Routine data extraction

Beginner

Overview

One of the key pillars of any SNT exercise is the review of the routine malaria data collected by the country’s national surveillance system. This section lists the most commonly collected data elements by countries’ Health Management Information Systems (HMIS) and considerations for its preparation and use.

In many countries, the HMIS uses the District Health Information System version 2 (DHIS2) platform to host the national database for routine health data. Furthermore, an increasing number of national malaria programs (NMPs) are establishing national malaria data repositories (NMDRs) linked to the HMIS so that routine data are easily accessible in a structured and organized fashion for data analysis.

The platform from which routine data should be extracted for SNT analysis (DHIS2, NMDR, or another platform) will be determined by the SNT team during the data collection and management step, and a person with access to and knowledge of the platform should be identified as the focal person for downloading data.

During the SNT process, it will be key to establish very clear data access mechanisms and ensure that the NMP and the Ministry of Health have full control of the individuals and partners accessing the data, as well as full access to all the information used.

Given that the data extraction process requires important governance discussions outside of the scope of this library, this page does not include instructions on how to perform the extraction. Instead, we list the key data elements that in our experience have been essential or helpful for SNT analyses, such that they can be identified for extraction. Additional data elements may also be relevant for your SNT, as every country’s context is different. Disaggregated information is highly valuable, although countries disaggregate their data differently, such as by age or sex.

In the code library, we use the column names from the Sierra Leone DHIS2 to provide an example to demonstrate data disaggregation and naming in one country.

Consult SNT team

Each country’s data is different!

Data element names, definitions, and disaggregations differ across countries. Although the conventions from the Sierra Leone DHIS2 are provided below, these are only examples, and your country will very likely use a somewhat different system.

Ask the SNT team for a data dictionary specific to the country’s data you are working with. This will help you better understand and analyze routine surveillance data. Expect to work closely with the NMP data manager to understand data element names, ensure that all necessary data fields are extracted, and that subsequent calculations are performed correctly.

Objectives

Understand which data elements from routine surveillance could be relevant for SNT
Gain general awareness of how elements may be disaggregated in routine reporting

Basic Data Elements

These core metadata columns provide the foundation for organizing and analyzing routine malaria surveillance data. While some elements may auto-populate from standard platform extractions, others often require explicit selection. Always verify which fields are included in extractions with the SNT team.

Health Facility ID: unique identification number for each health facility

If the health facility ID column was not extracted and you need to assign temporary health facility IDs for your analysis, the data preprocessing page provides an example of how to do that.
Health Facility Name: name of the health facility reporting the data

In Sierra Leone, this is found under the hf column of DHIS2.
Health Facility Type: classification of the facility (e.g., Hospital, Health Center, Clinic)

Some countries may include this information in DHIS2, otherwise it is often included in the master facility list (MFL).
Administrative Level 0 to X: hierarchy of geographic units in the country ranging from largest (administrative level 0 or national level) to smallest, to which each health facility is assigned

In Sierra Leone, administrative units from 0 to 4 are found under the columns adm0, adm1, adm2, adm3, and adm4.
Reporting Period: time frame for which data is reported

In Sierra Leone, the reporting period is found under the periodname column which includes both month and year, formatted as “January 2023” for example.

Epidemiological Data Elements

These columns contain epidemiological elements that report on disease burden, diagnosis and treatment, and health system utilization. Data elements on confirmed malaria cases form the basis of incidence calculations and stratification of malaria incidence.

All-Cause Outpatient Visits: total number of all-cause outpatient visits reported
Show Sierra Leone example

In Sierra Leone, all-cause outpatient visits are disaggregated by age. Two data elements need to be requested.
- OPD (New and follow-up curative) 0-59m_X
- OPD (New and follow-up curative) 5+y_X
Suspected Malaria Cases: reported count of cases with fever symptoms
Show Sierra Leone example

In Sierra Leone, suspected cases are disaggregated by age and reporting method (health facility or community health worker).
- Fever case - suspected Malaria 0-59m_X
- Fever case - suspected Malaria 5-14y_X
- Fever case - suspected Malaria 15+y_X
- Fever case in community (Suspected Malaria) 0-59m_X
- Fever case in community (Suspected Malaria) 5-14y_X
- Fever case in community (Suspected Malaria) 15+y_X
Malaria Tests Conducted: reported number of malaria tests conducted

Show Sierra Leone example

In Sierra Leone, tested cases are not directly reported, but they may be for your country. Sierra Leone reports positive and negative test results separately, which can be summed to calculate total tested cases as shown on the data preprocessing page.
Positive Malaria Tests: reported number of positive malaria tests (confirmed malaria cases)
Show Sierra Leone example

