Learning Path sandbox

authors: Phil Reed, Alban Gaignard, Leyla Jael Castro

contributors: Nick Juty, Roman Baum

Initially drafted the 20th of November 2025, as part of Bioschemas activities and ELIXIR BioHackathon Europe 2025.
Refined at de.NBI BioHackathon Germany 2025.
To be revised by the community.

Any questions, please contact [email protected], [email protected]

Aim of the repo

Report experiments to model Learning Paths with Schema.org ontology.

Content

A jupyter notebook showing :

How Schema.org can be used, especially the HowTo, HowToSection, and HowToStep types and the required properties to properly define order between steps.
Some code to query (SPARQL and property path) the semantic annotations and retrieve for a given step the learning prerequesites.
Some code to transform Schema.org markup into a Mermaid diagram

Results

First example

A sample Learning path:

https://tess.elixir-europe.org/learning_paths/introduction-to-galaxy-and-sequence-analysis-6384c0ed-3546-41cf-ac30-bff8680dd96c

LP structure:

Introduction to Galaxy and Sequence analysis [syllabusSections=M1,M2]

Module 1: Introduction to Galaxy [itemListElement=11,12] [nextItem=M2]
- (1.1) A short introduction to Galaxy [nextItem=12]
- (1.2) Galaxy Basics for genomics [nextItem=21]
Module 2: Basics of Genome Sequence Analysis [itemListElement=21,22,23,24]
- (2.1) Quality Control [nextItem=22]
- (2.2) Mapping [nextItem=23]
- (2.3) An Introduction to Genome Assembly [nextItem=24]
- (2.4) Chloroplast genome assembly

@prefix dct: <http://purl.org/dc/terms/> .
@prefix ex: <http://example.org/> .
@prefix schema: <https://schema.org/> .

ex:GA_learning_path a schema:Course ;
    dct:conformsTo <https://bioschemas.org/profiles/LearningPath> ;
    schema:courseCode "GSA101" ;
    schema:description "This learning path aims to teach you the basics of Galaxy and analysis of sequencing data. " ;
    schema:name "Introduction to Galaxy and Sequence analysis" ;
    schema:provider ex:ExampleUniversity ;
    schema:syllabusSections ex:Module_1,
        ex:Module_2 .

ex:Module_1 a schema:ItemList,
        schema:ListItem,
        schema:Syllabus ;
    dct:conformsTo <https://bioschemas.org/profiles/LearningPathModule> ;
    schema:itemListElement ex:TM11,
        ex:TM12 ;
    schema:name "Module 1: Introduction to Galaxy" ;
    schema:nextItem ex:Module_2 ;
    schema:teaches "Learn how to create a workflow" .

ex:TM11 a schema:LearningResource,
        schema:ListItem ;
    dct:conformsTo <https://bioschemas.org/profiles/TrainingMaterial> ;
    schema:description "What is Galaxy" ;
    schema:name "(1.1) A short introduction to Galaxy" ;
    schema:nextItem ex:TM12 ;
    schema:url "https://tess.elixir-europe.org/materials/hands-on-for-a-short-introduction-to-galaxy-tutorial?lp=1%3A1" .

And the complete diagram:

graph TD
N1["Module 1: Introduction to Galaxy"]
N3["(1.2) Galaxy Basics for genomics"]
N1 -- itemListElement --> N3
N1["Module 1: Introduction to Galaxy"]
N2["(1.1) A short introduction to Galaxy"]
N1 -- itemListElement --> N2
N4["Module 2: Basics of Genome Sequence Analysis"]
N8["(2.4) Chloroplast genome assembly"]
N4 -- itemListElement --> N8
N2["(1.1) A short introduction to Galaxy"]
N3["(1.2) Galaxy Basics for genomics"]
N2 -- nextItem --> N3
N1["Module 1: Introduction to Galaxy"]
N4["Module 2: Basics of Genome Sequence Analysis"]
N1 -- nextItem --> N4
N7["(2.3) An Introduction to Genome Assembly"]
N8["(2.4) Chloroplast genome assembly"]
N7 -- nextItem --> N8
N4["Module 2: Basics of Genome Sequence Analysis"]
N5["(2.1) Quality Control"]
N4 -- itemListElement --> N5
N4["Module 2: Basics of Genome Sequence Analysis"]
N6["(2.2) Mapping"]
N4 -- itemListElement --> N6
N4["Module 2: Basics of Genome Sequence Analysis"]
N7["(2.3) An Introduction to Genome Assembly"]
N4 -- itemListElement --> N7
N6["(2.2) Mapping"]
N7["(2.3) An Introduction to Genome Assembly"]
N6 -- nextItem --> N7
N3["(1.2) Galaxy Basics for genomics"]
N5["(2.1) Quality Control"]
N3 -- nextItem --> N5
N5["(2.1) Quality Control"]
N6["(2.2) Mapping"]
N5 -- nextItem --> N6

