Methane Chamber Database Structure
Methane Database Structure 
Naming Conventions for Attributes and Variables
24 April 2020
Overview
This page serves as guidance for the types and scope of data and metadata that will be archived as part of the Coastal Carbon Network’s developing methane chamber data synthesis. We propose the following data structure and standardized attribute names for metadata and data in order to make datasets machine-readable and interoperable. Each subheading lists a level of metadata or data hierarchy from site level to chamber level to timeseries information. Each subheading also represents separate tables which can be joined by common attributes such as study_id, site_id, and chamber_id. We also include accompanying sets of recommended controlled vocabulary for key categorical variables (also known as factors). Some attributes have controlled units that we wish to keep uniform across datasets.
Throughout the table key attributes are bolded. Please strive to provide data for these attributes whenever possible.
Site Level
Site information provides important context for your study. You should describe the site and how it fits into your broader study, provide geographic information, and add any relevant tags and notes regarding site vegetation and inundation.
| attribute_name | definition | unit, format, or codes |
|---|---|---|
| study_id | Unique identifier for the study made up of the first author's family name, as well as the second author's or 'et al' if more than three, then publication year seperated by underscores. | |
| site_id | Site identification code unique to each study. | |
| site_description | Site description including relevant study details and political geographic units. Some of these descriptions can be automated by the ingestion code. | |
| utc_offset | Offset from UTC of site data | hour |
| site_longitude | Positional longitude of the site in decimal degree WGS84. | degree |
| site_latitude | Positional latitude of the site in decimal degree WGS84. | degree |
| site_elevation | Site elevation relative to defined datum. | meter |
| site_elevation_datum | The datum relative to which the site elevation was measured against (For a complete list of datum names and aliases please refer to the ISO Geodedic Registry). | |
| site_elevation_MSL | Elevation of mean sea level relative to a given datum | meter |
| site_elevation_MSL_datum | The datum relative to which the mean sea level was measured against (For a complete list of datum names and aliases please refer to the ISO Geodedic Registry). | |
| site_elevation_MSL_station | Station used to determine MSL | free text |
| site_elevation_MSL_years | Period used to determine MSL | year |
| site_tidal_range | Mean tidal range calculated as the difference between Mean High Water and Mean Low water | meter |
| climate_classification | Köppen climate classification | Af; Am; Aw; Bsh; Bsk; Bwh; Bwk; Cfa; Cfb; Cfc; Csa; Csb; Cwa; Cwb; Cwc; Dfa; Dfb; Dfc; Dfd; Dsa; Dsb; Dsc; Dsd; Dwa; Dwb; Dwc; Dwd; EF; ET |
| land_cover_type_IGBP | Vegetation type based on the IGBP definition | Barren Sparse Vegetation; Croplands; Closed Shrublands; Cropland/Natural Vegetation Mosaics; Deciduous Broadleaf Forests; Deciduous Needleleaf Forests; Evergreen Broadleaf Forests; Evergreen Needleleaf Forests; Grasslands; Mixed Forests; Open Shrublands; Savannas; Snow and Ice; Urban and Built-Up Lands; Water Bodies; Permanent Wetlands; Woody Savannas |
| mean_annual_temp | Climatological long-term Mean Annual average air Temperature (MAT) | degreesCelsius |
| mean_annual_precipitation | Climatological long-term Mean Annual average Precipitation (MAP) | millimeter |
| salinity_class | Code based on submitter field observation or measurement indicating average annual salinity (Note: freshwater should only include tidal wetlands, or wetlands that are potentially/formerly tidal but artificially freshened due to artificial tidal restrictions). | fresh = <0.5 ppt.; oligohaline = 0.5-5 ppt.; mesohaline = 5-18 ppt.; polyhaline = 18-30 ppt.; mixoeuhaline = 30-40 ppt.; saline = 30-50 ppt.; brine = >50 ppt. |
| salinity_method | Indicate whether salinity_class was determined using a field observation or a measurement. | field observation = Salinity inferred by field observation such as vegetation.; measurement = Salinity observed from local instrument. |
| salinity_notes | Any relevant submitter generated notes on how salinity_class was determined. | |
