create_data_dictionary(metadata = airtable_metadata, table = "Activities") |>
(\(x) x$table_details)() |>
knitr::kable() |>
kableExtra::row_spec(row = 0, bold = TRUE) |>
kableExtra::kable_paper(lightable_options = "striped")7 Database
Airtable not anymore used to host the database
As of May 2024, the Africa CDC Database backend has shifted from Airtable to DoltHub.
This chapter has been kept here to document how the database started and to show the history of its development.
To read about DoltHub, see Chapter 2. To learn more about the use of dolt and DoltHub as the current backend for the database, read Chapter 6.
The current database is built using Airtable. The current database has the following schema:
This schema can be viewed interactively from here - https://airtable.com/appAL7fJUpBPYtOq4/tblt9ott045tWENcg/viwznxjIFAsTu0jzJ?blocks=bliZ6LV2bkGQNzgKF
7.1 Activities Table
7.1.1 Table details
Activities pertain to the formal/official title of the project that has been identified during the database search or survey.
Following are the different fields within the Activities table with their description.
7.1.2 Fields details
create_data_dictionary(metadata = airtable_metadata, table = "Activities") |>
(\(x) x$field_details)() |>
knitr::kable() |>
kableExtra::row_spec(row = 0, bold = TRUE) |>
kableExtra::kable_paper(lightable_options = "striped")| Field Name | Field Description | Field Type | Field Values |
|---|---|---|---|
| Activity | Activity name | singleLineText | NA |
| Source Name (from Primary Sources) | Name of primary source | multipleLookupValues | NA |
| Notes | Internal notes for maintenance | singleLineText | NA |
| Topic | Activity Topic | multipleRecordLinks | Topics |
| Grant ID | Grand Identifier | singleLineText | NA |
| Collaborators | Activity collaborators | multipleRecordLinks | Institutions |
| Researchers | Researchers involved in activity | multipleRecordLinks | Researchers |
| Published Work | Links to published work | singleLineText | NA |
| Activity Location alt | Activity location | multipleRecordLinks | Countries |
| UN Stats Sub-region Name (from Activity Location alt) | NA | multipleLookupValues | NA |
| Activity Outputs | Activity Outputs | multipleSelects | Data, Publication, Report, Guideline/SOP, Archive, Improving Diagnostics, Vaccine development, Therapeutics, Epidemic/Pandemic Preparedness, Biosurveillance technology, Prophylaxis, Surveillance, Improving Vaccine strategies, Training, Risk Assessment, Improving Capacity, Policies |
| Activity Status | Activity Status | singleSelect | Active, Completed |
| Activity Website | Activity Website | url | NA |
| Activity Identifier | Activity identifier | formula | NA |
| Primary Sources | Primary source of information | multipleRecordLinks | Sources |
| Date validated | Date when record was validated. | dateTime | NA |
| Validated | Indicate whether this record has been validated. | checkbox | NA |
| Additional Sources | Additional sources | singleLineText | NA |
| Continent Name (from Activity Location alt) | NA | multipleLookupValues | NA |
| AU Region Name (from Activity Location alt) | NA | multipleLookupValues | NA |
7.2 Countries Table
7.2.1 Table details
create_data_dictionary(metadata = airtable_metadata, table = "AU Countries") |>
(\(x) x$table_details)() |>
knitr::kable() |>
kableExtra::row_spec(row = 0, bold = TRUE) |>
kableExtra::kable_paper(lightable_options = "striped")List of countries used to indicate the location information for the researchers, topics, funders, sources, institutions, and activities tables
Following are the different fields within the Countries table with their description.
7.2.2 Fields details
create_data_dictionary(metadata = airtable_metadata, table = "Countries") |>
(\(x) x$field_details)() |>
knitr::kable() |>
kableExtra::row_spec(row = 0, bold = TRUE) |>
kableExtra::kable_paper(lightable_options = "striped")| Field Name | Field Description | Field Type | Field Values |
|---|---|---|---|
| Researchers | NA | multipleRecordLinks | Researchers |
| Funders | NA | multipleRecordLinks | Funders |
| AU Region Name | NA | singleSelect | Northern Africa, Eastern Africa, NA, Central Africa, Southern Africa, Western Africa |
| UN Stats Sub-region Name | Name of further sub-regional grouping to which country is usually classified within. This is based on the UN Statistics Division nomenclature. | singleSelect | NA, Eastern Africa, Middle Africa, Southern Africa, Western Africa, Channel Islands, Sark |
7.3 Description Table
7.3.1 Table details
create_data_dictionary(metadata = airtable_metadata, table = "Description") |>
(\(x) x$table_details)() |>
knitr::kable() |>
kableExtra::row_spec(row = 0, bold = TRUE) |>
kableExtra::kable_paper(lightable_options = "striped")The Description table provides overall description of this entire database.
