Tags

ARKs

Re-implementing the N2T ARK Resolver Apr 11, 2023

BEL

Referring to SARS-CoV-2 Proteins in BEL Sep 17, 2020
A Reading List of Academic Articles using the Biological Expression Language (BEL) May 22, 2020
A Listing of Publicly Available Content in the Biological Expression Language (BEL) Apr 30, 2020
An Incomplete History of Selventa and the Biological Expression Language (BEL) Apr 28, 2020

BioPortal

Extracting Semantic Mappings from BioPortal in SSSOM Nov 23, 2025

BiomarkerKB

The Bioregistry and BiomarkerKB Aug 22, 2025

Bioregistry

Validating Prefix Maps in LinkML Schemas Jan 6, 2026
Machine-Actionable Training Materials at BioHackathon Germany 2025 Dec 9, 2025
Exploring an unfamiliar SPARQL endpoint with the Bioregistry - a case study from NFDI4Culture Sep 11, 2025
Validating the FAIRness of knowledge graphs and ontologies in RDF using the Bioregistry Sep 4, 2025
Measuring the impact of the Bioregistry Aug 22, 2025
The Bioregistry and BiomarkerKB Aug 22, 2025
Semantic Pydantic Jan 10, 2024
Resources masquerading as OBO Foundry ontologies Mar 11, 2023
Compliance of Bioregistry Prefixes to the W3C Standard Jan 11, 2023
Global Core Biodata Resources in the Bioregistry Dec 19, 2022

CI/CD

Switching from using Tox to Just Sep 21, 2025

CURIEs

Validating Prefix Maps in LinkML Schemas Jan 6, 2026
Machine-Actionable Training Materials at BioHackathon Germany 2025 Dec 9, 2025
Validating the FAIRness of knowledge graphs and ontologies in RDF using the Bioregistry Sep 4, 2025
Measuring the impact of the Bioregistry Aug 22, 2025
Re-implementing the N2T ARK Resolver Apr 11, 2023
Idiomatic conversion between URIs and compact URIs Jan 10, 2023
What's a CURIE, and Why You Should be Using Them Sep 14, 2021

ChEBI

The EFO_ID column in ChEMBL's drug indications table isn't what you think it is Apr 17, 2025
Data Modeling and Integration with Clinical Trials Jan 23, 2025

ChEMBL

A historical analysis of ChEMBL Aug 26, 2025
The EFO_ID column in ChEMBL's drug indications table isn't what you think it is Apr 17, 2025
Reproducibly Loading the ChEMBL Relational Database Aug 5, 2021
Reproducibly Loading the ChEMBL SDF Aug 4, 2021

ClinicalTrials.gov

Data Modeling and Integration with Clinical Trials Jan 23, 2025

Cookiecutter

Dependency Groups and ReadTheDocs Nov 19, 2024

Disease Ontology

Data Modeling and Integration with Clinical Trials Jan 23, 2025

EFO

The EFO_ID column in ChEMBL's drug indications table isn't what you think it is Apr 17, 2025

Experimental Factor Ontology

The EFO_ID column in ChEMBL's drug indications table isn't what you think it is Apr 17, 2025

FastAPI

Semantic Pydantic Jan 10, 2024

GO

The EFO_ID column in ChEMBL's drug indications table isn't what you think it is Apr 17, 2025

Gene Ontology

The EFO_ID column in ChEMBL's drug indications table isn't what you think it is Apr 17, 2025

GraphViz

Building Graphviz when installing PyGraphviz Nov 5, 2024

HGNC

Databases as Ontologies Part 2 - A Case Study with HGNC Oct 14, 2025

Haskell

Some Haskell I Tried to Write Sep 26, 2024

IRIs

Validating the FAIRness of knowledge graphs and ontologies in RDF using the Bioregistry Sep 4, 2025
Measuring the impact of the Bioregistry Aug 22, 2025
Idiomatic conversion between URIs and compact URIs Jan 10, 2023

International Society of Biocuration

International Society of Biocuration Presents: Curate This! Mar 3, 2026
Discussions and Follow-ups from Biocuration 2024 Mar 11, 2024

