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Open Source Science

https://github.com/agentschapplantentuinmeise/midscalculator

https://github.com/agentschapplantentuinmeise/midscalculator

Science Score: 39.0%

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

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 6 DOI reference(s) in README
  • ○
    Academic publication links
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    Institutional organization owner
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    JOSS paper metadata
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    Scientific vocabulary similarity
    Low similarity (12.1%) to scientific vocabulary
Last synced: 10 months ago · JSON representation

Repository

Basic Info
  • Host: GitHub
  • Owner: AgentschapPlantentuinMeise
  • License: mit
  • Language: HTML
  • Default Branch: main
  • Size: 88.5 MB
Statistics
  • Stars: 6
  • Watchers: 2
  • Forks: 1
  • Open Issues: 11
  • Releases: 1
Created over 4 years ago · Last pushed 11 months ago
Metadata Files
Readme License

README.md

MIDSCalculator

This is the repository for the MIDSCalculator app, written initially by @LynnDelgat during an internship at Meise Botanic Garden in 2022. The MIDSCalculator is an Rshiny app that allows users to easily calculate MIDS scores for their natural history specimen datasets. The app currently supports data provided as Darwin Core Archives and Biocase ABCD archives.

Minimum Information about a Digital Specimen

Minimum Information about a Digital Specimen (MIDS) is a data standard which aims to describe four different levels of digitization status for biological and geological specimens from natural history collections, each level requiring certain information elements (referred to as MIDS elements from here on) to be digitally available. With this standard, users of collection data, as well as funders and collection curators will have a better overview of how comprehensively digitized a collection or any other set of specimens really is. The standard is currently still under development by a Task Group of the global Biodiversity Information Standards (“TDWG”) organization. While MIDS elements for digitization levels 0 and 1 have been specified, MIDS elements for levels 2 and 3 are still under discussion. For more details you can visit the GitHub repository https://github.com/tdwg/mids or the documentation website (still in draft stage) https://tdwg.github.io/mids.

MIDSCalculator App

The MIDSCalculator is a Shiny app written in R, which allows users to calculate MIDS scores for each record in a submitted dataset, and explore the results.

Mapping MIDS elements: use of a JSON schema

As the MIDS standard is agnostic to the data model of the sourced data, the app uses SSSOM mappings to map MIDS elements to properties of the sourced data. SSSOM mappings for Darwin Core archives and for Biocase ABCD archives are included in the app. Latest versions of SSSOM mappings can be found in the MIDS GitHub repository and more documentation can be viewed on the MIDS documentation website.

Data

Datasets

  • Example datasets for testing, GBIF Occurrence Downloads 10.15468/dl.e8jnan and 10.15468/dl.fuu99k, can be found as a zip file in the data folder for quick testing. Also included are an example Darwin Core archive from GBIF Norway's IPT server and a Biocase archive for the Herbarium Berolinense.

Owner

  • Name: Botanic Garden Meise
  • Login: AgentschapPlantentuinMeise
  • Kind: organization
  • Email: quentin.groom@plantentuinmeise.be
  • Location: Meise, Belgium

GitHub Events

Total
  • Issues event: 16
  • Watch event: 2
  • Issue comment event: 7
  • Push event: 13
  • Pull request event: 1
Last Year
  • Issues event: 16
  • Watch event: 2
  • Issue comment event: 7
  • Push event: 13
  • Pull request event: 1

Issues and Pull Requests

Last synced: 10 months ago

All Time
  • Total issues: 7
  • Total pull requests: 2
  • Average time to close issues: 11 months
  • Average time to close pull requests: 4 months
  • Total issue authors: 1
  • Total pull request authors: 1
  • Average comments per issue: 0.43
  • Average comments per pull request: 0.0
  • Merged pull requests: 1
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 5
  • Pull requests: 1
  • Average time to close issues: 4 months
  • Average time to close pull requests: about 20 hours
  • Issue authors: 1
  • Pull request authors: 1
  • Average comments per issue: 0.4
  • Average comments per pull request: 0.0
  • Merged pull requests: 1
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • matdillen (8)
  • snsb-seifert (1)
  • Rindiser (1)
Pull Request Authors
  • matdillen (3)
  • jrdh (1)
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Dependencies

Dockerfile docker
  • rocker/r-ver 4.2 build