diff --git a/diagrams/backbone_slice_2v2.drawio b/diagrams/backbone_slice_2v2.drawio new file mode 100644 index 00000000..eb88ac8c --- /dev/null +++ b/diagrams/backbone_slice_2v2.drawio @@ -0,0 +1,862 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/diagrams/data_and_var_source.drawio b/diagrams/data_and_var_source.drawio new file mode 100644 index 00000000..66b87fb0 --- /dev/null +++ b/diagrams/data_and_var_source.drawio @@ -0,0 +1,325 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/diagrams/geom_index.drawio b/diagrams/geom_index.drawio new file mode 100644 index 00000000..b025fbca --- /dev/null +++ b/diagrams/geom_index.drawio @@ -0,0 +1 @@ + \ No newline at end of file diff --git a/docs/background.html b/docs/background.html deleted file mode 100644 index a7c334af..00000000 --- a/docs/background.html +++ /dev/null @@ -1,620 +0,0 @@ - - - - - - - - - - - - - -background.knit - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
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-
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Problem Space

-

Geospatial data come in a variety of source formats with no -universal, interoperable standard representation. While working with a -single geospatial dataset has presents some technical challenges, the -complexity of using geospatial begins to compound when variables from -disparate datasets are needed for a single analysis study. As ad-hoc -solutions are introduced to deal with the increasing technical -complexity, the reproducibility of these studies plummets.

-

In order to enable reproducible studies that incorporate -place-related data with longitudinal patient-level data, it is first -necessary to develop functionality to automate retrieval and -transformation of publicly available place-related data into a standard -representation.

-
-
-

Goals

-

The overarching goal of the OHDSI GIS Workgroup is to develop -software and standards for incorporating place-based data into the OMOP -CDM and present this back to the OHDSI community. We reach these goals -through development in the four key areas below.

-
-

1) Infrastructure

-
    -
  • Functional Metadata Catalog
    • -
  • Harmonized geospatial data model
    • -
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2) Functionality

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  • Geocoding
    • -
  • Accessing geospatial datasets
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3) Vocabulary

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  • GIS specific concepts
    • -
  • SDoH vocabulary
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  • Toxin vocabulary
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4) Extensions

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  • Exposure_occurrence
    • -
-


-
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Publications/Presentation

-

OHDSI GIS Infrastructure (2023 OHDSI Symposium Poster, Abstract)

-

Toxins Vocabulary (2023 OHDSI Symposium Poster, Abstract)

-

OHDSI GIS Workgroup October 10, 2023 Update (video)

-

OHDSI GIS Workgroup 2023 Objectives and Key Results (video, -slides)

-

OHDSI GIS Workgroup August 23, 2022 Update (video)

