SDRF template for soil metaproteomics. Extends metaproteomics with soil-specific columns aligned with the GSC MIxS soil extension (0016012). Combine with ms-proteomics for MS acquisition columns.
The soil template adds soil-specific environmental metadata from the MIxS
soil extension. These columns describe soil properties, land use, and
chemical/physical context relevant to soil microbiome studies.
PRIDE ontology terms (PRIDE:0000828 children) include MIxS cross-references.
Usage: soil + ms-proteomics
| Column | Requirement | Source | Description | |
|---|---|---|---|---|
| characteristics[soil type] | recommended | soil | Soil classification type (ENVO term) | |
|
Soil classification type (ENVO term)
ontology
— ontologies: envo
Should be a valid ENVO soil type term
sandy loam, clay, peat, silt
|
||||
| characteristics[elevation] | optional | soil | Height of the sampling site above mean sea level. | |
|
Height of the sampling site above mean sea level.
values
— values:
10 feet, 30 feet, 2 cm
elevation with unit
|
||||
| characteristics[slope gradient] | optional | soil | The angle between ground surface and a horizontal line (MIxS:0000646). | |
|
The angle between ground surface and a horizontal line (MIxS:0000646).
values
— values:
10 %, 30 %
slope gradient with unit
|
||||
| characteristics[slope aspect] | optional | soil | The direction a slope faces (MIxS:0000647). | |
|
The direction a slope faces (MIxS:0000647).
values
— values:
300 degrees, north west, south
slope aspect
|
||||
| characteristics[profile position] | optional | soil | Cross-sectional position in the hillslope where sample was collected (MIxS:0001084). | |
|
Cross-sectional position in the hillslope where sample was collected (MIxS:0001084).
values
— values:
summit, shoulder, backslope
profile position
|
||||
| characteristics[drainage classification] | optional | soil | Drainage classification from a standard system such as the USDA system (MIxS:0001085). | |
|
Drainage classification from a standard system such as the USDA system (MIxS:0001085).
values
— values:
well drained, poorly drained, very poorly drained
drainage classification
|
||||
| characteristics[soil type method] | optional | soil | Method used to determine or classify soil type, including the classification system, field assess... | |
|
Method used to determine or classify soil type, including the classification system, field assessment protocol, or laboratory procedure applied (MIXS:0000334).
pattern
— pattern:
^.+$
Description of the soil type determination or classification method
USDA Soil Taxonomy classification, WRB soil classification system, Field assessment according to FAO Guidelines for Soil Description, National Soil Resources Institute classification protocol
|
||||
| characteristics[current land use] | optional | soil | Present state of sample site (MIXS:0001080). | |
|
Present state of sample site (MIXS:0001080).
pattern
— pattern:
^.+$
Land use type
agricultural, forest, urban, grassland, wetland
|
||||
| characteristics[current vegetation] | optional | soil | Current vegetation type at sampling site. Corresponds to MIxS cur_vegetation (MIXS:0000312). | |
|
Current vegetation type at sampling site. Corresponds to MIxS cur_vegetation (MIXS:0000312).
ontology
— ontologies: envo
Should be a valid ENVO vegetation term
grassland, deciduous forest, cropland
|
||||
| comment[current vegetation method] | optional | soil | method used in vegetation classification (MIXS:0000314). | |
|
method used in vegetation classification (MIXS:0000314).
values
— values:
vegetation survey, quadrant sampling
current vegetation method
|
||||
| characteristics[history of previous land use] | optional | soil | Previous land use and dates (MIXS:0000315). | |
|
Previous land use and dates (MIXS:0000315).
values
— values:
agricultural land 15 years, grassland forest 5 years
history of previous land use and dates
|
||||
| comment[history of previous land use method] | optional | soil | Reference or method used in determining previous land use (MIXS:0000316). | |
|
Reference or method used in determining previous land use (MIXS:0000316).
values
— values:
land registry records, historical archives
current vegetation method
|
||||
| characteristics[crop rotation] | optional | soil | Crop rotation history. Corresponds to MIxS crop_rotation (MIXS:0000318). | |
|
Crop rotation history. Corresponds to MIxS crop_rotation (MIXS:0000318).
