ChemOrigins: A Community Curated Database For Origins Of Life Chemistry

The origin of life is one of the most compelling questions in science. While experimental prebiotic chemistry has produced a wide range of reactions and plausible pathways, the resulting data remain fragmented across numerous publications and disciplinary journals.

ChemOrigins data life cycle: from curators, who create the original annotations, to end users through the graph database and the web interface. In gray, we included some of the components of ChemOrigins, such as the data processing pipelines or the version control system that enables collaborative curation of prebiotic chemistry. — biorxiv.org

Here, we introduce ChemOrigins, (https://chemorigins.bact.wisc.edu/) an open-access, community-curated knowledge graph that organizes experimentally supported prebiotic reactions. By representing molecules, reactions, conditions, and literature sources as interconnected nodes, ChemOrigins enables modular grouping of reactions and supports complex, query-driven exploration via a graph database architecture.

We demonstrate the utility of this framework through text-based searches, reaction network expansions, and the interactive visualization of user-annotated chemical modules. Unlike generative models, ChemOrigins prioritizes curated, evidence-based content and fosters community contributions through expert annotations and a user-friendly interface.

As a structured resource, ChemOrigins is designed to complement existing chemical databases and serve as a foundation for computational, educational, and theoretical research in the origins-of-life field.

Representation of the schema employed in ChemOrigins (https://chemorigins.bact.wisc.edu/). (a) Graph highlighting the different kinds of entities that we might find represented in ChemOrigins, together with some of their attributes (e.g., temperature, SMILES, etc) and the relationships between them. (b) Graph representation of the data associated with a given reaction (shown at the top of the figure), including substrate and product molecules (blue), the conditions at which those reactions took place (in this case, we highlight the temperature), the agents that allowed that reaction (in this case, different iron associated minerals) and finally, the source of the data, which is identified by its DOI. — biorxiv.org

Example visualizations of ChemOrigins data. (a) Pathways leading to alanine in our database. We find three different pathways: a pyruvate-based pathway, a Strecker synthesis pathway, and a reduction pathway from serine. (b) Pathways involving 1,3-oxazol-2-amine. This compound is an essential intermediate in the synthesis of nucleotides. (c) Possible prebiotic pathway enabling carbon fixation through a combination of environments. — biorxiv.org

ChemOrigins: A community curated database for origins of life chemistry, biorxiv.org

Astrobiology,