Documentation

Everything you need to read, contribute to, and build on PlasticDB.

What PlasticDB is

PlasticDB is a database of plastic-degrading microorganisms, proteins, and enzymes. Every entry is drawn from published literature — journal articles or preprints — and backed by a published experiment — the database contains no computationally predicted activity. It pairs a browsable evidence-linked catalogue with bioinformatics tools for sequence analysis and a structured system for contributing new data.

The platform has three areas:

  • Data browser — explore microorganisms, proteins, plastics, compounds, and papers, each with detail pages showing the degradation evidence behind them.
  • Bioinformatics tools — align your sequences against the PlasticDB enzyme database to annotate genes, genomes, and taxonomic tables.
  • Data submission — contribute new records from a paper through a guided form, or programmatically via the REST API.

Documentation map

Data Model

The evidence spine — how every degradation claim is anchored to the paper, actor, experiment, and measurement that support it.

Reading Results

How to interpret the badges, buckets and counts you see while browsing — positive vs. negative results, mixed evidence, and what the totals count.

Browsing the Database

The entity types and their list and detail pages: microorganisms, proteins, variants, plastics, compounds, papers, and the engineering view.

Contributing Data

A field-by-field reference for the Submit Data form: what each field means, whether it is required, and a worked example from a real paper.

Controlled Vocabularies

The allowed values for methods, measurement types, environments and the other controlled fields, mirrored from the live vocabulary endpoint.

REST API

Authentication, rate limits, and every public endpoint for reading data and submitting records programmatically.

Bioinformatics Tools

The sequence- and taxonomy-analysis pipelines: annotate a gene, a genome or a taxa table, compare genomes, map pathways, or build a tree.

Accounts & access

Browsing, searching, and bulk downloads are open to everyone — no account needed. An account adds the ability to run bioinformatics jobs, submit data, and manage API keys.

  • Register at /register with your email and a password (minimum 8 characters), then confirm your email.
  • API key — once logged in, generate one from Profile › API Keys. It is shown only once; store it securely. See the REST API page for how to send it.
  • Dashboard — after login, /dashboard is home base for your jobs, submissions, and profile.
Using PlasticDB in your research? See the About page for the citation and data-provenance details.