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EDGE Flowering Plants × Flora of the World — Documentation

Overview

This folder contains the data and scripts to cross-match the EDGE flowering plant dataset (Forest et al., Science) with the Flora of the World (FotW) occurrence database, in order to identify which EDGE-scored species are documented on FotW and to produce conservation-relevant statistics for a press release.

Matching strategy

The core challenge is that EDGE and FotW may use different accepted names for the same species — one dataset may follow a newer synonymy, use a different spelling, or apply a different circumscription. A naïve string match will therefore undercount the true overlap.

Our strategy is to normalise FotW taxonomy to the GBIF backbone first, then match against EDGE.

This is preferable to bidirectional on-the-fly synonym resolution because:

  1. GBIF is the shared backbone. The EDGE dataset is built on GBIF taxonomy. By aligning FotW names to GBIF accepted names, both datasets speak the same language before any comparison is made.
  2. FotW taxonomy is under our control. We can fix name discrepancies in FotW directly (and have done so for the names identified during earlier synonym resolution). This means the alignment is a one-time operation that improves the underlying database, not a workaround applied at query time.
  3. Cleaner and more reproducible. Once FotW names are resolved to GBIF accepted names, the EDGE match becomes a simple exact-key lookup with no ambiguity.

Pipeline overview

FotW taxonomy DB                        EDGE dataset (GBIF backbone)
        │                                          │
        ▼                                          ▼
[Step 1] Resolve FotW names           [Step 4a] Resolve EDGE names
         to GBIF accepted names                to GBIF accepted names
         (resolve_fotw_taxonomy.py)            (resolve_edge_taxonomy.py)
        │                                          │
        ▼                                          ▼
 FotW GBIF-normalised names           EDGE GBIF-normalised + new
        │                              accepted-name records
        │                              (build_edge_complete.py)
        ├──────────────────────────────────────────┤
        ▼                                          ▼
[Step 2] Exact match on              Joinable on accepted_gbif_id
         GBIF accepted name           for FotW website integration
         (match_EDGE_FotW_gbif.py)    (EDGE score embedding on
        │                              FotW taxon pages)
        ▼
[Step 3] Retrieve FotW taxon
         UUIDs for EDGE.List species
         (fetch_fotw_taxon_uuids.py)

Steps 1–3 produce the matched species list and FotW links used in the Science press release. Step 4 (the EDGE-side GBIF alignment) produces the FotW website deliverable: a single combined file that lets FotW import EDGE scores and resolve future taxon additions against the EDGE dataset.

Files

Scripts

File Location Description
resolve_fotw_taxonomy.py ../FotW_DB/ Step 1. Resolves all FotW taxon names against the GBIF backbone. Determines accepted/synonym status; for synonyms, retrieves the accepted name and its GBIF ID.
match_EDGE_FotW_gbif.py EDGE_flowering_plants/ Step 2. Exact-name match between GBIF-normalised FotW taxa and the EDGE dataset.
fetch_fotw_taxon_uuids.py EDGE_flowering_plants/ Step 3. Retrieves FotW taxon page UUIDs for matched EDGE.List species.
resolve_edge_taxonomy.py EDGE_flowering_plants/ Step 4a. Resolves all 335,497 EDGE species names against the GBIF backbone. Mirrors resolve_fotw_taxonomy.py. Resumable; supports --scope list | priority | all.
build_edge_complete.py EDGE_flowering_plants/ Step 4b. Builds the combined deliverable for the FotW website team: all EDGE rows + new accepted-name records inferred from synonym resolution. Collapses GBIF homonyms into canonical records.
generate_main_report.py EDGE_flowering_plants/ Generates EDGE_FotW_report.md / .pdf for the press article.
generate_press_article.py EDGE_flowering_plants/ Generates EDGE_FotW_press_article.docx BSU press article draft.
plot_EDGE_FotW.py EDGE_flowering_plants/ Generates figures from the matched species data.

