specimen_catalogue

https://github.com/oggioniale/specimen_catalogue

Science Score: 57.0%

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

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CITATION.cff file
Found CITATION.cff file
✓
codemeta.json file
Found codemeta.json file
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.zenodo.json file
Found .zenodo.json file
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DOI references
Found 3 DOI reference(s) in README
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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 (9.4%) to scientific vocabulary

Last synced: 9 months ago · JSON representation ·

Repository

Basic Info

Host: GitHub
Owner: oggioniale
License: apache-2.0
Language: JavaScript
Default Branch: main
Homepage: https://oggioniale.github.io/specimen_catalogue/
Size: 3.31 MB

Statistics

Stars: 3
Watchers: 3
Forks: 0
Open Issues: 2
Releases: 1

Created over 2 years ago · Last pushed over 1 year ago

Metadata Files

Readme License Citation Codemeta

README.md

Specimen catalogue

This repository includes a comprehensive solution to manage specimen information. The solution encompasses the following processes:

Data Collection: Collect information about specimens using an Excel file.
Data Transformation: Convert the collected information into XML and Turtle (TTL) formats using R functions.
Data Presentation: Translate the transformed data into HTML landing pages via XSLT.

Implementation Standards

The implementation adheres to several standards and recommendations to ensure compliance and interoperability.

ESIP: the solution follows the Physical Sample Curation recommendations;
SOSA Ontology: the main version of the SOSA ontology (19-10-2017) - W3C SOSA Ontology;
The extension of the SOSA ontology (05-09-2024) - W3C SOSA-SSN Draft and its GitHub repository;
SESAR (System for Earth Sample Registration) XSD schema solutions [1];
IGSN (International Generic Sample Number) CSIRO (Commonwealth Scientific and Industrial Research Organisation) schema compliance [2];
TDWG MIDS (Minimum Information about a Digital Specimen) specification at level 1.

By adhering to the above standards and schemas, the solution ensures compliance with DataCite requirements, facilitating standardized and interoperable specimen data management.

Production Flow The production flow of this implementation is illustrated in the figure below:

The workflow of this application consists of the following steps:

Fill the Spreadsheet: complete the specimen_template.xlsx spreadsheet with the relevant specimen information;
Generate XML and TTL: use the specimen_catalogue() function to generate IGSN CSIRO XML and TTL (Turtle) files based on the SOSA Ontology for each record present in the spreadsheet.

Owner

Name: Alessandro Oggioni
Login: oggioniale
Kind: user
Location: Milan - Italy
Company: CNR - IREA

Website: https://www.cnr.it/people/alessandro.oggioni
Repositories: 6
Profile: https://github.com/oggioniale

Citation (CITATION.cff)

# --------------------------------------------
# CITATION file created with {cffr} R package
# See also: https://docs.ropensci.org/cffr/
# --------------------------------------------
 
cff-version: 1.2.0
message: 'To cite package "Specimen" in publications use:'
type: software
title: 'Specimen: What the Package Does (One Line, Title Case)'
version: 0.0.0.9000
doi: 10.5281/zenodo.14517494
abstract: What the package does (one paragraph).
authors:
- family-names: Oggioni
  given-names: Alessandro
  email: alessandro.oggioni@cnr.it
  orcid: https://orcid.org/0000-0002-7997-219X
preferred-citation:
  type: generic
  title: Specimen
  authors:
  - family-names: Oggioni
    given-names: Alessandro
    email: alessandro.oggioni@cnr.it
    orcid: https://orcid.org/0000-0002-7997-219X
  year: '2024'
  notes: R package version v0.0.0.9000
repository-code: https://github.com/oggioniale/specimen_catalogue
url: https://oggioniale.github.io/specimen_catalogue/
contact:
- family-names: Oggioni
  given-names: Alessandro
  email: alessandro.oggioni@cnr.it
  orcid: https://orcid.org/0000-0002-7997-219X
references:
- type: software
  title: 'R: A Language and Environment for Statistical Computing'
  notes: Depends
  url: https://www.R-project.org/
  authors:
  - name: R Core Team
  institution:
    name: R Foundation for Statistical Computing
    address: Vienna, Austria
  year: '2024'
  version: '>= 2.10'
- type: software
  title: shiny
  abstract: 'shiny: Web Application Framework for R'
  notes: Suggests
  url: https://shiny.posit.co/
  repository: https://CRAN.R-project.org/package=shiny
  authors:
  - family-names: Chang
    given-names: Winston
    email: winston@posit.co
    orcid: https://orcid.org/0000-0002-1576-2126
  - family-names: Cheng
    given-names: Joe
    email: joe@posit.co
  - family-names: Allaire
    given-names: JJ
    email: jj@posit.co
  - family-names: Sievert
    given-names: Carson
    email: carson@posit.co
    orcid: https://orcid.org/0000-0002-4958-2844
  - family-names: Schloerke
    given-names: Barret
    email: barret@posit.co
    orcid: https://orcid.org/0000-0001-9986-114X
  - family-names: Xie
    given-names: Yihui
    email: yihui@posit.co
  - family-names: Allen
    given-names: Jeff
  - family-names: McPherson
    given-names: Jonathan
    email: jonathan@posit.co
  - family-names: Dipert
    given-names: Alan
  - family-names: Borges
    given-names: Barbara
  year: '2024'
  doi: 10.32614/CRAN.package.shiny
- type: software
  title: lifecycle
  abstract: 'lifecycle: Manage the Life Cycle of your Package Functions'
  notes: Imports
  url: https://lifecycle.r-lib.org/
  repository: https://CRAN.R-project.org/package=lifecycle
  authors:
  - family-names: Henry
    given-names: Lionel
    email: lionel@posit.co
  - family-names: Wickham
    given-names: Hadley
    email: hadley@posit.co
    orcid: https://orcid.org/0000-0003-4757-117X
  year: '2024'
  doi: 10.32614/CRAN.package.lifecycle

CodeMeta (codemeta.json)

{
  "@context": "https://doi.org/10.5063/schema/codemeta-2.0",
  "@type": "SoftwareSourceCode",
  "identifier": "Specimen",
  "description": "What the package does (one paragraph).",
  "name": "Specimen: What the Package Does (One Line, Title Case)",
  "codeRepository": "https://github.com/oggioniale/specimen_catalogue",
  "issueTracker": "https://github.com/oggioniale/specimen_catalogue/issues",
  "license": "`use_gpl3_license()`",
  "version": "0.0.0.9000",
  "programmingLanguage": {
    "@type": "ComputerLanguage",
    "name": "R",
    "url": "https://r-project.org"
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  "runtimePlatform": "R version 4.3.0 (2023-04-21)",
  "author": [
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      "familyName": "Oggioni",
      "email": "alessandro.oggioni@cnr.it",
      "@id": "https://orcid.org/0000-0002-7997-219X"
    }
  ],
  "funder": [
    {
      "@type": "Person",
      "givenName": "Alessandro",
      "familyName": "Oggioni",
      "email": "alessandro.oggioni@cnr.it",
      "@id": "https://orcid.org/0000-0002-7997-219X"
    }
  ],
  "maintainer": [
    {
      "@type": "Person",
      "givenName": "Alessandro",
      "familyName": "Oggioni",
      "email": "alessandro.oggioni@cnr.it",
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    }
  ],
  "softwareSuggestions": [
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        "name": "Comprehensive R Archive Network (CRAN)",
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      "sameAs": "https://CRAN.R-project.org/package=shiny"
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  "softwareRequirements": {
    "1": {
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  "fileSize": "0KB"
}

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