Technical reading list for a bioimaging + semantic web trip through Germany and Amsterdam

Tiago & AI — summary of an AI conversation that may be useful to others.

This is a reading list for a very specific kind of trip: attending a bioimaging community meeting (GerBI in Fulda), visiting friends in Jena and Bonn, and ending at SWAT4HCLS 2026 in Amsterdam. The person traveling works as a Research Software Engineer supporting the Zarr standard and bioimage metadata, does JSON-LD/RDF work, is very active on Wikidata and iNaturalist, and has a PhD on managing cell types in Wikidata. The recommendations lean technical and encyclopedic, meant for eReaders on planes and trains. Some are in German (B1/B2 level).

The list is split into two halves: general interest reading for airports and downtime, and deep technical reading that directly feeds into the work discussed at the conferences.

General interest

Plant systematics & botany

• The Plant Hunters by Carolyn Fry — history of botanical exploration, encyclopedic but readable.
• The Cabaret of Plants by Richard Mabey — cultural and scientific history of plants, touching on systematics and evolution.
• Plant Systematics: A Phylogenetic Approach by Judd et al. — the heavy reference classic. Good for dipping into on long flights.
• Die Botanik der Lust by Michael Pollan (German translation of The Botany of Desire) — four plants and how they shaped civilization. Accessible B1/B2 German.

Biodiversity & natural history

• The Song of the Dodo by David Quammen — island biogeography, extinction, and biodiversity. Long but compulsively readable.
• Das sechste Sterben by Elizabeth Kolbert (German translation of The Sixth Extinction) — biodiversity loss told through field reporting. Well-written, accessible German.
• An Immense World by Ed Yong — animal sensory biology (Umwelten). Light, encyclopedic, recent.
• Die Naturgeschichte by Pliny the Elder — the original encyclopedia of the natural world. Good abridged translations exist in both English and German.

Germany — history, culture & places

• Jena 1800: Die Republik der freien Geister by Peter Neumann — the remarkable intellectual circle in Jena around 1800 (Goethe, Schiller, Hegel, the Romantics). Perfect to read on the train to Jena. Accessible German.
• Die Vermessung der Welt by Daniel Kehlmann — a novel about Alexander von Humboldt and Carl Friedrich Gauss. Funny, clever, good B1/B2 German. Connects biodiversity and German intellectual history.
• German Genius by Peter Watson — encyclopedic (1000+ pages) history of German contributions to science, philosophy, and culture. Good for dipping in and out.

Cross-disciplinary classics

• Gödel, Escher, Bach by Douglas Hofstadter — logic, systems, patterns, creativity. Long but perfect for trains.
• The Information: A History, a Theory, a Flood by James Gleick — information theory from African drums to Wikipedia.
• Borges, Collected Fictions — short stories about infinite libraries, encyclopedias, and taxonomies. "The Library of Babel" and "Tlön, Uqbar, Orbis Tertius" are basically about classification systems and collaborative knowledge.

Deep technical reading

Zarr, OME-NGFF & bioimaging data

The Zarr v3 core specification (zarr-specs.readthedocs.io) deserves a careful end-to-end read. Not long, but the codec pipeline, sharding, and extension mechanism sections reward close attention. Print-to-PDF for eReader.

The OME-NGFF spec at ngff.openmicroscopy.org/latest defines how multiscale, multidimensional bioimaging arrays should be structured in Zarr — axes metadata, coordinate transformations, labeling. Read alongside the foundational 2021 Nature Methods paper:

• Moore et al., "OME-NGFF: a next-generation file format for expanding bioimaging data-access strategies" (Nature Methods, 2021).

The broader community companion piece:

• Moore, Basurto-Lozada, Besson et al., "OME-Zarr: a cloud-optimized bioimaging file format with international community support" (2023).

The 2024 OME-NGFF Hackathon preprint (Lüthi et al., 2025, BioHackrXiv) documents outcomes from the Zürich hackathon — workflow results and current tooling around OME-Zarr. Very fresh.

The OME-Zarr 1.0 RFC process is actively happening. The open RFCs on the ome/ngff GitHub repo (especially RFC5 on transforms) are worth reading closely. Download the markdown ahead of time.

