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"Abstracting the parameters of a Machine Learning Model", "url": "https://cthoyt.com/2022/02/06/model-abstraction.html", "published_at": "2022-02-06T18:00:00+00:00" }, { "id": "01a08765-4dab-73ed-aa17-d11c32d23749", "title": "Refactoring a Machine Learning Model", "url": "https://cthoyt.com/2022/02/06/model-refactoring.html", "published_at": "2022-02-06T15:45:00+00:00" }, { "id": "01a08765-4dab-73ed-aa17-d11c33398b3d", "title": "The Official Rules of Python Packaging Speedrunning", "url": "https://cthoyt.com/2022/01/24/packaging-speedrunning.html", "published_at": "2022-01-24T00:30:00+00:00" }, { "id": "01a08765-4dab-73ed-aa17-d11c33ed4cd1", "title": "How to Pick a Unique Prefix", "url": "https://cthoyt.com/2021/12/17/unique-prefix-picking.html", "published_at": "2021-12-17T13:17:00+00:00" }, { "id": "01a08765-4dab-73ed-aa17-d11c34b19089", "title": "A Glossary for the Bioregistry and Biopragmatics Stack", "url": "https://cthoyt.com/2021/10/07/biopragmatics-glossary.html", "published_at": "2021-10-07T13:26:00+00:00" }, { "id": "01a08765-4dab-73ed-aa17-d11c3561916e", "title": "How to Curate the INDRA Database", "url": "https://cthoyt.com/2021/09/16/curating-indra.html", "published_at": "2021-09-16T12:30:00+00:00" }, { "id": "01a08765-4dab-73ed-aa17-d11c358f2005", "title": "What’s a CURIE, and Why You Should be Using Them", "url": "https://cthoyt.com/2021/09/14/curies.html", "published_at": "2021-09-14T08:47:00+00:00" }, { "id": "01a08765-4dab-73ed-aa17-d11c35a22d0d", "title": "How to Code with Me - Beyond Linters", "url": "https://cthoyt.com/2021/09/13/beyond-linters.html", "published_at": "2021-09-13T23:18:00+00:00" }, { "id": "01a08765-4dab-73ed-aa17-d11c35dff40c", "title": "Pre-loading a PostgreSQL Docker Container", "url": "https://cthoyt.com/2021/08/28/biolookup-docker.html", "published_at": "2021-08-28T14:44:00+00:00" }, { "id": "01a08765-4dab-73ed-aa17-d11c3640cede", "title": "Machine Learning Needs More Generators", "url": "https://cthoyt.com/2021/08/18/streaming.html", "published_at": "2021-08-18T11:21:00+00:00" }, { "id": "01a08765-4dab-73ed-aa17-d11c3651986d", "title": "Organizing the Public Data about a Researcher", "url": "https://cthoyt.com/2021/08/17/self-organization.html", "published_at": "2021-08-17T11:21:00+00:00" }, { "id": "01a08765-4dab-73ed-aa17-d11c36de43d7", "title": "Reproducibly Loading the ChEMBL Relational Database", "url": "https://cthoyt.com/2021/08/05/taming-chembl-sql.html", "published_at": "2021-08-05T14:36:00+00:00" }, { "id": "01a08765-4dab-73ed-aa17-d11c3797b6a9", "title": "Reproducibly Loading the ChEMBL SDF", "url": "https://cthoyt.com/2021/08/04/taming-chembl-sdf.html", "published_at": "2021-08-04T12:46:00+00:00" }, { "id": "01a08765-4dab-73ed-aa17-d11c37ab8c36", "title": "Tales from the Bonner Ausländeramt", "url": "https://cthoyt.com/2021/07/26/tales-from-the-auslaenderamt.html", "published_at": "2021-07-26T12:46:00+00:00" }, { "id": "01a08765-4dab-73ed-aa17-d11c3861c678", "title": "Pythagorean Mean Rank