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- - - - - - - - - - - - - - - - diff --git a/docs/data/data_source_example.csv b/docs/data/data_source_example.csv new file mode 100644 index 00000000..5ffb55fb --- /dev/null +++ b/docs/data/data_source_example.csv @@ -0,0 +1,6 @@ +data_source_uuid,org_id,org_set_id,dataset_name,dataset_version,geom_type,geom_spec,boundary_type,has_attributes,download_method,download_subtype,download_data_standard,download_filename,download_url,download_auth,documentation_url +311,CDC/ATSDR,SVI,25-tract-2018,2018,,,tract,1,file,zip,gdb,SVI2018_MASSACHUSETTS_tract.gdb,https://svi.cdc.gov/Documents/Data/2018/db/states/Massachusetts.zip,,https://www.atsdr.cdc.gov/placeandhealth/svi/index.html +911,Census,TIGER/Line,25-tract-2018,2018,polygon,"""{""stage_transform"":[""dplyr::mutate(staged,geom_source_coding='GEOID',geom_source_value=GEOID,geom_name=dplyr::select(sf::st_drop_geometry(staged), n = if('NAME' %in% colnames(staged)) 'NAME' else 'NAMELSAD')$n,geom_local_value=geometry,geom_local_epsg=sf::st_crs(staged, paramaters=TRUE)$epsg)""]}""",tract,0,file,zip,shp,tl_2018_25_tract.shp,https://www2.census.gov/geo/tiger/TIGER2018/TRACT/tl_2018_25_tract.zip,,https://www.census.gov/geographies/mapping-files/time-series/geo/tiger-line-file.html +1234,Census,TIGER/Line,us-county-2018,2018,polygon,"{""stage_transform"":[""dplyr::mutate(staged,geom_source_coding='GEOID',geom_source_value=GEOID,geom_name=dplyr::select(sf::st_drop_geometry(staged), n = if('NAME' %in% colnames(staged)) 'NAME' else 'NAMELSAD')$n,geom_local_value=geometry,geom_local_epsg=sf::st_crs(staged, paramaters=TRUE)$epsg)""]}",county,0,file,zip,shp,tl_2018_us_county.shp,https://www2.census.gov/geo/tiger/TIGER2018/COUNTY/tl_2018_us_county.zip,,https://www.census.gov/geographies/mapping-files/time-series/geo/tiger-line-file.html +7777,EPA,AQS,annual_conc_by_monitor_2018,2018,point,,,1,file,zip,csv,annual_conc_by_monitor_2018.csv,https://aqs.epa.gov/aqsweb/airdata/annual_conc_by_monitor_2018.zip,,https://www.epa.gov/aqs +7778,EPA,AQS,annual_conc_by_monitor_2018,2018,point,"{""stage_transform"":[""dplyr::mutate(staged,geom_source_coding='state_count_site',geom_source_value=paste0(staged$State.Code, '_', staged$County.Code, '_', staged$Site.Num),geom_name=Local.Site.Name,geom_local_value=sf::st_as_binary(sf::st_as_sf(staged, coords=c('Latitude', 'Longitude'))$geometry,EWKB=TRUE, hex=TRUE),geom_local_epsg=dplyr::left_join(staged['Datum'], tibble(Datum = c('NAD83', 'WGS84'), epsg = c(4326, 4269)))[['epsg']])""]}",,1,file,zip,csv,annual_conc_by_monitor_2018.csv,https://aqs.epa.gov/aqsweb/airdata/annual_conc_by_monitor_2018.zip,,https://www.epa.gov/aqs diff --git a/docs/dataModelEditing.html b/docs/dataModelEditing.html deleted file mode 100644 index 9ff5a3ba..00000000 --- a/docs/dataModelEditing.html +++ /dev/null @@ -1,586 +0,0 @@ - - - - - - - - - - - - - -dataModelEditing.knit - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
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#Proposing changes to Gaia Data Models

-
-

Overview

-

The gaiaDB data model is still in early development. We hope to build -a model that suits a wide range of needs, and as such we encourage -interested parties to install, use, and provide feedback on the gaiaDB -backbone and harmonized data tables. This documentation demonstrates how -to create and submit “formal” change requests via pull requests. That -said, we always welcome ad-hoc feedback via email or GitHub issue -tracker.

-

The “official” data model at any given time is displayed on the Data Model page of -this website. This model reflects the csv files -gaiafieldLevel.csv and gaiatableLevel.csv that are -stored at ./inst/csv at the root of the OHDSI GIS WG git -repository.These csv files are used as the Single Source of Truth (SSoT) -throughout the project, meaning they are referenced in scripts that -create the SQL DDL scripts as well as functions in gaiaCore that operate -on gaiaDB.

-

The csv files, and their formatted counterpart on the Data Model -page, provide us a clear method proposing changes. Any changes to the -data model should be implemented directly (on a fork or branch of the -main repository) to csv files. After changes are made to the csv files, -the DDLs can be regenerated (see below), the website can be rerendered -to reflect these changes (see here), -a Pull Request can be opened, and a discussion about the changes can -begin.