pattern
— pattern:
^.+$
Crop rotation description
corn-soybean rotation, wheat-fallow, continuous corn
|
||||
| characteristics[history of agrochemical additions] | optional | soil | Addition of fertilizers, pesticides, etc. - amount and time of applications (MIXS:0000639). | |
|
Addition of fertilizers, pesticides, etc. - amount and time of applications (MIXS:0000639).
values
— values:
urea 2mg/L, 2020-01-01, superphosphate 5mg/L, 2019-02-19
agrochemical additions with amount and dates
|
||||
| characteristics[history of tillage] | optional | soil | tilling methods (MIXS:0001081). | |
|
tilling methods (MIXS:0001081).
values
— values:
chisel, digging spade
tillage classification
|
||||
| characteristics[history of fire] | optional | soil | evidence of fire (MIXS:0001086). | |
| characteristics[history of flooding] | optional | soil | evidence of flooding (MIXS:0000319). | |
| characteristics[history of extreme event] | optional | soil | events that may have affected microbial populations (MIXS:0000320). | |
|
events that may have affected microbial populations (MIXS:0000320).
date
09-10-2025, 10-02-2002
|
||||
| characteristics[soil horizon] | optional | soil | Soil horizon from which sample was collected | |
|
Soil horizon from which sample was collected
values
— values:
O horizon, A horizon, B horizon, C horizon, E horizon, R horizon
Soil horizon
|
||||
| comment[horizon method] | optional | soil | method used in determining the horizon (MIXS:0000321). | |
|
method used in determining the horizon (MIXS:0000321).
pattern
— pattern:
^.+$
Horizon method description
USDA Field Book, FAO Guidelines for Soil Profile Description, none
|
||||
| characteristics[soil taxonomic of FAO classification] | optional | soil | Soil classification from the FAO World soil distribution (MIxS:0001083) | |
|
Soil classification from the FAO World soil distribution (MIxS:0001083)
values
— values:
acrisols, calcisols, durisols, gleysols
FAO soil classification
|
||||
| characteristics[link classification information] | optional | soil | Link to digitized soil maps or other soil classification information (MIXS:0000329). | |
|
Link to digitized soil maps or other soil classification information (MIXS:0000329).
pattern
— pattern:
^(https?:\/\/|doi:|PMID:).+$
URL, DOI, or PMID linking to classification information
https://example.com/soil-map, doi:10.1000/xyz123, PMID:12345678
|
||||
| characteristics[soil taxonomic local classification] | optional | soil | Soil classification based on local soil classification system (MIXS:0000330). | |
|
Soil classification based on local soil classification system (MIXS:0000330).
pattern
— pattern:
^.+$
Local soil classification term or description
Chernozem, Podzol, Local classification type A
|
||||
| characteristics[soil local classification method] | optional | soil | Method used for local soil classification, including reference to the classification system or me... | |
|
Method used for local soil classification, including reference to the classification system or methodology applied (MIXS:0000331).
pattern
— pattern:
^.+$
Description or reference to the local soil classification method
FAO soil classification guidelines, USDA Soil Taxonomy methodology, National soil classification system (UK)
|
||||
| characteristics[soil texture] | optional | soil | The relative proportion of different grain sizes of mineral particles in a soil, expressed as per... | |
|
The relative proportion of different grain sizes of mineral particles in a soil, expressed as percentages of sand, silt, and clay, optionally including a textural class (MIXS:0000335).