| inundation_class | Code based on submitter field observation or measurement indicating how often the site location is inundated. | high = Study-Specific definition of an elevation relatively high in the tidal frame located above the Mean Highwater Mark (MHW), inundated infrequently either during high rainfall events, spring tides, or above normal high tides and typically defined by vegetation type (e.g., Spartina patens, Distichlis spicata, Salicornia sp., Juncus sp., and bulrush species).; mid = Study-specific definition of an elevation in the relative middle of the tidal frame, typically defined by vegetation type (e.g., Spartina patens).; low = Specific definition of an elevation relatively low in the tidal frame, typically defined by vegetation type (e.g., Spartina alterniflora).; levee = Study-specific definition of a relatively high elevation zone built up on the edge of a river, creek, or channel.; back = Study-specific definition of a relatively low elevation zone behind a levee. |
| inundation_method | Indicate whether inundation_class was determined using a field observation or a measurement | field observation = Inundation inferred by field observation such as vegetation.; measurement = Inundation class assessed from elevation and nearby tide gauge or other similar method. |
| inundation_time | Fraction of time the site location is inundated daily | fraction |
| inundation_notes | Any relevant submitter generated notes on how inundation/elevation was determined | |
| wetland_vegetation_class | Code based on submitter field observations or measurement indicating dominant wetland vegetation type. | mudflat = Describes unvegetated areas exposed and flooded by the tides.; emergent = Describes wetlands dominated by persistent emergent vascular plants.; scrub shrub = Describes wetlands dominated by woody vegetation less than or equal to 5 meters in height.; forested = Describes wetlands dominated by woody vegetation > 5 meters in height.; FO/SS = Dominated by forested to scrub/shrub biomass.; seagrass = Describes tidal or subtidal communities dominated by rooted vascular plants. |
| wetland_vegetation_method | Indicate whether wetland_vegetation_class was determined using a field observation or a measurement | field observation = Vegetation inferred by field observation.; measurement = Vegetation measured by counts or plots. |
| wetland_vegetation_notes | Any relevant submitter generated notes on how vegetation_class was were determined | |
| net_primary_productivity | Annual Net Primary Productivity measured at the site level. Negative values to indicate net uptake | gramsCarbonPerSquareMeterPerYear |
| ecosystem_respiration | Annual ecosystem respiration measured at the site level | gramsCarbonPerSquareMeterPerYear |
| impact_class | Code indicating any major anthropogenic and/or natural impacts historically and currently affecting the site dates of measurement. | undisturbed = No disturbance or management has occurred on the site.; tidally restricted = Tidal flow is muted or blocked by built structures.; impounded = Water level is raised artificially by a tidal restriction, resulting in ponding of water on the wetland and or upland surface.; managed impounded = Wetland is impounded seasonally, and other times natural or semi natural hydrology occurs.; ditched = Tidal hydrology is altered because artificial ditches have been cut to promote tidal flooding and drainage.; diked and drained = The wetland has been diked and drained, with or without flapper gates, pumping, or other means.; farmed = Managed impoundment or drainage in which wetland has been converted to agricultural land.; tidally restored = Tidal flow has been restored by removing an artificial obstruction.; submergence-salinization = due to sea level rise and salt water intrusion.; revegetated = Wetland vegetation has been reintroduced by replanting on unvegetated surfaces.; invasive plants removed = Natural plant communities have been restored by the active removal of invasive plant species.; invasive herbivores removed = Tidal wetland vegetation has been managed by the removal of invasive herbivores.; sediment added = Elevation has been managed by artificially adding sediment to the site using techniques such as thin layering or sediment diversion.; wetlands built = Constructed wetland using sediments such as dredge spoils or other sediment source.; fire = wildfire or managed burns.; land cover change = land use and land cover change.; invasion = woody or urban encroachment.; grazing = herbivory or browsing by mammals, managed or wild.; pests and disease = plant or soil damage from pests, insects, pathogens, blight, and other diseases.; storm or wind = Major storms including unusually high-precipitation and unusually high-wind events e.g. hurricane, hail, flooding from storm, etc. Temperature extreme + heat wave or freeze |
| ecosystem_age | If historically disturbed, time since disturbance | years |
| mean_dry_bulk_density | Mean soil bulk density | gramsPerCubicCentimeter |
| se_dry_bulk_density | Standard error of the mean bulk density | gramsPerCubicCentimeter |