Input data (not bundled — see links)

File Source Description
Forest_etal_EDGEangio_tableS1_EDGEspp_RL&Pred.csv Zenodo 10.5281/zenodo.17273037 Source EDGE dataset (Forest et al., Science, 2025). 335,497 flowering plant species with EDGE scores, ED, threat status, and EDGE.List flags.
taxon_DB_01May2026.csv FotW-taxonomy-GBIF-alignment FotW taxonomy DB export (12,838 taxa). Contains FotW taxon UUIDs and GBIF/CoL IDs in scientificNameID.
fotw_taxonomy_resolved.csv FotW-taxonomy-GBIF-alignment GBIF-resolved FotW taxonomy. Used by Steps 2 and 3 as the FotW-side join input.
occurrences.csv FotW Foundation (private export) FotW occurrence records, used by Step 2 for documentation counts and Step 3 for taxon-page lookups.

Output bundled with this repository

File Description
edge_taxonomy_complete.csv.gz Primary deliverable. 340,042 rows: 335,497 EDGE originals + 4,545 inferred accepted-name records. 38 columns (record_type + 14 GBIF + 22 EDGE-source + synonym_edge_keys). Compressed with gzip (~23 MB; decompresses to ~99 MB).
EDGE_CSV_data_dictionary.md Reference documentation for all 22 source EDGE columns (Species, EDGE.rank, edge.med, ed.med, threat, EDGE.List, …).

Other outputs (reproducible by running the scripts)

File Produced by Description
edge_taxonomy_resolved.csv resolve_edge_taxonomy.py --scope all Intermediate file. All 335,497 EDGE species with GBIF resolution (36 columns). Schema column-compatible with fotw_taxonomy_resolved.csv.
edge_new_accepted_names.csv build_edge_complete.py Subset of the deliverable: 4,545 inferred accepted-name records only.
EDGE_FotW_matched_species_gbif.csv match_EDGE_FotW_gbif.py 10,902 EDGE species matched against FotW with metadata and taxon URLs.
fotw_taxon_uuids.csv fetch_fotw_taxon_uuids.py FotW taxon UUIDs and URLs for EDGE.List species in FotW.
EDGE_FotW_report.md / .pdf generate_main_report.py Full report with statistics and clickable FotW links.
figures/ plot_EDGE_FotW.py Coverage, threat breakdown, top species, families, ED plots.

Reading the bundled deliverable

import pandas as pd
df = pd.read_csv("edge_taxonomy_complete.csv.gz")   # pandas reads .gz transparently
df <- read.csv(gzfile("edge_taxonomy_complete.csv.gz"))
gunzip -c edge_taxonomy_complete.csv.gz | head

Step 1 — Resolve FotW taxonomy to GBIF (resolve_fotw_taxonomy.py)

Located in ../FotW_DB/. Run from that directory:

cd ../FotW_DB
python3 resolve_fotw_taxonomy.py [--workers N] [--delay SECONDS]

How it works

For each of the 12,838 FotW taxa:

  • If a GBIF species ID is available (scientificNameID contains gbif.org/species/{id}): queries /v1/species/{id} directly. This is the most reliable method — no name-matching ambiguity.
  • Otherwise (CoL ID or no ID): queries /v1/species/match?kingdom=Plantae&name=Genus+epithet. Matches with confidence < 80 are flagged.

GBIF returns taxonomicStatus (ACCEPTED, SYNONYM, DOUBTFUL) and, for synonyms, the accepted name and its GBIF key. The script writes all results to fotw_taxonomy_resolved.csv.

Coverage of the 12,838 FotW taxa:

Lookup method Count
GBIF ID (direct) 8,798
CoL ID or no ID (name-match fallback) 4,040

The script is resumable — already-resolved taxon IDs are skipped on re-run.

Output — fotw_taxonomy_resolved.csv

Column Description
taxonID FotW taxon UUID
scientificName Original FotW name
genus, specificEpithet, infraspecificEpithet Name components
scientificNameID Original GBIF or CoL URL from FotW DB
gbif_id Extracted numeric GBIF species key
lookup_method gbif_id or name_match
gbif_status ACCEPTED, SYNONYM, DOUBTFUL, NO_MATCH, or ERROR
gbif_confidence Confidence score (name-match only)
accepted_name GBIF-accepted binomial
accepted_gbif_id GBIF key of the accepted name
accepted_gbif_url https://gbif.org/species/{accepted_gbif_id}
error Error message if lookup failed

Step 2 — Match FotW against EDGE (match_EDGE_FotW_gbif.py)

cd EDGE_flowering_plants
python3 match_EDGE_FotW_gbif.py                        # both phases (recommended)
python3 match_EDGE_FotW_gbif.py --phase 1              # Phase 1 only, no network
python3 match_EDGE_FotW_gbif.py --workers 8 --delay 0.3  # tune Phase 2 load

The GBIF backbone version mismatch problem

Although both FotW (after Step 1 normalisation) and EDGE use the GBIF backbone, they do not use the same version of it. The EDGE dataset was built on a GBIF snapshot that predates the current one. Some names that EDGE treats as accepted have since been synonymised by GBIF.

