist_source_field	marital_status	Shortlisted baseline source retained in the synthetic prototype (SOCDEM).
number_of_rooms	Number of rooms house has	shortlist_source_field	number_of_rooms	Shortlisted baseline source retained in the synthetic prototype (SOCDEM).
partner_hiv_status	What is your partner hiv status	shortlist_source_field	partner_hiv_status	Shortlisted baseline source retained in the synthetic prototype (SOCDEM).
partner_other_sexual_relations	Partner has other sexual relations	shortlist_source_field	partner_other_sexual_relations	Shortlisted baseline source retained in the synthetic prototype (SRHH).
people_sleep_in_room	How many people sleep in your room	shortlist_source_field	people_sleep_in_room	Shortlisted baseline source retained in the synthetic prototype (SOCDEM).
tap_water	Tap water in the premises	shortlist_source_field	tap_water	Shortlisted baseline source retained in the synthetic prototype (SOCDEM).
travel_time_to_clinic	Travel time from home to clinic	shortlist_source_field	travel_time_to_clinic	Shortlisted baseline source retained in the synthetic prototype (SOCDEM).
use_family_planning	Did you use family planning methods	shortlist_source_field	use_family_planning	Shortlisted baseline source retained in the synthetic prototype (SRHH).
work_status	Do you work	shortlist_source_field	work_status	Shortlisted baseline source retained in the synthetic prototype (SOCDEM).
ADTTE
PTB_STATUS	Preterm birth status	secondary_outcome	delivery outcomes	Synthetic secondary outcome.
SGA_STATUS	Small-for-gestational-age status	secondary_outcome	delivery outcomes	Synthetic secondary outcome.
SMO_DAYS	Days to severe maternal outcome or censoring	time_to_event	delivery/adverse event timing	Event timescale for Aim 4.
SMO_EVENT	Severe maternal outcome flag	time_to_event	pregnancy_outcome / adverse events	Primary dynamic prediction event indicator.
MPLUS_AIM2
aim2_social_mplus.dat	Wide categorical social indicator export	model_input	ADSL	Written from the centralized synthetic ADaM layer.
MPLUS_AIM3
aim3_logvl_wide.dat	Wide TSCORES export for LOG_VL	model_input	ADLB	Written from the centralized synthetic ADaM layer.
Current PME prototype data contract generated from the centralized synthetic ADaM builder.

Shortlist to ADaM Social-Derivation Map
Source variable	Source label	Source table	Aim scope	Derivation logic	Role
ECON - Economic strain indicator
highest_education	Your highest level of education	SOCDEM	aim_2;aim_4	Score lower educational attainment as structural economic vulnerability.	Latent social phenotype indicator
number_of_rooms	Number of rooms house has	SOCDEM	aim_2;aim_4	Score very low room count as constrained household resources.	Latent social phenotype indicator
work_status	Do you work	SOCDEM	aim_2;aim_4	Score unemployment/household work as material strain.	Latent social phenotype indicator
ECTV - Time-varying material strain signal
use_family_planning	Did you use family planning methods	SRHH	aim_2;aim_4	Use family-planning non-use as a proxy support signal layered onto baseline material strain.	Time-varying support flag
HOUS - Housing constraint indicator
kind_of_toilet	What kind of toilet do you have	SOCDEM	aim_2;aim_4	Flag lower-quality sanitation as household infrastructure strain.	Latent social phenotype indicator
number_of_rooms	Number of rooms house has	SOCDEM	aim_2;aim_4	Combine low room count with crowding to define housing constraint.	Latent social phenotype indicator
people_sleep_in_room	How many people sleep in your room	SOCDEM	aim_2;aim_4	Combine sleeping density with rooms to define crowding burden.	Latent social phenotype indicator
tap_water	Tap water in the premises	SOCDEM	aim_2;aim_4	Flag absent on-premises tap water as household infrastructure strain.	Latent social phenotype indicator
PART - Partner-context risk indicator
marital_status	Marital status	SOCDEM	aim_2;aim_4	Score unstable partner context as relational vulnerability.	Latent social phenotype indicator
partner_hiv_status	What is your partner hiv status	SOCDEM	aim_2;aim_4	Score partner HIV-positive status as partner-context vulnerability.	Latent social phenotype indicator
partner_other_sexual_relations	Partner has other sexual relations	SRHH	aim_2;aim_4	Score known partner concurrency as partner-context vulnerability.	Latent social phenotype indicator
PRTV - Time-varying partner-context signal
partner_other_sexual_relations	Partner has other sexual relations	SRHH	aim_2;aim_4	Carry partner-context instability into a time-varying support flag.	Time-varying support flag
TRNS - Transport barrier indicator
travel_time_to_clinic	Travel time from home to clinic	SOCDEM	aim_2;aim_4	Flag long clinic travel times as access-to-care barriers.	Latent social phenotype indicator
The social-risk indicators used in the PME prototype are now derived explicitly from shortlisted baseline fields rather than simulated directly in the aim scripts.