In Sierra Leone, positive tests results are disaggregated by age, test type, and test adminstrator (community health worker or health facility).
- Fever case in community tested for Malaria (RDT) - Positive 0-59m_X
- Fever case in community tested for Malaria (RDT) - Positive 5-14y_X
- Fever case in community tested for Malaria (RDT) - Positive 15+y_X
- Fever case tested for Malaria (Microscopy) - Positive 0-59m_X
- Fever case tested for Malaria (Microscopy) - Positive 5-14y_X
- Fever case tested for Malaria (Microscopy) - Positive 15+y_X
- Fever case tested for Malaria (RDT) - Positive 0-59m_X
- Fever case tested for Malaria (RDT) - Positive 5-14y_X
- Fever case tested for Malaria (RDT) - Positive 15+y_X
Negative Malaria Tests: reported number of negative malaria tests
Show Sierra Leone example

In Sierra Leone, negative tests results are disaggregated by age, test type, and test adminstrator (community health worker or health facility).
- Fever case in community tested for Malaria (RDT) - Negative 0-59m_X
- Fever case in community tested for Malaria (RDT) - Negative 5-14y_X
- Fever case in community tested for Malaria (RDT) - Negative 15+y_X
- Fever case tested for Malaria (Microscopy) - Negative 0-59m_X
- Fever case tested for Malaria (Microscopy) - Negative 5-14y_X
- Fever case tested for Malaria (Microscopy) - Negative 15+y_X
- Fever case tested for Malaria (RDT) - Negative 0-59m_X
- Fever case tested for Malaria (RDT) - Negative 5-14y_X
- Fever case tested for Malaria (RDT) - Negative 15+y_X
Presumed Malaria Cases: the reported number of clinically diagnosed malaria cases (based on symptoms like fever) without confirmatory testing

Show Sierra Leone example

In Sierra Leone, presumed cases are not reported, but they may be for your country. Presumed cases can also be calculated if they are not reported, with a few common options for calculations shown on the data preprocessing page.
Treated Malaria Cases: count of malaria cases reported as treated
Show Sierra Leone example

In Sierra Leone, treated cases are disaggregated by treatment window, age, and treatment administrator (community health worker or health facility). Malaria in pregnant women is also reported separately. The SNT team should be consulted regarding whether treated cases in pregnant women should be added to the number treated for adults, or if they are already included in those counts.
- Malaria treated in community with ACT <24 hours 0-59m_X
- Malaria treated in community with ACT >24 hours 0-59m_X
- Malaria treated in community with ACT <24 hours 5-14y_X
- Malaria treated in community with ACT >24 hours 5-14y_X
- Malaria treated in community with ACT <24 hours 15+y_X
- Malaria treated in community with ACT >24 hours 15+y_X
- Malaria treated with ACT <24 hours 0-59m_X
- Malaria treated with ACT >24 hours 0-59m_X
- Malaria treated with ACT <24 hours 5-14y_X
- Malaria treated with ACT >24 hours 5-14y_X
- Malaria treated with ACT <24 hours 15+y_X
- Malaria treated with ACT >24 hours 15+y_X
- Malaria in 1st trimester treated
- Malaria in 2nd or 3rd trimester treated
Severe Malaria Cases: reported number of confirmed malaria cases meeting severe malaria criteria

Show Sierra Leone example

In Sierra Leone, there is no specific reporting of severe malaria cases.
All-Cause Hospital Admissions: reported total all-cause inpatient admissions
Show Sierra Leone example

In Sierra Leone, all-cause hospital admissions are diaggregated by age, and are either total general admissions (for children uner 5) or the sum of admissions from specific conditions (other age groups):
- All-Cause Admission U5yr: sum of
  - Admission - Child 1–59 months
  - Admission - Stabilisation Centre
- All-Cause Admission 05–14yr: sum of
  - Admission - Child with malaria 5–14 years
  - Admission - Child with diarrhoea
  - Admission - Child with pneumonia
- All-Cause Admission 15yr+: sum of
  - Admission - Malaria 15+ years
  - Admission - Maternity
  - Admission - Medical
  - Admission - Psychiatric
  - Admission - Surgical
  - Admission - TB
Malaria Hospital Admissions: reported count of patients hospitalized with malaria
Show Sierra Leone example