Second example

This is a module of a learning path graph where each item is a course instance (event), not a training material. They provide a linear reduction which we will model. This reduction supports the prerequisites in a simplified way, and ignores courses from other modules (Open Oriented Programming).

https://www.helmholtz-hida.de/en/discover-hida/helmholtz-information-data-science-framework/data-science-course-portfolio/

LP structure:

Helmholtz Data Science Course Portfolio [syllabusSections=M1]

Module: Open Research [itemListElement=1,2,3,4,5,6,7]
- (1) Kickstart Shell & Git [nextItem=2]
  - 22-23 September 2025
- (2) Introduction to Git & GitLab [nextItem=3]
  - 15-16 September 2025
  - 24-25 November 2025
- (3) Foundations of Research Software Publication [nextItem=4]
  - 6-7 November 2025
- (4) Continuous Integration [nextItem=5]
  - 28-29 October 2025
  - 16-17 December 2025
- (5) Fundamentals of Software Testing [nextItem=6]
  - No instances yet
- (6) Reproducible and Open Research [nextItem=7]
  - 19 November 2025
- (7) AI Ethics: Model Cards for Model Reporting
  - 17 October 2025

Each course may have multiple course instances.

hz:HZ_learning_path a schema:Course ;
    dct:conformsTo <https://bioschemas.org/profiles/LearningPath> ;
    schema:courseCode "data-science-course-portfolio" ;
    schema:description "The platforms of the Information & Data Science Framework have developed a coordinated course offer that covers a wide array of topics." ;
    schema:name "Helmholtz Data Science Course Portfolio" ;
    schema:provider hz:Helmholtz ;
    schema:syllabusSections hz:Module_1 .

hz:Module_1 a schema:Course,
        schema:ItemList,
        schema:ListItem,
        schema:Syllabus ;
    dct:conformsTo <https://bioschemas.org/profiles/LearningPathModule> ;
    schema:description "Unlock the potential of open science through courses on collaborative research practices and project management, open-source tools and software, and publishing ethically sound, reproducible, and transparent results." ;
    schema:itemListElement hz:TM1,
        hz:TM2,
        hz:TM3,
        hz:TM4,
        hz:TM5,
        hz:TM6,
        hz:TM7 ;
    schema:name "Open Research" ;
    schema:teaches "Learn how to support open science" .

hz:TM1 a schema:Course,
        schema:ListItem ;
    dct:conformsTo <https://bioschemas.org/profiles/Course> ;
    schema:description "Boost your research efficiency with this workshop on Bash scripting and Git version control. Learn to automate tasks with custom scripts and track your work with Git" ;
    schema:hasCourseInstance hz:TM1a ;
    schema:name "(1) Kickstart Shell & Git" ;
    schema:nextItem hz:TM2 ;
    schema:url "https://www.helmholtz-hida.de/en/lernen-vernetzen/data-science-course-portfolio/kickstart-shell-git/" .

hz:TM1a a schema:CourseInstance ;
    dct:conformsTo <https://bioschemas.org/profiles/CourseInstance> ;
    schema:courseMode "online" ;
    schema:endDate "2025-09-23T17:00:00" ;
    schema:startDate "2025-09-22T09:00:00" .

And the complete diagram:

