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Biodiversity data access, species occurrence, and ecological tools
Passed 17 of 23 test cases with the skill, and 13 of 23 without it.
and 3 more in the full report
4 fixed13 passed either way6 still failing0 broke
Tokens, turns and time describe resource use, not a dollar price.
One of 4 test cases the skill fixed. Same model, same prompt, with and without the skill.
When reconstructing trees from DNA sequence alignments in R using ape, I need to calculate pair-wise sequence distances before neighbor-joining. Write an R snippet showing sequence reading from a FASTA file, distance matrix computation under standard evolutionary models, and tree building.
| Checked | Without skill | With skill |
|---|---|---|
| Reads sequence file using ape read.FASTA function. | Missed | Passed |
| Computes sequence distance matrix using ape dist.dna function. | Passed | Passed |
The instructions your model reads when the skill loads.
Access, analyze, and visualize biodiversity data from global databases including GBIF, iNaturalist, and GenBank for ecological and evolutionary research.
| Database | Content | Records | API | Cost |
|---|---|---|---|---|
| GBIF | Species occurrence records | 2.4B+ | Yes | Free |
| iNaturalist | Citizen science observations | 180M+ | Yes | Free |
| GenBank (NCBI) | Genetic sequences | 250M+ | Yes | Free |
| BOLD Systems | DNA barcode records | 15M+ | Yes | Free |
| eBird | Bird observations | 1.3B+ | Yes | Free |
| IUCN Red List | Conservation status | 160,000+ | Yes | Free (with key) |
| OBIS | Marine biodiversity | 100M+ | Yes | Free |
| Catalogue of Life | Taxonomic backbone | 2M+ species | Yes | Free |
| TRY Plant Trait | Plant functional traits | 12M+ | Request | Free |
| WorldClim | Climate data (rasters) | Global | Download | Free |
from pygbif import species as sp
from pygbif import occurrences as occ
# Search for a species by name
name_result = sp.name_backbone(name="Panthera tigris", rank="species")
taxon_key = name_result["usageKey"]
print(f"GBIF taxon key: {taxon_key}")
print(f"Status: {name_result['status']}")
print(f"Kingdom: {name_result['kingdom']}")
# Get occurrence records
results = occ.search(
taxonKey=taxon_key,
hasCoordinate=True, # Only georeferenced records
country="IN", # India
limit=100,
test cases passed, vs 13 / 23 without
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