This creates a one-sided blind spot:

Dataset Name used GBIF current status
EDGE Aneulophus congoensis SYNONYM of A. africanus
FotW (normalised) Aneulophus africanus ACCEPTED

After Step 1, FotW correctly carries Aneulophus africanus. But this name does not appear in EDGE (which has Aneulophus congoensis), so a Phase 1-only match produces no hit. The problem is on the EDGE side: its names are frozen at an older GBIF version.

Two-phase solution

Phase 1 — FotW → GBIF → EDGE (no network calls; uses pre-resolved taxonomy from Step 1)

For every FotW taxon, the GBIF-accepted name is looked up from fotw_taxonomy_resolved.csv and checked against the EDGE dataset. Catches:

  • direct — FotW name = EDGE name (same current GBIF accepted name on both sides)
  • fotw_synonym — FotW carried an old name; its GBIF accepted name = EDGE name

Phase 2 — EDGE.List → GBIF → FotW (~9,700 network queries; ~10 min)

For each EDGE.List species not yet matched, the EDGE name is queried against GBIF. If GBIF returns a different accepted name and that name is present in FotW's normalised taxonomy, a match is recorded. These are labelled edge_synonym matches.

Together, the two phases ensure that name-version differences on either side of the GBIF snapshot boundary do not cause missed matches.

Output — EDGE_FotW_matched_species_gbif.csv

Columns: EDGE_rank, species, family, order, edge_med, ed_med, tbl_med, pext_med, threat, RL_ERP, EDGE_List, EDGE_Borderline, EDGE_Research, EDGE_Watch, fotw_original_name, fotw_gbif_status, fotw_taxon_id, match_method, n_fotw_records, taxon_url

The match_method column records how each species was found:

Value Meaning
direct FotW name = EDGE name
fotw_synonym FotW name was a GBIF synonym; accepted name = EDGE name
edge_synonym EDGE name was a GBIF synonym; accepted name is in FotW (Phase 2)

Step 3 — Retrieve FotW taxon UUIDs (fetch_fotw_taxon_uuids.py)

python3 fetch_fotw_taxon_uuids.py [--workers N] [--delay SECONDS]

For each EDGE.List species matched in FotW, queries the FotW search page and parses the taxon page UUID from the HTML. Resumable. Output: fotw_taxon_uuids.csv with columns species_key, genus, epithet, taxon_uuid, taxon_url.

All EDGE.List species in FotW have complete UUID entries (2 were supplied manually: Nasa aequatoriana and Tecunumania stothertiae).

Step 4 — EDGE taxonomy GBIF alignment & FotW deliverables

This is the EDGE-side counterpart to Step 1. It produces a single combined file that lets the FotW website team (i) import EDGE scores onto existing FotW taxon pages and (ii) resolve any future FotW taxon addition against the EDGE dataset via the GBIF backbone.

Step 4a — Resolve EDGE names against GBIF (resolve_edge_taxonomy.py)

python3 resolve_edge_taxonomy.py --scope all          # full 335,497-row table (~17 h)
python3 resolve_edge_taxonomy.py --scope priority     # list+borderline+research+watch (~28 min)
python3 resolve_edge_taxonomy.py --scope list         # EDGE.List only (~6 min)

For each EDGE species, queries /v1/species/match?kingdom=Plantae&name=Genus epithet against the current GBIF backbone. Mirrors resolve_fotw_taxonomy.py (same 14 GBIF-derived columns, identical names and order). Resumable — already-resolved species are skipped on re-run.