JATS

Some Haskell I Tried to Write Sep 26, 2024

JSKOS

Mapping from SSSOM to JSKOS Jan 15, 2026

LinkML

Validating Prefix Maps in LinkML Schemas Jan 6, 2026
Machine-Actionable Training Materials at BioHackathon Germany 2025 Dec 9, 2025

MeSH

Annotating the Literature with Named Entity Recognition Dec 19, 2025

N2T

Re-implementing the N2T ARK Resolver Apr 11, 2023

NFDI

Bridging NFDI's culture and chemistry knowledge graphs Oct 7, 2025
Exploring an unfamiliar SPARQL endpoint with the Bioregistry - a case study from NFDI4Culture Sep 11, 2025

OBI

Data Modeling and Integration with Clinical Trials Jan 23, 2025

OBO

Resources masquerading as OBO Foundry ontologies Mar 11, 2023
Ooh Na Na, What's My Name? Apr 18, 2020

ORCID

Easier ORCID Jun 8, 2024

OWL

Databases as Ontologies Part 2 - A Case Study with HGNC Oct 14, 2025
Databases as Ontologies Part 1 - Background and Software Oct 14, 2025

OntoPortal

Extracting Semantic Mappings from BioPortal in SSSOM Nov 23, 2025

PHP

Programmatic Access to a Wordpress User List Sep 20, 2024

PIDs

Re-implementing the N2T ARK Resolver Apr 11, 2023

Pandoc

Some Haskell I Tried to Write Sep 26, 2024

PubMed

Annotating the Literature with Named Entity Recognition Dec 19, 2025

PyBEL

A Listing of Publicly Available Content in the Biological Expression Language (BEL) Apr 30, 2020

PyOBO

Annotating the Literature with Named Entity Recognition Dec 19, 2025

Pydantic

Semantic Pydantic Jan 10, 2024

Python

Switching from using Tox to Just Sep 21, 2025
I wish I could unpack Callables in Python type annotations Apr 23, 2025
Using ParamSpec with Python Generics Apr 22, 2025
A dilemma with PEP-696 default generics when using optional static typing in Python Apr 19, 2025
Dependency Groups and ReadTheDocs Nov 19, 2024
Building Graphviz when installing PyGraphviz Nov 5, 2024
Programmatic Access to a Wordpress User List Sep 20, 2024
Semantic Pydantic Jan 10, 2024
Compliance of Bioregistry Prefixes to the W3C Standard Jan 11, 2023
Idiomatic conversion between URIs and compact URIs Jan 10, 2023
Abstracting the parameters of a Machine Learning Model Feb 6, 2022
Refactoring a Machine Learning Model Feb 6, 2022
Adding Structured Data to Docstrings Feb 20, 2021

ROR

Suggesting new relations in ROR from Wikidata Sep 25, 2025

SDF

Reproducibly Loading the ChEMBL SDF Aug 4, 2021

SKOS

Mapping from SSSOM to JSKOS Jan 15, 2026
Mapping from SSSOM to Wikidata Jan 8, 2026

SPARQL

Bridging NFDI's culture and chemistry knowledge graphs Oct 7, 2025
Exploring an unfamiliar SPARQL endpoint with the Bioregistry - a case study from NFDI4Culture Sep 11, 2025

SQL

Reproducibly Loading the ChEMBL Relational Database Aug 5, 2021

SSSLM

Annotating the Literature with Named Entity Recognition Dec 19, 2025

SSSOM

Challenges with Semantic Mappings Jan 20, 2026
Semantic Mappings Enable Automated Assembly Jan 16, 2026
Mapping from SSSOM to JSKOS Jan 15, 2026
Mapping from SSSOM to Wikidata Jan 8, 2026
Extracting Semantic Mappings from BioPortal in SSSOM Nov 23, 2025

Tox

Switching from using Tox to Just Sep 21, 2025

UBERON

The EFO_ID column in ChEMBL's drug indications table isn't what you think it is Apr 17, 2025

UMLS

Unlocking UMLS Sep 1, 2023

URIs

Validating Prefix Maps in LinkML Schemas Jan 6, 2026
Machine-Actionable Training Materials at BioHackathon Germany 2025 Dec 9, 2025
Validating the FAIRness of knowledge graphs and ontologies in RDF using the Bioregistry Sep 4, 2025
Measuring the impact of the Bioregistry Aug 22, 2025
Idiomatic conversion between URIs and compact URIs Jan 10, 2023