-
-
-

Generating DDL scripts

-

The “official” DDL scripts at any given time are stored at -./inst/ddl. The only time these need to be regenerated is when there are -changes or proposed changes to the data model. If you just need to -implement the DDL in your database, simply run the scripts in that -directory against your Postgres database.

-

To regenerate the DDL scripts, simply run the scripts -gaiaCore::writeGaiaDdl(gaiaVersion, outputfolder), -gaiaCore::writePrimaryKeys(gaiaVersion, outputfolder), and -gaiaCore::writeForeignKeys(gaiaVersion, outputfolder).

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This is the specification document for the gaiaDB Data Model. -This data model is still under development and likely to -change. Each table is represented with a high-level description -and ETL conventions that should be followed. This is continued with a -discussion of each field in each table, any conventions related to the -field, and constraints that should be followed (like primary key, -foreign key, etc). Should you have questions please feel free to visit -the forums or the github issue page. -

-
-

Backbone

-
-

data_source

-

Table Description

-

This table contains records that catalog external (or local) -web-hosted entities. All source data in gaiaDB must be referenced in -this table.

-

User Guide

-

All records in this table are sources of geospatial data. They can be -sources of geometry data, such as point, line, or polygon, or they can -be attribute data with an identifier that relates them to geometry data, -such as a FIPS code or GEOID.

-

ETL Conventions

-

All sources of data that should be included in gaiaDB must have an -entry in this table. Geometry data sources require a “geom_spec”: a -lightweight transformation from the source data to the standardized -format, written in R and serialized as JSON.

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Gaia Field - -User Guide - -ETL Conventions - -Datatype - -Required - -Primary Key - -Foreign Key - -FK Table - -FK Domain -
-data_source_uuid - - - -int4 - -Yes - -Yes - -No - - -
-org_id - - - -varchar(100) - -Yes - -No - -No - - -
-org_set_id - - - -varchar(100) - -Yes - -No - -No - - -
-dataset_name - - - -varchar(100) - -Yes - -No - -No - - -
-dataset_version - - - -varchar(100) - -Yes - -No - -No - - -
-geom_type - - - -varchar(100) - -No - -No - -No - - -
-geom_spec - - - -text - -No - -No - -No - - -
-boundary_type - - - -varchar(100) - -No - -No - -No - - -
-has_attributes - - - -int4 - -No - -No - -No - - -
-download_method - - - -varchar(100) - -Yes - -No - -No - - -
-download_subtype - - - -varchar(100) - -Yes - -No - -No - - -
-download_data_standard - - - -varchar(100) - -Yes - -No - -No - - -
-download_filename - - - -varchar(100) - -Yes - -No - -No - - -
-download_url - - - -varchar(100) - -Yes - -No - -No - - -
-download_auth - - - -varchar(100) - -No - -No - -No - - -
-documentation_url - - - -varchar(100) - -No - -No - -No - - -
-
-
-

variable_source

-

Table Description

-

This table contains records that describe the distinct variables in a -data source enabling downstream data integrations. All variables from -attribute source data must be catalogued in this table.

-

User Guide

-

All records in this table describe distinct variables from attribute -source data. For example, consider a weather dataset that is being added -to gaiaDB. First, the entire dataset is catalogued in the data_source -table. Then, the distinct variables of that dataset (temperature in -fahrenheit, temperature in celsius, inches of rain, wind direction, -etc.) each become a single record in this table. All records in this -table are related back to their parent source dataset via a foreign key -relationship to the data_source table. Many variable_source records can -be related to a single data_source record.

-

ETL Conventions

-

Every individual variable from a source dataset must have an entry in -this table. Likewise, any source attribute dataset that gets included in -the data_source table will likely have many “children” in this table. -All records in this table contain an “attr_spec”: a lightweight -transformation of a single variable into the standardized table -format.

