Scientific open source Software (SOSS)

A repository that given an software arfefact DOI, it will computationally reproduce the software environment of the package.

Description

This project aims to: (1) extract and link scientific software metadata from package files in a RDF KG and (2) recreate the software artefacts to compare with FAIR Maturity Evaluation services.

Overview of the methodology:

From a collection of software projects on 4TU, it produces reproducible sets of software artefacts and compare with FAIR evaluator.

graph LR
A[Collect software artefacts] -->B(Identify single-software artefacts)
    B --> C{Processes}
    C -->|data collection| D[Scan software artefacts API-4TU] --> Z(inspect source code e.g py file, readme for metadata extraction) --> F(GUIX package definition RDF) --> G(RDF/validation output)
    C -->|verify reproducible worflow| E[Scan open-source software] --> U(Select projects that are able to run as command-line tool) --> H(run command-line) --> J(JSON output)
    C -->|FAIR calculator| J(JSON output)

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Expected contributions

Support researchers reusing software artefacts by adding discoverability, traceability and reproducibility functionalities in 4TUResearchData using semantic technology approaches:

• 1. Add descriptors on the existing RDF data model (annotate with GUIX Package standards)
• 2. A framework to generate the dataset in RDF. It includes scripts for the collection of data and execution of the FAIR tests discrepancies in a sandbox environment
• 3. Raw data files from the dataset generation that can be reused for futher researcher

Materials and resources

Available software repositories

A list of research software registries (also known as catalog, index, warehouse, repository, hub, platform, and other terms) can be found here: Awesome Research Software Registries

• Research software directory
• 4TUResearchData repository
• TUD
• Research Software Heritage
• Marven Central Repository
• Apache projects
• ORKG
• Codewithpapers

Available ontologies

Concepts and properties are annotated with:

• GUIX Package difinitions
• Semanticscience Integrated Ontology (SIO)
• Software Ontology (SWO)
• Research Software Ontology (RO)
• Ontology of Software Depencencies (OSD)
• OKG-Soft
• ML Schedma Core Specification

Data Model

Explaining the elements of a knowledge graph for the research software artefacts:

• Source code repo: entity that host +1 packages/module
• Package: a sub-module that provides a reusable piece of software
• Version: a tag associated with a repo or package that identifies the unique instance or release of the source
• djht:software: a computational related flaw associated with versions of a repo or package

graph TD
   A((Repo)) -->|rdf:has dependecy| B((ml: version))
   A((Repo)) -->|ml: has transitive dependency| B
   C((ml: package)) -->|ml: has version| B
   B -->|has software| D((djht: software))
   D -->|fixed version| B
   D --> |djht: has author| E((ORCID))
   D --> |has source| F((Source Code))
   D --> |has categories| G((Tags))
   D --> |has files| H((djht:files))

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Example RDF (turtle):

# metamodel_version: 1.7.0
@prefix djht: <http://djht.org/ontology/djht/> .
@prefix mls: <http://www.w3.org/ns/mls#> .
@prefix schema: <http://schema.org/> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .

<https://doi.org/10.4121/19145426.v1> a mls:Software ;
    djht:authors "0000-0002-9994-1462, 0000-0002-9994-XXXXX" ;
    djht:files 8 ;
    djht:funding "EU-horizon" ;
    djht:tags "data science" ;
    schema:name "Characterizing single-molecule dynamics of viral RNA-dependent RNA polymerases with a multiplexed magnetic tweezers" ;
    mls:function "1-800" .

<https://doi.org/10.4121/19145426.v2> a mls:Software ;
    djht:dependencies 90 ;
    djht:funding "none" ;
    djht:references "none" ;
    djht:tags "AI" ;
    schema:name "Characterizing single-molecule dynamics of viral RNA-dependent RNA polymerases with a multiplexed magnetic tweezers" ;
    mls:function "1-800" .

[] a djht:Container ;
    djht:softwares <https://doi.org/10.4121/19145426.v1>,
        <https://doi.org/10.4121/19145426.v2> .

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License

Copyright (C) 2023 - MIT License

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