Derived Analytical Objects
Derived object	Analytical role	Mplus name	Purpose
Social risk phenotyping
Social risk phenotype class	Latent baseline social-vulnerability phenotype	XSRP	Represents the derived latent social-risk grouping used in causal mixture analyses for obstetric HIV.
Posterior social-risk probability	Class-membership uncertainty summary for social-risk models	PSRP	Retains posterior uncertainty so social-risk class assignment is not treated as fixed in downstream estimation.
Maternal burden phenotyping
Maternal burden phenotype class	Latent longitudinal physiological-burden phenotype	XMBP	Represents the derived multivariate maternal-risk trajectory grouping under irregular longitudinal follow-up.
Outcome endpoint
Severe maternal outcome endpoint	Binary downstream maternal endpoint	YSMO	Defines the derived severe maternal outcome target used for modeling and translational interpretation.
Prediction objects
Dynamic landmark risk estimate	Updated individualized risk at clinical prediction landmarks	RDLM	Stores updated patient-level risk predictions generated from the joint longitudinal-event modeling framework.
Uncertainty objects
BCH / posterior uncertainty weights	Uncertainty control for latent-class and mixture-model estimation	WBCH	Carries BCH-style or posterior-probability uncertainty adjustments into distal outcome and prediction models.

Observed Variable Maps

Social Risk Phenotypes and the Maternal Burden of Obstetric HIV: A Causal Mixture Modeling Approach

