Biopragmatics

A resolver is a web application that returns a redirect response for the uniform resource identifier (URI) expansion of a compact URI (CURIE).

This post describes how I extended the work in my previous post that axiomatizes neutron numbers and nucleon numbers for isotopes that appear in ChEBI as children of atom terms, then materializes isotope (same atomic number), isotone (same neutron number),

I submitted an abstract to the 3rd Base4NFDI User Conference (UC4B2026) on behalf of the NFDI Section Metadata Working Group for Ontology Harmonization and Mapping describing the current uses and future prospects for the Semantic Farm throughout the NFDI…

This post describes how I produced a novel ontology module that axiomatizes the atomic numbers for ChEBI terms representing atoms (i.e., subclasses of CHEBI:33250) using subclass expressions with data restrictions, and the ROBOT template magic that made it

This post describes several complementary workflows for reviewing semantic mappings in the Simple Standard for Sharing Ontological Mappings (SSSOM) generated either by manual curation or (semi-)automated methods.

This is the second of a two-part blog post on the past and future of automated evaluation of predicted semantic mappings.

This is the first of a two-part blog post on the past and future of automated evaluation of predicted semantic mappings.

The Simple Standard for Sharing Ontological Mappings (SSSOM) specifies a transformation from its data model to the to Web Ontology Language (OWL) its documentation.

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).

Generative artificial intelligence, large language models (LLMs), and agentic artificial intelligence have become unavoidable topics of conversation for programmers and scientists alike.

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 labor…

The data model in PyOBO closely resembles the Web Ontology Language (OWL) and macros in the OBO Flat File format.

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, and semapv:MappingChaining.

The 7th NFDI4Chem consortium meeting took place last week in Jena.

While researchers typically communicate their work through poster presentations, oral presentations, and written communication, programmers often give (live) demonstrations.

OpenCitations aggregates and deduplicates bibliographic information from CrossRef, Europe PubMed Central, and other sources to construct a comprehensive, open index of citations between scientific works.

There are many challenges associated with the curation, publication, acquisition, and usage of semantic mappings.

Data and knowledge originating from heterogeneous sources often use heterogeneous controlled vocabularies and/or ontologies for annotating named entities.

JSKOS (JSON for Knowledge Organization Systems) is a JSON-based data model for representing terminologies, thesauri, classifications, and other semantic artifacts.

At the 4th Ontologies4Chem Workshop in Limburg an der Lahn, I proposed an initial crosswalk between the Simple Standard for Sharing Ontological Mappings (SSSOM) and the Wikidata semantic mapping data model.

LinkML enables defining data models and data schemas in YAML informed by semantic web best practices.

Here are the books I read in 2025.

Annotating the literature with mentions of key concepts from a given domain is often the first step towards extracting more substantial structured knowledge.

I recently attended the 4th BioHackathon Germany hosted by the German Network for Bioinformatics Infrastructure (de.NBI).

Earlier this week, a question was asked on OBO Foundry Slack on where to find semantic mappings to terms in the Systematized Nomenclature of Medicine - Clinical Terms (SNOMED-CT).

This is the second of a two-part post about encoding databases as ontologies.

This is the first of a two-part post about encoding databases as ontologies.

Representing negative knowledge in the semantic web is an open problem.

At the sixth NFDI4Chem consortium meeting, Torsten Schrade from the NFDI4Culture consortium gave a lovely and whimsical talk entitled A Data Alchemist’s Journey through NFDI which explored ways that we might federate and jointly query both consortia’s kno…

I was looking at the different NFDI consortia in the Research Organization Registry (ROR), and found that the only two that have a parent relations to the NFDI (ror:05qj6w324) are NFDI4DS (ror:00bb4nn95) and MaRDI (ror:04ncnzm65).

I became aware of just while watching Hynek’s second video on uv a few months ago.

Earlier this week at the sixth NFDI4Chem consortium meeting, Torsten Schrade from the NFDI4Culture consortium gave a lovely and whimsical talk entitled A Data Alchemist’s Journey through NFDI which explored ways that we might federate and jointly query bo…

Using standard CURIE prefixes and URI prefixes in semantic web artifacts such as Resource Description Framework (RDF) promotes interoperability, enables reuse in downstream data integration, and makes data more FAIR.

I’ve recently submitted an article to the Journal of Open Source Software (JOSS) describing chembl-downloader, a Python package for automating downloading and using ChEMBL data in a reproducible way.

The Bioregistry is a database and toolchain for standardization of prefixes, CURIEs, and URIs that appear in linked (open) data.

The Bioregistry is a community-driven registry of semantic spaces and their metadata.

The Ontology Lookup Service (OLS) is now indexing dense embeddings for ontology terms constructed from term labels, synonyms, and descriptions using LLMs.

Assembling and inferring missing semantic mappings is a timely problem in biomedical data and knowledge integration.

Following the theme of my previous two posts, I’ve run into another typing conundrum where I want to unpack a pre-existing Callable into a class with Generic[P, T] where P is a parameter specification type (i.e.

I’ve been working on applying strict static typing to my Python package class-resolver and ran into an interesting way of using generics in combination with parameter specification variables (i.e., ParamSpecs).

This post describes an issue I’ve had with writing correct types when using PEP-696 defaults in typing.TypeVar.

ChEMBL periodically curates clinical trial information into its DRUG_INDICATION table.

I’ve recently worked with clinical studies from ClinicalTrials.gov and other international registries.

Here’s the books I read in 2024.

I was working on making data about scholarly conferences more FAIR and a big question crossed my mind: what are all the conference venues?

This stub post contains my notes about funding for open source software.

Brandon Sanderson has been releasing a few chapters a week of his upcoming novel, Wind and Truth, on his publisher’s website leading up to its December 6th release.

PEP 735 introduced dependency groups in packaging metadata, which are complementary to optional dependencies in that they might not correspond to features in the package, but rather be something like development or release dependencies.

Graphviz is software for graph visualization written in C.

I’m working through making a contribution to pandoc that adds first-class support for author role annotations using the Contribution Role Taxonomy (CRediT) and also outputs compliant Journal Publishing Tag Set (JATS) XML.