In Sierra Leone, malaria admissions are disaggregated by age.
- Admission - Child with malaria 0-59 months_X
- Admission - Child with malaria 5-14 years_X
- Admission - Malaria 15+ years_X
All-Cause Deaths: reported total of all-cause patient deaths
Show Sierra Leone example

In Sierra Leone, all-cause deaths are diaggregated by age, and are the sum of deaths from specific conditions:
- All-Cause Deaths - U5yr: sum of
  - Child death - Cause unspecified 01-59m
  - Child death - Diarrhoea 01-59m
  - Child death - HIV 01-59m
  - Child death - Malaria 01-59m
  - Child death - Malnutrition 01-59m
  - Child death - Other specified causes 01-59m
  - Child death - Pneumonia 01-59m
  - Child death - Trauma 01-59m
  - Separation - Child 1-59 months Death
- All-Cause Deaths - 05 - 14yr: sum of
  - Child death - Cause unspecified 05-09y
  - Child death - Cause unspecified 10-14y
  - Child death - Diarrhoea 05-09y
  - Child death - Diarrhoea 10-14y
  - Child death - HIV 05-09y
  - Child death - HIV 10-14y
  - Child death - Malaria 05-09y
  - Child death - Malaria 10-14y
  - Child death - Malnutrition 05-09y
  - Child death - Malnutrition 10-14y
  - Child death - Other specified causes 05-09y
  - Child death - Other specified causes 10-14y
  - Child death - Pneumonia 05-09y
  - Child death - Pneumonia 10-14y
  - Child death - Trauma 05-09y
  - Child death - Trauma 10-14y
  - Separation - Child with malaria 5-14 years Death
  - Separation - Child with diarrhoea Death
  - Separation - Child with pneumonia Death
- All-Cause Deaths - 15yr: sum of
  - Death malaria 15+ years Female
  - Death malaria 15+ years Male
  - Death other 15+ yrs Male
  - Death other 15+ yrs Female
  - Separation - Medical Death
  - Separation - Surgical Death
Malaria Deaths: reported deaths attributed to malaria
Show Sierra Leone example

In Sierra Leone, malaria deaths are diaggregated by age, sex, and inpatient records (separation). Whether only hospital deaths or also community deaths should be included in SNT analysis should be discussed with the SNT team.
- Deaths in Community
- Child death - Malaria 1-59m_X
- Child death - Malaria 10-14y_X
- Child death - Malaria 5-9y_X
- Death malaria 15+ years Female
- Death malaria 15+ years Male
- Separation - Child with malaria 0-59 months_X Death
- Separation - Child with malaria 5-14 years_X Death
- Separation - Malaria 15+ years_X Death

Consult SNT Team

Sometimes health facilities act as sentinel sites for the collection of deaths that occur at the community. Whether or not this is happening should be confirmed with the NMP surveillance focal point. If facilities are also collecting community death information, there will be many more facilities reporting malaria deaths than reporting inpatients, and the specificity of this variable will be low: there will be many reported malaria deaths without confirmation of malaria as cause of death.

Anemia outpatients, admissions and deaths: reported outpatients, hospital admissions, and deaths associated with anemia. While data quality may not be high, anemia is an important burden outcome for malaria and should be tracked and analyzed when possible.

Show Sierra Leone example

In Sierra Leone, there is no specific reporting of anemia.

Intervention Data Elements

Both malaria-specific and non-malaria interventions from routine data can be informative for SNT. Routine intervention data is also available in DHIS2 – note that campaign data such as for SMC or mass ITN campaigns is usually collected in a separate system and will need to be accessed and managed separately for SNT, unless countries already have an NMDR in place where all information can be accessible.

Routine intervention data can be extracted, managed, and analyzed by adapting the code provided in this library. Some routine intervention data that may be relevant for your SNT include:

Malaria Interventions

Routine ITN Distribution: distribution of insecticide-treated nets through health facilities and outreach programs. These routine distributions could happen at antenatal care (ANC) visits, with vaccination in infancy through the Expanded Programme on Immunization (EPI), through school-based distribution, or other mechanisms. You will need to know which distribution systems are relevant to your SNT context, and which ones report into DHIS2, to ensure that all the necessary data elements are extracted to appropriately calculate population and operational coverages and other relevant indicators.
Show Sierra Leone example

