Browsing the Database
The entity types in PlasticDB and where to find them.
Entity types
PlasticDB is organised around a handful of entity types, each with a searchable list page and a detail page:
| Entity | List | Detail | What the detail page shows |
|---|---|---|---|
| Microorganisms | /microorganisms | /microorganisms/{tax_id} |
Species name, NCBI tax ID, lineage breadcrumb with clickable ranks, growth-temperature profile, the plastics it degrades, the enzymes it expresses, and the papers behind each claim. |
| Proteins | /proteins | /proteins/{accession} |
PlasticDB accession, enzyme name, GenBank / UniProt IDs, amino-acid sequence, signal peptide, EC number, target plastics, source organism, engineered variants, and a 3D structure viewer (iCn3D) when a structure exists. |
| Protein variants | via Engineering | /variants/{id} |
An engineered variant as a first-class record: its own accession, parent enzyme, mutations, engineering method, reported kinetics and stability, and the plastics it acts on. Variants have no separate list page — they surface through the Engineering view and search. |
| Plastics | /plastics | /plastics/{id} |
Polymer abbreviation (PET, PHB, PBAT…), full chemical name, a statistics sidebar, and paginated tables of degrading organisms and active enzymes split by result. |
| Compounds | /compounds | /compounds/{id} |
Chemical compounds — monomers, additives, and degradation / pathway intermediates. Name, formula, type, and an additive flag. |
| Papers | /papers | /papers/{id} |
Citation, DOI, year, journal, and the microorganisms, proteins, and variants derived from the interactions the paper supports. |
List pages support free-text search and column filters (for example, filtering microorganisms by plastic, environment, taxonomic rank, or growth-temperature class). Detail pages show every related entity, so you can pivot from an organism to the enzymes it expresses, or from a plastic to everything shown to degrade it.
Protein Engineering view
The Engineering page (/engineering, detail
/engineering/{accession}) is a focused view of enzyme engineering: it
lists only enzymes that have at least one recorded engineered variant, and lets you
pick a parent enzyme to compare its variants' mutations, kinetics, and stability
side by side. This is the primary way to discover and navigate between variants.
Search
The search bar in the header runs a cross-entity search: a query is matched against microorganisms, proteins, protein variants, plastics, and papers at once, and results are grouped by type. Variant matches route to the variant's own page, not to the parent enzyme. Use the filter chips beside the search box to restrict results to a single entity type, or open the full search page for the complete ranked list.
Interpreting what you see
The tables, badges, and headline counts on these pages follow consistent rules — which results count as “degrading”, how disagreeing papers are shown, and what the totals include. The Reading Results page explains all of it, and Data Model covers how the underlying records connect.