graph TD
N2["(1) Kickstart Shell & Git"]
N3["(2) Introduction to Git & GitLab"]
N2 -- nextItem --> N3
N1["Open Research"]
N8["(7) AI Ethics: Model Cards for Model Reporting"]
N1 -- itemListElement --> N8
N5["(4) Continuous Integration"]
N6["(5) Fundamentals of Software Testing"]
N5 -- nextItem --> N6
N3["(2) Introduction to Git & GitLab"]
N4["(3) Foundations of Research Software Publication"]
N3 -- nextItem --> N4
N1["Open Research"]
N5["(4) Continuous Integration"]
N1 -- itemListElement --> N5
N1["Open Research"]
N3["(2) Introduction to Git & GitLab"]
N1 -- itemListElement --> N3
N1["Open Research"]
N7["(6) Reproducible and Open Research"]
N1 -- itemListElement --> N7
N4["(3) Foundations of Research Software Publication"]
N5["(4) Continuous Integration"]
N4 -- nextItem --> N5
N1["Open Research"]
N2["(1) Kickstart Shell & Git"]
N1 -- itemListElement --> N2
N6["(5) Fundamentals of Software Testing"]
N7["(6) Reproducible and Open Research"]
N6 -- nextItem --> N7
N1["Open Research"]
N4["(3) Foundations of Research Software Publication"]
N1 -- itemListElement --> N4
N1["Open Research"]
N6["(5) Fundamentals of Software Testing"]
N1 -- itemListElement --> N6
N7["(6) Reproducible and Open Research"]
N8["(7) AI Ethics: Model Cards for Model Reporting"]
N7 -- nextItem --> N8

Schema structure

We propose two new Bioschemas profiles and a small change to one Bioschemas profile:

LearningPath: inherits from Course
LearningPathModule: inherits from Course and Syllabus and ListItem and ItemList
TrainingMaterial: inherits from LearningResource and ListItem

A LearningPath has zero or more LearningPathModule. A LearningPathModule has zero or more LearningResource. These relationships are (ordered) lists or steps, using the ItemList and Syllabus Schema.org types.

Class diagram, where 🔺 is Schema.org type, 🟩 is Bioschemas profile, 🔵 is new profile:

classDiagram
direction TB
    class Event["Event🔺"] {
    }
    class CourseInstance["CourseInstance🔺🟩"]  {
    }
    class Course["Course🔺🟩"] {
        syllabusSections
    }
    class new_LearningPath["new:LearningPath🔵"] {
        Syllabus[] syllabusSections
    }
    class ListItem["ListItem🔺"] {
	    nextItem
    }
    class Syllabus["Syllabus🔺"] {   
    }
    class new_LearningPathModule["new:LearningPathModule🔵"] {
        ListItem[] itemListElement
        LearningPathTopic nextItem
    }
    class LearningResource["LearningResource🔺"] {
    }
    class bio_TrainingMaterial["bio:TrainingMaterial🟩"] {
    }
    Course <|-- new_LearningPath
    Course <|-- new_LearningPathModule
    Syllabus <|-- new_LearningPathModule
    ListItem <|-- new_LearningPathModule
    LearningResource <|-- Course
    LearningResource <|-- bio_TrainingMaterial
    LearningResource <|-- Syllabus
    Event <|-- CourseInstance

More detailed class diagram, including the distinction where there is a Schema.org type with the same name as a Bioschemas profile:

classDiagram
direction TB
    class CourseInstance["CourseInstance🔺"] {
    }
    class bio_CourseInstance["bio:CourseInstance🟩"] {
    }
    class bio_Course["bio:Course🟩"] {
    }
    class Course["Course🔺"] {
	    syllabusSections
    }
    class new_LearningPath["new:LearningPath🔵"] {
	    Syllabus[] syllabusSections
    }
    class ListItem["ListItem🔺"] {
	    nextItem
    }
    class Syllabus["Syllabus🔺"] {
    }
    class new_LearningPathModule["new:LearningPathModule🔵"] {
	    ListItem[] itemListElement
	    LearningPathTopic nextItem
    }
    class LearningResource["LearningResource🔺"] {
    }
    class bio_TrainingMaterial["bio:TrainingMaterial🟩"] {
    }
    class CreativeWork["CreativeWork🔺"] {
    }
    class Event["Event🔺"] {
    }
    Course <|-- bio_Course
    Course <|-- new_LearningPath
    Course <|-- new_LearningPathModule
    Syllabus <|-- new_LearningPathModule
    ListItem <|-- new_LearningPathModule
    CreativeWork <|-- LearningResource
    CreativeWork <|-- Course
    LearningResource <|-- Course
    LearningResource <|-- Syllabus
    Event <|-- CourseInstance
    CourseInstance <|-- bio_CourseInstance
    LearningResource <|-- bio_TrainingMaterial

Name		Name	Last commit message	Last commit date
Latest commit History 27 Commits
README.md		README.md
Tests_LearningPath.ipynb		Tests_LearningPath.ipynb
lp1.jsonld		lp1.jsonld
lp1.mmd		lp1.mmd
lp1.ttl		lp1.ttl
lp2.jsonld		lp2.jsonld
lp2.mmd		lp2.mmd
lp2.ttl		lp2.ttl
model.py		model.py

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