water

v1.0.0 sample

SDRF template for aquatic metaproteomics. Extends metaproteomics with water-specific columns aligned with the GSC MIxS water extension (0016014). Combine with ms-proteomics for MS acquisition columns.

Key Guidance

The water template adds aquatic environment metadata from the MIxS water

extension. These columns describe water body properties, chemical/physical

measurements, and sampling context for aquatic microbiome studies.

PRIDE ontology terms (PRIDE:0000829 children) include MIxS cross-references.

Usage: water + ms-proteomics

Inheritance

base → metaproteomics → water

Combination Rules

Mutually exclusive with: human-gut, soil

Columns

81 own + 27 inherited = 108 total · click a row for details

	Column	Requirement	Source	Description
▶	source name	required	base	Unique identifier for the biological sample
Description Unique identifier for the biological sample Ontology PRIDE:0000623 Properties
▶	assay name	required	base	Unique identifier for the data acquisition run
Description Unique identifier for the data acquisition run Ontology NCIT:C178857 Properties
▶	technology type	required	base	Type of technology used
Description Type of technology used Ontology PRIDE:0000663 Properties Validators single_cardinality_validator values — values: `proteomic profiling by mass spectrometry`, `protein expression profiling by antibody array`, `protein expression profiling by aptamer array`
▶	comment[technical replicate]	required	base	Identifier for the technical replicate (integer starting from 1)
Description Identifier for the technical replicate (integer starting from 1) Ontology MS:1001808 Properties type: integer
▶	comment[data file]	required	base	Name of the raw data file
Description Name of the raw data file Ontology MS:1003083 Properties
▶	characteristics[environmental sample type]	required	metaproteomics	Type of environmental sample analyzed (ENVO or EFO term). Corresponds to MIxS env_medium (MIXS:0000014).
Description Type of environmental sample analyzed (ENVO or EFO term). Corresponds to MIxS env_medium (MIXS:0000014). Ontology PRIDE:0000993 Properties Validators ontology — ontologies: envo, efo Should be a valid ENVO or EFO term Examples `soil`, `seawater`, `gut microbiome`, `wastewater`, `biofilm`
▶	source name[sample name]	required	water	Reference to the Sample. This term is used for cross-reference samples in SDRF for proteomics (MI...
Description Reference to the Sample. This term is used for cross-reference samples in SDRF for proteomics (MIXS:0001107). Ontology PRIDE:0000623 Properties allows N/A Validators identifier sample name identifier Examples `Sample_1`, `Sample_2`
▶	project name	required	water	Name of the project within which the sequencing was organized (MIXS:0000092).
Description Name of the project within which the sequencing was organized (MIXS:0000092). Ontology PRIDE:0000676 Properties allows N/A Validators identifier project name identifier Examples `Bermuda_Atlantic_Time-series_Study`, `Metaproteomes_of_Seawater_Microbial_Communities`
▶	comment[sdrf version]	recommended	base	Version of the SDRF-Proteomics specification used to annotate this file
Description Version of the SDRF-Proteomics specification used to annotate this file Ontology PRIDE:0000839 Properties Validators semver SDRF specification version Examples `v1.1.0`, `v2.0.0-dev`
▶	characteristics[geographic location]	recommended	metaproteomics	Geographic location where sample was collected (GAZ term or coordinates). Corresponds to MIxS geo...
Description Geographic location where sample was collected (GAZ term or coordinates). Corresponds to MIxS geo_loc_name (MIXS:0000010). Ontology PRIDE:0000995 Properties allows N/A allows not available Validators ontology — ontologies: gaz Should be a valid GAZ term or coordinates Examples `Pacific Ocean`, `Amazon rainforest`, `47.6062 N, 122.3321 W`
▶	characteristics[environmental medium]	recommended	metaproteomics	Environmental material from which the sample was obtained (ENVO term). Corresponds to MIxS env_me...
Description Environmental material from which the sample was obtained (ENVO term). Corresponds to MIxS env_medium (MIXS:0000014). Ontology PRIDE:0000994 Properties allows N/A allows not available Validators ontology — ontologies: envo Should be a valid ENVO environmental material term Examples `soil`, `seawater`, `freshwater`, `feces`, `biofilm`
▶	characteristics[sampling depth zone]	recommended	water	Ecological depth zone of the sampling site
Description Ecological depth zone of the sampling site Ontology PRIDE:0001005 Properties allows N/A allows not available Validators values — values: `epipelagic`, `mesopelagic`, `bathypelagic`, `abyssopelagic`, `hadopelagic`, `benthic`, … Ocean depth zone
▶	characteristics[elevation]	recommended	water	Height of the sampling site above mean sea level.
Description Height of the sampling site above mean sea level. Ontology PRIDE:0000712 Properties allows N/A allows not available Validators number_with_unit elevation with unit Examples `10 feet`, `30 feet`, `2 cm`