Following are the different fields within the Description table with their description.
7.3.2 Fields details
create_data_dictionary(metadata = airtable_metadata, table = "Description") |>
(\(x) x$field_details)() |>
knitr::kable() |>
kableExtra::row_spec(row = 0, bold = TRUE) |>
kableExtra::kable_paper(lightable_options = "striped")| Field Name | Field Description | Field Type | Field Values |
|---|---|---|---|
| Email for primary contact | NA | ||
| Primary Contact | Person to correspond with about the base | singleLineText | NA |
| IRB | Optional: Link to IRB | url | NA |
| Base Description | Characterization of the base. What is the base describing? | multilineText | NA |
7.4 Funder Table
7.4.1 Table details
create_data_dictionary(metadata = airtable_metadata, table = "Funders") |>
(\(x) x$table_details)() |>
knitr::kable() |>
kableExtra::row_spec(row = 0, bold = TRUE) |>
kableExtra::kable_paper(lightable_options = "striped")Funders pertain to the entities funding each activity.
The funders’ information is retrieved from declared funders for the activities identified during the database search or the survey.
Following are the different fields within the Funders table with their description.
7.4.2 Fields details
create_data_dictionary(metadata = airtable_metadata, table = "Funders") |>
(\(x) x$field_details)() |>
knitr::kable() |>
kableExtra::row_spec(row = 0, bold = TRUE) |>
kableExtra::kable_paper(lightable_options = "striped")| Field Name | Field Description | Field Type | Field Values |
|---|---|---|---|
| Funder Type | Type of funder | singleSelect | Charitable organization, Foundation, Pharmaceutical company , Not-for-profit Partnership, NGO, Government Agency, University, Research Institut, Public- public partnership , Public-private partnership |
| Funder Website | Website of funder | url | NA |
| Source Name (from Primary Sources) | Source from where funder was identified | multipleLookupValues | NA |
| Activities | Activities supported by funder | multipleRecordLinks | Activities |
| WHO Region Name (from Funder Location alt) | NA | multipleLookupValues | NA |
| Continent Name (from Funder Location alt) | NA | multipleLookupValues | NA |
| Primary Sources | Source from where funder was identified | multipleRecordLinks | Sources |
7.5 Institutions Table
7.5.1 Table details
create_data_dictionary(metadata = airtable_metadata, table = "Institutions") |>
(\(x) x$table_details)() |>
knitr::kable() |>
kableExtra::row_spec(row = 0, bold = TRUE) |>
kableExtra::kable_paper(lightable_options = "striped")Institutions pertain to the entities directly related to or implementing the activity and/or the affiliation of the researcher implementing the activity.
Following are the different fields within the Institutions table with their description.
7.5.2 Fields details
create_data_dictionary(metadata = airtable_metadata, table = "Institutions") |>
(\(x) x$field_details)() |>
knitr::kable() |>
kableExtra::row_spec(row = 0, bold = TRUE) |>
kableExtra::kable_paper(lightable_options = "striped")| Field Name | Field Description | Field Type | Field Values |
|---|---|---|---|
| Institution Email | Email of institution | NA | |
| Institution Website | Institution Website | url | NA |
| Activities | Name of activity identified with institution | multipleRecordLinks | Activities |
| Sources | Name of primary source | multipleRecordLinks | Sources |
| Institution Type | Institution Type | singleSelect | Research Institute, University, NGO, National Government Institution, Non-profit Organisation , Hospital, Government Agency, Consortium, Partnership of Institutes, Industry, Charity, Public-private partnetship, International Coalition , Inter-governmental Organisation, Medical Service Provider, Network |
| Institution Location | Institution location | multipleRecordLinks | WHO Countries |
| Notes | Internal notes (for maintenance) | singleLineText | NA |
| Topic (from Activities) | Name of topic identified with the institution | multipleLookupValues | NA |
7.6 Researchers Table
7.6.1 Table details
create_data_dictionary(metadata = airtable_metadata, table = "Researchers") |>
(\(x) x$table_details)() |>
knitr::kable() |>
kableExtra::row_spec(row = 0, bold = TRUE) |>
kableExtra::kable_paper(lightable_options = "striped")Researchers pertains to the people involved in the activities contained in this database, and maybe involved in a variety of activity types. including but not limited to, research.
Researchers identified during the database search. Information on researchers are primarily retrieved once activities have been identified from the database search process. It is possible that researchers are identified apriori and from which information on topics, funders, sources, institutions, and activities may be identified relevant to the specific researcher. This may happen when the planned/proposed survey is implemented and sent to known researchers who may or may not be in the database to begin with.