URNs

Validating the FAIRness of knowledge graphs and ontologies in RDF using the Bioregistry Sep 4, 2025
Measuring the impact of the Bioregistry Aug 22, 2025

W3C

Compliance of Bioregistry Prefixes to the W3C Standard Jan 11, 2023

Wikidata

Mapping from SSSOM to Wikidata Jan 8, 2026
Suggesting new relations in ROR from Wikidata Sep 25, 2025
Exploring Event Venues in Wikidata Jan 17, 2025
Querying Journals and Publishers in Wikidata Jun 22, 2023
Modeling and Querying Awards in Wikidata Jun 8, 2023
Adding New Literature Sources to the Wikidata Integrator Jan 23, 2021

Wordpress

Programmatic Access to a Wordpress User List Sep 20, 2024

automation

Switching from using Tox to Just Sep 21, 2025
Downloading Audio from Soundcloud Dec 3, 2024

bert

Text-based embeddings of ontology terms Aug 4, 2025

bibliometrics

Efficient Bulk Access to Citations in OpenCitations Feb 10, 2026
Suggesting new relations in ROR from Wikidata Sep 25, 2025
A historical analysis of ChEMBL Aug 26, 2025
Exploring Event Venues in Wikidata Jan 17, 2025
Easier ORCID Jun 8, 2024
Querying Journals and Publishers in Wikidata Jun 22, 2023
Modeling and Querying Awards in Wikidata Jun 8, 2023
Connecting Preprints to Peer-reviewed Articles on Wikidata Jan 2, 2023
A First Look at OpenCheck Nov 15, 2022
Curating Publications on Wikidata Feb 12, 2022
You Should Use a Private Email on Publications Feb 6, 2022
Organizing the Public Data about a Researcher Aug 17, 2021
Adding New Literature Sources to the Wikidata Integrator Jan 23, 2021
Organizing the Public Data about your Research Organization Jan 17, 2021
Summarizing ChemRxiv Apr 15, 2020

biocuration

International Society of Biocuration Presents: Curate This! Mar 3, 2026
Discussions and Follow-ups from Biocuration 2024 Mar 11, 2024
Promoting the longevity of curated scientific resources through open code, open data, and public infrastructure Jan 3, 2023
How to Curate the INDRA Database Sep 16, 2021

bioinformatics

Inference over Semantic Mappings with SeMRA Apr 28, 2025
Current Perspectives on KGEMs in and out of Biomedicine Apr 5, 2021
Explaining MCI Conversion with Path Queries to NeuroMMSig Feb 23, 2021

biomarker

The Bioregistry and BiomarkerKB Aug 22, 2025

biopragmatics

Validating the FAIRness of knowledge graphs and ontologies in RDF using the Bioregistry Sep 4, 2025
Measuring the impact of the Bioregistry Aug 22, 2025

books

cheminformatics

A historical analysis of ChEMBL Aug 26, 2025
Reproducibility Pilot in the Journal of Cheminformatics Aug 27, 2023
Reproducibly Loading the ChEMBL Relational Database Aug 5, 2021
Reproducibly Loading the ChEMBL SDF Aug 4, 2021

chemistry

Bridging NFDI's culture and chemistry knowledge graphs Oct 7, 2025
A historical analysis of ChEMBL Aug 26, 2025

citation networks

Efficient Bulk Access to Citations in OpenCitations Feb 10, 2026

citations

Efficient Bulk Access to Citations in OpenCitations Feb 10, 2026

clinical trials

The EFO_ID column in ChEMBL's drug indications table isn't what you think it is Apr 17, 2025
Data Modeling and Integration with Clinical Trials Jan 23, 2025

code with me

How to Code with Me - Beyond Linters Sep 13, 2021
How to Code with Me - Wrapping a Flask App in a CLI Jan 11, 2021
How to Code with Me - Making a CLI Jun 11, 2020
How to Code with Me - Organizing a Package Jun 3, 2020
How to Code with Me - Flake8 Hell Apr 25, 2020
How to Fix Your Monolithic Pull Request Mar 20, 2020