▶	characteristics[tidal stage]	recommended	water	Stage of tide (MIXS:0000750).
Description Stage of tide (MIXS:0000750). Ontology PRIDE:0000820 Properties allows N/A allows not available Validators values — values: `high tide`, `low tide` tidal stage wth term
▶	characteristics[total depth of water volume]	recommended	water	Measurement of total depth of water column (MIXS:0000634).
Description Measurement of total depth of water column (MIXS:0000634). Ontology PRIDE:0000821 Properties allows N/A allows not available Validators number_with_unit total depth of water volume with unit Examples `35 m`, `10 m`, `200 m`
▶	characteristics[water current]	recommended	water	Measured speed and direction of water flow
Description Measured speed and direction of water flow Ontology PRIDE:0001006 Properties allows N/A allows not available Validators number_with_unit water current with unit Examples `0.35 m/s`, `0.10 m/s`
▶	characteristics[mean friction velocity]	recommended	water	Measurement of mean friction velocity (MIXS:0000498).
Description Measurement of mean friction velocity (MIXS:0000498). Ontology PRIDE:0000794 Properties allows N/A allows not available Validators number_with_unit mean friction velocity with unit Examples `0.035 m/s`, `0.010 m/s`
▶	characteristics[mean peak friction velocity]	recommended	water	Measurement of mean peak friction velocity (MIXS:0000502).
Description Measurement of mean peak friction velocity (MIXS:0000502). Ontology PRIDE:0000795 Properties allows N/A allows not available Validators number_with_unit mean peak friction velocity with unit Examples `0.015 m/s`, `0.045 m/s`
▶	characteristics[pressure]	recommended	water	Pressure to which the sample is subject to, in atmospheres (MIXS:0000412)
Description Pressure to which the sample is subject to, in atmospheres (MIXS:0000412) Ontology PRIDE:0000809 Properties allows N/A allows not available Validators number_with_unit pressure with unit Examples `15 dbar`, `25 dbar`
▶	comment[sdrf template]	optional	base	Template name and version used for annotation. Two formats are supported - key=value format (NT=t...
Description Template name and version used for annotation. Two formats are supported - key=value format (NT=template_name;VV=vX.Y.Z) or simple format (template_name vX.Y.Z). Multiple templates can be specified using multiple columns. Ontology PRIDE:0000832 Properties allows not available multiple cardinality Validators pattern — pattern: `^(NT=[\w-]+;VV=v\d+\.\d+\.\d+(-[\w.]+)?\|[\w-]+ v\d+\.\d+\.\d+(-[\w.]+)?)$` Template can be specified as 'NT=name;VV=vX.Y.Z' or 'name vX.Y.Z' Examples `NT=human;VV=v1.1.0`, `human v1.1.0`, `NT=ms-proteomics;VV=v1.1.0`, `ms-proteomics v1.1.0`
▶	comment[sdrf annotation tool]	optional	base	Software tool or method used to generate or annotate the SDRF file. Two formats are supported - k...
Description Software tool or method used to generate or annotate the SDRF file. Two formats are supported - key=value format (NT=tool_name;VV=vX.Y.Z) or simple format (tool_name vX.Y.Z). Ontology PRIDE:0000840 Properties allows not available Validators pattern — pattern: `^(NT=[\w-]+;VV=v[\d.]+[\w.-]\|[\w-]+ v[\d.]+[\w.-]\|manual curation)$` Annotation tool can be specified as 'NT=name;VV=vX.Y.Z' or 'name vX.Y.Z' or 'manual curation' Examples `NT=lesSDRF;VV=v0.1.0`, `lesSDRF v0.1.0`, `NT=sdrf-pipelines;VV=v1.0.0`, `sdrf-pipelines v1.0.0`, `manual curation`
▶	comment[sdrf validation hash]	optional	base	Hash value for SDRF validation integrity checking
Description Hash value for SDRF validation integrity checking Properties allows N/A allows not available Validators pattern — pattern: `^.+$` Validation hash string
▶	characteristics[collection date]	optional	metaproteomics	Date when sample was collected (ISO 8601)
Description Date when sample was collected (ISO 8601) Ontology PRIDE:0000996 Properties allows N/A allows not available Validators date Sample collection date Examples `2024`, `2024-01`, `2024-01-15`
▶	characteristics[sample collection method]	optional	metaproteomics	Method used to collect the environmental sample
Description Method used to collect the environmental sample Ontology PRIDE:0000997 Properties allows N/A allows not available Validators pattern — pattern: `^.+$` Collection method description Examples `grab sample`, `core sample`, `swab`, `filtration`
▶	characteristics[depth]	optional	metaproteomics	Depth at which sample was collected. Corresponds to MIxS depth (MIXS:0000018).
Description Depth at which sample was collected. Corresponds to MIxS depth (MIXS:0000018). Ontology PRIDE:0000711 Properties allows N/A allows not available Validators number_with_unit Depth with unit Examples `10 m`, `50 cm`, `100 m`
▶	characteristics[altitude]	optional	metaproteomics	Altitude or elevation of sampling site. Corresponds to MIxS elevation (MIXS:0000093).