Social Risk Phenotypes and the Maternal Burden of Obstetric HIV: A Causal Mixture Modeling Approach
Source	Original variable	Mplus name	Label	Role in analysis	Join keys	Justification
Arv Treatment
ARV	drg1	ARD1	Drug 1	treatment_exposure	usubjid|dsta	Primary regimen component for therapy exposure grouping.
ARV	dsta	ARDS	Date started	treatment_exposure	usubjid|dsta	Treatment exposure start needed for ART-time alignment.
ARV	dsto	ARDE	Date stopped	treatment_exposure	usubjid|dsta	Treatment exposure stop needed for treatment dynamics and censoring.
Clinical Sti
SRHH	abnormal_vaginal_discharge	SRAV	Last 3 months-abnormal vag discharge	clinical_covariate	usubjid|visitnum	Clinical STI symptom indicator; model separately from social exposure constructs.
SRHH	genital_herpes	SRGH	In the last 3 months-genital herpes	clinical_covariate	usubjid|visitnum	Clinical STI diagnosis indicator; model separately from social exposure constructs.
SRHH	syphilis	SRSY	In the last 3 months-syphilis	clinical_covariate	usubjid|visitnum	Clinical STI diagnosis indicator; model separately from social exposure constructs.
Obstetric History
OBSH	number_abortions	OBAB	Number of abortions/miscarriages	baseline_covariate	usubjid|visitnum	Baseline reproductive history risk profile.
OBSH	number_premature_births	OBPB	Premature births	baseline_covariate	usubjid|visitnum	Baseline reproductive history risk profile.
OBSH	number_stillbirths	OBST	Number stillbirths >20 weeks	baseline_covariate	usubjid|visitnum	Baseline reproductive history risk profile.
OBSH	outcome_last_pregnancy	OBOP	Outcome of the last pregnancy	baseline_covariate	usubjid|visitnum	Baseline reproductive history risk profile.
OBSH	total_number_pregnancies	OBTP	Total number of pregnancies	baseline_covariate	usubjid|visitnum	Baseline reproductive history risk profile.
Sexual Reproductive
SRHH	currently_pregnant	SRCP	Currently pregnant	covariate	usubjid|visitnum	Sexual/reproductive and STI vulnerability profile.
Site Context
CNTRYST	country	CNCO	Country	design_covariate	siteid	Country-level context for health-system and policy heterogeneity adjustment.
CNTRYST	siteid	CNSI	Site ID	design_covariate	siteid	Primary site-level clustering and stratification covariate across aims.
CNTRYST	sitenm	CNS1	Site Name	design_covariate	siteid	Readable site label for outputs and quality control checks.
Social
SRHH	partner_other_sexual_relations	SRPO	Partner has other sexual relations	covariate	usubjid|visitnum	Social relationship-risk context indicator; keep in social exposure domain.
SRHH	use_family_planning	SRUF	Did you use family planning methods	covariate	usubjid|visitnum	Behavior/access indicator in reproductive social context; model with social determinants.
Social Baseline
SOCDEM	age	SDAG	Age	covariate	usubjid|visitnum	Baseline demographic confounder for all models.
SOCDEM	highest_education	SDHE	Your highest level of education	covariate	usubjid|visitnum	Socioeconomic confounder and social phenotype component.
SOCDEM	kind_of_toilet	SDTO	What kind of toilet do you have	covariate	usubjid|visitnum	Baseline social determinants and access profile.
SOCDEM	marital_status	SDMS	Marital status	covariate	usubjid|visitnum	Baseline social determinants and access profile.
SOCDEM	number_of_rooms	SDRO	Number of rooms house has	covariate	usubjid|visitnum	Baseline social determinants and access profile.
SOCDEM	partner_hiv_status	SDPH	What is your partner hiv status	covariate	usubjid|visitnum	Baseline social determinants and access profile.