Metrics", "url": "https://cthoyt.com/2021/04/19/pythagorean-mean-ranks.html", "published_at": "2021-04-19T12:46:00+00:00" }, { "id": "01a08765-4dab-73ed-aa17-d11c39381605", "title": "Current Perspectives on KGEMs in and out of Biomedicine", "url": "https://cthoyt.com/2021/04/05/kgem-perspectives.html", "published_at": "2021-04-05T12:13:00+00:00" }, { "id": "01a08765-4dab-73ed-aa17-d11c39c94fd5", "title": "Explaining MCI Conversion with Path Queries to NeuroMMSig", "url": "https://cthoyt.com/2021/02/23/cpath-visit.html", "published_at": "2021-02-23T22:53:00+00:00" }, { "id": "01a08765-4dab-73ed-aa17-d11c3a10dc31", "title": "Adding Structured Data to Docstrings", "url": "https://cthoyt.com/2021/02/20/docdata.html", "published_at": "2021-02-20T20:12:00+00:00" }, { "id": "01a08765-4dab-73ed-aa17-d11c3af4c0c6", "title": "Adding New Literature Sources to the Wikidata Integrator", "url": "https://cthoyt.com/2021/01/23/updating-the-wikidata-integrator.html", "published_at": "2021-01-23T20:12:00+00:00" }, { "id": "01a08765-4dab-73ed-aa17-d11c3b4ee41c", "title": "Organizing the Public Data about your Research Organization", "url": "https://cthoyt.com/2021/01/17/organization-organization.html", "published_at": "2021-01-17T18:23:00+00:00" }, { "id": "01a08765-4dab-73ed-aa17-d11c3bd659bd", "title": "How to Code with Me - Wrapping a Flask App in a CLI", "url": "https://cthoyt.com/2021/01/11/click-and-flask.html", "published_at": "2021-01-11T00:14:00+00:00" }, { "id": "01a08765-4dab-73ed-aa17-d11c3c31468f", "title": "Pathway Relationships", "url": "https://cthoyt.com/2020/12/30/pathway-relationships.html", "published_at": "2020-12-30T08:00:00+00:00" }, { "id": "01a08765-4dab-73ed-aa17-d11c3caeee06", "title": "Making DrugBank Reproducible", "url": "https://cthoyt.com/2020/12/14/taming-drugbank.html", "published_at": "2020-12-14T08:00:00+00:00" }, { "id": "01a08765-4dab-73ed-aa17-d11c3ce9521d", "title": "Scoring Inverse Triples", "url": "https://cthoyt.com/2020/12/11/inverse-triple-scoring.html", "published_at": "2020-12-11T08:00:00+00:00" }, { "id": "01a08765-4dab-73ed-aa17-d11c3d7340e1", "title": "Generating Testing Knowledge Graphs with Literals", "url": "https://cthoyt.com/2020/12/07/generating-literal-datasets.html", "published_at": "2020-12-07T08:00:00+00:00" }, { "id": "01a08765-4dab-73ed-aa17-d11c3daab400", "title": "Referring to SARS-CoV-2 Proteins in BEL", "url": "https://cthoyt.com/2020/09/17/sars-cov-2-proteins-in-bel.html", "published_at": "2020-09-17T00:05:00+00:00" }, { "id": "01a08765-4dab-73ed-aa17-d11c3e1b4ed1", "title": "How to Code with Me - Making a CLI", "url": "https://cthoyt.com/2020/06/11/click.html", "published_at": "2020-06-11T15:48:00+00:00" }, { "id": "01a08765-4dab-73ed-aa17-d11c3e4a8441", "title": "The Curation of Neurodegeneration Supporting Ontology", "url": "https://cthoyt.com/2020/06/09/conso.html", "published_at": "2020-06-09T19:31:00+00:00" }, { "id": "01a08765-4dab-73ed-aa17-d11c3eb5a073", "title": "How to Code with Me - Organizing a Package", "url": "https://cthoyt.com/2020/06/03/how-to-code-with-me-organization.html", "published_at": "2020-06-03T08:00:00+00:00" } ] posts Claim your blog