pattern
— pattern:
^[0-9]+(\.[0-9]+)?( *- *[0-9]+(\.[0-9]+)?)? *.+$
Soil texture expressed as percentages and/or textural class
40% sand 40% silt 20% clay, 30-50 silty clay loam, silty clay loam
|
||||
| characteristics[soil texture method] | optional | soil | Method used to determine soil texture, including reference to the analytical or classification ap... | |
|
Method used to determine soil texture, including reference to the analytical or classification approach applied.(MIXS:0000336)
pattern
— pattern:
^.+$
Description or reference to the soil texture determination method
Hydrometer method, Laser diffraction particle size analysis, Pipette method
|
||||
| characteristics[link climate information] | optional | soil | Link to climate resource associated with the sampling site. (MIXS:0000328) | |
|
Link to climate resource associated with the sampling site. (MIXS:0000328)
pattern
— pattern:
^(https?:\/\/|doi:|PMID:).+$
URL, DOI, or PMID linking to climate information
https://climate-data.org/location123, doi:10.1000/climate456, PMID:98765432
|
||||
| characteristics[mean annual temperature] | optional | soil | Mean annual temperature at the sampling site, typically expressed in degrees Celsius.(MIXS:0000135) | |
|
Mean annual temperature at the sampling site, typically expressed in degrees Celsius.(MIXS:0000135)
values
Mean annual temperature in °C
12.5 oC, 25 oC
|
||||
| characteristics[mean seasonal temperature] | optional | soil | Mean seasonal temperature range or average during a defined season at the sampling site. (MIXS:0000136) | |
|
Mean seasonal temperature range or average during a defined season at the sampling site. (MIXS:0000136)
pattern
— pattern:
^.+$
Seasonal temperature description or value
summer 18°C, winter -2 to 5°C
|
||||
| characteristics[mean annual precipitation] | optional | soil | Total annual precipitation at the sampling site, typically measured in millimeters per year.(MIXS... | |
|
Total annual precipitation at the sampling site, typically measured in millimeters per year.(MIXS:0000140)
numeric
Annual precipitation in mm/year
800/year, 1200.5/year
|
||||
| characteristics[mean seasonal precipitation] | optional | soil | Precipitation amount during a defined season at the sampling site. (MIXS:0000141) | |
|
Precipitation amount during a defined season at the sampling site. (MIXS:0000141)
pattern
— pattern:
^.+$
Seasonal precipitation description or value
summer 120 mm, winter 300 mm
|
||||
| characteristics[pH method] | optional | soil | Method used to determine pH in the sample.(MIXS:0001106) | |
|
Method used to determine pH in the sample.(MIXS:0001106)
pattern
— pattern:
^.+$
Description of pH measurement method
pH measured in water (1:2.5 soil:solution ratio), pH measured in CaCl2 solution
|
||||
| characteristics[organic matter] | optional | soil | Organic matter content of the sample.(MIXS:0000204) | |
|
Organic matter content of the sample.(MIXS:0000204)
number_with_unit
Organic matter content (%)
5.2 %, 12 %
|
||||
| characteristics[total organic carbon] | optional | soil | Total organic carbon content. Corresponds to MIxS tot_org_carb (MIXS:0000533). | |
|
Total organic carbon content. Corresponds to MIxS tot_org_carb (MIXS:0000533).
pattern
— pattern:
^[\d.]+\s*(mg/kg|g/kg|%)$
Total organic carbon with unit
15.2 g/kg, 2.5 %
|
||||
| characteristics[total organic carbon method] | optional | soil | Method used to determine total organic carbon.(MIXS:0000337) | |
|
Method used to determine total organic carbon.(MIXS:0000337)
pattern
— pattern:
^.+$
Description of TOC measurement method
dry combustion method, Walkley-Black method
|
||||
| characteristics[organic nitrogen] | optional | soil | Organic nitrogen content of the sample.(MIXS:0000205) | |
|
Organic nitrogen content of the sample.(MIXS:0000205)
number_with_unit
Organic nitrogen (%)
0.2 %, 1.5 %
|
||||
| characteristics[total nitrogen content] | optional | soil | Total nitrogen content of the sample.(MIXS:0000530) | |
|
Total nitrogen content of the sample.(MIXS:0000530)
number_with_unit
Total nitrogen (%)
0.5 %, 2.1 %
|
||||
| characteristics[total nitrogen content method] | optional | soil | Method used to determine total nitrogen content.(MIXS:0000338) | |
|
Method used to determine total nitrogen content.(MIXS:0000338)
pattern
— pattern:
^.+$
Description of nitrogen measurement method
Kjeldahl method, Dumas combustion method
|
||||
| characteristics[water content] | optional | soil | Water content of soil sample. Corresponds to MIxS water_content (MIXS:0000185). | |
|
Water content of soil sample. Corresponds to MIxS water_content (MIXS:0000185).
