Data

Tools

Indexes

Applications

Experiments

Open Source Science

species_genbankbold

Getting data from GenBank and Bold for further analyses

https://github.com/ronaldvisser/species_genbankbold

Science Score: 57.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ✓
    CITATION.cff file
    Found CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 4 DOI reference(s) in README
  • ○
    Academic publication links
  • ○
    Academic email domains
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (4.2%) to scientific vocabulary
Last synced: 6 months ago · JSON representation ·

Repository

Getting data from GenBank and Bold for further analyses

Basic Info
  • Host: GitHub
  • Owner: RonaldVisser
  • License: gpl-3.0
  • Language: R
  • Default Branch: main
  • Size: 9.16 MB
Statistics
  • Stars: 1
  • Watchers: 1
  • Forks: 0
  • Open Issues: 0
  • Releases: 0
Created over 2 years ago · Last pushed about 1 year ago
Metadata Files
Readme License Citation

README.md

Species_GenBankBold

Getting data from GenBank and Bold for further analyses

Usage

The file gettingcombiningdata.R is used to get data from GenBank and Bold on basis os the trnL marker. The species list of plants (see data) is used to select only plant DNA.

ncbi_download.R is a function to download data from the NCBI databank, used by the aforementioned script.

refdbimportBOLD.R is an adapted version of the function from https://github.com/fkeck/refdb/blob/main/R/import_NCBI.R. See also:

Keck, F., & Altermatt, F. (2023). Management of DNA reference libraries for barcoding and metabarcoding studies with the R package refdb. Molecular Ecology Resources, 23(2), 511-518. https://doi.org/10.1111/1755-0998.13723.

Data

The file SL2020 Checklist Flora NL.xlsx was taken from

Duistermaat, H., Sparrius, L.B., & Denters, T. (2021). Standaardlijst van de Nederlandse Flora 2020 [Data set]. In Gorteria. Zenodo. https://doi.org/10.5281/zenodo.5596206

Owner

  • Login: RonaldVisser
  • Kind: user

Citation (CITATION.cff) 

cff-version: 1.2.0
message: "If you use this software, please cite it as below."
authors:
  - family-names: Visser
    given-names: Ronald
    orcid: "https://orcid.org/0000-0001-6966-1729"
title: "Combining data from GenBank and Bold"
version: 0.3.0
doi: xxx
date-released: 2024-12-04
url: "https://github.com/RonaldVisser/Species_GenBankBold"

GitHub Events

Total
  • Issues event: 1
  • Watch event: 1
  • Issue comment event: 2
  • Push event: 6
Last Year
  • Issues event: 1
  • Watch event: 1
  • Issue comment event: 2
  • Push event: 6