Description Altitude or elevation of sampling site. Corresponds to MIxS elevation (MIXS:0000093). Ontology PRIDE:0000712 Properties allows N/A allows not available Validators number_with_unit Altitude with unit Examples `500 m`, `1200 m`, `0 m`
▶	characteristics[temperature]	optional	metaproteomics	Temperature at sampling location. Corresponds to MIxS temperature (MIXS:0000113).
Description Temperature at sampling location. Corresponds to MIxS temperature (MIXS:0000113). Ontology PRIDE:0000703 Properties allows N/A allows not available Validators number_with_unit Temperature in Celsius Examples `25 °C`, `4 °C`, `-20 °C`
▶	characteristics[ph]	optional	metaproteomics	pH at sampling location
Description pH at sampling location Ontology PRIDE:0000746 Properties allows N/A allows not available Validators pattern — pattern: `^\d+(\.\d+)?$` pH value Examples `7.0`, `5.5`, `8.2`
▶	characteristics[sample storage]	optional	metaproteomics	Storage conditions for the sample before analysis
Description Storage conditions for the sample before analysis Ontology PRIDE:0000730 Properties allows N/A allows not available Validators pattern — pattern: `^.+$` Storage conditions Examples `-80C`, `liquid nitrogen`, `4C`
▶	comment[metagenome accession]	optional	metaproteomics	Accession number for matched metagenome data
Description Accession number for matched metagenome data Ontology PRIDE:0000956 Properties allows N/A allows not available Validators accession Database accession number Examples `MGYA00001234`, `SRP123456`
▶	characteristics[microbiome source]	optional	metaproteomics	Source of the microbiome being studied (e.g., gut microbiome, rhizosphere microbiome)
Description Source of the microbiome being studied (e.g., gut microbiome, rhizosphere microbiome) Ontology PRIDE:0000986 Properties allows N/A allows not available Validators pattern — pattern: `^.+$` Microbiome source description Examples `gut microbiome`, `rhizosphere microbiome`, `oral microbiome`, `skin microbiome`
▶	characteristics[biomass estimation]	optional	metaproteomics	Estimated microbial biomass in the sample
Description Estimated microbial biomass in the sample Ontology PRIDE:0000990 Properties allows N/A allows not available Validators pattern — pattern: `^.+$` Biomass estimation Examples `1e9 cells/g`, `high biomass`, `low biomass`
▶	characteristics[host contamination]	optional	metaproteomics	Level of host protein contamination if known
Description Level of host protein contamination if known Ontology PRIDE:0000991 Properties allows N/A allows not available Validators pattern — pattern: `^.+$` Host contamination level Examples `low (<5%)`, `moderate (5-20%)`, `high (>20%)`
▶	comment[contaminant database]	optional	metaproteomics	Contaminant database(s) used in database search
Description Contaminant database(s) used in database search Ontology PRIDE:0000992 Properties allows N/A allows not available Validators pattern — pattern: `^.+$` Contaminant database name(s) Examples `cRAP`, `MaxQuant contaminants`, `cRAP;MaxQuant contaminants`
▶	characteristics[mock community]	optional	metaproteomics	Identifier or name of mock community standard used
Description Identifier or name of mock community standard used Ontology PRIDE:0000987 Properties allows N/A allows not available Validators pattern — pattern: `^.+$` Mock community identifier Examples `ZymoBIOMICS Microbial Community Standard`, `ATCC MSA-1000`
▶	characteristics[mock community composition]	optional	metaproteomics	Description of mock community composition (species and ratios)
Description Description of mock community composition (species and ratios) Ontology PRIDE:0000988 Properties allows N/A allows not available Validators pattern — pattern: `^.+$` Community composition description Examples `8 bacteria + 2 yeasts at defined ratios`, `even mix of 10 species`
▶	comment[expected organism list]	optional	metaproteomics	Semicolon-separated list of organisms expected in mock community
Description Semicolon-separated list of organisms expected in mock community Ontology PRIDE:0000989 Properties allows N/A allows not available Validators pattern — pattern: `^.+$` Semicolon-separated organism list Examples `E. coli;B. subtilis;S. cerevisiae;L. fermentum`, `Bacillus subtilis;Staphylococcus aureus`
▶	characteristics[salinity]	optional	water	Salinity measurement. Corresponds to MIxS salinity (MIXS:0000183).
Description Salinity measurement. Corresponds to MIxS salinity (MIXS:0000183). Ontology PRIDE:0000701 Properties allows N/A allows not available Validators pattern — pattern: `^[\d.]+\s*(PSU\|ppt\|g/L)$\|^(freshwater\|brackish\|marine)$` Salinity value with unit or descriptive term Examples `35 PSU`, `freshwater`, `brackish`
▶	characteristics[conductivity]	optional	water	Electrical conductivity of water sample. Corresponds to MIxS conduc (MIXS:0000544).
Description Electrical conductivity of water sample. Corresponds to MIxS conduc (MIXS:0000544). Ontology PRIDE:0000776 Properties allows N/A allows not available Validators pattern — pattern: `^[\d.]+\s*(uS/cm\|mS/cm\|S/m)$` Conductivity with unit Examples `450 uS/cm`, `1.2 mS/cm`
