Building LUMIS together

04 | 09 | 2025 by Yann Le Franc (eSDF) Building LUMIS together Welcome and introduction 02 | 10 | 2025 Yann Le Franc (eSDF) DOI: 10.5281/zenodo.17397077 Introduction to LUMEN 1 ●Presenting the LUMIS platform to LUMEN and GRAPHIA partners ●Dive into the world of semantic artefact creation ●Engage in a co-creation activity with the partners to define a Minimum Viable Product Why this workshop? Introduction to LUMEN 2 How are we planning to work together ? Three working groups to address different aspects of LUMIS development ●Group 1: User stories and mapping with functional needs (technical) ●Group 2: Defining a first architecture diagram for the LUMIS platform (technical) ●Group 3: How can we design the platform to support the collaboration between the domain experts and the semantic artefacts experts? (non technical) Introduction to LUMEN 3 Agenda ●Short introduction to LUMIS - 30 minutes ●Q&A - 10 minutes ●Working together - 70 minutes ○Group 1: User story mapping with functionalities and prioritisation ○Group 2: Design the workspace architecture ○Group 3: How can we make LUMIS usable by non-ontologist? ●Wrap-Up - 10 minutes Introduction to LUMEN 4 ●Define a Minimum Viable Product for LUMIS ○Prioritize user stories, features, and user paths ○Define an initial architecture for the LUMIS Workspace ●Identify needed features to enable collaboration between domain experts and ontologists/taxonomists ●Identify needed features for a newcomer into ontology/taxonomy design What do we want to get out of this workshop? 04 | 09 | 2025 by Julien Homo (Foxcub) Building LUMIS together Introduction to LUMIS 02 | 10 | 2025 Yann Le Franc (eSDF) Introduction to LUMEN 6 What do semantic artefacts represent? from https://www.businessinsider.com/different-types-of-beer-2016-13?r =US&IR=T Conceptual models of the world which describes the concepts and their relations necessary to describe data and its context. From Di Iorio, Angelo & Peroni, Silvio & Vitali, Fabio. (2012). OWiki: Enabling an Ontology-Led Creation of Semantic Data. 10.1007/978-3-642-23172-8_24. Introduction to LUMEN 7 The diversity of Semantic artefacts Introduction to LUMEN 8 Examples of generic conceptual models DCAT PROV Introduction to LUMEN 15 Examples of practices in various communities Marine, Agriculture, Food, Biomedical science Introduction to LUMEN 16 Examples of practices in various communities Marine, Agriculture, Food, Biomedical science Introduction to LUMEN 17 Examples of practices in various communities Marine, Agriculture, Food, Biomedical science Introduction to LUMEN 18 Examples of practices in various communities Marine, Agriculture, Food, Biomedical science Introduction to LUMEN Examples of practices in various communities Linguistics, Humanities Introduction to LUMEN Examples of practices in various communities Linguistics, Humanities Introduction to LUMEN Examples of practices in various communities Material Science and Manufacturing https://doi.org/10.5281/zenodo.6504553 Introduction to LUMEN Semantic artefacts as part of standardisation landscape StandICT.eu, Sarkar, Arkopaul, Frost, Lindsay, Walshe, Ray, & Muscella, Silvana. (2023). Report of TWG Ontologies: Landscape of Ontologies Standards. Zenodo. https://doi.org/10.5281/zenodo.7907025 Large diversity of Semantic Artefact representations, coupled with difficulty to find, interoperate and reuse which impair semantic interoperability How can we resolve this situation? Introduction to LUMEN Applying the FAIR principles to S.A. • 17 generic recommendations and 12 Best Practices • Recommendation aligned with RFC 2119 (MUST, SHOULD, MAY) • 9 MUST • 7 SHOULD • 1 MAY • 1 Undetermined • Minimum metadata profile for FAIR Semantic Artefacts https://doi.org/10.5281/zenodo.6675295 Clement Jonquet, Biswanath Dutta, Luiz O. Bonino da Silva Santos, Robert Pergl, Yann Le Franc. Common Minimum Metadata for FAIR Semantic Artefacts. 