pattern
— pattern:
^[\d.]+\s*(g/g|%)$
Water content with unit
25 %, 0.25 g/g
|
||||
| characteristics[soil water content method] | optional | soil | Method used to determine soil water content.(MIXS:0000323) | |
|
Method used to determine soil water content.(MIXS:0000323)
pattern
— pattern:
^.+$
Description of water content measurement method
gravimetric method, time-domain reflectometry
|
||||
| comment[microbial biomass] | optional | soil | Microbial biomass present in the sample.(MIXS:0000650) | |
|
Microbial biomass present in the sample.(MIXS:0000650)
number_with_unit
Microbial biomass concentration
250 mg/kg, 1200 mg/kg
|
||||
| comment[microbial biomass method] | optional | soil | Method used to determine microbial biomass.(MIXS:0000339) | |
|
Method used to determine microbial biomass.(MIXS:0000339)
pattern
— pattern:
^.+$
Description of microbial biomass measurement method
chloroform fumigation extraction, substrate-induced respiration
|
||||
| characteristics[extreme unusual properties of heavy metals] | optional | soil | Concentration of heavy metals in the sample, including elements such as lead, cadmium, mercury, a... | |
|
Concentration of heavy metals in the sample, including elements such as lead, cadmium, mercury, and others.(MIXS:0000652)
pattern
— pattern:
^.+$
Heavy metal concentrations with units or description
Pb 50 mg/kg; Cd 2 mg/kg, Hg 0.5 mg/kg
|
||||
| characteristics[extreme unusual properties of heavy metals method] | optional | soil | Method used to determine heavy metal concentrations in the sample.(MIXS:0000343) | |
|
Method used to determine heavy metal concentrations in the sample.(MIXS:0000343)
pattern
— pattern:
^.+$
Description of heavy metal measurement method
ICP-MS analysis, Atomic absorption spectroscopy
|
||||
| characteristics[aluminum saturation] | optional | soil | Aluminum saturation of the soil, typically expressed as a percentage of cation exchange capacity ... | |
|
Aluminum saturation of the soil, typically expressed as a percentage of cation exchange capacity occupied by aluminum.(MIXS:0000607)
number_with_unit
Aluminum saturation (%)
15 %, 45.5 %
|
||||
| characteristics[aluminum saturation method] | optional | soil | Method used to determine aluminum saturation in the sample.(MIXS:0000324) | |
|
Method used to determine aluminum saturation in the sample.(MIXS:0000324)
pattern
— pattern:
^.+$
Description of aluminum saturation measurement method
KCl extraction followed by titration, ICP-OES after extraction
|
||||
| characteristics[sieving] | optional | soil | Size of mesh used to sieve the sample prior to analysis.(MIXS:0000322) | |
|
Size of mesh used to sieve the sample prior to analysis.(MIXS:0000322)
pattern
— pattern:
^.+$
Sieve size or description
2 mm mesh, 500 µm sieve
|
||||
| comment[sample volume or weight for DNA extraction] | optional | soil | Volume or weight of sample used for DNA extraction.(MIXS:0000111) | |
|
Volume or weight of sample used for DNA extraction.(MIXS:0000111)
pattern
— pattern:
^[0-9]+(\.[0-9]+)?\s?(g|mg|kg|mL|L)$
Sample amount with unit
0.5 g, 10 mL
|
||||
| characteristics[pooling of DNA extracts] | optional | soil | Whether multiple DNA extracts were pooled prior to sequencing.(MIXS:0000325) | |
|
Whether multiple DNA extracts were pooled prior to sequencing.(MIXS:0000325)
pattern
— pattern:
^(yes|no|pooled|not pooled).*$
Indication of DNA extract pooling
yes, pooled from 3 replicates, no
|
||||
| comment[storage conditions] | optional | soil | Storage conditions of the sample prior to analysis, including temperature and duration if known.(... | |
|
Storage conditions of the sample prior to analysis, including temperature and duration if known.(MIXS:0000327)
pattern
— pattern:
^.+$
Storage condition description
-80°C for 6 months, 4°C short-term storage, room temperature
|
||||
| comment[link to additional analysis] | optional | soil | Link to additional analysis results or external resources related to the sample.(MIXS:0000340) | |
|
Link to additional analysis results or external resources related to the sample.(MIXS:0000340)
pattern
— pattern:
^(https?:\/\/|doi:|PMID:).+$
URL, DOI, or PMID linking to additional analysis
https://example.com/analysis-results, doi:10.1000/analysis123, PMID:12345678
|
||||
| comment[miscellaneous parameter] | optional | soil | Any additional parameter not captured by other fields; should include a name and value.(MIXS:0000752) | |
|
Any additional parameter not captured by other fields; should include a name and value.(MIXS:0000752)
pattern
— pattern:
^.+:.+$
Parameter name and value in key:value format
{'enzyme_activity': 'high'}, {'soil_color': 'dark brown'}
|
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