In Sierra Leone, ITN distribution is disggregated by setting (facility or outreach campaign) and age. For example, ITNs given with the 3rd dose of immunization with the pentavalent vaccine, and ITNs given at ANC visit, are reported in these columns:
- LLITN given at Pentavalent 3rd dose In_Facility, 0-11m
- LLITN given at Pentavalent 3rd dose In_Facility, 12-59m
- LLITN given at Pentavalent 3rd dose Outreach, 0-11m
- LLITN given at Pentavalent 3rd dose Outreach, 12-59m
- Antenatal client given LLITN In_Facility
- Antenatal client given LLITN Outreach
Intermittent Preventive Treatment in Pregnancy (IPTp): reported number of pregnant women receiving doses of sulfadoxine-pyrimethamine for malaria prevention
Show Sierra Leone example

In Sierra Leone, IPTp treatments are disaggregated by visit number and setting (facility, community, or outreach). Up to three doses are recorded. Note that the number of nationally recommended doses of IPTp can vary by country.
- Antenatal client IPTp 1st dose in community
- Antenatal client IPTp 2nd dose in community
- Antenatal client IPTp 3rd dose in community
- Antenatal client IPT 1st dose In_Facility
- Antenatal client IPT 1st dose Outreach
- Antenatal client IPT 2nd dose In_Facility
- Antenatal client IPT 2nd dose Outreach
- Antenatal client IPT 3rd dose In_Facility
- Antenatal client IPT 3rd dose Outreach
Perennial Malaria Chemoprevention (PMC): preventive sulfadoxine-pyrimethamine doses given periodically to children in the first one or two years of life.
Show Sierra Leone example

In Sierra Leone, PMC is called IPTi, and the schedule includes 3 doses during routine vaccination visits. Routine IPTi doses are disaggregated by dose, setting, and infant age.
- IPTi 1st dose given In_Facility, 0-11m
- IPTi 1st dose given In_Facility, 12-59m
- IPTi 1st dose given Outreach, 0-11m
- IPTi 1st dose given Outreach, 12-59m
- IPTi 2nd dose given In_Facility, 0-11m
- IPTi 2nd dose given In_Facility, 12-59m
- IPTi 2nd dose given Outreach, 0-11m
- IPTi 2nd dose given Outreach, 12-59m
- IPTi 3rd dose given In_Facility, 0-11m
- IPTi 3rd dose given In_Facility, 12-59m
- IPTi 3rd dose given Outreach, 0-11m
- IPTi 3rd dose given Outreach, 12-59m
Malaria Vaccine: administration of malaria vaccines (RTS,S/AS01 or R21). The schedule for both vaccines includes a 3-dose priming series, which may be followed by one or more boosters.
Show Sierra Leone example

In Sierra Leone, malaria vaccine doses are disaggregated by age, setting, and dose.
- Malaria 1st dose In_Facility, 0-11m
- Malaria 1st dose In_Facility, 12-59m
- Malaria 1st dose Outreach, 0-11m
- Malaria 1st dose Outreach, 12-59m
- Malaria 2nd dose In_Facility, 0-11m
- Malaria 2nd dose In_Facility, 12-59m
- Malaria 2nd dose Outreach, 0-11m
- Malaria 2nd dose Outreach, 12-59m
- Malaria 3rd dose In_Facility, 0-11m
- Malaria 3rd dose In_Facility, 12-59m
- Malaria 3rd dose Outreach, 0-11m
- Malaria 3rd dose Outreach, 12-59m
- Malaria 4th dose In_Facility, 0-11m
- Malaria 4th dose In_Facility, 12-59m
- Malaria 4th dose Outreach, 0-11m
- Malaria 4th dose Outreach, 12-59m

Data Elements to Inform Coverage of Routine Interventions

ANC (Antenatal Care) Visits: routine antenatal care attendance tracking for maternal health monitoring. ANC visits are important to understand for several aspects, including:
1. understanding operational coverage of IPTp,
2. understanding access to care, through the lens of pregnant women, including the timing of first and follow-up visits and dropout rates through time, and
3. if pregnant women at ANC, or a specific ANC visit, are universally tested for malaria, the test positivity rate (TPR) can be used to monitor trends in malaria transmission.
Show Sierra Leone example

In Sierra Leone, antenatal care is disaggregated by visit number, trimester, and setting, up to 8 visits.
- Antenatal client 1st visit In_Facility
- Antenatal client 1st visit Outreach
- Antenatal client 1st visit under 12 weeks In_Facility
- Antenatal client 1st visit under 12 weeks Outreach
- Antenatal client 4th visit In_Facility
- Antenatal client 4th visit Outreach
- Antenatal client 8th visit In_Facility
- Antenatal client 8th visit Outreach

Consult SNT Team

It is important to understand certain data practices around ANC:

Is there any information on the average gestational period of the women who attend ANC1? This is to understand which ANC visit should be used to calculate the coverage of IPTp1, 2, and 3. If ANC1 is attended by women before week 12, which is not common in many parts of Africa but still possible, then these women will not be eligible for IPTp until they reach an ANC visit when they are in the 2nd trimester.
Is the number of ANC visit associated to the timing of the pregnancy, or does it follow each woman through time regardless of gestational age? For example, for a woman who goes to her first ANC visit in the 3rd trimester, will her visit be counted as ANC1 or as ANC-X associated to her gestational age?

