metadata.json

{
  "title": "NCBITaxonomy.jl - rapid biological names finding and reconciliation",
  "authors": [
    {
      "affiliations": [
        "Université de Montréal, Départment de Sciences Biologiques, Montréal QC, Canada",
        "Québec Centre for Biodiversity Science, Montréal, QC, Canada"
      ],
      "familyname": "Poisot",
      "givennames": "Timothée",
      "email": "timothee.poisot@umontreal.ca",
      "orcid": "0000-0002-0735-5184",
      "status": ["corresponding"]
    },
    {
      "affiliations": [
        "Centre on Climate Change and Planetary Health, London School of Hygiene and Tropical Medicine, London, UK",
        "Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene and Tropical Medicine, London, UK",
        "Current address: Centre for Biodiversity and Environment Research, University College London, London, UK"
      ],
      "familyname": "Gibb",
      "givennames": "Rory",
      "orcid": "0000-0002-0965-1649"
    },
    {
      "affiliations": [
        "Emerging Pathogens Institute, University of Florida, Gainesville, FL, United States of America",
        "School of Life Sciences, University of KwaZulu-Natal, Durban, South Africa",
        "Department of Geography, University of Florida, Gainesville, FL, United States of America"
      ],
      "familyname": "Ryan",
      "givennames": "Sadie J.",
      "orcid": "0000-0002-4308-6321"
    },
    {
      "affiliations": [
        "Department of Microbiology and Immunology, Georgetown University Medical Center, Georgetown University, Washington, D.C., United States of America",
        "Center for Global Health Science and Security, Georgetown University Medical Center, Georgetown University, Washington, D.C., United States of America"
      ],
      "familyname": "Carlson",
      "givennames": "Colin J.",
      "orcid": "0000-0001-6960-8434"
    }
  ],
  "abstract": "`NCBITaxonomy.jl` is a package designed to facilitate the reconciliation and cleaning of taxonomic names, using a local copy of the NCBI taxonomic backbone [@Federhen2012NcbTax; @Schoch2020NcbTax]; The basic search functions are coupled with quality-of-life functions including case-insensitive search and custom fuzzy string matching to facilitate the amount of information that can be extracted automatically while allowing efficient manual curation and inspection of results. `NCBITaxonomy.jl` works with version 1.6 of the Julia programming language [@Bezanson2017JulFre], and relies on the Apache Arrow format to store a local copy of the NCBI raw taxonomy files. The design of `NCBITaxonomy.jl` has been inspired by similar efforts, like the R package `taxadb` [@Norman2020TaxHig], which provides an offline alternative to packages like `taxize` [@Chamberlain2013TaxTax].",
  "keywords": [
    "biodiversity",
    "taxonomy",
    "NCBI",
    "fuzzy matching"
  ],
  "citationstyle": "ecography"
}