FGSCdb
Georeferenced database of Fusarium graminearum species complex (FGSC) isolates identified to species and
trichothecene genotype, compiled from the literature. The website is static (no server, no database) and is
served by Netlify from the docs/ folder at https://fgsc.netlify.app.
Del Ponte et al. 2022. Phytopathology 112:741–751. https://doi.org/10.1094/PHYTO-06-21-0277-RVW
Repository layout
| Path | What it holds |
|---|
docs/ | The published site: index.html and data/ (built files, do not edit by hand) |
site-src/page.html | Source of the web page (map, charts, table, sources) |
data/ | Curated tables exported from the master Google Sheet: isolates, articles, counts, changelog, flags |
vocab/ | Controlled vocabularies and the gazetteer used to geocode localities |
scripts/ | R pipeline (see below) |
raw/ | The 2021 Google Sheet used by the old Shiny app, kept for provenance |
legacy-distill/ | Sources of the previous distill site |
Data flow
Master Google Sheet (FGSCdb_clean) scripts/00_fetch_sheet.R -> data/*.csv, vocab/*.csv
tabs: isolates, articles, counts, vocab scripts/03_validate.R -> stops on invalid values
scripts/02_site_data.R -> docs/index.html, docs/data/
- isolates: one row per isolate, in standard vocabulary.
coord_precision records how the coordinate was
obtained: reported, locality (from same-location records), municipality (geocoded), county centroid,
country centroid.
- articles: one row per source (
article_id, reference, doi, data_level = isolate | aggregate | both).
- counts: aggregated data from sources without isolate-level tables (geo unit × period × host × species ×
TRI genotype →
n_isolates); use not crossed when a source gives species and genotype counts separately.
A source must not appear in both isolates and counts.
- vocab: controlled vocabularies; the validator rejects values that are not listed.
scripts/01_clean.R is the one-time 2026 cleanup of the 2021 sheet (raw/). It needs Natural Earth country
boundaries and US county shapes in geo/ (not versioned). Every change it made is in data/changelog.csv, and
records to review are in data/flags.csv.
Rebuild the site
Locally, after the data CSVs are up to date:
source("scripts/03_validate.R"); source("scripts/02_site_data.R")
Open docs/index.html directly or serve docs/ with any static server.
On GitHub: Actions > "Build FGSCdb" > Run workflow. It downloads the master sheet, validates, rebuilds docs/
and commits; Netlify then redeploys. The sheet must be shared as "Anyone with the link can view".
Netlify
Publish directory: docs. No build command.
