Unraveling complex biology with biological knowledge graphs. Content licensed under CC BY 4.0.

Charles Tapley Hoyt

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. I am slowly working towards updating my cookiecutter template cookiecutter-snekpack to use PEP 735. So far, uv and tox have released support - all that’s left is ReadTheDocs.

Dependency Groups and ReadTheDocs

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. This has lead me down a (losing) journey with learning the Haskell programming language, so I thought I would post a short note on a function I tried to understand.

Some Haskell I Tried to Write

Graphviz is software for graph visualization written in C. PyGraphviz provides a nice Python wrapper for it. The issue is that getting Python to know about the C headers changes every few months. I’ll try and keep this blog post updated every time there are some changes.

Building Graphviz when installing PyGraphviz

Several controlled vocabularies and ontologies that aren’t themselves OBO Foundry ontologies use unsanctioned OBO PURLs. This post is about how to use the Bioregistry to identify which resources are doing this and to give some insight into how we arrived in this situation. Background on the OBO Foundry   The OBO Foundry is a set of independent, interoperable biomedical ontologies that aspire to using shared development principles.

Resources masquerading as OBO Foundry ontologies

Today’s short post is about three SPARQL queries I wrote to get bibliometric information about journals and publishers out of Wikidata. Each of the following queries can be readily copy-pasted into the Wikidata Query Service and run in the browser.

Querying Journals and Publishers in Wikidata

I’ve just returned from the 17

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Annual International Biocuration Conference at the Indian Biological Data Centre (IBDC) in Faridabad, India.

Discussions and Follow-ups from Biocuration 2024

Using Pydantic for encoding data models and FastAPI for implementing APIs on top of them has become a staple for many Python programmers.

Semantic Pydantic

I finally got back into reading! Over winter break 2022, I started the Stormlight Archive then followed up in 2023 by reading the entirety of Brandon Sanderson’s

 Cosmere

, as well as a some other fantasy, science fiction, and literary fiction. Here’s the list.

Books I Read in 2023

Archival Resource Keys (ARKs) are flavor of persistent identifiers like DOIs, URNs, and Handles that have the benefit of being free, flexible with what metadata gets attached, and natively able to resolve to web pages. Name-to-Thing (N2T) implements a resolver for a variety of ARKs, so this blog post is about how that resolver can be re-implemented with the curies Python package. In a lot of ways, ARKs look and act like CURIEs.

Re-implementing the N2T ARK Resolver

This blog is normally about

 very serious science

, but I’m taking a break from that for the evening to advertize my band’s upcoming show on April 8

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in the SPH Music Masters Finale (aka, the German Battle of the Bands). We need your support!

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

Authorships are

The Open Researcher and Contributor Identifier (ORCID) database is an invaluable resource that supports the unambiguous identification of researchers. However, its first party data dump is too complex, verbose, and unstandardized for many use cases. This post describes open source software I wrote that automates downloading, processing, and exporting ORCID into a more usable form. I put the results on Zenodo under the CC0 license.

Easier ORCID

The International Society of Biocuration (ISB) partners with the journal Database to get discounts for its members when they publish there. This means the ISB’s executive committee needs to send a member list to the journal’s editor.

Programmatic Access to a Wordpress User List

The Unified Medical Language System (UMLS) is a widely used biomedical and clinical vocabulary maintained by the United States National Library of Medicine. However, it is notoriously difficult to access and work with due to licensing restrictions and its complex download system. In the same vein as my previous posts about DrugBank and ChEMBL, this post describes open source software I’ve developed for downloading and working with this data.

Unlocking UMLS

I was recently nominated for the International Society for Biocuration’s Excellence in Biocuration Early Career Award (results will be announced on June 14

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!). This made me curious about how to model nominations and awards on Wikidata. In this post, I’ll describe how to curate awards, nominations, recipients, and how to make SPARQL queries to get them.

Modeling and Querying Awards in Wikidata

I’ve been working on improving reproducibility in the field of cheminformatics for some time now. For example, I’ve written posts about making data from DrugBank and ChEMBL more actionable. Over the last year, I’ve been preparing a concept with the editors of the Journal of Cheminformatics on how to include an assessment of reproducibility to reviews of manuscripts submitted to the journal.

Reproducibility Pilot in the Journal of Cheminformatics

Biopragmatics

I finally got back into reading! Over winter break 2022, I started the
Stormlight Archive then followed up in 2023 by reading the entirety of
Brandon Sanderson's *Cosmere*, as well as a some other fantasy, science
fiction, and literary fiction. Here's the list.

