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React4Cat: classifying reaction via functional groups and SHACL-AF

Borgelt, Hendrik

Publisher
Zenodo
DOI
10.5281/zenodo.17831171
Repository
zenodo.org
Language
en

Abstract

Presentation given at the Ontologies4Chem Workshop 2025. Abstract: Classifying datasets based on their content is an important task for making data FAIR. In the domains of chemistry and, more specifically, the subdomain of catalysis, this is most often not a trivial task, since experiments usually lead to side reactions, which should also be documented. This is where an optimized Reac4Cat aims to ease this task by classifying datasets against established reaction databases and by comparing and classifying reactions based on functional group chemistry. To facilitate this, classic ontology logic is not sufficient. Therefore, an additional classifying mechanism based on SHACL’s advanced feature set is implemented, using SAPRQL-based construct queries to establish new relations and add an extra layer of logic. --- This research was funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation), grant number 441926934 (NFDI4Cat).

Full text

1 Shaping the Digital Future of Catalysis React4Cat Visit Our Website nfdi4cat.org Limburg | Wednesday, 12 November 2025 classifying reaction via functional groups and SHACL-AF 2 Topics 1. Classifying catalysis data from experiments „Digital Agent” as added value for researchers 2. Design Pattern extensions and SHACL-Shapes for existing ontologies → Reac4Cat’s Design patterns as additions to RXMO? → SHACL shape documentation Hendrik Borgelt | Limburg | Wednesday, 12 November 2025 3 Introduction Reaction Classification Laboratory Reality vs Theoretical Background: “5 Liters of Isoamylacetate react in an aerated reactor after half an hour to produce Isoamylol” Stoichiometrically correct Ontology Representation Main reaction Consecutive reaction Isoamyl acetate Isoamylol Isoamyl aldehyde Example Reaction: We need ways to classify even semantically incorrect representations ! Hendrik Borgelt | Limburg | Wednesday, 12 November 2025 4 Data processing and semantic enrichment Pipeline Data Extraction & Standardization Modification of the Base Ontology Semantic Enrichement through Structural Analysis Automated Analysis Options 1. Convert data into a digital representation 2. Normalize and extract functional groups 3. Generate Ontological representation 4. Reason and Classify via OWL reasoning and SHACLAdvanced Features 1. 2. 3. 4. Hendrik Borgelt | Limburg | Wednesday, 12 November 2025 5 ▪“ChEBI” extension: ▪Local classes for functional group alignment ▪Functional group fragments for modeling purposes ▪RXNO extension: Addition of specific reaction types currently missing (overspecification compared to RXNO) Isoamylol monohydric alcohols Isoamylol Ester Hydrolysis Reaction (base catalysed) Modified Class Hierarchies: [1, 2] Fat Saponification Ester hydrolysis Reaction (neutral) OH_single OH_double OH_triple Class of butanols Class of Isoamylols Class of Glycerols substances processes funct. groups monohydric alcohol dihydric alcohol trihydric alcohol Local Extension of ChEBI & RXNO Extensions only intended for this “Application-Ontology” 6 Import routes & Substructure Search Ref. Data Search for FGs Exp. Data KG pyEnzyme Regex KEGG entry Stand. Lists RD-Kit Instantiation owlready2 Hendrik Borgelt | Limburg | Wednesday, 12 November 2025 7 API request response Creating Instances and relations Reference Reaction: Hydrolysis of Isoamylacetate Reaction Instance Implementing Reactions and Structure Analysis Hendrik Borgelt | Limburg | Wednesday, 12 November 2025 8 API request response Creating Instances and relations Reference Reaction: Hydrolysis of Isoamylacetate CC(C)CCOC(=O)CCC(C)CCOC(=O)C SMILES Reaction Instance Isoamylacetat Implementing Reactions and Structure Analysis Hendrik Borgelt | Limburg | Wednesday, 12 November 2025 9 API request response Creating Instances and relations Reference Reaction: Hydrolysis of Isoamylacetate Isoamyl residue '[CH3][CH]([CH3])[CH2][C;D2]' CC(C)CCOC(=O)C Isoamylacetat CC(C)CCOC(=O)C SMILES SMARTS Reaction Instance Implementing Reactions and Structure Analysis Hendrik Borgelt | Limburg | Wednesday, 12 November 2025 16 How do I Document SHACL Logic SHACL-Advanced Feature Inferencing Shapes are basically equivalent to a design pattern ▪Should I document it as metadata in the Ontology? ▪In the Ontology Documentation/Tutorial? ▪Should SHACL Shapes get their own standalone Documentation? Hendrik Borgelt | Limburg | Wednesday, 12 November 2025 17 linkedin.com/company/nfdi4cat [email protected] Would you like to exchange ideas or become a part of the community? www.nfdi4cat.org Dr. Sara Espinoza Phone +49-69-7564-354 Email sara.espinoz[email protected] Melusine Billig Phone +49-69-7564-524 Email [email protected] @[email protected]