SOCDEM	people_sleep_in_room	SDPS	How many people sleep in your room	covariate	usubjid|visitnum	Baseline social determinants and access profile.
SOCDEM	tap_water	SDTW	Tap water in the premises	covariate	usubjid|visitnum	Baseline social determinants and access profile.
SOCDEM	travel_time_to_clinic	SDTT	Travel time from home to clinic	covariate	usubjid|visitnum	Access-to-care proxy affecting both exposure and outcomes.
SOCDEM	work_status	SDWS	Do you work	covariate	usubjid|visitnum	Economic vulnerability indicator for social phenotype classes.
Baseline social structure, reproductive history, STI context, and treatment covariates used for latent social-risk phenotyping and causal mixture modeling.

Multivariate Maternal Risk Phenotyping: Handling Time-Unstructuredness in Growth Mixture Models

Multivariate Maternal Risk Phenotyping: Handling Time-Unstructuredness in Growth Mixture Models
Source	Original variable	Mplus name	Label	Role in analysis	Join keys	Justification
Arv Treatment
ARV	drg1	ARD1	Drug 1	treatment_exposure	usubjid|dsta	Primary regimen component for therapy exposure grouping.
ARV	dsta	ARDS	Date started	treatment_exposure	usubjid|dsta	Treatment exposure start needed for ART-time alignment.
ARV	dsto	ARDE	Date stopped	treatment_exposure	usubjid|dsta	Treatment exposure stop needed for treatment dynamics and censoring.
Biochemistry
LFT	creatinine1	LFCR	Creatinine	biomarker	usubjid|visitnum	Core renal dysfunction marker relevant to severe maternal outcomes.
LFT	total_bilirubin	LFTB	Total bilirubin	biomarker	usubjid|visitnum	Core hepatic dysfunction marker relevant to severe maternal outcomes. Methodologically essential despite higher missingness; use missing-data strategy.
Hematology
FBC	haemoglobin	FBHB	Haemoglobin	biomarker	usubjid|visitnum	Core anemia marker for maternal risk phenotyping.
FBC	platelet_count	FBPL	Platelet count	biomarker	usubjid|visitnum	Core coagulation/hematologic risk marker.
Hiv Markers
HIVM	cd4_count	HIC4	Cd4 count	biomarker	usubjid|visitnum	Core immune status marker for risk adjustment and phenotyping. Methodologically essential despite higher missingness; use missing-data strategy.
HIVM	viral_load	HIVL	Viral load copies	biomarker	usubjid|visitnum	Core HIV disease activity marker for maternal risk stratification. Methodologically essential despite higher missingness; use missing-data strategy.
Site Context
CNTRYST	country	CNCO	Country	design_covariate	siteid	Country-level context for health-system and policy heterogeneity adjustment.
CNTRYST	siteid	CNSI	Site ID	design_covariate	siteid	Primary site-level clustering and stratification covariate across aims.
CNTRYST	sitenm	CNS1	Site Name	design_covariate	siteid	Readable site label for outputs and quality control checks.
Vitals
VIT	bmi	VTBM	Bmi	biomarker	usubjid|visitnum	Core maternal physiologic trajectory measures.
VIT	diastolic_bp	VTDB	Diastolic bp	biomarker	usubjid|visitnum	Core maternal hemodynamic marker linked to obstetric risk.
VIT	systolic_bp	VTSB	Systolic bp	biomarker	usubjid|visitnum	Core maternal hemodynamic marker linked to obstetric risk.
VIT	weight	VTWT	Weight	biomarker	usubjid|visitnum	Core maternal physiologic trajectory measures.
Who Stage
WHO	who_clinical_classification	WHWC	Who clinical classification	disease_severity_covariate	usubjid|visitnum	Global HIV clinical severity summary for baseline adjustment.
Physiological and HIV-related markers used to characterize multivariate maternal risk trajectories under irregular follow-up.