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Gaia Field - -User Guide - -ETL Conventions - -Datatype - -Required - -Primary Key - -Foreign Key - -FK Table - -FK Domain -
-variable_source_id - - - -serial4 - -Yes - -Yes - -No - - -
-geom_dependency_uuid - - - -int4 - -No - -No - -Yes - -data_source - -
-variable_name - - - -varchar - -Yes - -No - -No - - -
-variable_desc - - - -text - -Yes - -No - -No - - -
-data_source_uuid - - - -int4 - -Yes - -No - -Yes - -data_source - -
-attr_spec - - - -text - -Yes - -No - -No - - -
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attr_index

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Table Description

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A programmatically derived index table of all the attribute source -datasets included in the data_source table.

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User Guide

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This table can be (re)generated after new entries are added to the -data_source table by running the gaiaCore createIndices() function.

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ETL Conventions

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Run the createIndices() function to (re)generate this table.

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Gaia Field - -User Guide - -ETL Conventions - -Datatype - -Required - -Primary Key - -Foreign Key - -FK Table - -FK Domain -
-attr_index_id - - - -numeric - -Yes - -Yes - -No - - -
-variable_source_id - - - -numeric - -Yes - -No - -Yes - -variable_source - -
-attr_of_geom_index_id - - - -numeric - -Yes - -No - -Yes - -geom_index - -
-database_schema - - - -varchar(255) - -Yes - -No - -No - - -
-table_name - - - -varchar(255) - -Yes - -No - -No - - -
-data_source_id - - - -numeric - -Yes - -No - -Yes - -data_source - -
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geom_index

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Table Description

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A programmatically derived index table of all the geometry source -datasets included in the data_source table.

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User Guide

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This table can be (re)generated after new entries are added to the -data_source table by running the gaiaCore createIndices() function.

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ETL Conventions

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Run the createIndices() function to (re)generate this table.

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Gaia Field - -User Guide - -ETL Conventions - -Datatype - -Required - -Primary Key - -Foreign Key - -FK Table - -FK Domain -
-geom_index_id - - - -numeric - -Yes - -Yes - -No - - -
-data_type_id - - - -numeric - -No - -No - -No - - -
-data_type_name - - - -varchar(255) - -Yes - -No - -No - - -
-geom_type_concept_id - - - -numeric - -No - -No - -Yes - -concept - -
-geom_type_source_value - - - -varchar(255) - -No - -No - -No - - -
-database_schema - - - -varchar(255) - -Yes - -No - -No - - -
-table_name - - - -varchar(255) - -Yes - -No - -No - - -
-table_desc - - - -varchar(255) - -Yes - -No - -No - - -
-data_source_id - - - -numeric - -Yes - -No - -Yes - -data_source - -
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attr_template

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Table Description

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This table is a template for the standardized attribute table that -get created.

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User Guide

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No action necessary. This table must simply exist (with no entries) -in the backbone schema.

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ETL Conventions

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No action necessary.

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Gaia Field - -User Guide - -ETL Conventions - -Datatype - -Required - -Primary Key - -Foreign Key - -FK Table - -FK Domain -
-attr_record_id - - - -serial4 - -Yes - -Yes - -No - - -
-geom_record_id - - - -int4 - -Yes - -No - -Yes - -geom_template - -
-variable_source_record_id - - - -int4 - -Yes - -No - -Yes - -variable_source - -
-attr_concept_id - - - -int4 - -No - -No - -Yes - -concept - -
-attr_start_date - - - -date - -Yes - -No - -No - - -
-attr_end_date - - - -date - -Yes - -No - -No - - -
-value_as_number - - - -float8 - -No - -No - -No - - -
-value_as_string - - - -varchar - -No - -No - -No - - -
-value_as_concept_id - - - -int4 - -No - -No - -Yes - -concept - -
-unit_concept_id - - - -int4 - -No - -No - -Yes - -concept - -
-unit_source_value - - - -varchar - -No - -No - -No - - -
-qualifier_concept_id - - - -int4 - -No - -No - -Yes - -concept - -
-qualifier_source_value - - - -varchar - -No - -No - -No - - -
-attr_source_concept_id - - - -int4 - -No - -No - -Yes - -concept - -
-attr_source_value - - - -varchar - -Yes - -No - -No - - -
-value_source_value - - - -varchar - -Yes - -No - -No - - -
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geom_template

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Table Description

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This table is a template for the standardized geometry tables that -get created.

