# Data Access Requirements

This document specifies exactly what data sources, systems, and contact points are needed to unlock each dashboard module beyond the current evidence scan capability.

## Current Data Status

| Source | Access | Data Available | Modules Enabled |
|---|---|---|---|
| INSP SitRep (via INRB-UMIE GitHub) | Public | Daily zone-level cases, contacts, hospitalisation | Situation, Time (notification), Place, Contacts (partial) |
| WorldPop (via INRB-UMIE) | Public | Population by health zone | Attack rates |
| INRB-UMIE testing_capacity | Public | PCR machines by zone | Lab (capacity only) |
| WHO DON602/603 | Public | National case counts, risk assessment | Situation, Response |
| ECDC Threat Assessment | Public | EU/EEA risk, preparedness | Response |
| Pathoplexus | Restricted | 16 outbreak genomes (metadata) | Genomics (partial) |
| NCBI GenBank | Public | 34 historical genomes | Genomics (historical QC) |

## What Is Missing and How to Get It

### 1. Individual Case Linelist

**Unlocks:** B. Cases (filterable table), C. Time (onset-based epi curve), E. Person (demographics), J. Data Quality (missingness, duplicates)

| Field | Required For |
|---|---|
| case_id | Deduplication, drill-down |
| age, sex | Age/sex pyramid, demographic targeting |
| onset_date | Onset-based epi curve (vs notification date) |
| notification_date | Reporting delay analysis |
| classification (suspect/probable/confirmed/discarded) | Case classification cascade |
| outcome (alive/dead/unknown) | CFR by subgroup |
| health_zone, GPS | Sub-zone mapping, cluster detection |
| occupation | HCW risk, exposure groups |
| pregnancy_status | Maternal risk |
| idp_refugee_status | Vulnerability targeting |
| exposure_type | Transmission chain inference |

**Source system:** DRC Ministry of Health (Direction de la Surveillance Epidemiologique)

**Data format:** Likely DHIS2 export (CSV/JSON) or Go.Data linelist export

**Contact:**
- INSP (Institut National de Sante Publique): pierre.akilimali@insp.cd
- INRB: dav.ebengo@umie-inrb.org
- WHO Country Office DRC: afrowcocd@who.int

**Access mechanism:** Formal data sharing agreement (DSA) between requesting organisation (MSF, WHO, research institution) and DRC MoH. Standard WHO outbreak data sharing framework applies.

**Ingestion path:** Drop CSV as `data/incoming/linelist.csv` -- pipeline auto-processes into dashboard.

---

### 2. Contact Tracing Database

**Unlocks:** H. Contacts (follow-up rates, transmission chains, lost-to-follow-up, unknown-source cases)

| Field | Required For |
|---|---|
| contact_id, case_id (source) | Transmission chain reconstruction |
| date_listed | Timeliness: case-to-listing delay |
| daily_follow_up_status | Follow-up completion rate |
| symptom_onset (if converted to case) | Secondary attack rate |
| outcome (completed 21d / lost / became case) | Tracing effectiveness |
| relationship_to_case | Exposure classification |

**Source system:** WHO Go.Data or MSF Epi Info / KoboToolbox field systems

**Contact:**
- WHO Go.Data team: godata@who.int
- MSF Epicentre: epicentre@paris.msf.org

**Access mechanism:** Operational data; typically shared within the response coordination structure (IMS). Request through WHO Health Cluster or MSF coordination.

**Ingestion path:** Drop as `data/incoming/contacts.csv`

---

### 3. Laboratory Information (Sample Cascade)

**Unlocks:** F. Lab (full testing cascade: collected, transported, received, tested, pending, rejected)

| Field | Required For |
|---|---|
| sample_id, case_id | Link lab to case |
| date_collected | Timeliness: onset-to-sample |
| date_received_lab | Transport time |
| date_result | Lab turnaround time |
| result (positive/negative/indeterminate/rejected) | Positivity rate, rejection rate |
| test_type (PCR/RDT/culture) | Diagnostic method breakdown |
| ct_value | Viral load proxy |
| reason_rejected | Quality improvement |

**Source system:** INRB LIMS (Laboratory Information Management System)

**Contact:**
- INRB Kinshasa: Prof. Placide Mbala-Kingebeni
- INRB Bunia field lab: via INRB coordination

**Access mechanism:** Typically shared through WHO Health Cluster lab working group. May require specific DSA with INRB.

**Ingestion path:** Drop as `data/incoming/lab_results.csv`

---

### 4. Onset-Based Epi Curve Data

**Unlocks:** C. Time (true epi curve reflecting transmission dynamics rather than reporting patterns)

**Source:** Derived from linelist (field: onset_date). Not available separately.

**Alternative:** If linelist access is not possible, request WHO to publish onset-date aggregated epi curve in situation reports (this has been done in previous DRC Ebola outbreaks).

