Controlled Vocabularies

The allowed values for the controlled fields used when contributing data.

Several fields accept only values from a fixed list (the Submit Data form offers them as drop-downs). If a paper's term doesn't map to any option, pick the closest one and add detail in a notes/description field rather than inventing a value. These lists are the same ones the extraction pipeline validates against.

The authoritative, always-current lists are served live at GET /api/v1/vocabularies (see the REST API page). The tables below mirror that endpoint.

Experiment methods (field: method)

The technique used in an experiment. Grouped by category for readability; any value from any group is valid.

Gravimetric:

weight_loss mass_remaining

Plate / culture:

clear_zone growth_on_plastic

Respirometry:

co2_evolution o2_consumption

Chemical analysis:

cod toc titration chn_analysis

Imaging:

sem afm tem clsm optical_microscopy visual_inspection

Spectroscopy:

ftir nmr uv_vis raman xps cd eds

Chromatography:

hplc lc_ms gc_ms gc gpc_sec tlc

Mass spectrometry:

maldi_tof ms

Enzymatic / biochemical:

enzyme_assay zymogram dcpip fluorescent_assay ros_assay biosensor

Optical:

luminescence dls turbidity

Surface:

contact_angle qcm ssa

Mechanical / rheology:

tensile_strength viscometry

Thermal / diffraction:

dsc tga xrd

Other:

radiolabeling fcm

Measurement types (field: measurement_type)

What a measurement quantified — distinct from the method that produced it. Note the deliberate naming split: the method is co2_evolution / o2_consumption, while the measurement it yields is co2_evolved / o2_consumed. When a value is omitted, the default unit below is applied.

ValueCategoryDefault unit
weight_lossgravimetric%
mass_remaininggravimetric%
clear_zone_diameterplate_assaymm
monomer_releasedchromatographymM
co2_evolvedrespirometry%
o2_consumedrespirometry%
molecular_weight_changechromatography%
crystallinity_changethermal%
depolymerization_rateenzymaticmg/L/h
depolymerization_extentenzymatic%
degradation_half_lifeenzymatich
tensile_strength_changemechanical%
elongation_at_breakmechanical%
contact_angle_changesurfacedegree
soluble_carbon_releasedchemical_analysismg/L
surface_morphologyimagingqualitative
surface_roughnessimagingqualitative
product_identifiedchemical_analysisqualitative
functional_group_changespectroscopyqualitative
growth_observedculturequalitative
activity_detectedenzymaticqualitative
thermal_degradationthermalqualitative
turbidity_changeopticalqualitative
weight_loss is the weight lost, not the weight remaining. If your paper reports what was left, use mass_remaining rather than converting — entering one under the other is an easy mistake and nothing can detect it afterwards.
FTIR and Raman results go under functional_group_change — bands appearing, disappearing or shifting in the polymer itself, and the indices computed from them (carbonyl index, oxidation index; put the number in value). product_identified is for a released species named by a separative technique such as HPLC/GC-MS, not for a change in the solid polymer's own spectrum.
Three terms exist so that their neighbours stop absorbing them. A water contact angle is contact_angle_change in degrees, not surface_morphology, which is qualitative imaging. Bulk dissolved carbon — TOC, DOC, COD — is soluble_carbon_released in mg/L; monomer_released is for a named monomer in mM. Tensile extension is elongation_at_break, while tensile_strength_change is the stress at break.
How much, how fast, and how long are three different measurements. depolymerization_rate is a quantity per unit time. A dimensionless conversion — %, fold, % of wild type, % of theoretical — is depolymerization_extent, whatever produced it: pH-stat titration, HPLC monomer quantification converted to conversion, or a gravimetric conversion. weight_loss stays narrower still: mass lost from the specimen on a balance. A paper that prints a titration conversion beside its gravimetric weight loss is reporting two measurements, not one.
degradation_half_life is the substrate's half-life — the time for half the polymer to be degraded, in hours or days. It is not the enzyme's thermal half-life, which belongs in the protein's properties.half_life alongside half_life_temperature. One is how long the protein survives at a temperature; the other is how long the plastic survives the protein.

Other controlled fields

FieldAllowed values
resultpositive negative inconclusive
actor_typemicroorganism protein protein_variant
substrate_formmodel_substrate amorphous_film crystalline_film film powder emulsion granule particle whole_polymer
aerobicityaerobic anaerobic microaerophilic not_reported
environment_typesoil marine_sediment marine_water freshwater compost wastewater activated_sludge landfill gut plastic_surface industrial hot_spring deep_sea mangrove coastal rhizosphere plant_material other
experimental_systemwhole_organism cell_free_enzyme
enzyme_production_contextnative heterologous not_reported
enzyme_preparationcrude_extract partially_purified purified immobilized not_reported
variant_typewild_type engineered truncated fusion synthetic predicted
fraction_basisweight mole volume unspecified
extraction_confidencehigh medium low

Convention, not enforced: duration_unit (h, d, w, mo) and temperature_unit (C) are free-text fields with recommended codes rather than validated vocabularies — but staying with these codes keeps the data consistent. oxygen_requirement on the microorganism is likewise free text.