▶	characteristics[density]	optional	water	Density of the sample, which is its mass per unit volume (aka volumetric mass density) (MIXS:0000435).
Description Density of the sample, which is its mass per unit volume (aka volumetric mass density) (MIXS:0000435). Ontology PRIDE:0000777 Properties allows N/A allows not available Validators number_with_unit density with unit Examples `1022 kg/m3`, `1050 kg/m3`
▶	characteristics[redox potential]	optional	water	Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potentia...
Description Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential (MIXS:0000182). Ontology PRIDE:0000811 Properties allows N/A allows not available Validators number_with_unit redox potential with unit Examples `1.2 V`, `0.80 V`
▶	characteristics[fluorescence]	optional	water	Raw or converted fluorescence of water (MIXS:0000704).
Description Raw or converted fluorescence of water (MIXS:0000704). Ontology PRIDE:0000790 Properties allows N/A allows not available Validators number_with_unit redox potential with unit Examples `1.2 RFU`, `3.8 RFU`
▶	characteristics[light intensity]	optional	water	Light intensity at sampling depth. Corresponds to MIxS light_intensity (MIXS:0000706).
Description Light intensity at sampling depth. Corresponds to MIxS light_intensity (MIXS:0000706). Ontology PRIDE:0000792 Properties allows N/A allows not available Validators pattern — pattern: `^[\d.]+\s*(lux\|umol/m2/s)$` Light intensity with unit Examples `500 lux`, `100 umol/m2/s`
▶	characteristics[turbidity]	optional	water	Turbidity measurement. Corresponds to MIxS turbidity (MIXS:0000191).
Description Turbidity measurement. Corresponds to MIxS turbidity (MIXS:0000191). Ontology PRIDE:0000827 Properties allows N/A allows not available Validators pattern — pattern: `^[\d.]+\s*(NTU\|FNU)$` Turbidity with unit Examples `5.2 NTU`, `12 FNU`
▶	characteristics[downward PAR]	optional	water	Visible waveband radiance and irradiance measurements in the water column (MIXS:0000703).
Description Visible waveband radiance and irradiance measurements in the water column (MIXS:0000703). Ontology PRIDE:0000789 Properties allows N/A allows not available Validators number_with_unit downward PAR with unit Examples `120 µmol`, `15 µmol`
▶	characteristics[photon flux]	optional	water	Measurement of photon flux (MIXS:0000725).
Description Measurement of photon flux (MIXS:0000725). Ontology PRIDE:0000807 Properties allows N/A allows not available Validators number_with_unit photon flux with unit Examples `120 µmol`, `15 µmol`
▶	characteristics[nitrate]	optional	water	Nitrate concentration. Corresponds to MIxS nitrate (MIXS:0000425).
Description Nitrate concentration. Corresponds to MIxS nitrate (MIXS:0000425). Ontology PRIDE:0000796 Properties allows N/A allows not available Validators number_with_unit Nitrate concentration with unit Examples `0.5 mg/L`, `10 umol/L`
▶	characteristics[nitrite]	optional	water	Nitrite concentration. Corresponds to MIxS nitrite (MIXS:0000426).
Description Nitrite concentration. Corresponds to MIxS nitrite (MIXS:0000426). Ontology PRIDE:0000797 Properties allows N/A allows not available Validators number_with_unit Nitrite concentration with unit Examples `0.5 mg/L`, `1 mg/L`
▶	characteristics[nitrogen]	optional	water	Nitrogen concentration. Corresponds to MIxS nitrogen (MIXS:0000504).
Description Nitrogen concentration. Corresponds to MIxS nitrogen (MIXS:0000504). Ontology PRIDE:0000798 Properties allows N/A allows not available Validators number_with_unit Nitrogen concentration with unit Examples `10 mg/L`, `15 mg/L`
▶	characteristics[ammonium]	optional	water	Ammonium concentration. Corresponds to MIxS ammonium (MIXS:0000427).
Description Ammonium concentration. Corresponds to MIxS ammonium (MIXS:0000427). Ontology PRIDE:0000764 Properties allows N/A allows not available Validators number_with_unit ammonium concentration with unit Examples `1 mg/L`, `1.5 mg/L`
▶	characteristics[phosphate]	optional	water	Phosphate concentration. Corresponds to MIxS phosphate (MIXS:0000505).
Description Phosphate concentration. Corresponds to MIxS phosphate (MIXS:0000505). Ontology PRIDE:0000805 Properties allows N/A allows not available Validators number_with_unit Phosphate concentration with unit Examples `0.1 mg/L`, `1.5 umol/L`
▶	characteristics[dissolved inorganic nitrogen]	optional	water	Dissolved inorganic nitrogen concentration (MIXS:0000698).
Description Dissolved inorganic nitrogen concentration (MIXS:0000698). Ontology PRIDE:0000784 Properties allows N/A allows not available Validators number_with_unit dissolved inorganic nitrogen concentration with unit Examples `761 mmol/L`, `500 mmol/L`
▶	characteristics[total inorganic nitrogen]	optional	water	total inorganic nitrogen concentration (MIXS:0000745).
Description total inorganic nitrogen concentration (MIXS:0000745). Ontology PRIDE:0000828 Properties allows N/A allows not available Validators number_with_unit total inorganic phosphoruss concentration with unit Examples `76 mg/L`, `40 mg/L`