The Zarr v3 extension registry on GitHub (zarr-developers/zarr-extensions) maps the current extension landscape. Worth reviewing for anyone working at the OME-NGFF/Zarr intersection.

Semantic web, JSON-LD, RDF & knowledge graphs

• Semantic Web for the Working Ontologist by Allemang & Hendler (3rd edition) — covers RDF 1.1, SPARQL 1.1, OWL 2, and JSON-LD. The single best book for SWAT4HCLS prep.
• Learning SPARQL by Bob DuCharme (O'Reilly) — more practical and query-focused. Pairs well with the Wikibooks SPARQL tutorial for Wikidata-specific patterns.
• The W3C JSON-LD 1.1 spec — reads surprisingly well as a document. Understanding framing, compaction, and context resolution deeply helps with metadata work. Free at w3.org.
• Knowledge Graphs by Aidan Hogan et al. (2021, MIT Press / free preprint from authors) — the rigorous encyclopedic textbook. Covers RDF, SPARQL, OWL, SHACL, knowledge graph embeddings.
• Linked Data Patterns by Leigh Dodds & Ian Davis — free online, short, practical. A pattern language for linked data design decisions.
• The SHACL specification and SHACL Advanced Features spec — increasingly important for anyone doing validation of metadata in RDF.

Wikidata, biodiversity informatics & ontologies

• Waagmeester, Stupp, Burgstaller-Muehlbacher et al., "Wikidata as a FAIR knowledge graph for the life sciences" (2020) — the canonical paper on biomedical Wikidata.
• The 2024 framework paper on integrating biomedical knowledge in Wikidata with OBO ontologies and MeSH keywords (Heliyon) — evaluates semantic alignment gaps and proposes automated enrichment methods.
• Smith et al., "The OBO Foundry: coordinated evolution of ontologies" (Nature Biotechnology, 2007) and the updated 2024 community paper — foundational for understanding how biomedical ontologies are governed.
• Ontology Engineering by Keet (Springer, free chapters online) — the best modern textbook on building and maintaining ontologies.
• The TDWG Darwin Core specification and recent papers on Wikidata for biodiversity (connecting iNaturalist, GBIF, and Wikidata).

RSE practice, FAIR software & infrastructure

• The Turing Way (book.the-turing-way.org) — community-maintained handbook for reproducible, ethical, and collaborative data science. The FAIR data and FAIR software chapters especially. Free, works well as PDF on eReader.
• The Research Software Engineering book by Matt Bannister (Chapman & Hall/CRC, free online at rse-book.github.io) — big picture overview of software carpentry-level skills, automation, and reproducibility for researchers.
• Barker et al., "Introducing the FAIR Principles for Research Software" (Scientific Data, 2022) — the FAIR4RS Principles paper. Short but foundational.
• The NFDI working group on RSE has published a layered model of RSE roles and responsibilities in research data infrastructure, connecting FAIR4RS principles with practical tooling — relevant for anyone working in the German research infrastructure ecosystem (NFDI4BIOIMAGE, GerBI).
• Software Engineering at Google (Winters, Manshreck, Wright) — free online. Not research-specific, but the chapters on code review, testing culture, and dependency management are useful for any RSE thinking about long-term maintainability.

Conference-specific prep

For GerBI in Fulda (March 16–18): the OME-NGFF specs, RFCs, and NFDI4BIOIMAGE publications are the most directly relevant reading. The hackathon preprint and the Zarr v3 extension registry map the current state of the community.

For SWAT4HCLS in Amsterdam (March 23–26): the Allemang book, the JSON-LD spec, and the Wikidata-as-FAIR-KG paper are the core prep. The BioHackathon project pitches are already posted on the SWAT4HCLS website — reviewing them on the train is good preparation for joining a hackathon project. The conference accepts short papers, position papers, demos, and posters on topics including bioimaging, biodiversity, knowledge graphs, and FAIR data.

The itinerary works well for reading progression: specs and bioimaging reading on the outbound flights, semantic web and SPARQL on the trains through Jena and Bonn, arrive in Amsterdam with context for the hackathon.