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2026

Deploying a Resolver using the CURIEs Package original ↗

24 Sept 2026

Axiomatizing Nuclides in ChEBI original ↗

24 Sept 2026

Semantic Farm and the 3rd Base4NFDI User Conference original ↗

15 Sept 2026

Axiomatizing Atomic Numbers in ChEBI original ↗

4 Sept 2026

Semantic Mapping Review Workflows original ↗

27 Aug 2026

Automating the Evaluation of Predicted Semantic Mappings Part 2: A New Workflow original ↗

17 Aug 2026

Automating the Evaluation of Predicted Semantic Mappings Part 1: Opportunities for OAEI original ↗

17 Aug 2026

Mapping from SSSOM to OWL original ↗

7 Aug 2026

Standards Don’t Succeed Without Community Work original ↗

7 Aug 2026

LLM Notes and Policies original ↗

18 Jul 2026

Comparing manually curated semantic mappings in SSSOM original ↗

19 Jun 2026

A practical approach to translate OWL to SKOS original ↗

3 Jun 2026

Transparent provenance for derived semantic mappings in SSSOM original ↗

29 May 2026

Discussions at the 7th NFDI4Chem Consortium Meeting original ↗

18 May 2026

International Society of Biocuration Presents: Curate This!original ↗

3 Mar 2026

Efficient Bulk Access to Citations in OpenCitations original ↗

10 Feb 2026

Challenges with Semantic Mappings original ↗

20 Jan 2026

Semantic Mappings Enable Automated Assembly original ↗

16 Jan 2026

Mapping from SSSOM to JSKOS original ↗

15 Jan 2026

Mapping from SSSOM to Wikidata original ↗

8 Jan 2026

Validating Prefix Maps in LinkML Schemas original ↗

6 Jan 2026

Books I Read in 2025 original ↗

1 Jan 2026

2025

Annotating the Literature with Named Entity Recognition original ↗

19 Dec 2025

Machine-Actionable Training Materials at BioHackathon Germany 2025 original ↗

9 Dec 2025

Extracting Semantic Mappings from BioPortal in SSSOM original ↗

23 Nov 2025

Databases as Ontologies Part 1 - Background and Software original ↗

14 Oct 2025

Databases as Ontologies Part 2 - A Case Study with HGNC original ↗

14 Oct 2025

Bridging NFDI’s culture and chemistry knowledge graphs original ↗

7 Oct 2025

Representing Negative Knowledge original ↗

7 Oct 2025

Suggesting new relations in ROR from Wikidata original ↗

25 Sept 2025

Switching from using Tox to Just original ↗

21 Sept 2025

Exploring an unfamiliar SPARQL endpoint with the Bioregistry - a case study from NFDI4Culture original ↗

11 Sept 2025

Validating the FAIRness of knowledge graphs and ontologies in RDF using the Bioregistry original ↗

4 Sept 2025

A historical analysis of ChEMBL original ↗

26 Aug 2025

Measuring the impact of the Bioregistry original ↗

22 Aug 2025

The Bioregistry and BiomarkerKB original ↗

22 Aug 2025

Text-based embeddings of ontology terms original ↗

4 Aug 2025

Inference over Semantic Mappings with SeMRA original ↗

28 Apr 2025

I wish I could unpack Callables in Python type annotations original ↗

23 Apr 2025

Using ParamSpec with Python Generics original ↗

22 Apr 2025

A dilemma with PEP-696 default generics when using optional static typing in Python original ↗

19 Apr 2025

The EFO_ID column in ChEMBL’s drug indications table isn’t what you think it is original ↗