▶	characteristics[total dissolved nitrogen]	optional	water	total dissolved nitrogen concentration (MIXS:0000744).
Description total dissolved nitrogen concentration (MIXS:0000744). Ontology PRIDE:0000822 Properties allows N/A allows not available Validators number_with_unit total dissolved nitrogen concentration with unit Examples `76 mg/L`, `40 mg/L`
▶	characteristics[dissolved inorganic phosphorus]	optional	water	Dissolved inorganic phosphorus concentration (MIXS:0000106).
Description Dissolved inorganic phosphorus concentration (MIXS:0000106). Ontology PRIDE:0000785 Properties allows N/A allows not available Validators number_with_unit dissolved inorganic phosphorus concentration with unit Examples `76 mmol/L`, `56 mmol/L`
▶	characteristics[total nitrogen concentration]	optional	water	total nitrogen concentration (MIXS:0000102).
Description total nitrogen concentration (MIXS:0000102). Ontology PRIDE:0000824 Properties allows N/A allows not available Validators number_with_unit total nitrogen concentration with unit Examples `76 mmol/L`, `56 mmol/L`
▶	characteristics[total phosphorus]	optional	water	total phosphorus concentration. Corresponds to MIxS total phosphorus (MIXS:0000117).
Description total phosphorus concentration. Corresponds to MIxS total phosphorus (MIXS:0000117). Ontology PRIDE:0000826 Properties allows N/A allows not available Validators number_with_unit total phosphorus concentration with unit Examples `0.03 mg/L`, `0.05mg/L`
▶	characteristics[soluble reactive phosphorus]	optional	water	soluble reactive phosphorus concentration (MIXS:0000738).
Description soluble reactive phosphorus concentration (MIXS:0000738). Ontology PRIDE:0000816 Properties allows N/A allows not available Validators number_with_unit soluble reactive phosphorus concentration with unit Examples `0.1 mg/L`, `0.2 mg/L`
▶	characteristics[silicate]	optional	water	ssilicate concentration. Corresponds to MIxS(MIXS:0000184).
Description ssilicate concentration. Corresponds to MIxS(MIXS:0000184). Ontology PRIDE:0000812 Properties allows N/A allows not available Validators number_with_unit soluble reactive phosphorus concentration with unit Examples `0.05 mmol/L`, `0.08 mmol/L`
▶	characteristics[alkalinity]	optional	water	Alkalinity measurement. Corresponds to MIxS alkalinity (MIXS:0000421).
Description Alkalinity measurement. Corresponds to MIxS alkalinity (MIXS:0000421). Ontology PRIDE:0000760 Properties allows N/A allows not available Validators number_with_unit Alkalinity with unit Examples `120 mg/L`, `2.5 meq/L`
▶	characteristics[alkalinity method]	optional	water	Method used for alkalinity measurement (MIXS:0000298).
Description Method used for alkalinity measurement (MIXS:0000298). Ontology PRIDE:0000761 Properties allows N/A Validators identifier Alkalinity method identifier Examples `titration`
▶	characteristics[calcium]	optional	water	Calcium concentration. Corresponds to MIxS(MIXS:0000421).
Description Calcium concentration. Corresponds to MIxS(MIXS:0000421). Ontology PRIDE:0000772 Properties allows N/A allows not available Validators number_with_unit Calcium with unit Examples `0.2 mmol/L`, `2.5 mmol/L`
▶	characteristics[magnesium]	optional	water	Magnesium concentration. Corresponds to MIxS(MIXS:0000431).
Description Magnesium concentration. Corresponds to MIxS(MIXS:0000431). Ontology PRIDE:0000793 Properties allows N/A allows not available Validators number_with_unit Magnesium with unit Examples `25 mmol/kg`, `52.8 mmol/kg`
▶	characteristics[potassium]	optional	water	Potassium concentration. Corresponds to MIxS(MIXS:0000430).
Description Potassium concentration. Corresponds to MIxS(MIXS:0000430). Ontology PRIDE:0000808 Properties allows N/A allows not available Validators number_with_unit Potassium with unit Examples `463 mg/L`, `300 mg/L`
▶	characteristics[sodium]	optional	water	Sodium concentration. Corresponds to MIxS(MIXS:0000428).
Description Sodium concentration. Corresponds to MIxS(MIXS:0000428). Ontology PRIDE:0000815 Properties allows N/A allows not available Validators number_with_unit Sodium with unit Examples `10.5 mg/L`, `12 mg/L`
▶	characteristics[chloride]	optional	water	Sodium concentration. Corresponds to MIxS(MIXS:0000429).
Description Sodium concentration. Corresponds to MIxS(MIXS:0000429). Ontology PRIDE:0000774 Properties allows N/A allows not available Validators number_with_unit Chloride with unit Examples `5000 mg/L`, `3500 mg/L`
▶	characteristics[sulfate]	optional	water	Sulfate concentration. Corresponds to MIxS(MIXS:0000423).
Description Sulfate concentration. Corresponds to MIxS(MIXS:0000423). Ontology PRIDE:0000817 Properties allows N/A allows not available Validators number_with_unit Sulfate with unit Examples `5 mmol/L`, `3.5 mmol/L`
▶	characteristics[sulfide]	optional	water	Sulfide concentration. Corresponds to MIxS(MIXS:0000424).