Routine childhood immunizations other than malaria: vaccination data (e.g. pentavalent vaccine, measles, polio, etc.) that counts the number of children vaccinated at the same time as when an ITN, PMC or the malaria vaccine are, should be, or could be delivered. This information helps measure operational coverage for different interventions and also helps assess access and strength of the immunization system to the target community population.
Show Sierra Leone example

In Sierra Leone, other routine immunizations include pentavalent vaccines.
- Pentavalent 1st dose In_Facility, 0-11m
- Pentavalent 1st dose In_Facility, 12-59m
- Pentavalent 1st dose Outreach, 0-11m
- Pentavalent 1st dose Outreach, 12-59m
- Pentavalent 2nd dose In_Facility, 0-11m
- Pentavalent 2nd dose In_Facility, 12-59m
- Pentavalent 2nd dose Outreach, 0-11m
- Pentavalent 2nd dose Outreach, 12-59m
- Pentavalent 3rd dose In_Facility, 0-11m
- Pentavalent 3rd dose In_Facility, 12-59m
- Pentavalent 3rd dose Outreach, 0-11m
- Pentavalent 3rd dose Outreach, 12-59m
Eligible populations: number of children eligible for each vaccination touchpoint, or expected number of pregnant women. These population denominators are important for understanding effective coverage of vaccinations, ANC, and IPTp.
Show Sierra Leone example

In Sierra Leone, eligible EPI populations are reported in DHIS2. While the expected number of pregnant women is also reported, this variable is not regularly updated, and therefore in practice the NMP instead uses estimates number of pregnant women as 4.4% of the total population.
- EPI_12-23 months
- EPI_12-59 months
- EPI_9 months - 14 yrs
- EPI_HPV target
- EPI_Live births
- EPI_Non Pregnant Women
- EPI_Population total
- EPI_Pregnant Women
- EPI_Surviving Infants
- EPI_Under 15 years
- EPI_Under 5 years
- EPI_Women of child bearing age

Stock Data Elements

Stock data tracks the availability of essential malaria commodities.

In SNT, stock information can be used to identify facilities to target for performance improvement, interpret epidemiological data such as when testing rate or treatment rate is unexpectedly low, and included in analysis of risk factors associated with malaria burden, among other uses. Therefore, during SNT all available stock data should be extracted and reviewed.

If there is data on absolute stock numbers, these can be compared to the number of treatments given and/or tests conducted for the same period of time, to evaluate coherency across datasets and potentially explain certain incoherencies.

If there are stockouts, it is important to understand the definition of stockouts and the ways that they are reported. Ask if there is any information that will allow understanding why the stockouts took place: for example, there may be archived reports or bulletins on stockout events.

Stock information is reported through the Logistics Management Information System (LMIS), but health facilities may also report on the number of days each month for which they have stockouts and the number of months for which stock is available into the HMIS. Consult the SNT team to determine where stockout indicators can be sourced for analysis.

Show Sierra Leone example

In Sierra Leone, stockout data for antimalarials are reported by type, and for ACTs, also by dosages (for example, pediatric and adult). This example only shows stockout data for RDTs and antimalarials, but during SNT it is also advised to review stockouts for other routine commodities (ITNs, malaria vaccine, etc.) and absolute available stock if possible.

Malaria Rapid Diagnostic Test Kit - Stockout
Artemether 20mg/ml, Inj - Stockout
Artesunate 50mg, Suppository - Stockout
Artesunate 60mg/ml, Inj, Vial - Stockout
Sulphadoxine & Pyrimethamine 500mg & 25mg, Tab - Stockout
Artemether & Lumefantrine (ACT) 20mg & 120mg, 6 Tabs - Stockout
Artemether & Lumefantrine (ACT) 20mg & 120mg, 12 Tabs - Stockout
Artemether & Lumefantrine (ACT) 20mg & 120mg, 18 Tabs - Stockout
Artemether & Lumefantrine (ACT) 20mg & 120mg, 24 Tabs - Stockout
Artesunate 20mg/ml, Inj - Stockout