Multidimensional Latent Burden and Translational Stratification: A Dynamic Prediction Framework

Multidimensional Latent Burden and Translational Stratification: A Dynamic Prediction Framework
Source	Original variable	Mplus name	Label	Role in analysis	Join keys	Justification
Adverse Events
AE	ae_severity	AESE	Adverse event severity	outcome_support	usubjid|vstdt	Supports severe-event capture beyond delivery record fields.
AE	serious_adverse_event	AESA	Is this a serious adverse event	outcome_support	usubjid|vstdt	Captures severe intercurrent maternal morbidity events.
Arv Treatment
ARV	drg1	ARD1	Drug 1	treatment_exposure	usubjid|dsta	Primary regimen component for therapy exposure grouping.
ARV	dsta	ARDS	Date started	treatment_exposure	usubjid|dsta	Treatment exposure start needed for ART-time alignment.
ARV	dsto	ARDE	Date stopped	treatment_exposure	usubjid|dsta	Treatment exposure stop needed for treatment dynamics and censoring.
Biochemistry
LFT	creatinine1	LFCR	Creatinine	biomarker	usubjid|visitnum	Core renal dysfunction marker relevant to severe maternal outcomes.
LFT	total_bilirubin	LFTB	Total bilirubin	biomarker	usubjid|visitnum	Core hepatic dysfunction marker relevant to severe maternal outcomes. Methodologically essential despite higher missingness; use missing-data strategy.
Clinical Sti
SRHH	abnormal_vaginal_discharge	SRAV	Last 3 months-abnormal vag discharge	clinical_covariate	usubjid|visitnum	Clinical STI symptom indicator; model separately from social exposure constructs.
SRHH	genital_herpes	SRGH	In the last 3 months-genital herpes	clinical_covariate	usubjid|visitnum	Clinical STI diagnosis indicator; model separately from social exposure constructs.
SRHH	syphilis	SRSY	In the last 3 months-syphilis	clinical_covariate	usubjid|visitnum	Clinical STI diagnosis indicator; model separately from social exposure constructs.
Delivery Outcomes
LDR	deldt	LDDD	Delivery date	outcome	usubjid|visitnum	Defines pregnancy and delivery endpoints.
LDR	gestational_diabetes	LDGD	Gestational diabetes	outcome	usubjid|visitnum	Defines pregnancy and delivery endpoints.
LDR	high_blood_pressure	LDHB	High blood pressure	outcome	usubjid|visitnum	Defines pregnancy and delivery endpoints.
LDR	obstetrics_complications	LDOC	Any obstetric complications	outcome	usubjid|visitnum	Defines pregnancy and delivery endpoints.
LDR	pregnancy_outcome	LDPO	2 indicate pregnancy outcome	outcome	usubjid|visitnum	Primary maternal outcome definition for SMO trajectory and endpoint modeling.
LDR	type_delivery	LDTD	Type of delivery	outcome	usubjid|visitnum	Defines pregnancy and delivery endpoints.
LDR	vaginal_bleeding	LDVB	Vaginal bleeding	outcome	usubjid|visitnum	Defines pregnancy and delivery endpoints.
Hematology
FBC	haemoglobin	FBHB	Haemoglobin	biomarker	usubjid|visitnum	Core anemia marker for maternal risk phenotyping.
FBC	platelet_count	FBPL	Platelet count	biomarker	usubjid|visitnum	Core coagulation/hematologic risk marker.
Hiv Markers
HIVM	cd4_count	HIC4	Cd4 count	biomarker	usubjid|visitnum	Core immune status marker for risk adjustment and phenotyping. Methodologically essential despite higher missingness; use missing-data strategy.
HIVM	viral_load	HIVL	Viral load copies	biomarker	usubjid|visitnum	Core HIV disease activity marker for maternal risk stratification. Methodologically essential despite higher missingness; use missing-data strategy.
Hospital Admissions
HOSP	admdt	HOAD	Admission date	outcome_support	usubjid|admdt	Hospitalization timing signal for acute decompensation episodes.
HOSP	diag	HODG	Diagnosis	outcome_support	usubjid|admdt	Captures acute clinical deterioration episodes.
Maternal Followup
MAFU	admitted_hospital	MFAH	Been admitted to hospital	time_varying_covariate	usubjid|visitnum	Time-varying maternal clinical status and symptoms.
MAFU	current_health_status	MFHS	General health status	time_varying_covariate	usubjid|visitnum	Time-varying maternal clinical status and symptoms.
MAFU	current_pregnancy_status	MFPS	Current pregnancy status	time_varying_covariate	usubjid|visitnum	Time-varying maternal clinical status and symptoms.
Obstetric History
OBSH	number_abortions	OBAB	Number of abortions/miscarriages	baseline_covariate	usubjid|visitnum	Baseline reproductive history risk profile.
OBSH	number_premature_births	OBPB	Premature births	baseline_covariate	usubjid|visitnum	Baseline reproductive history risk profile.
OBSH	number_stillbirths	OBST	Number stillbirths >20 weeks	baseline_covariate	usubjid|visitnum	Baseline reproductive history risk profile.
OBSH	outcome_last_pregnancy	OBOP	Outcome of the last pregnancy	baseline_covariate	usubjid|visitnum	Baseline reproductive history risk profile.
OBSH	total_number_pregnancies	OBTP	Total number of pregnancies	baseline_covariate	usubjid|visitnum	Baseline reproductive history risk profile.
Pregnancy Followup
ANCF	admitted_hospital	ANAH	Admitted to hospital since last visit	time_varying_covariate	usubjid|visitnum	Antenatal follow-up status and interim clinical changes.
ANCF	change_in_arv_regimen	ANCA	Change in arv regimen since last visit	time_varying_covariate	usubjid|visitnum	Antenatal follow-up status and interim clinical changes.