---

### 5. Demographic Breakdown

**Unlocks:** E. Person (age/sex pyramid, occupation, vulnerability)

**Source:** Derived from linelist (fields: age, sex, occupation, pregnancy, idp_status).

**Alternative:** Request WHO/ECDC to publish age/sex disaggregated case counts in DON updates. ECDC has done this for other outbreaks.

---

### 6. Response Operations Data

**Unlocks:** I. Response (team deployment, IPC audits, safe burial coverage, WASH interventions, vaccination/trial readiness)

| Data | Source |
|---|---|
| Mobile team deployment | MSF operations, WHO Health Cluster |
| IPC audit results | WHO IPC pillar |
| Safe burial coverage | Red Cross/IFRC |
| WASH interventions | UNICEF WASH Cluster |
| Vaccination campaign status | WHO EPI, Africa CDC |
| Clinical trial enrolment | WHO R&D Blueprint, trial sponsors |

**Contact:** These data streams flow through the IMS (Incident Management System) coordination structure. Request via WHO Health Cluster lead or MSF coordination.

**Ingestion path:** Drop as `data/incoming/response_ops.csv` (format flexible)

---

### 7. Linked Genomic-Epidemiological Data

**Unlocks:** G. Genomics (linked map + tree + case drill-down)

**Requirement:** Link Pathoplexus sequence accessions to linelist case_ids and contact tracing data.

| Field | Source |
|---|---|
| sequence_id / Pathoplexus accession | Pathoplexus |
| case_id | Linelist |
| onset_date, health_zone | Linelist |
| contact_links | Contact tracing DB |

**Source:** Requires coordination between INRB (sequences) and INSP/MoH (linelist). This linkage is typically done within the national response.

**Contact:**
- INRB: Prof. Mbala-Kingebeni, Dr. Ssewanyana (CPHL)
- Pathoplexus data use: contact before publication

**Ingestion path:** Drop as `data/incoming/genomic_linkage.csv`

---

## Ingestion Pipeline

When any of the above data files are placed in `data/incoming/`, the ingestion pipeline (`ingest_data.py`) automatically:

1. Validates the file against expected schema
2. Cleans and standardises field names
3. Merges with existing data (health zone join key: canonical `nom`)
4. Updates the dashboard JSON data files
5. Regenerates affected plots
6. Logs the ingestion with timestamp, source, record count

**File naming convention:** `data/incoming/{dataset}_{date}.csv`

Examples:
- `data/incoming/linelist_2026-06-01.csv`
- `data/incoming/contacts_2026-06-01.csv`
- `data/incoming/lab_results_2026-06-01.csv`

The pipeline will not overwrite existing data without confirmation. Previous versions are archived in `data/incoming/archive/`.

---

## Priority Order

| Priority | Data Source | Impact | Difficulty |
|---|---|---|---|
| 1 | Linelist (onset dates + demographics) | Unlocks 4 modules (Cases, Time, Person, Quality) | High (DSA required) |
| 2 | Contact tracing database | Unlocks Contacts tab fully | Medium (operational data) |
| 3 | Lab sample cascade | Unlocks Lab tab fully | Medium (INRB LIMS access) |
| 4 | Response operations | Unlocks Response tab fully | Low-Medium (multiple sources) |
| 5 | Genomic-epi linkage | Unlocks linked drill-down | High (cross-system coordination) |

## Data Sharing Frameworks

Relevant frameworks for requesting access:

- **WHO International Health Regulations (2005):** Obligation to share data for PHEIC response
- **WHO Policy Statement on Data Sharing (2016):** Timely sharing of epidemiological data during public health emergencies
- **Nagoya Protocol:** Does not apply to pathogen sequence data under PHEIC
- **Pathoplexus Restricted Use:** Contact lead investigators before publication; public health use permitted
- **DRC National Data Governance:** MoH approval required for individual-level data export

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*Document maintained by Atlas Outbreak Intelligence. Contact: office@loew-beer.at*
*Last updated: 2026-05-30*