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User Guide

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No action necessary. This table must simply exist (with no entries) -in the backbone schema.

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ETL Conventions

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No action necessary.

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Gaia Field - -User Guide - -ETL Conventions - -Datatype - -Required - -Primary Key - -Foreign Key - -FK Table - -FK Domain -
-geom_record_id - - - -serial4 - -Yes - -Yes - -No - - -
-geom_name - - - -varchar - -Yes - -No - -No - - -
-geom_source_coding - - - -varchar - -Yes - -No - -No - - -
-geom_source_value - - - -varchar - -Yes - -No - -No - - -
-geom_wgs84 - - - -geometry - -No - -No - -No - - -
-geom_local_epsg - - - -int4 - -Yes - -No - -No - - -
-geom_local_value - - - -geometry - -Yes - -No - -No - - -
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CDM Extension

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exposure_occurrence

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Table Description

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This table is used to interface with ATLAS and OHDSI tool stack

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User Guide

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NA

-

ETL Conventions

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NA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Gaia Field - -User Guide - -ETL Conventions - -Datatype - -Required - -Primary Key - -Foreign Key - -FK Table - -FK Domain -
-exposure_occurrence_id - - - -integer - -Yes - -Yes - -No - - -
-location_id - - - -integer - -Yes - -No - -Yes - -location - -
-person_id - - - -integer - -Yes - -No - -Yes - -person - -
-cohort_definition_id - - - -integer - -No - -No - -No - - -
-exposure_concept_id - - - -integer - -Yes - -No - -Yes - -concept - -
-exposure_start_date - - - -date - -Yes - -No - -No - - -
-exposure_start_datetime - - - -datetime - -No - -No - -No - - -
-exposure_end_date - - - -date - -Yes - -No - -No - - -
-exposure_end_datetime - - - -datetime - -No - -No - -No - - -
-exposure_type_concept_id - - - -integer - -Yes - -No - -Yes - -concept - -Type Concept -
-exposure_relationship_concept_id - - - -integer - -Yes - -No - -Yes - -concept - -
-exposure_source_concept_id - - - -integer - -No - -No - -Yes - -concept - -
-exposure_source_value - - - -varchar(50) - -No - -No - -No - - -
-exposure_relationship_source_value - - - -varchar(50) - -No - -No - -No - - -
-dose_unit_source_value - - - -varchar(50) - -No - -No - -No - - -
-quantity - - - -integer - -No - -No - -No - - -
-modifier_source_value - - - -varchar(50) - -No - -No - -No - - -
-operator_concept_id - - - -integer - -No - -No - -Yes - -concept - -
-value_as_number - - - -float - -No - -No - -No - - -
-value_as_concept_id - - - -integer - -No - -No - -Yes - -concept - -
-unit_concept_id - - - -integer - -No - -No - -Yes - -concept - -Unit -
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#Editing the OHDSI GIS WG documentation website

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Overview

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We encourage contributions to our software documentation and our -website. Follow these guidelines for making and proposing changes.

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Website

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This section explains how to edit the content of the website. In this -context, the website refers to everything at https://ohdsi.github.io/GIS/ except for the https://ohdsi.github.io/GIS/gaiaCore content which is -covered in the next section.

