Powered by OpenAIRE graph
Found an issue? Give us feedback
ZENODOarrow_drop_down
ZENODO
Software . 2025
License: CC BY
Data sources: Datacite
ZENODO
Software . 2024
License: CC BY
Data sources: Datacite
versions View all 2 versions
addClaim

This Research product is the result of merged Research products in OpenAIRE.

You have already added 0 works in your ORCID record related to the merged Research product.

GBIF Taxonomy OWLizer

Authors: Miranda Soares, Filipi;
Abstract

This version includes the documentation of the web-based app developed for this script, available at https://filipi-soares.github.io/TaxonOWLConverter/. Overview This script fetches taxonomic classification data for given species names from the GBIF API and generates an OWL ontology representation of the taxonomy. It ensures that only accepted scientific names are included in the OWL representation, ignoring synonyms. Requirements Python 3.x requests library Functions fetch_gbif_data(scientific_name) Fetches taxonomic classification from the GBIF API for a given scientific name. Parameters: scientific_name (str) - The scientific name of the species. Returns: dict - The JSON response from the API containing taxonomic data, or None if the request fails. Example: data = fetch_gbif_data("Apis mellifera") fetch_synonyms(species_key) Fetches synonyms for a given species key from the GBIF API. Parameters: species_key (int): The unique key identifying the species in the GBIF database. Returns: list: A list of dictionaries, each representing a synonym of the species, or an empty list if the request fails. Example: synonyms = fetch_synonyms(1341976) accumulate_taxa(data, taxa) Accumulates unique taxa and their relationships from the provided taxonomic data into the taxa dictionary. Parameters: data (dict): The taxonomic data for a species. taxa (dict): A dictionary to store unique taxa and their relationships. validate_accepted_name(data, taxa) Ensures that only the accepted scientific name is included in the taxa dictionary by validating against synonyms. Parameters: generate_owl(taxa) Generates an OWL representation from the accumulated taxa. Parameters: taxa (dict) - A dictionary containing unique taxonomic information. Returns: A string containing the OWL representation of the taxonomy. Usage Define a list of species names you want to include in the ontology. species_names = [ "Apis mellifera", "Bos taurus", "Capra aegagrus hircus", "Ovis aries", "Sus", "Prochilodus cearensis", "Prochilodus scrofa", "Prochilodus margravii", "Semaprochilodus insignis", "Semaprochilodus taeniurus", "Colossoma mitrei", "Arapaima gigas", "Tilapia" ] Iterate through the list of species names, fetch their taxonomic data, accumulate the taxa, and validate accepted names. taxa = {} for name in species_names: data = fetch_gbif_data(name) if data: accumulate_taxa(data, taxa) validate_accepted_name(data, taxa) Generate the OWL representation from the accumulated taxa. owl_data = generate_owl(taxa) print(owl_data) The program generates an OWL representation of the accumulated taxonomy, ensuring that each taxonomic level is included only once, and prints it to the console.

Related Organizations
  • BIP!
    Impact byBIP!
    citations
    This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
    0
    popularity
    This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
    Average
    influence
    This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
    Average
    impulse
    This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
    Average
Powered by OpenAIRE graph
Found an issue? Give us feedback
citations
This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Citations provided by BIP!
popularity
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
BIP!Popularity provided by BIP!
influence
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Influence provided by BIP!
impulse
This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
BIP!Impulse provided by BIP!
0
Average
Average
Average
Related to Research communities