| mean_soil_organic | Mean Soil organic matter conent | fraction |
| se_soil_organic | Standard error of mean soil organic matter conent | fraction |
| mean_soil_carbon | Mean soil organic carbon conent | fraction |
| se_soil_carbon | Standard error of mean soil organic carbon conent | fraction |
| mean_soil_total_nitrogen | Mean soil total nitrogen conent | fraction |
| se_soil_total_nitrogen | Standard error of mean soil total nitrogen conent | fraction |
| mean_soil_total_phosphorous | Mean soil total phosphorous conent | fraction |
| se_soil_total_phosphorous | Standard error of mean soil total phosphorous conent | fraction |
| mean_soil_CN_ratio | Mean soil C:N | dimensionless |
| se_soil_CN_ratio | Standard error of mean soil C:N | dimensionless |
| mean_soil_clay | Mean fraction of clay (<4 microns) in soil (0-1) | fraction |
| se_soil_clay | Standard error of mean fraction of clay | fraction |
| mean_soil_silt | Mean fraction of silt (4 - 63 microns) in soil (0-1) | fraction |
| se_soil_silt | Standard error mean fraction of silt | fraction |
| mean_soil_sand | Mean fraction of sand (>63 microns) in soil (0-1) | fraction |
| se_soil_sand | Standard error of mean fraction of sand | fraction |
Chamber Level
| attribute_name | definition | unit, format, or codes |
|---|---|---|
| study_id | Unique identifier for the study made up of the first author's family name, as well as the second author's or 'et al' if more than three, then publication year seperated by underscores. | |
| site_id | Site identification code unique to each study. | |
| chamber_id | Chamber identification code unique to each site. | |
| chamber_year | Year of chamber installation | YYYY |
| chamber_type | Chamber type | static; automated |
| collar_installation_date | Date of chamber collar installation. | YYYY-MM-DD |
| collar_installation_period | Code indicating how far in advance collars were installed, if collar installation date is unknown. | less than one week prior to sampling event; between one week and one month prior to sampling event; between one month and one year prior to sampling event; more than one year prior to sampling event |
| collar_insertion_depth | Depth of collar insertion | centimeter |
| chamber_volume | Chamber volume. | cubicMeter |
| chamber_area | Collar area. | squareMeter |
| chamber_opacity | chamber opacity | clear; opaque |
| mixing_fan_present | Chamber mixing fan present and operating | TRUE; FALSE |
| path_to_chamber | Was there a boardwalk or other means to approach the chamber without compressing the soil? | TRUE; FALSE |
| chamber_location_notes | chamber location comment (hummock/hollow, wetland edge, ditch, etc) | free text |
| chamber_notes | Any other relevant submitter generated notes on chambers. | |
| chamber_longitude | Positional longitude of the chamber in decimal degree WGS84. | degree |
| chamber_latitude | Positional latitude of the chamber in decimal degree WGS84. | degree |
| chamber_position_accuracy | Accuracy of latitude and longitude measurement, if determined and recorded. | meter |
| chamber_position_method | Code indicating how latitude and longitude were determined. | RTK; handheld; other high resolution; other moderate resolution; other low resolution |
| chamber_elevation | Surface elevation of the chamber relative to defined datum. | meter |
| chamber_elevation_datum | The datum relative to which the chamber elevation was measured against (For a complete list of datum names and aliases please refer to the ISO Geodedic Registry). | |
| chamber_elevation_accuracy | Accuracy of elevation measurement, if determined and recorded | meter |
| chamber_elevation_method | Code indicating how elevation was determined | RTK; other high resolution; LiDAR; DEM; other low resolution |
| chamber_elevation_MSL | Surface elevation of the chamber relative to mean sea level | meter |
| chamber_elevation_notes | Any relevant submitter generated notes on how elevation was determined | |
| salinity_class | If salinity was determined at the site level, please leave it blank here. Code based on submitter field observation or measurement indicating average annual salinity (Note: freshwater should only include tidal wetlands, or wetlands that are potentially/formerly tidal but artificially freshened due to artificial tidal restrictions). | fresh = <0.5 ppt.; oligohaline = 0.5-5 ppt.; mesohaline = 5-18 ppt.; polyhaline = 18-30 ppt.; mixoeuhaline = 30-40 ppt.; saline = 30-50 ppt.; brine = >50 ppt. |
| salinity_method | Indicate whether salinity_class was determined using a field observation or a measurement | field observation = Salinity inferred by field observation such as vegetation.; measurement = Salinity observed from local instrument. |
| salinity_notes | Any relevant submitter generated notes on how salinity_class was determined | |