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The source of the website’s content are contained in the ./rmd/ -directory at the root of this repository. Most of the content in the -./rmd/ directory are RMarkdown files which are rendered to HTML, stored -in the ./docs/ directory, and served as a website using GitHub Pages. -Along with RMD files, there are images, stylesheets (CSS), and a file -called _site.yml. The _site.yml file specifies the website structure and -defines the elements on the site’s navbar.

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To edit existing pages on the website, simply find and edit the -corresponding RMD file. To add new pages to the website, create an RMD -file, fill it with content, and then add it to _site.yml in a fitting -place. Whether you are editing existing pages or creating new ones, the -function RMarkdown::render_site() can be run to regenerate -the HTML files docs directory. More on rendering below.

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R Package Documentation

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R Package documentation is created using ROxygen within R scripts. -The ROxygen is rendered to .Rd files by running -devtools::document(). After documentation is created, the -function pkgdown::build_site() can be run to render the .Rd -files into HTML, which automatically ends up in ./docs/gaiaCore/ and can -be accessed from the website. More on rendering below.

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Rendering

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If you’ve been keeping track, there are three functions which need to -be called to generate the HTML for the website: 1. -devtools::document() creates .Rd files from inline ROxygen -2. RMarkdown::render_site() creates HTML for website -content 3. pkgdown::build_site() creates HTML for the R -Package documentation

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Running three functions each time you need to regenerate the website -can be a drag. Even worse, the website won’t generate correctly if they -are run out of order.

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To make things easier, there is a helper R script, -render_gaia_site.R, that can be run using -source('./render_gaia_site.R'). This simply calls those -three functions in the correct order. It makes life just a bit -easier.

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Publishing

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Finally, after changes have been made to the website or documentation -and the new HTML has been rendered, simply commit your changes and -create a Pull Request on the OHDSI GIS WG repository. A maintainer will -review your changes, provide feedback if necessary, and accept your -changes when they are ready.

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Gaia Framework Overview

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The Gaia Framework provides the highest-level view of the components -that compose Gaia; the framework is divided into three main parts, a -functional metadata repository (Catalog), staging database and execution -engine (Core), and ecosystem of Gaia-compatible software packages -(Extensions):

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Gaia Catalog

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A readily-extensible catalog of source datasets. Gaia Catalog -contains metadata for public geospatial datasets. Descriptive metadata -facilitates search and discovery of relevant datasets. Functional -metadata (machine-actionable instructions) enables automated retrieval, -extraction, transformation, and loading of public datasets and their -constituent variables.

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Gaia Core

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Gaia Core is the central functionality and storage of Gaia and itself -consists of two main features: a staging database and -an execution engine.

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The staging database is a PostGIS database with a replica copy of the -Gaia Catalog installed in a schema named “backbone”. In this database, -public datasets that are registered in Gaia Catalog can be “staged”: -transformed and then loaded as tables in a standardized -Entity-Attribute-Value format. Other geospatial data, such as geocoded -addresses, can also be loaded into the staging database for use in -conjunction with the staged data.

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All operations on the staging database (creating tables, inserting -data, accessing data, etc.) are performed through the “execution -engine”. The execution engine can be any software package (e.g. R -package, Python library, CLI) that connects to the database and -functionalizes the logic required to write or read data to and from the -standard format. Currently, there is one execution engine: an R Package -named gaiaCore.

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Extensions

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Any functionality that falls outside of Gaia Core’s scope (basic -Create, Read, Update and Delete operations) can be encapsulated in an -Extension. An extension can be thought of as a software package or -library that interfaces with Gaia Core (through the execution engine) -that collects similar functionality. Extensions can be grouped by the -communities they serve or by the functionality they provide. For -example, the gaiaOHDSI -extension is built to provide members of the OHDSI community useful -connectors between Gaia Core and an OMOP database and various OHDSI -tools. On the other hand, general (hypothetical) extensions like gaiaVis -or gaiaLayer provide visualization and layer building software to Gaia -Core, respectively.

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