Output — edge_taxonomy_resolved.csv (36 columns):

Block Columns
GBIF-derived (14 — same schema as fotw_taxonomy_resolved.csv) taxonID, scientificName, genus, specificEpithet, infraspecificEpithet, scientificNameID, gbif_id, lookup_method, gbif_status, gbif_confidence, accepted_name, accepted_gbif_id, accepted_gbif_url, error
EDGE source (22, verbatim from input) Species, EDGE.rank, Family, Order, edge.med, ed.med, tbl.med, above.med.tot, above.med.perc, pext.med, total.thr.draws, perc.thr.draws, threat, RL.ERP, thr.or.not, in.backbone, above.med, EDGE.List, EDGE.Borderline, EDGE.Research, EDGE.Watch, useful.plant

Resolution results (335,497 rows):

GBIF status Count %
ACCEPTED 326,159 97.22%
SYNONYM 9,051 2.70%
HETEROTYPIC_SYNONYM 6 0.00%
DOUBTFUL 19 0.01%
NO_MATCH 0 0%
ERROR (transient GBIF timeouts; retryable) 262 0.08%

All synonyms have accepted_name and accepted_gbif_id populated.

Step 4b — Build the combined deliverable (build_edge_complete.py)

python3 build_edge_complete.py

Reads edge_taxonomy_resolved.csv and produces:

  1. edge_taxonomy_complete.csv — the primary deliverable. Single combined file containing:
    • All 335,497 EDGE rows tagged record_type = edge_original
    • 4,545 new accepted-name records tagged record_type = gbif_accepted_new, generated when an EDGE synonym resolves to a GBIF-accepted binomial that is not itself in the EDGE Species list. Each new row carries synonym_edge_keys — a semicolon-separated list of the EDGE synonym(s) that point to that accepted name.
  2. edge_new_accepted_names.csv — the 4,545 new rows only, for review.

GBIF homonym handling: some accepted binomials exist as multiple GBIF taxa (homonyms, or GBIF's own duplicate records — e.g. Morella salicifolia has 5 distinct GBIF keys). The script collapses these into one canonical record per binomial, picked by (a) most synonym pointers, (b) tie-break by lowest GBIF key. The dropped homonym GBIF ids are preserved on the canonical row in the error column (merged_homonyms:<id1>,<id2>,...). 64 GBIF entries collapsed into 45 canonical winners.

Combined file integrity:

Check Result
Total rows 340,042
Duplicate taxonID 0
Duplicate scientificName 0
Source EDGE table duplicate Species 0
Groups sharing accepted_gbif_id (synonym↔accepted links, not duplicates) 7,356

Schema (38 columns): record_type + the 36 columns of edge_taxonomy_resolved.csv + synonym_edge_keys.

How to join with FotW:

FotW (fotw_taxonomy_resolved.csv).accepted_gbif_id
    ↔
EDGE (edge_taxonomy_complete.csv).accepted_gbif_id

The two files share 10,299 unique accepted_gbif_id values; 10,902 EDGE rows have a FotW match, including 231 EDGE.List priority species (up from 229 with the older direct-name pipeline — the gain comes from deeper synonym resolution applied to every EDGE row).

What to display on the FotW taxon page

Of the 22 EDGE source columns, only a subset is meaningful for end users — many are MCMC sampling statistics that justify the methodology but don't belong on a public page. The recommendations below are organised by display priority. The full column glossary is in EDGE_CSV_data_dictionary.md.

Tier 1 — show on the taxon page (initial release)

Column Suggested label / UI treatment Meaning
is_edge_species (derived boolean) No badge — gates the entire EDGE panel Computed during import: true if a matching row was found in edge_taxonomy_complete.csv when joining on accepted_gbif_id (either record_type = edge_original, or record_type = gbif_accepted_new with a resolvable synonym_edge_keys link). Use this as the master gate for whether the EDGE panel is rendered at all.
is_edge_list_priority (derived boolean) Badge: "EDGE Priority Species" Computed during import: true if EDGE.List = "y". Member of the global priority list of 9,945 species that are both threatened AND robustly above the median EDGE score. The single most actionable flag on the page.
EDGE.rank "EDGE rank: #N of 335,497" Global rank by combined EDGE score. #1 is the top priority overall. Rank #1,140 = top 0.3%. Useful for context even when not on the priority list.
edge.med "EDGE score: X.XX" The composite metric itself (range 0–54.9). Higher = greater conservation priority. Best paired with the rank for interpretation.
ed.med "Evolutionary Distinctiveness: X Myr" How isolated this species is on the flowering-plant tree of life, in millions of years. Long branches with few close relatives = high ED (max 139.4 Myr for Amborella trichopoda).
threat IUCN-style tag (CR / EN / VU / NT / LC / EW / EX) with the standard IUCN colour coding; or "Predicted: threatened / not threatened" when from the expert panel Either the IUCN Red List category or a modelled equivalent. Always pair with RL.ERP so the attribution is honest.
RL.ERP Small tag next to threat: "IUCN-assessed" (RL) or "Modelled — Expert Review Panel" (ERP) Distinguishes formal IUCN assessments (49,800 species) from model predictions (285,700 species). Critical for honest presentation — predicted threat is not the same as assessed.

