Through my position at RWTH Aachen University, I’m establishing academic collaborations through German, European, and international grants and developing project-based contracts for organizations with unmet business needs addressed by the semantic technologies and capabilities that I’ve developed and write about here. Privately, I can offer consulting services, speaking engagements, and training for organizations interested in these topics.
Here’s some more details about me and my research. You
can download my résumé
(single page), CV, or see
my ORCiD page at
https://orcid.org/0000-0003-4423-4370.
Content on this site is licensed as
CC BY 4.0. See
also my family recipe blog.
Recent Posts
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Automating the Evaluation of Predicted Semantic Mappings Part 2: A New Workflow
This is the second of a two-part blog post on the past and future of automated evaluation of predicted semantic mappings. This part describes the implementation of a new automated workflow for the evaluation of predicted semantic mappings that consumes arbitrary Simple Standard for Sharing Ontological Mappings (SSSOM), stratifies mappings as manually curated or predicted, then produces an evaluation for each source-target ontology pair present.
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Automating the Evaluation of Predicted Semantic Mappings Part 1: Opportunities for OAEI
This is the first of a two-part blog post on the past and future of automated evaluation of predicted semantic mappings. I describe some of the challenges and opportunities for challenges like the Ontology Alignment Evaluation Initiative (OAEI) and how they could be addressed with Simple Standard for Sharing Ontological Mappings (SSSOM), and its ecosystem. In the second part, I present a concrete implementation of a new automated evaluation system that address some of those challenges.
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Mapping from SSSOM to OWL
The Simple Standard for Sharing Ontological Mappings (SSSOM) specifies a transformation from its data model to the to Web Ontology Language (OWL) its documentation. This post is about implementing and extending that transformation in the sssom-pydantic Python package and the implications for ontology curation and maintenance, especially within the context of NFDI4Chem.
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Standards Don't Succeed Without Community Work
In March 2026, the NIH Common Fund Data Ecosystem issued a request for comments for a proposal for a knowledge graph exchange format entitled JSON Knowledge Graph Exchange Format (JKG). This post is about the burden of proposing yet another standard and highlights sage wisdom from Nico Matentzoglu about the importance of community work in pushing standards.
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LLM Notes and Policies
Generative artificial intelligence, large language models (LLMs), and agentic artificial intelligence have become unavoidable topics of conversation for programmers and scientists alike. This post comprises links to external writing about these topics from which I would like to draw inspiration when crafting my own communication and policies.
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Comparing manually curated semantic mappings in SSSOM
I am currently supporting Philip Strömert and Noura Rayya in the efforts to modernize and revitalize the Chemical Methods Ontology (CHMO) to support annotation of instrumentation used to produce experimental data captured in the Chemotion electronic laboratory notebook as part of NFDIChem. This post is about the adoption of Simple Standard for Sharing Ontological Mappings (SSSOM) to support interoperability between CHMO and other resources, and the workflow I developed to compare overlapping manual curations from different researchers.
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A practical approach to translate OWL to SKOS
The data model in PyOBO closely resembles the Web Ontology Language (OWL) and macros in the OBO Flat File format. However, some communities prefer the simplified nature of the SKOS data model compared to the highly precise (and sometimes burdensome) nature of OWL semantics. This post describes the workflow I implemented to downscale OWL to SKOS.
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Transparent provenance for derived semantic mappings in SSSOM
The Simple Standard for Sharing Ontological Mappings (SSSOM) requires semantic mappings to annotate a justification from the Semantic Mapping Vocabulary (SEMAPV) such as
semapv:ManualMappingCuration,semapv:MappingInversion, andsemapv:MappingChaining. However, SSSOM did not have a mechanism for tracking which mappings were used during inference workflows like inversion or chaining. This post is about my recent SSSOM enhancement proposal to add a new fieldderived_fromto support this. -
Discussions at the 7th NFDI4Chem Consortium Meeting
The 7th NFDI4Chem consortium meeting took place last week in Jena. This post is a summary of some of the interesting discussions I had there.
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International Society of Biocuration Presents: Curate This!
While researchers typically communicate their work through poster presentations, oral presentations, and written communication, programmers often give (live) demonstrations. I’m not aware of any technical nor practical barriers for why curators couldn’t do the same, and always wished that curators did this more often. This post is about how I planned to make this a reality by starting a podcast with the International Society for Biocuration (ISB) entitled ISB Presents: Curate This!.