| inundation_class | If inundation was determined at the site level, please leave it blank here. Code based on submitter field observation or measurement indicating how often the chamber location is inundated. | high = Study-Specific definition of an elevation relatively high in the tidal frame located above the Mean Highwater Mark (MHW), inundated infrequently either during high rainfall events, spring tides, or above normal high tides and typically defined by vegetation type (e.g., Spartina patens, Distichlis spicata, Salicornia sp., Juncus sp., and bulrush species).; mid = Study-specific definition of an elevation in the relative middle of the tidal frame, typically defined by vegetation type (e.g., Spartina patens).; low = Specific definition of an elevation relatively low in the tidal frame, typically defined by vegetation type (e.g., Spartina alterniflora).; levee = Study-specific definition of a relatively high elevation zone built up on the edge of a river, creek, or channel.; back = Study-specific definition of a relatively low elevation zone behind a levee. |
| inundation_method | Indicate whether inundation_class was determined using a field observation or a measurement | field observation = Inundation inferred by field observation such as vegetation.; measurement = Inundation class assessed from elevation and nearby tide gauge or other similar method. |
| inundation_time | Fraction of time the chamber location is inundated daily | fraction |
| inundation_notes | Any relevant submitter generated notes on how inundation/elevation was determined | |
| wetland_vegetation_class | If wetland veg class was determined at the site level, please leave it blank here. Code based on submitter field observations or measurement indicating dominant wetland vegetation type. | mudflat = Describes unvegetated areas exposed and flooded by the tides.; emergent = Describes wetlands dominated by persistent emergent vascular plants.; scrub shrub = Describes wetlands dominated by woody vegetation less than or equal to 5 meters in height.; forested = Describes wetlands dominated by woody vegetation > 5 meters in height.; FO/SS = Dominated by forested to scrub/shrub biomass.; seagrass = Describes tidal or subtidal communities dominated by rooted vascular plants. |
| wetland_vegetation_method | Indicate whether vegetation_class was determined using a field observation or a measurement | field observation = Vegetation inferred by field observation.; measurement = Vegetation measured by counts or plots. |
| wetland_vegetation_notes | Any relevant submitter generated notes on how vegetation_class and dominant_species were determined. | |
| field_or_manipulation_code | Code to indicate whether this is a field study or an artificial growing manipulation like a marsh organ or mesocosm. | field; marsh organ; mesocosm |
| chamber_treatment_code | Code indicating whether there was an experimental treatment at the plot (as opposed to an unmanipulated control). | control; treatment |
| chamber_treatment_notes | Any relevant submitter generated notes on how chamber_treatment_code was determined. | |
| chamber_species | Species (Latin binomial) according to the most up to date classification. If multiple species per chamber, separate species name by semicolons | |
| chamber_species_date | Measurement date of species fraction cover, biomass, leaf area, LAI or height | YYYY-MM-DD |
| fraction_cover | Estimated ground area coverage of species or vegetation type in chamber (0-1). If multiple species per chamber, separate each species cover by semicolons following the same order as the chamber_species | fraction |
| fraction_cover_method | Method used to calculate fraction cover | number; mass; area; abundance |
| clipping | Was vegetation clipped before measurement period? | TRUE; FALSE |
| biomass | Live plant mass within chamber footprint. If multiple species per chamber, separate each species biomass by semicolons following the same order as the chamber_species | gC/m2 |
| specific_leaf_area | Specific leaf area of plants in chamber | squareCentimetersPerGram |
| leaf_area_index | Leaf area index of plants in chamber | m2/m2 |
| species_CN_ratio | carbon/nitrogen ratio in vegetation in chamber or representative of chamber | dimensionless |
| height | average plant height within chamber | meter |
| species_notes | Any other submitter defined notes regarding the species. | |
| dry_bulk_density | Soil bulk density | gramsPerCubicCentimeter |
| soil_organic | Soil organic matter conent | fraction |
| soil_carbon | Soil organic carbon conent | fraction |
| soil_CN_ratio | Soil C:N | dimensionless |
Chamber Time Series
This level of hierarchy contains the actual time series information. Sample ID’s should be used in the case that there are multiple replicates of a measurements.