1.  Oathbringer (Stormlight Archive \#3) by Brandon Sanderson
2.  Rhythm of War (Stormlight Archive \#4) by Brandon Sanderson
3.  The Final Empire (Mistborn \#1) by Brandon Sanderson
4.  The Well of Ascension (Mistborn \#2) by Brandon Sanderson
5.  The Hero of Ages (Mistborn \#3) by Brandon Sanderson
6.  The Alloy of Law (Mistborn \#4) by Brandon Sanderson
7.  Shadows of Self (Mistborn \#5) by Brandon Sanderson
8.  The Bands of Mourning (Mistborn \#6) by Brandon Sanderson
9.  Warbreaker by Brandon Sanderson
10. Elantris by Brandon Sanderson
11. The Shadow of the Wind (The Cemetery of Forgotten Books \#1) by
    Carlos Ruiz Zafón
12. The Angel's Game (The Cemetery of Forgotten Books \#2) by Carlos
    Ruiz Zafón
13. The Emperor's Soul by Brandon Sanderson
14. The Hope of Elantris by Brandon Sanderson
15. The Eleventh Metal by Brandon Sanderson
16. Mistborn: Secret History by Brandon Sanderson
17. Shadows for Silence in the Forests of Hell by Brandon Sanderson
18. Sixth of Dusk by Brandon Sanderson
19. White Sands by Brandon Sanderson
20. The Lost Metal (Mistborn \#7) by Brandon Sanderson
21. Edgedancer (Stormlight Archive \#2.5) by Brandon Sanderson
22. What It Means When a Man Falls from the Sky by Lesley Nneka Arimah
23. Tress of the Emerald Sea by Brandon Sanderson
24. The Prisoner of Heaven (The Cemetery of Forgotten Books \#3) by
    Carlos Ruiz Zafón
25. The Name of the Wind (The Kingkiller Chronicle \#1) by Patrick
    Rothfuss
26. The Wise Man's Fear (The Kingkiller Chronicle \#2) by Patrick
    Rothfuss
27. The Labyrinth of Spirits (The Cemetery of Forgotten Books \#4) by
    Carlos Ruiz Zafón
28. Yumi and the Nightmare Painter by Brandon Sanderson
29. Hyperion (The Hyperion Cantos \#1) by Dan Simmons
30. The Fall of Hyperion (The Hyperion Cantos \#2) by Dan Simmons
31. Dawnshard (Stormlight Archive \#3.5) by Brandon Sanderson
32. The Sunlit Man by Brandon Sanderson
33. All Systems Red (Murderbot Dairies \#1) by Martha Wells
34. Endymion (The Hyperion Cantos \#3) by Dan Simmons
35. The Rise of Endymion (The Hyperion Cantos \#4) by Dan Simmons
36. A Memory Called Empire (Teixcalaan \#1) by Arkady Martine
37. A Desolation Called Peace (Teixcalaan \#2) by Arkady Martine
38. Crime and Punishment by Fyodor Dostoevsky
39. The Strange Case of Dr. Jekyll and Mr. Hyde by Robert Louis
    Stevenson
40. Anna Karenina by Leo Tolstoy
41. Red Rising (Red Rising Saga \#1) by Pierce Brown
42. Golden Son (Red Rising Saga \#2) by Pierce Brown
43. This is How You Lose the Time War by Amal El-Mohtar and Max
    Gladstone

Cosmere moments I really enjoyed (spoilers):

1.  Every single oath (finished or not), particularly Elhokar and
    Eshonai
2.  I guessed the twist in Tress of the Emerald Sea
3.  Kelsier's not dead!
4.  Dalinar Kholin's entire character arc
5.  Wayne, Pattern, and Nightblood being hilarious
6.  Michael Kramer and Kate Reading's voices
7.  All the tidbits in Sunlit Man... I can't wait for Stormlight 5 to
    fill in some of the gaps.

Other non-Cosmere highlights (spoilers):

1.  Narrator reveal at the end of The Labyrinth of Spirits
2.  Anna Karenina's inner monologue as she commits suicide was
    devastating
3.  Rothfuss's prose is like honey
4.  The messiah arc in the second Hyperion duology is really nice. It's
    a much better version of the awful "love connects the universe"
    cliché at the end of Interstellar that actually creates plot- and
    character-driven relevance.

Disappointments:

1.  Knowing the Doors of Stone might never come out but reading
    Kingkiller Chronicle \#1 and \#2 anyway
2.  I didn't like that All Systems Red had the entire plot get resolved
    off-screen. My sisters were really hoping I'd like this book, and I
    was only neutral. I'll still give the next one a try.
3.  I missed the Year of Sanderson Kickstarter (and the hilarity of the
    announcement video). I hadn't really started until after.
4.  The Russian classics were pretty slow, but I guess that's how it
    goes.

My goal in 2024 is to read more books from different genres, especially
ones I've never touched before.