ANCF	current_pregnancy_status	ANPS	Current pregnancy status	time_varying_covariate	usubjid|visitnum	Antenatal follow-up status and interim clinical changes.
Pregnancy Registration
PRF	conceive_on_arvs	PRCA	Conceive while taking arvs	pregnancy_timing_covariate	usubjid|visitnum	Pregnancy registration and gestational timing anchors.
PRF	edddt	PRED	Expected delivery date	pregnancy_timing_covariate	usubjid|visitnum	Pregnancy time anchor for gestational alignment and dynamic prediction windows.
PRF	est_gestational_age_wks	PREG	Estimated gestational age-weeks	pregnancy_timing_covariate	usubjid|visitnum	Core gestational timing covariate for longitudinal models.
PRF	last_menstrual_period	PRMP	Date of last menstrual period	pregnancy_timing_covariate	usubjid|visitnum	Pregnancy registration and gestational timing anchors.
Sexual Reproductive
SRHH	currently_pregnant	SRCP	Currently pregnant	covariate	usubjid|visitnum	Sexual/reproductive and STI vulnerability profile.
Site Context
CNTRYST	country	CNCO	Country	design_covariate	siteid	Country-level context for health-system and policy heterogeneity adjustment.
CNTRYST	siteid	CNSI	Site ID	design_covariate	siteid	Primary site-level clustering and stratification covariate across aims.
CNTRYST	sitenm	CNS1	Site Name	design_covariate	siteid	Readable site label for outputs and quality control checks.
Social
SRHH	partner_other_sexual_relations	SRPO	Partner has other sexual relations	covariate	usubjid|visitnum	Social relationship-risk context indicator; keep in social exposure domain.
SRHH	use_family_planning	SRUF	Did you use family planning methods	covariate	usubjid|visitnum	Behavior/access indicator in reproductive social context; model with social determinants.
Social Baseline
SOCDEM	age	SDAG	Age	covariate	usubjid|visitnum	Baseline demographic confounder for all models.
SOCDEM	highest_education	SDHE	Your highest level of education	covariate	usubjid|visitnum	Socioeconomic confounder and social phenotype component.
SOCDEM	kind_of_toilet	SDTO	What kind of toilet do you have	covariate	usubjid|visitnum	Baseline social determinants and access profile.
SOCDEM	marital_status	SDMS	Marital status	covariate	usubjid|visitnum	Baseline social determinants and access profile.
SOCDEM	number_of_rooms	SDRO	Number of rooms house has	covariate	usubjid|visitnum	Baseline social determinants and access profile.
SOCDEM	partner_hiv_status	SDPH	What is your partner hiv status	covariate	usubjid|visitnum	Baseline social determinants and access profile.
SOCDEM	people_sleep_in_room	SDPS	How many people sleep in your room	covariate	usubjid|visitnum	Baseline social determinants and access profile.
SOCDEM	tap_water	SDTW	Tap water in the premises	covariate	usubjid|visitnum	Baseline social determinants and access profile.
SOCDEM	travel_time_to_clinic	SDTT	Travel time from home to clinic	covariate	usubjid|visitnum	Access-to-care proxy affecting both exposure and outcomes.
SOCDEM	work_status	SDWS	Do you work	covariate	usubjid|visitnum	Economic vulnerability indicator for social phenotype classes.
Termination Death
TERM	cause_of_death	TRCD	Cause of death	outcome	usubjid|visitnum	Captures terminal outcomes and death attribution.
TERM	dthdt	TRDT	Date of death	outcome	usubjid|visitnum	Maternal death timing anchor for severe outcome endpoint.
TERM	reason_for_termination	TRRF	Reason for termination	outcome	usubjid|visitnum	Captures terminal outcomes and death attribution.
Vitals
VIT	bmi	VTBM	Bmi	biomarker	usubjid|visitnum	Core maternal physiologic trajectory measures.
VIT	diastolic_bp	VTDB	Diastolic bp	biomarker	usubjid|visitnum	Core maternal hemodynamic marker linked to obstetric risk.
VIT	systolic_bp	VTSB	Systolic bp	biomarker	usubjid|visitnum	Core maternal hemodynamic marker linked to obstetric risk.
VIT	weight	VTWT	Weight	biomarker	usubjid|visitnum	Core maternal physiologic trajectory measures.
Who Stage
WHO	who_clinical_classification	WHWC	Who clinical classification	disease_severity_covariate	usubjid|visitnum	Global HIV clinical severity summary for baseline adjustment.
Outcome, timing, biomarker, follow-up, and support variables used for severe maternal outcome definition and dynamic prediction.

Immediate Data Domains

The current metadata work is centered on the domains that directly support the proposed framework:

• Baseline social and demographic structure for latent social risk phenotypes.
• Obstetric and reproductive history for baseline maternal vulnerability profiling.
• ART exposure and treatment timing for longitudinal alignment.
• Vital signs, hematology, renal, hepatic, and HIV markers for physiological burden phenotyping.
• Delivery, hospitalization, adverse event, and termination records for severe maternal outcome definition and support.

Next Documentation Steps

1. Finalize a controlled registry for severe maternal outcome derivation variables and supporting event fields.
2. Document gestational and clinical time anchors used for irregular longitudinal alignment.
3. Add a formal join-specification layer for participant, visit, admission, and delivery records.
4. Extend the registry with derived-variable documentation for phenotype classes, dynamic prediction inputs, and final endpoint-construction rules once the live data pipeline is linked.

Open standalone PhDDesk project