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.
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
Spectroscopy:
ftir nmr uv_vis raman xps cd eds
Chromatography:
hplc lc_ms gc_ms 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.
| Value | Category | Default unit |
|---|---|---|
weight_loss | gravimetric | % |
mass_remaining | gravimetric | % |
clear_zone_diameter | plate_assay | mm |
monomer_released | chromatography | mM |
co2_evolved | respirometry | % |
o2_consumed | respirometry | % |
molecular_weight_change | chromatography | % |
crystallinity_change | thermal | % |
depolymerization_rate | enzymatic | mg/L/h |
tensile_strength_change | mechanical | % |
surface_morphology | imaging | qualitative |
surface_roughness | imaging | qualitative |
product_identified | chemical_analysis | qualitative |
functional_group_change | spectroscopy | qualitative |
growth_observed | culture | qualitative |
activity_detected | enzymatic | qualitative |
thermal_degradation | thermal | qualitative |
turbidity_change | optical | qualitative |
mass_remaining rather than converting — entering one under
the other is an easy mistake and nothing can detect it afterwards.
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.
Other controlled fields
| Field | Allowed values |
|---|---|
result | positive negative inconclusive |
actor_type | microorganism protein protein_variant |
substrate_form | model_substrate amorphous_film crystalline_film film powder emulsion granule whole_polymer |
aerobicity | aerobic anaerobic microaerophilic not_reported |
environment_type | soil 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_system | whole_organism cell_free_enzyme |
enzyme_production_context | native heterologous not_reported |
enzyme_preparation | crude_extract partially_purified purified immobilized not_reported |
variant_type | wild_type engineered truncated fusion synthetic predicted |
fraction_basis | weight mole volume unspecified |
extraction_confidence | high 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.