2nd Workshop on Ontologies for FAIR and FAIR Ontologies (Onto4FAIR), Cassia Trojahn; Luiz Olavo Bonino da Silva Santos; Giancarlo Guizzardi; Clement Jonquet, Jul 2023, Sherbrooke, Canada. ⟨hal-04106533v2⟩ Introduction to LUMEN Summary of the recommendations ● Usage of globally unique persistent and resolvable identifiers for semantic artefacts, their content (i.e. concept/term/class and relation) and their version, ● Minimum machine-readable metadata to describe the semantic artefacts themselves and their content, ● Usage of repositories/catalogs to share, publish and retrieve semantic artefacts and their content ● Defining common API(s) to access and index semantic artefacts and their content, ● Interoperability approaches to make sure that semantic artefacts of various degrees of complexity and encoding format should work together including publishing FAIR mappings and crosswalks between semantic artefacts, ● Semantic artefacts and their content should be retrievable through search engines. 04 | 09 | 2025 by Julien Homo (Foxcub) Building LUMIS together A first mock-up of the LUMIS platform 02 | 10 | 2025 Julien Homo (Foxcub) Introduction to LUMEN LUMEN | LUMIS https://lumis.lumenproject.eu powered by About |Legal notice|FAQ|Contact Version 1.1.12 You must log in or sign up before continuing. Welcome to LUMIS, the LUMEN Infrastructure for Semantics! Sign in with MyAccessID using existing accounts such asGoogle,ORCID,DARIAH,eduTEAMSand multiple academic accounts. Please take a moment to read our documentation. Sign in with MyAccessID LUMIS is an open platform designed to support ontology-driven research and metadata curation workflows. It is developed as part of the LUMEN project, with contributions from multiple partners across the EOSC ecosystem. The LUMIS Platform is supported by the LUMEN consortium, with funding from the European Commission’s Horizon Europe programme, and developed in collaboration with leading research infrastructures in the LUMEN Federation. Portail d’authentification https://lumis.myaccessid.org Contact us – Privacy Policy Introduction to LUMEN LUMEN | LUMIS https://lumis.lumenproject.eu powered by Version 1.1.12 About |Legal notice|FAQ|Contact Julien Homo DocsWorkspace Search artefacts Semantic artefacts 12 My artefacts (3) JulienHomo/Climate-Change-Ontology OWL ontology • Current LOT phase: Requirements • Updated about 2 hours JulienHomo/research-funding-schemes-v1 SKOS vocabulary • Current LOT phase: Implementation • Updated about 2 days ago JulienHomo/Material-Science-Properties OWL ontology • Current LOT phase: Maintenance • Updated about 3 months ago Other artefacts available in the workspace (9) AliceDurand/Educational-Competence-Model OWL ontology • Current LOT phase: Implementation • Updated about 3 days ago OpenLex/Legal-Reference-Alignment SKOS vocabulary • Current LOT phase: Publication • Updated about 2 months ago AgroOnto/Food-Terminology-vocab OWL ontology • Current LOT phase: Maintenance • Updated about 3 months ago AliceDurand/Environmental-Indicators OWL ontology • Current LOT phase: Maintenance • Updated about 3 months ago View all other artefacts Sort: Recently updated Sort: Recently updated Create a new semantic artefact Create Univ Grenoble Alpes 130,7 MB 2 Semantic artefacts12 Introduction to LUMEN LUMEN | LUMIS https://lumis.lumenproject.eu powered by Version 1.1.12 About |Legal notice|FAQ|Contact Julien Homo DocsWorkspace Title Climate Change Ontology Abstract Controlled vocabulary capturing terms related to climate change scenarios Author(s) Jane Doe (INRAE), Miguel Alvarez (CSIC) Contributor(s) FAIRIMPACT Consortium Artefact type OWL Ontology Keywords climate, emission, carbon sink, adaptation Theme(s) Environment, Climate Subject