Description Sulfide concentration. Corresponds to MIxS(MIXS:0000424). Ontology PRIDE:0000818 Properties allows N/A allows not available Validators number_with_unit Sulfide with unit Examples `2 mmol/L`, `1.5 mmol/L`
▶	characteristics[bromide]	optional	water	Bromide concentration. Corresponds to MIxS(MIXS:0000176).
Description Bromide concentration. Corresponds to MIxS(MIXS:0000176). Ontology PRIDE:0000771 Properties allows N/A allows not available Validators number_with_unit Bromide with unit Examples `0.05 ppm`, `0.01 ppm`
▶	characteristics[atmospheric data]	optional	water	Measurement of atmospheric data; can include multiple data (MIXS:0001097).
Description Measurement of atmospheric data; can include multiple data (MIXS:0001097). Ontology PRIDE:0000765 Properties allows N/A allows not available Validators pattern — pattern: `^.+$` Diet description Examples `wind speed; 9 knots`, `humidity; 75%`
▶	characteristics[dissolved organic carbon]	optional	water	Dissolved organic carbon concentration. Corresponds to MIxS (MIXS:0000433)
Description Dissolved organic carbon concentration. Corresponds to MIxS (MIXS:0000433) Ontology PRIDE:0000786 Properties allows N/A allows not available Validators number_with_unit Dissolved orgainic carbon concentration with unit Examples `197 mmol/L`, `75 mmol/L`
▶	characteristics[dissolved inorganic carbon]	optional	water	Dissolved inorganic carbon concentration. Corresponds to MIxS (MIXS:0000434)
Description Dissolved inorganic carbon concentration. Corresponds to MIxS (MIXS:0000434) Ontology PRIDE:0000781 Properties allows N/A allows not available Validators number_with_unit Dissolved inorgainic carbon concentration with unit Examples `2059 mmol/kg`, `1075 mmol/kg`
▶	characteristics[dissolved carbon dioxide]	optional	water	Dissolved carbon dioxide concentration. Corresponds to MIxS (MIXS:0000436)
Description Dissolved carbon dioxide concentration. Corresponds to MIxS (MIXS:0000436) Ontology PRIDE:0000779 Properties allows N/A allows not available Validators number_with_unit Dissolved carbon dioxide concentration with unit Examples `5 mg/L`, `10 mg/L`
▶	characteristics[dissolved oxygen]	optional	water	Dissolved oxygen concentration. Corresponds to MIxS diss_oxygen (MIXS:0000119).
Description Dissolved oxygen concentration. Corresponds to MIxS diss_oxygen (MIXS:0000119). Ontology PRIDE:0000788 Properties allows N/A allows not available Validators pattern — pattern: `^[\d.]+\s*mg/L$\|^(hypoxic\|anoxic\|oxic)$` Dissolved oxygen with unit or descriptive term Examples `8.5 mg/L`, `hypoxic`, `anoxic`
▶	characteristics[dissolved hydrogen]	optional	water	Dissolved hydrogen concentration. Corresponds to MIxS (MIXS:0000205).
Description Dissolved hydrogen concentration. Corresponds to MIxS (MIXS:0000205). Ontology PRIDE:0000780 Properties allows N/A allows not available Validators number_with_unit Dissolved hydrogen concentration with unit Examples `0.3 mmol/L`, `0.5 mmol/L`
▶	characteristics[dissolved organic nitrogen]	optional	water	Dissolved organic nitrogen concentration. Corresponds to MIxS (MIXS:0000162).
Description Dissolved organic nitrogen concentration. Corresponds to MIxS (MIXS:0000162). Ontology PRIDE:0000787 Properties allows N/A allows not available Validators number_with_unit Dissolved organic nitrogen concentration with unit Examples `0.04 mmol/L`, `0.05 mmol/L`
▶	characteristics[organic carbon]	optional	water	Organic carbon concentration. Corresponds to MIxS (MIXS:0000508).
Description Organic carbon concentration. Corresponds to MIxS (MIXS:0000508). Ontology PRIDE:0000799 Properties allows N/A allows not available Validators number_with_unit Organic carbon concentration with unit Examples `1.5 ug/L`, `1 ug/L`
▶	characteristics[organic matter]	optional	water	Organic matter concentration. Corresponds to MIxS (MIXS:0000204).
Description Organic matter concentration. Corresponds to MIxS (MIXS:0000204). Ontology PRIDE:0000748 Properties allows N/A allows not available Validators number_with_unit Organic matter concentration with unit Examples `1.75 ug/L`, `1 ug/L`
▶	characteristics[organic nitrogen]	optional	water	Organic nitrogen concentration. Corresponds to MIxS (MIXS:0000205).
Description Organic nitrogen concentration. Corresponds to MIxS (MIXS:0000205). Ontology PRIDE:0000800 Properties allows N/A allows not available Validators number_with_unit Organic matter concentration with unit Examples `4 umol/L`, `1 umol/L`
▶	characteristics[particulate organic carbon]	optional	water	Particulate organic carbon concentration. Corresponds to MIxS (MIXS:0000515).
Description Particulate organic carbon concentration. Corresponds to MIxS (MIXS:0000515). Ontology PRIDE:0000801 Properties allows N/A allows not available Validators number_with_unit Particulate organic carbon concentration with unit Examples `1.92 umol/L`, `1 umol/L`
▶	characteristics[particulate organic nitrogen]	optional	water	Particulate organic nitrogen concentration. Corresponds to MIxS (MIXS:0000719).
