@cthoyt@scholar.social

Charles Tapley Hoyt @cthoyt@scholar.social

· 2mo ago

I have an opening in my group at RWTH Aachen University for a research internship for a bachelor or master's student in chemistry or computer science who would like to learn about cheminformatics methods in catalyst design for plastics recycling

more info: https://zenodo.org/records/20758266

#cheminformatics #circulareconomy #recycling #chemistry #internship #informatics #inorganic

Zenodo

Research Internship Opportunity - Initial application of cheminformatics methods for bioinorganic catalyst design

The Chair of Bioinorganic Chemistry in the Institute of Inorganic Chemistry at RWTH Aachen University is offering a research internship opportunity in Summer/Fall 2026 for bachelor's or master's students interested in exploring the intersection between chemistry and informatics. The flyer is attached to this Zenodo record. This research internship will be supervised by Dr. Charles Tapley Hoyt within the Herres-Pawlis group. Prior knowledge in programming is preferred, but not required for studen

2

0

18

0

Charles Tapley Hoyt @cthoyt@scholar.social

· 3mo ago

a blog post on comparing overlapping SSSOM curations from two different curators, as part of @NFDI4Chem@nfdi.social

https://cthoyt.com/2026/06/19/comparing-sssom.html

#sssom #semanticweb #owl #ontologies

Biopragmatics

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 man

3

0

2

0

Charles Tapley Hoyt @cthoyt@scholar.social

· 8mo ago

I blogged about software I wrote for efficiently downloading and querying @opencitations@scicomm.xyz in bulk

📖 blog: https://cthoyt.com/2026/02/10/opencitations-client.html

💽 code: https://github.com/cthoyt/opencitations-client

#opencitations #bibliometrics #opensource #python #knowledgegraphs

Biopragmatics

Efficient Bulk Access to Citations in OpenCitations

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. This post describes the opencitations-client package which wraps the OpenCitations API and implements an automated pipeline for locally downloading, caching, and accessing OpenCitations in bulk.

5

0

1

0

Charles Tapley Hoyt @cthoyt@scholar.social

· 10mo ago

Replying to

@deNBI @dalia a big output here was the development of the OERbservatory Python package (https://github.com/data-literacy-alliance/oerbservatory) which serves as an interoperability hub with the DALIA, TeSS, and Schemas.org data models for open educational resources (OERs), learning materials, and later, learning paths

GitHub

GitHub - data-literacy-alliance/oerbservatory: An interoperability layer for open educational resources and learning materials

An interoperability layer for open educational resources and learning materials - data-literacy-alliance/oerbservatory

7

0

5

0

Charles Tapley Hoyt @cthoyt@scholar.social

· 6mo ago

that feeling when someone sends a pull request that includes modifications to turn off linter checks they didn't pass

3

0

1

0

Charles Tapley Hoyt @cthoyt@scholar.social

· 5mo ago

Replying to

@janmartinkeil@mstdn.social @helmholtz_hmc@helmholtz.social maybe you want to add in using @bioregistry@hachyderm.io to make sure all of the prefixes defined at the top are standardized

2

3

0

Charles Tapley Hoyt @cthoyt@scholar.social

· 5mo ago

do i just dislike the font that AI-generated (scientific) images use?

Is it that I can see the kerning is bad?

Or do I just have disdain that they are AI-generated?

2

4

1

0

Charles Tapley Hoyt @cthoyt@scholar.social

· 5mo ago

Replying to

@anja_g_werder @nfdi4objects @nfdi4culture @Textplus @klassikstiftung @textgrid it would be on brand if each mug had its own PID

2

0

Charles Tapley Hoyt @cthoyt@scholar.social

· 6mo ago

SSSOM now specifies an algorithm for hashing records (i.e., rows in a SSSOM TSV file) to support interoperability across implementations and make semantic mappings more FAIR

📖 https://mapping-commons.github.io/sssom/spec-support-hashing

Implementations are already available in SSSOM-Java and sssom-pydantic

huge thanks to @dgouttegattat for leading the development of this part of the SSSOM spec!

#sssom #owl #semanticweb #obo #fair

mapping-commons.github.io

2

0

3

0

Charles Tapley Hoyt @cthoyt@scholar.social

· 6mo ago

RE: https://sigmoid.social/@osma/116328364922932251

cool stuff from the SKOS and SKOSMOS crew :)

sigmoid.social

Osma Suominen: "I made Super Finto - a novel way of exploring and…" - Sigmoid Social

2

0

2

0

Charles Tapley Hoyt @cthoyt@scholar.social

· 5mo ago

Replying to

@khinsen thanks for sharing

1

0

Charles Tapley Hoyt @cthoyt@scholar.social

· 5mo ago

Replying to

@Floppy @andrewnez which toolchain is appropriate if we treated people as markdown files? Should I YOLO and just push to main? Should I use a linter that reports erorrs? Or a formatter that fixes them?

1

0

Charles Tapley Hoyt @cthoyt@scholar.social

· 5mo ago

Replying to

@meanmicio@todon.eu @biocurator@genomic.social cool! for some context, here are our first two episodes on YouTube: https://www.youtube.com/playlist?list=PLYM0tkKvhlX54EMQGIbAOOhMKlDDPF21P and this is more or less the question list that we go through: https://cthoyt.com/2026/03/03/curate-this.html have a look and if you're still interested let's take discussion to email (cthoyt@gmail.com)

YouTube

Curate This!