categories Automatically assigned from reference taxonomy Thesaurus used Agrovoc, GEMET Language en Creation Date 2025-06-12 Last Modified 2025-07-20 Version 1.1 Publisher EOSC Future via LUMIS Primary Producer LUMEN WP4 Aggregator EarthPortal License CC-BY 4.0 Landing page https://lumis.lumenproject.eu/ontologies/climatechange Sources information Based on IPCC terminology and UNEP glossary Sources URL https://data.ipcc.ch/glossary, https://unep.org/semantic-vocabularies Spatial coverage Global Temporal coverage 2005–2023 Define URI strategy Check for existing artefacts Declare source & licence Add competency questions Validate minimum metadata REQUIREMENTS Edit in WebProtégé Edit in VocBench Synchronise with Git Run SHACL validation Run quality checks Manage labels & languages Create mappings Convert / export formats IMPLEMENTATION PUBLICATION MAINTENANCE Artefact metadata Artefact files Current LOT status Recent activities FAIRness overview OVERVIEW This view displays the core metadata of your semantic artefact. You can edit or complete fields at any time to improve the quality and reusability of your artefact. Create Univ Grenoble Alpes 130,7 MB 2 Semantic artefacts12 JulienHomo/Climate-Change-Ontology OWL ontology • Current LOT phase: Requirements • Updated about 2 hours Introduction to LUMEN LUMEN | LUMIS https://lumis.lumenproject.eu powered by Version 1.1.12 About |Legal notice|FAQ|Contact Julien Homo DocsWorkspace Define URI strategy Check for existing artefacts Declare source & licence Add competency questions Validate minimum metadata REQUIREMENTS Edit in WebProtégé Edit in VocBench Synchronise with Git Run SHACL validation Run quality checks Manage labels & languages Create mappings Convert / export formats IMPLEMENTATION PUBLICATION MAINTENANCE Artefact metadata Artefact files Current LOT status Recent activities FAIRness overview OVERVIEW This view displays the internal package structure of the semantic artefact. The folder layout is predefined by LUMIS to ensure consistency and interoperability across all tools and LOT activities. You can upload, replace, or delete files within each folder, but the structure itself cannot be modified by users. More details about the LUMIS semantic artefact structure Import from disk Climate-Change-Ontology Climate-Change-Ontology > ontology > 1.1.0 Search files Filename Modified date Size Refresh ontology shapes queries mappings docs reports 1.0.0 1.1.0 ontology.xml ontology.ttl ontology.json 24 octobre 2025 08:15 19 octobre 2025 14:12 21 octobre 2025 16:09 12.1 MB 7.99 MB 2.51 MB Download XML JSON TTL NT NQ TRIX Import from catalog Create Univ Grenoble Alpes 130,7 MB 2 Semantic artefacts12 JulienHomo/Climate-Change-Ontology OWL ontology • Current LOT phase: Requirements • Updated about 2 hours Introduction to LUMEN LUMEN | LUMIS https://lumis.lumenproject.eu powered by Version 1.1.12 About |Legal notice|FAQ|Contact Julien Homo DocsWorkspace Define URI strategy Check for existing artefacts Declare source & licence Add competency questions Validate minimum metadata REQUIREMENTS Edit in WebProtégé Edit in VocBench Synchronise with Git Run SHACL validation Run quality checks Manage labels & languages Create mappings Convert / export formats IMPLEMENTATION PUBLICATION MAINTENANCE Artefact metadata Artefact files Current LOT status Recent activities FAIRness overview OVERVIEW PHASE 1 - ONTOLOGY REQUIREMENTS SPECIFICATION Use case specification: Edit metadata Data exchange identification: Check for existing artefacts • Declare source & licence Purpose and scope identification: Edit metadata Functional Ontology requirements proposal: Add competency questions Functional Ontology requirements completion: Link CQs to SPARQL tests ORSD formalization: Generate ORSD (preview) • Export ORSD (PDF/Markdown) Functional requirements formalization: Attach acceptance criteria to CQs PHASE 2 - ONTOLOGY IMPLEMENTATION Ontology conceptualization: Open in WebProtégé • Open in VocBench Ontology encoding: Manage labels & languages • Convert/export formats Ontology evaluation: Run SHACL validation • Run quality checks Ontology reuse: Create mappings • Check for existing artefacts PHASE 3 - ONTOLOGY PUBLICATION Proposal release update: Create release / tag • Pre-publish checklist Documentation: Sync README from repo • Generate documentation site / landing page Online publication: Publish to OntoPortal • Publish to Git repository (fallback) • Register PID (DOI/PURL) This view shows your progress along the LOT methodology. Complete the required items in Requirements to unlock Implementation. Use the action links on each activity to move forward. More details about LOT PHASE 4 - ONTOLOGY PUBLICATION Create Univ Grenoble Alpes 130,7 MB 2 Semantic artefacts12 JulienHomo/Climate-Change-Ontology OWL ontology • Current LOT phase: Requirements • Updated about 2 hours Introduction to LUMEN LUMEN | LUMIS https://lumis.lumenproject.eu powered by Version 1.1.12 About |Legal notice|FAQ|Contact Julien Homo DocsWorkspace Define URI strategy Check for existing artefacts Declare source & licence Add competency questions Validate minimum metadata REQUIREMENTS Edit in WebProtégé Edit in VocBench Synchronise with Git Run SHACL validation Run quality checks Manage labels & languages Create mappings Convert / export formats IMPLEMENTATION PUBLICATION MAINTENANCE Artefact metadata Artefact files Current LOT status Recent activities FAIRness overview OVERVIEW This view lists recent actions performed through LUMIS on this artefact, with status and quick links to continue or fix issues. Only operations triggered from LUMIS are recorded (no external tool logs). Time (UTC) Level LOT phase Action Actor Status Evidence / Details 2025-08-27 10:42:18 INFO Implementation Run quality checks (OOPS!) LUMIS Bot Success 2 critical, 5 minor issues • Report rep_6ae2 2025-08-27 10:32:01 WARN Publication Publish to OntoPortal Julien Homo Blocked Pre-publish checklist failed: license missing 2025-08-27 10:15:34 INFO Implementation Run SHACL validation LUMIS Bot Success 12 450 triples checked • 0 violations • Duration 2.1s 2025-08-27 09:58:22 INFO Requirements Edit metadata (license) Julien Homo Success License updated — CC0-1.0 (was CC-BY-4.0) 2025-08-27 09:40:09 INFO Requirements Add competency questions Julien Homo Success +3 CQs (IDs: CQ-01..03) 2025-08-26 16:20:11 INFO Implementation Create mappings (SKOS align) Julien Homo Success climate:HeatWave exactMatch who:HeatwaveTerm 2025-08-26 15:55:47 INFO Implementation Manage labels & languages Julien Homo Success Added en, fr labels on 18 classes 2025-08-26 15:32:10 INFO Implementation Synchronise with Git (PR-based) LUMIS Bot Success PR #17 opened on main • 5 files changed (+42/-12) 2025-08-26 15:05:03 ERROR Implementation Synchronise with Git (push) LUMIS Bot Failed Permission denied on repo • Ref main 2025-08-26 11:12:55 INFO Requirements Check for existing artefacts Julien Homo Success 4 candidates found (EarthPortal ×3, LOV ×1) 2025-08-25 18:03:41 INFO Publication Pre-publish checklist LUMIS Bot Failed Missing: License, PID policy • 2/6 checks passed View more logs Create Univ Grenoble Alpes 130,7 MB 2 Semantic artefacts12 JulienHomo/Climate-Change-Ontology OWL ontology • Current LOT phase: Requirements • Updated about 2 hours Introduction to LUMEN LUMEN | LUMIS https://lumis.lumenproject.eu powered by Version 1.1.12 About |Legal notice|FAQ|Contact Create Julien Homo DocsWorkspace Univ Grenoble Alpes 130,7 MB 2 Semantic artefacts12 JulienHomo/Climate-Change-Ontology OWL ontology • Current LOT phase: Requirements • Updated about 2 hours Define URI strategy Check for existing artefacts Declare source & licence Add