Available but deferred to a future release

These columns carry meaningful information and can be added to the EDGE panel in a future iteration, but are not part of the initial design.

  • pext.med — modelled probability of extinction within 100 years (the GE term in the EDGE formula, ~0.04 for LC, ~0.97 for CR).
  • useful.plant — has a documented economic or cultural use per Plants of the World Online (~34,400 species). Good candidate for a "documented human use" icon.
  • EDGE.Borderline — meets EDGE.List criteria with lower statistical confidence (50–95% of phylogenetic draws above median).
  • EDGE.Research — EDGE.List species lacking adequate data; flagged for targeted fieldwork or Red List assessment.
  • EDGE.Watch — EDGE.List species whose status is improving or stabilising but still require active monitoring.

Do not display (internal / methodological)

These columns underpin the analysis but are not user-relevant. Keep them in the database for reproducibility, but do not surface them on taxon pages.

  • tbl.med — terminal branch length (Myr). Technical phylogenetics; redundant with ed.med for most users.
  • above.med — statistical robustness flag (above-median in ≥ 95% of draws). Methodological — already baked into EDGE.List membership.
  • above.med.tot — internal MCMC counter (draws above median).
  • above.med.perc — internal MCMC counter (proportion of draws above median).
  • total.thr.draws — internal MCMC counter (draws classified as threatened).
  • perc.thr.draws — internal MCMC counter (proportion of draws classified as threatened).
  • thr.or.not — binary derived from threat; redundant for display.
  • in.backbone — whether the EDGE name was on the WFO/GBIF backbone snapshot used to build the phylogeny. Internal metadata.

Design hints

  • Use the official IUCN palette for the threat tag (CR red, EN orange-red, VU orange, NT amber, LC green, EW/EX black). For ERP-predicted species, use a desaturated version of the same colour to signal lower certainty.
  • Where RL.ERP = RL, link the threat tag to the species' IUCN Red List page. Doable now via the IUCN Red List API v4; an enrichment step can attach the IUCN URL for the ~49,800 RL-assessed species.
  • For is_edge_list_priority = true species, consider a dedicated EDGE panel near the top of the page. For non-priority species with a notably high EDGE.rank (say top 10,000), a smaller inline note keeps context without implying priority.
  • ed.med is the most intuitive metric for a general audience ("this species sits on a 50-million-year branch with no close relatives") — worth a one-line plain-language gloss next to the number.

Input data details

EDGE dataset columns

Column Description
Species Binomial name with underscore separator (e.g. Gomortega_keule)
EDGE.rank Global EDGE rank among all 335,497 species (1 = highest)
Family / Order Taxonomic placement
edge.med Median EDGE score
ed.med Median Evolutionary Distinctiveness (millions of years)
tbl.med Median terminal branch length (millions of years)
pext.med Median probability of extinction
threat IUCN Red List category or predicted status (thr / not)
RL.ERP Assessment source: RL = IUCN Red List, ERP = Expert Review Panel
EDGE.List y if on EDGE priority list (threatened + robustly above-median EDGE score)
EDGE.Borderline y if borderline EDGE.List candidate
EDGE.Research y if flagged for research priority
EDGE.Watch y if flagged for monitoring

EDGE rank vs. EDGE.List

EDGE.rank sorts all 335,497 species by EDGE score. EDGE.List is a binary filter: only species that are both threatened and robustly above the median EDGE score (≥ 95% of phylogenetic draws). A species can rank highly but be off the EDGE.List if it is not threatened — e.g. Amborella trichopoda (ED = 139.4 Myr, LC, rank #1,140, not on EDGE.List) vs. Amorphophallus lewallei (ED = 50.9 Myr, CR, rank #2, EDGE.List).

