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Proposed Schema: Ecosystem Component

Status: Draft for team discussion Team lead: Chris Mull Column prefix: eco_ Source: David Ruiz Garcia's reference paper (Issue #2), adapted for elasmobranch context

Validation

Extracted classifications for this schema can be reviewed at https://simondedman.github.io/elasmo_analyses/validate/. Validators are encouraged to check papers associated with their own work and submit corrections via their OpenAlex author page.

Purpose

Classify each paper by the ecosystem component(s) it studies. This enables filtering like "show all papers studying demersal elasmobranchs in coastal habitats" or "which techniques are used for pelagic vs reef species?"

Extraction Method

Search terms are matched against the full text of each paper (title, abstract, keywords, and body where available), not keywords alone. A term like "seagrass" appearing anywhere in the paper will trigger eco_seagrass = 1. For papers without full text, title + abstract + keywords are searched.

LLM-based extraction (Phase 2) will supplement keyword matching to catch implicit habitat references that keywords miss (e.g., a paper studying Triaenodon obesus on a reef without using the word "reef").

Proposed Categories

Level 1: Realm (broad)

Column Label Search Terms
eco_marine Marine marine, ocean, sea, saltwater
eco_freshwater Freshwater freshwater, river, lake, estuarine*, brackish
eco_brackish Brackish/Estuarine estuar*, brackish, lagoon, mangrove

Level 2: Zone/Habitat

Column Label Search Terms
eco_pelagic Pelagic/Open Ocean pelagic, open ocean, oceanic, offshore, epipelagic, mesopelagic, bathypelagic
eco_coastal Coastal/Neritic coastal, neritic, inshore, nearshore, continental shelf
eco_demersal Demersal/Benthic demersal, benthic, bottom-dwelling, epibenthic, benthopelagic
eco_reef Coral/Rocky Reef coral reef, reef-associated, rocky reef
eco_deepwater Deep-water deep-sea, deep-water, abyssal, hadal, bathyal, seamount
eco_intertidal Intertidal intertidal, tide pool, littoral
eco_mangrove Mangrove mangrove
eco_seagrass Seagrass seagrass, eelgrass, Posidonia, Zostera, Thalassia
eco_kelp Kelp Forest kelp forest, kelp bed, macroalgal
eco_polar Polar/Ice polar, arctic, antarctic, ice-edge, sea ice
eco_riverine Riverine river shark, freshwater stingray, bull shark river

Functional Habitats (cross-cutting)

Column Label Search Terms
eco_nursery Nursery Habitat nursery habitat, nursery ground, nursery area, essential fish habitat, juvenile habitat
eco_pupping Pupping Ground pupping ground, pupping area, parturition site, birthing ground

Level 3: Depth Zone (where stated)

Column Label Search Terms
eco_epipelagic Epipelagic (0-200m) epipelagic, surface, photic zone
eco_mesopelagic Mesopelagic (200-1000m) mesopelagic, twilight zone
eco_bathypelagic Bathypelagic (1000-4000m) bathypelagic, deep scattering layer
eco_abyssal Abyssal (4000m+) abyssal, hadal

Depth Data Columns (numeric extraction)

Column Type Description
depth_range text Stated depth range as text, e.g., "0-200", "150", ">500", "<50"
depth_min_m float Minimum depth in metres (parsed from depth_range)
depth_max_m float Maximum depth in metres (parsed from depth_range)

Confidence / Guess Columns

When the extraction process can't confidently assign an ecosystem level, a guess system is used rather than leaving data blank:

Column Type Description
eco_1_guess text Best guess for Level 1 realm if not confidently determined (e.g., "eco_marine")
eco_2_guess text Best guess for Level 2 zone if not confidently determined (e.g., "eco_kelp")
eco_3_guess text Best guess for Level 3 depth zone if not confidently determined

Rules:

  • Binary eco_* columns are only set to 1 when the extraction is confident.
  • If an eco level has no confident match, the relevant binary columns stay 0, and the eco_N_guess column is populated with the best-guess category name.
  • This avoids polluting numeric binary columns with non-numeric characters while preserving uncertain classifications for later review.

Discussion Points

  1. Multiple habitats per paper: Papers often span habitats (e.g., "movement between reef and pelagic zones"). Binary columns handle this naturally.
  2. Level 3 depth zones vs. numeric depth: Depth zones provide quick filtering; depth_range/depth_min_m/depth_max_m provide precise data. Both are useful.
  3. "Not stated": All eco_ columns default to 0 when habitat isn't stated. No guessing into binary columns. Guesses go to eco_N_guess text columns only.

Expected Coverage

Based on typical elasmobranch literature:

  • Pelagic + coastal + demersal should cover ~70-80% of papers
  • Reef, mangrove, deep-water cover most of the remainder
  • Freshwater is a small but distinct subset (~2-3% of papers)
  • Nursery/pupping grounds are a cross-cutting functional subset (~5-10% of papers)

Draft created: 2026-03-10 for team review