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 | |
|---|---|---|---|---|
| source name[sample name] | required | soil | Reference to the Sample. This term is used for cross-reference samples in SDRF for proteomics (MI... | |
|
Reference to the Sample. This term is used for cross-reference samples in SDRF for proteomics (MIXS:0001107).
identifier
sample name identifier
Sample_1, Sample_2
|
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| project name | required | soil | Name of the project within which the sequencing was organized (MIXS:0000092). | |
|
Name of the project within which the sequencing was organized (MIXS:0000092).
identifier
project name identifier
Bermuda_Atlantic_Time-series_Study, Metaproteomes_of_Seawater_Microbial_Communities
|
||||
| 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
|
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| 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[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
|
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| 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
|
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| 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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