competency questions Validate minimum metadata REQUIREMENTS Edit in WebProtégé Edit in VocBench Synchronise with Git Run SHACL validation Run quality checks Manage labels & languages Create mappings Convert / export formats IMPLEMENTATION PUBLICATION MAINTENANCE Artefact metadata Artefact files Current LOT status Recent activities FAIRness overview OVERVIEW This view aggregates FAIR assessments from multiple tools. Results are guidance, not certification. Checks run on the artefact saved in LUMIS (not on external tool logs). FINDINGS BY PRINCIPLE MULTI-TOOL PANEL RESULTS O’FAIRe score: 74/100 (F: 74 · A: 61 · I: 67 · R: 86) · See details FOOPS! score: 68/100 (F: 70 · A: 55 · I: 62 · R: 85) · See details Last run: 2025-08-27 10:22 UTC · By: Alice Durand · Run FAIRness checks Findable (F) Accessible (A) PID / stable URI policy: ⚠ Missing PID (DOI/PURL) → Register PID Indexed in relevant SAC(s): ⚠ Not published → Configure publication targets Metadata completeness: Minimum set OK (title, desc, keywords, domain) → View metadata Access protocol not declared: ⚠ Missing access info → Declare source & licence License not machine-readable: ⚠ Text only → Attach acceptance criteria Vocabulary mappings incomplete: ⚠ No alignments provided → Create mappings SHACL validation not run: ⚠ Pending structural check → Run SHACL validation Provenance missing: ⚠ No contributor metadata → Artefact metadata / Add competency questions Documentation incomplete: ⚠ Pending LODE documentation → Generate doc site Reusable (R) Interoperable (I) Introduction to LUMEN LUMEN | LUMIS https://lumis.lumenproject.eu powered by Julien Homo DocsWorkspace Create Univ Grenoble Alpes 130,7 MB 2 Semantic artefacts12 JulienHomo/Climate-Change-Ontology OWL ontology • Current LOT phase: Requirements • Updated about 2 hours Version 1.1.12 About |Legal notice|FAQ|Contact Define URI strategy Check for existing artefacts Declare source & licence Add competency questions Validate minimum metadata REQUIREMENTS IMPLEMENTATION PUBLICATION MAINTENANCE Artefact metadata Artefact files Current LOT status Recent activities FAIRness overview OVERVIEW This view aggregates FAIR assessments from multiple tools. Results are guidance, not certification. Checks run on the artefact saved in LUMIS (not on external tool logs). FINDINGS BY PRINCIPLE MULTI-TOOL PANEL RESULTS O’FAIRe score: 74/100 (F: 74 · A: 61 · I: 67 · R: 86) · See details FOOPS! score: 68/100 (F: 70 · A: 55 · I: 62 · R: 85) · See details Last run: 2025-08-27 10:22 UTC · By: Alice Durand · Run FAIRness checks Findable (F) Accessible (A) PID / stable URI policy: ⚠ Missing PID (DOI/PURL) → Register PID Indexed in relevant SAC(s): ⚠ Not published → Configure publication targets Metadata completeness: Minimum set OK (title, desc, keywords, domain) → View metadata Access protocol not declared: ⚠ Missing access info → Declare source & licence License not machine-readable: ⚠ Text only → Attach acceptance criteria Vocabulary mappings incomplete: ⚠ No alignments provided → Create mappings SHACL validation not run: ⚠ Pending structural check → Run SHACL validation Provenance missing: ⚠ No contributor metadata → Artefact metadata / Add competency questions Documentation incomplete: ⚠ Pending LODE documentation → Generate doc site Reusable (R) Interoperable (I) Edit in WebProtégé Edit in VocBench Synchronise with Git Run SHACL validation Run quality checks Manage labels & languages Create mappings Convert / export formats You are leaving LUMIS Edits will now take place in an external tool. LUMIS cannot track individual actions performed inside this tool. Changes will only be visible in LUMIS once you save and synchronize the artefact back. OK Don’t worry, once your edits are saved, LUMIS will automatically detect the changes and help you continue your workflow smoothly. Do not show this again