controlled vocabularies

Inference over Semantic Mappings with SeMRA Apr 28, 2025

cosine similarity

Text-based embeddings of ontology terms Aug 4, 2025

cultural heritage

Bridging NFDI's culture and chemistry knowledge graphs Oct 7, 2025

culture

Bridging NFDI's culture and chemistry knowledge graphs Oct 7, 2025

curation

International Society of Biocuration Presents: Curate This! Mar 3, 2026
Explaining MCI Conversion with Path Queries to NeuroMMSig Feb 23, 2021
Pathway Relationships Dec 30, 2020
Referring to SARS-CoV-2 Proteins in BEL Sep 17, 2020
The Curation of Neurodegeneration Supporting Ontology Jun 9, 2020
The Trouble with Ontologies, or, How to Build an Ontology May 12, 2020

data integration

Data Modeling and Integration with Clinical Trials Jan 23, 2025

deep learning

Abstracting the parameters of a Machine Learning Model Feb 6, 2022
Refactoring a Machine Learning Model Feb 6, 2022

docker

Pre-loading a PostgreSQL Docker Container Aug 28, 2021

doctoral thesis

Host a Graduate Seminar Before Writing Your Thesis Feb 9, 2020

documentation

Dependency Groups and ReadTheDocs Nov 19, 2024

embeddings

Text-based embeddings of ontology terms Aug 4, 2025

environments

Building Graphviz when installing PyGraphviz Nov 5, 2024

expat

Tales from the Bonner Ausländeramt Jul 26, 2021

funding

Notes on Open Source Funding Dec 3, 2024
Long-term Funding for Small Biomedical Databases Jan 4, 2023

genes

Databases as Ontologies Part 2 - A Case Study with HGNC Oct 14, 2025
Databases as Ontologies Part 1 - Background and Software Oct 14, 2025

graph database

Data Modeling and Integration with Clinical Trials Jan 23, 2025

graph query

Data Modeling and Integration with Clinical Trials Jan 23, 2025

identifier schema

Validating the FAIRness of knowledge graphs and ontologies in RDF using the Bioregistry Sep 4, 2025
Measuring the impact of the Bioregistry Aug 22, 2025

identifiers

Validating the FAIRness of knowledge graphs and ontologies in RDF using the Bioregistry Sep 4, 2025
Measuring the impact of the Bioregistry Aug 22, 2025

indra

How to Curate the INDRA Database Sep 16, 2021

interoperability

Mapping from SSSOM to JSKOS Jan 15, 2026
Mapping from SSSOM to Wikidata Jan 8, 2026

just

Switching from using Tox to Just Sep 21, 2025

knowledge graphs

Challenges with Semantic Mappings Jan 20, 2026
Semantic Mappings Enable Automated Assembly Jan 16, 2026
Representing Negative Knowledge Oct 7, 2025
Bridging NFDI's culture and chemistry knowledge graphs Oct 7, 2025
Data Modeling and Integration with Clinical Trials Jan 23, 2025
Scoring Inverse Triples Dec 11, 2020
Generating Testing Knowledge Graphs with Literals Dec 7, 2020
Encoding Biology in Knowledge Graphs Jan 23, 2020

lexica

Ooh Na Na, What's My Name? Apr 18, 2020

longevity

Long-term Funding for Small Biomedical Databases Jan 4, 2023

machine learning

Abstracting the parameters of a Machine Learning Model Feb 6, 2022
Refactoring a Machine Learning Model Feb 6, 2022
Machine Learning Needs More Generators Aug 18, 2021

mappings

Mapping from SSSOM to JSKOS Jan 15, 2026
Mapping from SSSOM to Wikidata Jan 8, 2026
Inspector Javert's Xref Database Apr 19, 2020

medical subject headings

Annotating the Literature with Named Entity Recognition Dec 19, 2025

meta

Biosemantics vs. Biopragmatics Jan 22, 2020

music

The Representatives of Monkey Jack - German Battle of the Bands Finale Mar 29, 2023

mypy

I wish I could unpack Callables in Python type annotations Apr 23, 2025
Using ParamSpec with Python Generics Apr 22, 2025
A dilemma with PEP-696 default generics when using optional static typing in Python Apr 19, 2025