Following are the different fields within the Researchers table with their description.
7.6.2 Fields details
create_data_dictionary(metadata = airtable_metadata, table = "Researchers") |>
(\(x) x$field_details)() |>
knitr::kable() |>
kableExtra::row_spec(row = 0, bold = TRUE) |>
kableExtra::kable_paper(lightable_options = "striped")| Field Name | Field Description | Field Type | Field Values |
|---|---|---|---|
| WHO Region Name (from Researcher Country Location alt) | NA | multipleLookupValues | NA |
| ACDC Status | Is researcher from the Africa CDC? | singleSelect | Non-member, Member |
| Sources | Name of source | multipleRecordLinks | Sources |
| UN Stats Region Name (from Researcher Country Location alt) | NA | multipleLookupValues | NA |
| Affiliation | Institution researcher is affiliated with. Choices from the institutions table | multipleRecordLinks | Institutions |
| Institution Location alt (from Affiliation) | NA | multipleLookupValues | NA |
| Topic (from Activity) | Name of topic | multipleLookupValues | NA |
| Researcher Name | Full name of researcher identified in the search | singleLineText | NA |
| Notes | Internal notes (for maintenance) | singleLineText | NA |
| Source Name (from Sources) | Name of source | multipleLookupValues | NA |
| Additional Sources | Additional sources | singleLineText | NA |
| Activity Type (from Activity) | Type of activity | multipleLookupValues | NA |
| Topic (from Activity) 2 | NA | multipleLookupValues | NA |
| Website | Personal website of researcher (if any) | singleLineText | NA |
| Activity | Activity/activities researchers is involved in | multipleRecordLinks | Activities |
| Institution Location (from Affiliation) | Name of location where institution is based | multipleLookupValues | NA |
| Willing to be contacted | Is the researcher willing to be contacted? | checkbox | NA |
| Continent Name (from Researcher Country Location alt) | NA | multipleLookupValues | NA |
7.7 Sources Table
7.7.1 Table details
create_data_dictionary(metadata = airtable_metadata, table = "Sources") |>
(\(x) x$table_details)() |>
knitr::kable() |>
kableExtra::row_spec(row = 0, bold = TRUE) |>
kableExtra::kable_paper(lightable_options = "striped")Sources contain initial set of sources (primarily funders) identified to initiate the database search. These original sources are fully described here - https://ecohealthalliance.github.io/rig-handbook/sources.html.
From the initial search, other sources were identified from which additional streams of searches were performed. Currently, the sources table is updated through a primary search of possible sources in addition to the search performed on the original sources list.
Following are the different fields within the Sources table with their description.
7.7.2 Fields details
create_data_dictionary(metadata = airtable_metadata, table = "Sources") |>
(\(x) x$field_details)() |>
knitr::kable() |>
kableExtra::row_spec(row = 0, bold = TRUE) |>
kableExtra::kable_paper(lightable_options = "striped")| Field Name | Field Description | Field Type | Field Values |
|---|---|---|---|
| Source Type | Type of primary source | singleSelect | Website text page, Website table, Website search, Downloadable document in PDF, Downloadable document in XLSX, Downloadable document in CSV, Downloadable document in DOCX, A form of database, Website text page, Website search, Links to downloadable documents in PDF, Website table, Website search |
| Source Notes | Internal notes for primary source (for maintenance) | multilineText | NA |
| Topics | Topics identified from primary source | multipleRecordLinks | Topics |
| Relevant tables | Notes on relevant tables found from primary source | multipleSelects | Researchers, Topics, Activities, Funders, Institutions, Countries |
| Funders | Funders identified from primary source | multipleRecordLinks | Funders |
| Source Name | Name of primary source | singleLineText | NA |
| Created By | Person who created the entry | createdBy | NA |
| Researchers | Name of researcher identified from primary source | multipleRecordLinks | Researchers |
7.8 Survey Results Table
7.8.1 Table details
create_data_dictionary(metadata = airtable_metadata, table = "Survey Results") |>
(\(x) x$table_details)() |>
knitr::kable() |>
kableExtra::row_spec(row = 0, bold = TRUE) |>
kableExtra::kable_paper(lightable_options = "striped")NA
Following are the different fields within the Survey Results table with their description.