International Society for Biocuration

1

0

Charles Tapley Hoyt @cthoyt@scholar.social

· 5mo ago

Replying to

@andrewnez i have the same sentiment. In my job, I'm often trying to integrate different scientific databases that all have pretty high overlap, but aren't quite similar enough to integrate without writing some code as an abstraction between them (mostly for drug discovery/medicine)

1

0

Charles Tapley Hoyt @cthoyt@scholar.social

· 5mo ago

Replying to

@meanmicio@todon.eu @EUCommission@ec.social-network.europa.eu agree with the sentiment, but I can't help notice... what are you curating back there? want to show us how this works on the @biocurator@genomic.social podcast? we did 2 episodes so far where we interviewed people about how they do curation

1

3

0

Charles Tapley Hoyt @cthoyt@scholar.social

· 6mo ago

Astral (makers of uv and ruff) will be acquired by OpenAI (https://openai.com/index/openai-to-acquire-astral) 😐

#python

OpenAI

OpenAI to acquire Astral

Accelerates Codex growth to power the next generation of Python developer tools

1

5

0

Charles Tapley Hoyt @cthoyt@scholar.social

· 6mo ago

Replying to

@sethmlarson@mastodon.social thanks for posting this! i gave some feedback I think you already saw :)

1

0

Charles Tapley Hoyt @cthoyt@scholar.social

· 7mo ago

RE: https://mastodon.social/@sethmlarson/116229292847984092

I just added a human.json to my blog too! I like writing and creating and won't start offloading that to AI anytime soon.

commit: https://github.com/cthoyt/cthoyt.github.io/commit/9bae6226153749ba966fcb1f657f0c913c4ecad4

mastodon.social

Seth Larson: "Probably going to implement this for my website, …" - Mastodon

1

0

Charles Tapley Hoyt @cthoyt@scholar.social

· 7mo ago

RE: https://genomic.social/@biocurator/116165946498006598

lots of work went into planning the virtual conference series this year. please join, especially if you're not in the bio- part of the curation and FAIR data world to have cross-disciplinary exchange!

genomic.social

Int Soc Biocuration: "we're hosting our next virtual conference series …" - genomic.social

1

0

Charles Tapley Hoyt @cthoyt@scholar.social

· 8mo ago

Replying to

@cas@social.treehouse.systems I guess the question is what percentage of those would be interested in taking up more responsibility. I can imagine that's a big ask for a community that's also busy with their own things, and until now were happy that your component in their ecosystem was taken care of just for context, I am thinking about similar things, but for much smaller academic projects with a smaller pool of more busy people 🙃

1

0

Charles Tapley Hoyt @cthoyt@scholar.social

· 34mo ago

Replying to

@hynek@mastodon.social I really enjoyed that, thanks. Will try using it in my next app!

1

0

Charles Tapley Hoyt @cthoyt@scholar.social

· 5mo ago

Replying to

@janmartinkeil@mstdn.social for context, the file you pointed to is the curation file, which has all sorts of stuff that aren't needed for consumers

0

Charles Tapley Hoyt @cthoyt@scholar.social

· 8mo ago

Replying to

@cas I'm curious how many external contributors you already have / how consistent they are?

0

3

0

Charles Tapley Hoyt @cthoyt@scholar.social

· 3mo ago

RE: https://mastodon.social/@egonw/116753932826141631

my biocurator blood makes me a sucker for doing more curation to make metadata completeness numbers go up

@rogue_scholar@wisskomm.social is there documentation somewhere on how to encode metadata in my posts to get my ORCiD, ROR, and other metadata propagated correctly?

mastodon.social

Egon Willigh☮gen 🟥: "Rogue Scholar (@rogue_scholar@wisskomm.social) la…" - Mastodon

0

2

0

Charles Tapley Hoyt @cthoyt@scholar.social

· 6mo ago

Replying to

@nedbat@hachyderm.io publish it? it would be cool to have a "stumbleupon" -like thing that picks a random human website to show you

0

2

0

Charles Tapley Hoyt @cthoyt@scholar.social

· 5mo ago

Replying to

@rodlux@maly.io welcome back !

0

1

0

Charles Tapley Hoyt @cthoyt@scholar.social

· 6mo ago

Replying to

@jonafato@mastodon.social you should check out @andrewnez@mastodon.social on fedi and his blog, he's been writing about this topic a lot in the last few months

0

3

0

Charles Tapley Hoyt @cthoyt@scholar.social

· 5mo ago

Replying to

@janmartinkeil@mstdn.social You'll probably want to use the data dump from https://w3id.org/biopragmatics/bioregistry/registry.json (if you want to get reconciliation for prefix synonyms) or the JSON-LD context from https://github.com/biopragmatics/bioregistry/raw/refs/heads/main/exports/contexts/bioregistry.context.jsonld (if you just want to check if valid) all of the outputs are CC0. There's also the Python package built around it, in case you want to reuse validation code

w3id.org

0

1

0

Charles Tapley Hoyt @cthoyt@scholar.social

· 5mo ago

Replying to

@dgouttegattat it's all three probably plus some other things I am noticing subconsciously

0