17 Apr 2025

Data Modeling and Integration with Clinical Trials original ↗

23 Jan 2025

Books I Read in 2024 original ↗

18 Jan 2025

Exploring Event Venues in Wikidata original ↗

17 Jan 2025

2024

Notes on Open Source Funding original ↗

3 Dec 2024

Downloading Audio from Soundcloud original ↗

3 Dec 2024

Dependency Groups and ReadTheDocs original ↗

19 Nov 2024

Building Graphviz when installing PyGraphviz original ↗

5 Nov 2024

Some Haskell I Tried to Write original ↗

26 Sept 2024

Programmatic Access to a Wordpress User List original ↗

20 Sept 2024

Easier ORCID original ↗

8 Jun 2024

Discussions and Follow-ups from Biocuration 2024 original ↗

11 Mar 2024

Semantic Pydantic original ↗

10 Jan 2024

Books I Read in 2023 original ↗

1 Jan 2024

2023

Unlocking UMLS original ↗

1 Sept 2023

Reproducibility Pilot in the Journal of Cheminformatics original ↗

27 Aug 2023

Querying Journals and Publishers in Wikidata original ↗

22 Jun 2023

Modeling and Querying Awards in Wikidata original ↗

8 Jun 2023

Re-implementing the N2T ARK Resolver original ↗

11 Apr 2023

The Representatives of Monkey Jack - German Battle of the Bands Finale original ↗

29 Mar 2023

Resources masquerading as OBO Foundry ontologies original ↗

11 Mar 2023

Compliance of Bioregistry Prefixes to the W3C Standard original ↗

11 Jan 2023

Idiomatic conversion between URIs and compact URIs original ↗

10 Jan 2023

Long-term Funding for Small Biomedical Databases original ↗

4 Jan 2023

Promoting the longevity of curated scientific resources through open code, open data, and public infrastructure original ↗

3 Jan 2023

Connecting Preprints to Peer-reviewed Articles on Wikidata original ↗

2 Jan 2023

2022

Global Core Biodata Resources in the Bioregistry original ↗

19 Dec 2022

A First Look at OpenCheck original ↗

15 Nov 2022

Curating Publications on Wikidata original ↗

12 Feb 2022

You Should Use a Private Email on Publications original ↗

6 Feb 2022

Abstracting the parameters of a Machine Learning Model original ↗

6 Feb 2022

Refactoring a Machine Learning Model original ↗

6 Feb 2022

The Official Rules of Python Packaging Speedrunning original ↗

24 Jan 2022

2021

How to Pick a Unique Prefix original ↗

17 Dec 2021

A Glossary for the Bioregistry and Biopragmatics Stack original ↗

7 Oct 2021

How to Curate the INDRA Database original ↗

16 Sept 2021

What’s a CURIE, and Why You Should be Using Them original ↗

14 Sept 2021

How to Code with Me - Beyond Linters original ↗

13 Sept 2021

Pre-loading a PostgreSQL Docker Container original ↗

28 Aug 2021

Machine Learning Needs More Generators original ↗

18 Aug 2021

Organizing the Public Data about a Researcher original ↗

17 Aug 2021

Reproducibly Loading the ChEMBL Relational Database original ↗

5 Aug 2021

Reproducibly Loading the ChEMBL SDF original ↗

4 Aug 2021

Tales from the Bonner Ausländeramt original ↗

26 Jul 2021

Pythagorean Mean Rank Metrics original ↗

19 Apr 2021

Current Perspectives on KGEMs in and out of Biomedicine original ↗

5 Apr 2021

Explaining MCI Conversion with Path Queries to NeuroMMSig original ↗

23 Feb 2021

Adding Structured Data to Docstrings original ↗

20 Feb 2021

Adding New Literature Sources to the Wikidata Integrator original ↗

23 Jan 2021

Organizing the Public Data about your Research Organization original ↗

17 Jan 2021

How to Code with Me - Wrapping a Flask App in a CLI original ↗

11 Jan 2021

2020

Pathway Relationships original ↗

30 Dec 2020

Making DrugBank Reproducible original ↗

14 Dec 2020

Scoring Inverse Triples original ↗

11 Dec 2020

Generating Testing Knowledge Graphs with Literals original ↗

7 Dec 2020

Referring to SARS-CoV-2 Proteins in BEL original ↗

17 Sept 2020

How to Code with Me - Making a CLI original ↗

11 Jun 2020

The Curation of Neurodegeneration Supporting Ontology original ↗

9 Jun 2020

How to Code with Me - Organizing a Package original ↗

3 Jun 2020