FotW occurrence database columns

Column Description
genus Genus name
specificEpithet Species epithet
family Family name
occurrenceID UUID of the occurrence record
country, stateProvince, county, locality Geographic provenance
decimalLatitude, decimalLongitude Coordinates
eventDate Collection or observation date
recordedBy Collector name (one row per collector)

Key results (current)

EDGE × FotW matching

Metric Value
EDGE species matched in FotW 10,902 / 335,497 (3.25%)
EDGE.List species in FotW 231 / 9,945 (2.32%)
Unique GBIF accepted ids shared (EDGE ∩ FotW) 10,299
Best EDGE rank in FotW #2 (Amorphophallus lewallei, CR)
EW EDGE.List species in FotW 4 (Franklinia alatamaha, Brugmansia suaveolens, B. vulcanicola, B. sanguinea)

EDGE × GBIF resolution (Step 4)

Metric Value
EDGE rows resolved against GBIF 335,497 (100%)
ACCEPTED 326,159 (97.22%)
SYNONYM (incl. HETEROTYPIC) 9,057 (2.70%)
DOUBTFUL 19
ERROR (retryable) 262 (0.08%)
New accepted-name records created 4,545
Combined deliverable rows 340,042

Planned next steps

  1. GBIF taxonomy alignment of FotW — DONE; deposited at Flora-of-the-World/FotW-taxonomy-GBIF-alignment.
  2. EDGE-side GBIF taxonomy alignment — DONE 2026-05-18; produces edge_taxonomy_complete.csv.
  3. FotW website team to import edge_taxonomy_complete.csv: update existing taxon pages with EDGE scores (join on accepted_gbif_id), and add the 4,545 new accepted-name records.
  4. EDGE score integration on FotW taxon pages — embed edge.med, ed.med, threat, and EDGE.List flag.
  5. (Optional) Retry the 262 ERROR rows from Step 4a — delete those rows from edge_taxonomy_resolved.csv and re-run resolve_edge_taxonomy.py --scope all (resumable).
  6. Press release species selection — shortlist the most compelling EDGE.List species in FotW.

Citation

If you use this repository, please cite both the source publication and the underlying dataset.

Publication

Forest, F., Brown, R., Buerki, S., Colville, J. F., Moat, J., Nic Lughadha, E., Owen, N. R., Raimondo, D. C., Rivers, M., Rosindell, J., Walker, B. E., Bachman, S. P., Pipins, S., Gumbs, R., Brown, M. J. M. (2025). High risk of extinction across the flowering plant tree of life. Science. https://doi.org/10.1126/science.adz0773

Dataset

Forest, F., Brown, R., Buerki, S., Colville, J. F., Moat, J., Nic Lughadha, E., Owen, N. R., Raimondo, D. C., Rivers, M., Rosindell, J., Walker, B. E., Bachman, S. P., Pipins, S., Gumbs, R., Brown, M. J. M. (2025). High risk of extinction across the flowering plant tree of life — codes. Zenodo. https://doi.org/10.5281/zenodo.17273037

The source EDGE table redistributed in this repository (Forest_etal_EDGEangio_tableS1_EDGEspp_RL&Pred.csv) is Supplementary Table S1 of the publication above and is also available through the Zenodo deposit.

License

This repository is released under the Creative Commons Attribution 4.0 International (CC BY 4.0) license. The full legal code is included in the LICENSE file.

You are free to share and adapt the material — including the code, the GBIF-resolved EDGE taxonomy outputs, and the combined deliverable — for any purpose, including commercially, provided that you give appropriate credit to the source publication and dataset cited above, indicate any changes made, and do not suggest endorsement by the authors of either work.

Maintainer

Flora of the World Foundation, Boise, ID, USA — https://floraoftheworld.org

About

GBIF-aligned EDGE flowering plants taxonomy and Flora of the World matching pipeline (Forest et al. 2025, Science)

floraoftheworld.org

Topics

taxonomy edge conservation phylogenetics biodiversity gbif iucn-red-list angiosperms flora-of-the-world flowering-plants

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