Description Particulate organic nitrogen concentration. Corresponds to MIxS (MIXS:0000719). Ontology PRIDE:0000802 Properties allows N/A allows not available Validators number_with_unit Particulate organic nitrogen concentration with unit Examples `0.3 umol/L`, `0.5 umol/L`
▶	characteristics[total particulate carbon]	optional	water	Total particulate carbon content. Corresponds to MIxS (MIXS:0000747).
Description Total particulate carbon content. Corresponds to MIxS (MIXS:0000747). Ontology PRIDE:0000825 Properties allows N/A allows not available Validators number_with_unit Particulate organic carbon concentration with unit Examples `35 umol/L`, `5 ug/L`
▶	characteristics[carbon nitrogen ratio]	optional	water	Carbon to nitrogen concentration. Corresponds to MIxS (MIXS:0000310).
Description Carbon to nitrogen concentration. Corresponds to MIxS (MIXS:0000310). Ontology PRIDE:0000773 Properties allows N/A allows not available Validators pattern — pattern: `^[\d.]+$` carbon nitrogen measurement value Examples `0.475`, `0.34576`
▶	characteristics[suspended particulate matter]	optional	water	Suspended particulate matter concentration. Corresponds to MIxS (MIXS:0000741).
Description Suspended particulate matter concentration. Corresponds to MIxS (MIXS:0000741). Ontology PRIDE:0000819 Properties allows N/A allows not available Validators number_with_unit Particulate organic carbon concentration with unit Examples `0.5 mg/L`, `1 mg/L`
▶	characteristics[chlorophyll]	optional	water	Chlorophyll concentration if measured
Description Chlorophyll concentration if measured Ontology PRIDE:0000775 Properties allows N/A allows not available Validators number_with_unit Chlorophyll concentration with unit Examples `2.5 ug/L`, `0.1 mg/L`
▶	characteristics[primary production]	optional	water	Primary production measurement
Description Primary production measurement Ontology PRIDE:0000810 Properties allows N/A allows not available Validators number_with_unit primary production measurement with unit Examples `100 mg/m3/day`, `10 g/m2/day`
▶	comment[bacterial production]	optional	water	bacterial production measurement (MIXS:0000683)
Description bacterial production measurement (MIXS:0000683) Ontology PRIDE:0000767 Properties allows N/A allows not available Validators number_with_unit bacterial production measurement with unit Examples `5 mg/m3/day`, `10 mg/m3/day`
▶	characteristics[bacterial respiration]	optional	water	bacterial respiration measurement (MIXS:0000684)
Description bacterial respiration measurement (MIXS:0000684) Ontology PRIDE:0000768 Properties allows N/A allows not available Validators number_with_unit bacterial respiration measurement with unit Examples `300 umolO2/L/hr`, `100 umolO2/L/hr`
▶	characteristics[bacterial carbon production]	optional	water	bacterial carbon production measurement (MIXS:0000173)
Description bacterial carbon production measurement (MIXS:0000173) Ontology PRIDE:0000766 Properties allows N/A allows not available Validators number_with_unit bacterial carbon production with unit Examples `2.53 ug/L/hr`, `1.23 ug/L/hr`
▶	characteristics[aminopeptidase activity]	optional	water	Aminopeptidase activity measurement (MIXS:0000172)
Description Aminopeptidase activity measurement (MIXS:0000172) Ontology PRIDE:0000763 Properties allows N/A allows not available Validators number_with_unit aminopeptidase activity with unit Examples `0.253 mol/L/hr`, `0.123 mol/L/hr`
▶	characteristics[glucosidase activity]	optional	water	glucosidase activity measurement (MIXS:0000137)
Description glucosidase activity measurement (MIXS:0000137) Ontology PRIDE:0000791 Properties allows N/A allows not available Validators number_with_unit glucosidase activity with unit Examples `5 mol/L/hr`, `3 mol/L/hr`
▶	characteristics[phaeopigments]	optional	water	phaeopigments concentration (MIXS:0000180)
Description phaeopigments concentration (MIXS:0000180) Ontology PRIDE:0000804 Properties allows N/A allows not available Validators number_with_unit phaeopigments with unit Examples `2.5 mg/m3`, `3 mg/m3`
▶	characteristics[biomass]	optional	water	Total cell count of any organism (MIXS:0000174)
Description Total cell count of any organism (MIXS:0000174) Ontology PRIDE:0000769 Properties allows N/A allows not available Validators number_with_unit biomass with unit Examples `25 g`, `3 kg`
▶	comment[organism count]	optional	water	phaeopigments concentration (MIXS:0000103)
Description phaeopigments concentration (MIXS:0000103) Ontology PRIDE:0000704 Properties allows N/A allows not available Validators number_with_unit organism count in CFU/ml Examples `500 CFU/ml`, `2000 CFU/ml`
▶	comment[oxygenation status of sample]	optional	water	Oxygenation status of sample (MIXS:0000753).
Description Oxygenation status of sample (MIXS:0000753). Ontology PRIDE:0000702 Properties allows N/A allows not available Validators number_with_unit Oxygenation status of sample in mmHg Examples `80 mmHg`, `100 mmHg`