7.8.2 Field details
create_data_dictionary(metadata = airtable_metadata, table = "Survey Results") |>
(\(x) x$field_details)() |>
knitr::kable() |>
kableExtra::row_spec(row = 0, bold = TRUE) |>
kableExtra::kable_paper(lightable_options = "striped")| Field Name | Field Description | Field Type | Field Values |
|---|---|---|---|
| Activity description/ purpose | Description of activity | multilineText | NA |
| Sharing with Colleagues | Is respondent going to share with colleagues? | singleLineText | NA |
| Lead Researcher | Name of lead researcher | singleLineText | NA |
| Created By | Name of survey respondent | createdBy | NA |
| Other websites listing this project | Other website listings for this project | singleLineText | NA |
| Funder | Name of funder for this project | singleLineText | NA |
| Official Project Title | Official project title | singleLineText | NA |
| Official Project website | Official project website | singleLineText | NA |
7.9 Topics Table
7.9.1 Table details
create_data_dictionary(metadata = airtable_metadata, table = "Topics") |>
(\(x) x$table_details)() |>
knitr::kable() |>
kableExtra::row_spec(row = 0, bold = TRUE) |>
kableExtra::kable_paper(lightable_options = "striped")Topics pertain to the disease names and disease types.
The topics table contains disease types/disease entities of interest to the Africa CDC based on their priorities (as described in their Framework document) and is continually updated with whatever disease/disease entity/disease type were deemed relevant by the database contributor.
Following are the different fields within the Topics table with their description.
7.9.2 Fields details
create_data_dictionary(metadata = airtable_metadata, table = "Topics") |>
(\(x) x$field_details)() |>
knitr::kable() |>
kableExtra::row_spec(row = 0, bold = TRUE) |>
kableExtra::kable_paper(lightable_options = "striped")| Field Name | Field Description | Field Type | Field Values |
|---|---|---|---|
| Sources | Name of Source | multipleRecordLinks | Sources |
| Diseases | Disease entity related/relevant to the field/topic of interest | multipleSelects | HIV, TB, COVID-19, Monkeypox, Lassa fever, Bat flu, Avian flu, Swine flu, Ebola virus disease, Marburg virus disease, Marburg haemorrhagic fever, H7N9, H5N1, H1N1, H1N2, H3N2, Plague, Anthrax, Crimean-Congo Haemorrhagic Fever, Rift Valley Fever, Nipah Virus, Brucellosis, undulant fever, Malta fever, Mediterranean fever, Hantavirus haemorrhagic fever with renal syndrome, Hantavirus pulmonary syndrome, Q fever, Chikungunya, Henipavirus, Ghanaian bat henipavirus, Leptospirosis, Weill's disease, West Nile Fever, Zika fever, Dengue fever, African trypanosomiasis, Chagas disease, Yellow fever, Malaria, Re-emerging viruses, Visceral Leishmaniasis, Kala-azar, Cutaneous leishmaniasis , Hepatitis E , Viral Hepatitis, Hepatitis C, Hepatitis B, Leprosy, Hookworm, Schistosomiasis, Ascariasis, Trichuriasis, Lymphatic filariasis, Trachoma, Buruli ulcer, Dracunculiasis, Bilharzia, Whipworm Infection, Elephantiasis, Guinea-worm disease , Burkitt lymphoma, Cryptococcal meningitis, Kaposi sarcoma, schistosomiasis, Viral haemorrhagic fever, Rabies |
| Activity Location (from Activities) | Name of location of activity in which topic was identified | multipleLookupValues | NA |
| Survey Results | Results from survey | multipleRecordLinks | Survey Results |
| Search terms | Search terms used to identify topic | multipleSelects | antimycobacterial, anti-mycobacterial, COVID-19, coronavirus, omicron, rifampicin, ritonavir, darunavir, dolutegravir, MIS-C, HVTN, ART, antiretroviral, lopinavir, bedaquiline, clofazimine, isoniazid, pyrazinamide, antitubercular, tenofovir disoproxil fumarate, emtricitabine, dolutegravir , efavirenz, tubercular, drug-resistant, AMR, raltegravir, DR-, DR-TB, helminth, TBM, fluke, wildlife sampling, biosurveillance, surveillance network, seroprevalence, detection of __, monitoring of __, seroevidence, identification of __, seropositive, seroepidemiological, survey, screened, __ prevalence |
| Disease Types | Type/category to which disease is grouped under | multipleSelects | infectious disease, viral, bacterial, parasitic, vector-bourne, zoonotic, virus, soil-transmitted |
| Continent Name (from Activity Location alt) (from Activities) | NA | multipleLookupValues | NA |
| Activity Location alt (from Activities) | NA | multipleLookupValues | NA |
| Institutions | Institutions | multipleRecordLinks | Institutions |
| Region (from Activity Location) (from Activities) | Name of region where topic was identified | multipleLookupValues | NA |
| AU Region Name (from Activity Location alt) (from Activities) | NA | multipleLookupValues | NA |