named entity normalization

Annotating the Literature with Named Entity Recognition Dec 19, 2025

named entity recognition

Annotating the Literature with Named Entity Recognition Dec 19, 2025

natural language processing

Annotating the Literature with Named Entity Recognition Dec 19, 2025

nlp

How to Curate the INDRA Database Sep 16, 2021

ontologies

Inference over Semantic Mappings with SeMRA Apr 28, 2025
Data Modeling and Integration with Clinical Trials Jan 23, 2025
Resources masquerading as OBO Foundry ontologies Mar 11, 2023

ontology

Databases as Ontologies Part 2 - A Case Study with HGNC Oct 14, 2025
Databases as Ontologies Part 1 - Background and Software Oct 14, 2025
Text-based embeddings of ontology terms Aug 4, 2025
Pre-loading a PostgreSQL Docker Container Aug 28, 2021
Pathway Relationships Dec 30, 2020
The Curation of Neurodegeneration Supporting Ontology Jun 9, 2020
The Trouble with Ontologies, or, How to Build an Ontology May 12, 2020

ontology merging

Inference over Semantic Mappings with SeMRA Apr 28, 2025

open data

Exploring Event Venues in Wikidata Jan 17, 2025

open source

Notes on Open Source Funding Dec 3, 2024

organizations

Suggesting new relations in ROR from Wikidata Sep 25, 2025

packaging

Switching from using Tox to Just Sep 21, 2025
Dependency Groups and ReadTheDocs Nov 19, 2024

philosophy

Promoting the longevity of curated scientific resources through open code, open data, and public infrastructure Jan 3, 2023

prefix maps

Validating Prefix Maps in LinkML Schemas Jan 6, 2026
Machine-Actionable Training Materials at BioHackathon Germany 2025 Dec 9, 2025

prefixes

Compliance of Bioregistry Prefixes to the W3C Standard Jan 11, 2023
Idiomatic conversion between URIs and compact URIs Jan 10, 2023

programming

Abstracting the parameters of a Machine Learning Model Feb 6, 2022
Refactoring a Machine Learning Model Feb 6, 2022
The Official Rules of Python Packaging Speedrunning Jan 24, 2022

publishing

Some Haskell I Tried to Write Sep 26, 2024

pykeen

Pythagorean Mean Rank Metrics Apr 19, 2021
Current Perspectives on KGEMs in and out of Biomedicine Apr 5, 2021
Scoring Inverse Triples Dec 11, 2020
Generating Testing Knowledge Graphs with Literals Dec 7, 2020

reading

Downloading Audio from Soundcloud Dec 3, 2024

reproducibility

Data Modeling and Integration with Clinical Trials Jan 23, 2025
Unlocking UMLS Sep 1, 2023
Reproducibility Pilot in the Journal of Cheminformatics Aug 27, 2023
Making DrugBank Reproducible Dec 14, 2020

sbert

Text-based embeddings of ontology terms Aug 4, 2025

semantic mappings

Challenges with Semantic Mappings Jan 20, 2026
Semantic Mappings Enable Automated Assembly Jan 16, 2026
Mapping from SSSOM to JSKOS Jan 15, 2026
Mapping from SSSOM to Wikidata Jan 8, 2026
Inference over Semantic Mappings with SeMRA Apr 28, 2025

semantic spaces

The Bioregistry and BiomarkerKB Aug 22, 2025

semantic web

Inference over Semantic Mappings with SeMRA Apr 28, 2025
Semantic Pydantic Jan 10, 2024
Idiomatic conversion between URIs and compact URIs Jan 10, 2023

semantics

How to Pick a Unique Prefix Dec 17, 2021
A Glossary for the Bioregistry and Biopragmatics Stack Oct 7, 2021
What's a CURIE, and Why You Should be Using Them Sep 14, 2021
Biosemantics vs. Biopragmatics Jan 22, 2020

similarity

Text-based embeddings of ontology terms Aug 4, 2025

snekpack

Switching from using Tox to Just Sep 21, 2025

static typing

I wish I could unpack Callables in Python type annotations Apr 23, 2025
Using ParamSpec with Python Generics Apr 22, 2025
A dilemma with PEP-696 default generics when using optional static typing in Python Apr 19, 2025

sustainability

Long-term Funding for Small Biomedical Databases Jan 4, 2023

teaching

Host a Graduate Seminar Before Writing Your Thesis Feb 9, 2020

text mining

Annotating the Literature with Named Entity Recognition Dec 19, 2025