▶	characteristics[alkyl diethers]	optional	water	Alkyl diethers concentration (MIXS:0000490).
Description Alkyl diethers concentration (MIXS:0000490). Ontology PRIDE:0000762 Properties allows N/A allows not available Validators number_with_unit Alkyl diethers in unit Examples `0.005 mol/L`, `0.003 mol/L`
▶	characteristics[diether lipids]	optional	water	Diether lipids concentration (MIXS:0000178).
Description Diether lipids concentration (MIXS:0000178). Ontology PRIDE:0000778 Properties allows N/A allows not available Validators number_with_unit Diether lipids in unit Examples `0.5 ng/L`, `0.3 ng/L`
▶	characteristics[bishomohopanol]	optional	water	Bishomohopanol concentration (MIXS:0000175).
Description Bishomohopanol concentration (MIXS:0000175). Ontology PRIDE:0000770 Properties allows N/A allows not available Validators number_with_unit bishomohopanol in unit Examples `14 ug/L`, `4 ug/g`
▶	characteristics[phospholipid fatty acid]	optional	water	Phospholipid fatty acid concentration (MIXS:0000181).
Description Phospholipid fatty acid concentration (MIXS:0000181). Ontology PRIDE:0000806 Properties allows N/A allows not available Validators pattern — pattern: `^.+$` Phospholipid fatty acid name and measurement value Examples `Linoleic acid; 2.8 mg/L`, `Palmitic acid; 1.5 mg/L`
▶	characteristics[petroleum hydrocarbon]	optional	water	Petroleum hydrocarbon concentration (MIXS:0000516).
Description Petroleum hydrocarbon concentration (MIXS:0000516). Ontology PRIDE:0000803 Properties allows N/A allows not available Validators number_with_unit petroleum hydrocarbon in unit Examples `0.05 umol/L`, `0.02 umol/L`
▶	comment[sample storage temperature]	optional	water	Temperature at which sample was stored (MIXS:0000110).
Description Temperature at which sample was stored (MIXS:0000110). Ontology PRIDE:0000705 Properties Validators number_with_unit temperature in Celsius Examples `-80 °C`, `-20 °C`
▶	comment[sample storage location]	optional	water	Location at which sample was stored (MIXS:0000755).
Description Location at which sample was stored (MIXS:0000755). Ontology PRIDE:0000709 Properties allows N/A allows not available Validators pattern — pattern: `^.+$` storage location description Examples `freezer`, `room`
▶	comment[sample storage duration]	optional	water	Duration for which the sample was stored (MIXS:0000116).
Description Duration for which the sample was stored (MIXS:0000116). Ontology PRIDE:0000707 Properties allows N/A allows not available Validators pattern — pattern: `^.+$` storage duration description Examples `40 days`, `6 months`
▶	comment[sample volume or weight for DNA extraction]	optional	water	Volume or weight of sample used for DNA extraction.(MIXS:0000111)
Description Volume or weight of sample used for DNA extraction.(MIXS:0000111) Ontology PRIDE:0000706 Properties allows N/A allows not available Validators pattern — pattern: `^[0-9]+(\.[0-9]+)?\s?(g\|mg\|kg\|mL\|L)$` Sample amount with unit Examples `0.5 g`, `10 mL`
▶	comment[size-fraction lower threshold]	optional	water	mesh/pore size used to pre-filter/pre-sort the sample (MIXS:0000735).
Description mesh/pore size used to pre-filter/pre-sort the sample (MIXS:0000735). Ontology PRIDE:0000813 Properties allows N/A allows not available Validators number_with_unit size-fraction lower threshold in unit Examples `0.1 um`, `0.2 um`
▶	comment[size-fraction upper threshold]	optional	water	Mesh or pore size of the device used to retain the sample (MIXS:0000736).
Description Mesh or pore size of the device used to retain the sample (MIXS:0000736). Ontology PRIDE:0000814 Properties allows N/A allows not available Validators number_with_unit size-fraction upper threshold in unit Examples `10 um`, `20 um`
▶	characteristics[perturbation]	optional	water	Type of perturbation applied. Corresponds to MIxS perturbation (MIXS:0000754).
Description Type of perturbation applied. Corresponds to MIxS perturbation (MIXS:0000754). Ontology PRIDE:0000700 Properties allows N/A allows not available Validators pattern — pattern: `^.+$` Perturbation description Examples `antibiotic administration`, `dietary intervention`, `none`
▶	comment[miscellaneous parameter]	optional	water	Any additional parameter not captured by other fields; should include a name and value.(MIXS:0000752)
Description Any additional parameter not captured by other fields; should include a name and value.(MIXS:0000752) Ontology PRIDE:0000710 Properties allows N/A allows not available Validators pattern — pattern: `^.+:.+$` Parameter name and value in key:value format Examples `{'enzyme_activity': 'high'}`, `{'soil_color': 'dark brown'}`

Contributors

Yasset Perez-Riverol (yperez@ebi.ac.uk) - EMBL-EBI
Deepti Jaiswal Kundu (jaiswal@ebi.ac.uk) - EMBL-EBI
Nithu Sara John (nithu@ebi.ac.uk) - EMBL-EBI
Nandana Madhusoodanan (nandana@ebi.ac.uk) - EMBL-EBI
Asier Larrea (alarre@ebi.ac.uk) - EMBL-EBI
Toan Phung (TPhung001@dundee.ac.uk) - University of Dundee
Timo Sachsenberg (timo.sachsenberg@uni-tuebingen.de) - University of Tübingen