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Origin Story & Mission

Marine biogeochemistry needs a shared vocabulary between experimentalists and modelers for cross-disciplinary work to advance the field. Yet, to integrate disciplines successfully, researchers need to be vocal about discrepancy and uncertainty, and realize caveats of how values are determined. This community-driven collection of biogeochemical output began at the BioGeoScapes modelling workshop and the following PRiMO session at Woods Hole Oceanographic Institution in September 2025. To highlight cross-discipline implications like What data was particularly helpful to inform a model? or How can a model help constrain experimental parameters?, the idea arose to create a Wiki that provided a central repository for basic information related to interdisciplinary biogeochemistry science. This emerged as a way to address needs that have arisen in conversations specifically:

• defining key terms used across disciplines
• explain types of data generated by different methods, assumptions, and potential biases
• describe different types of models, required data inputs, computational demand, and limitations

Content

The Oceancyclopedia is an encyclopedia of marine biogeochemistry, and consists of three components:

Lexicon

A dictionary with definitions from both experimentalists, observationalists, and modelers.

Data wiki

Types of data from experimental observations and how they are obtained, grouped by the process they investigate.

Primary Production

Photoautotrophy | Nitrogen Fixation | Phytoplankton C/N-Based Growth Rates | Chemoautotrophy

Secondary Production

Enzyme Activity | Growth Rate | Respiration

Nutrient Fluxes

Nitrogen | Phosphorous | Sulfur | Trace Metals | Biomineralization

Interactions

Grazing | Mixotrophy | Viruses | Allelopathy | Life cycles

Model wiki

Types of models explained grouped by the scales they function at.

Cellular scale

Flux Balance Analysis | Proteome Allocation Models | Particle Simulation | Bio Particle Simulation

Biome scale

Community Flux Balance Analysis | GENOME

Global scale

CMIP | MARBL | Darwin | AWESOME-OCIM

These pages contain definitions, limitations, context, and references.
They are populated by researchers, naming responsible authors for context and credit.

Teaching material

This was a suggestion from the BioGeoScapes leadership and we are working on incorporating it.