| attribute_name | definition | unit, format, or codes |
|---|---|---|
| study_id | Unique identifier for the study made up of the first author's family name, as well as the second author's or 'et al' if more than three, then publication year seperated by underscores. | |
| site_id | Site identification code unique to each study. | |
| chamber_id | Chamber identification code unique to each site. Use chamber_id followed by a position and aggregation qualifiers H_V_R (horizontal_ vertical_replicate). For example two replicate chambers (Ch_1_1_1 and Ch_1_1_2), two different chambers in the same site (Ch_1_1_1 and Ch_2_1_1) | |
| sample_id | Unique identifier for samples if there are more than one replicate per sampling event. | |
| sample_year | Year of the sampling event. | YYYY |
| sample_month | Month of the sampling event. | MM |
| sample_day | Day of the sampling event. If DD was not recorded, use NA | DD |
| chamber_eq_time | Length of time the chamber equilibrated before measurements were taken. | minutes |
| chamber_measurement_length | Measurement length | minutes |
| chamber_volume | Chamber volume. | cubicMeter |
| sample_start_time_hour | Start of measurement period, local time, no DST. | HH |
| sample_start_time_minutes | Start of measurement period, local time, no DST. | MM |
| sample_start_time_seconds | Start of measurement period, local time, no DST. If seconds were not recorded use NA | SS |
| sample_end_time_hour | End of measurement period, local time, no DST | HH |
| sample_end_time_minutes | End of measurement period, local time, no DST | MM |
| sample_end_time_seconds | End of measurement period, local time, no DST. Use NA if seconds were not recorded | SS |
| chamber_measurement_mode | Measurement mode | Close flow, open flow or point measurement |
| chamber_flow_rate | Chamber flow rate | L min-1 |
| light_treatment | Fraction (0-1) describing any light/dark treatment the sampling event was subjected too. | Fraction ambient light (0 is dark) |
| ch4_analyzer | model of analyzer(s) used for fluxes | free text |
| ch4_flux | Methane flux (CH4) inside chamber. Positive fluxes are net emissions to atmosphere. | nanoMolPersquareMeterPerSecond |
| ch4_flux_model | Specify model/method used to calculate flux over sampling period. | linear; exponential ; summation of fluxes during specific time intervals; internal vs external gas concentration |
| ch4_flux_se | The standard error of CH4 flux. | |
| ch4_flux_n | Typical number of sampling events within sampling period. | |
| ch4_flux_r2 | The R^2 value of the model used to calculate flux over sampling period. | dimensionless |
| ch4_flux_pvalue_threshold | p-value threshold of significance of the slope parameter | |
| ch4_flux_notes | Any user submitted notes about CH4 during the sampling period. | |
| co2_flux | Carbon dioxide (CO2) flux inside chamber. Positive fluxes are net emissions to atmosphere. | microMolPersquareMeterPerSecond |
| co2_flux_model | Specify model used to calculate flux over sampling period. | linear; exponential ; summation of fluxes during specific time intervals; internal vs external gas concentration |
| co2_flux_se | The standard error of CO2 flux. | |
| co2_flux_n | Number of sampling events within sampling period. It is valid to report a typical number for continuous measurements | |
| co2_flux_r2 | The R^2 value of the model used to calculate flux over sampling period. | dimensionless |
| co2_flux_notes | Any user submitted notes about CO2 during the sampling period. | |
| n2o_flux | The flux of N2O between the chamber and environment over the sampling period. | nanoMolPersquareMeterPerSecond |
| n2o_flux_model | Specify model used to calcuate flux over sampling period. | linear; exponential ; summation of fluxes during specific time intervals; internal vs external gas concentration |
| n2o_flux_se | The standard error of N2O flux. | |
| n2o_flux_n | Typical number of sampling events within sampling period. | |
| n2o_flux_r2 | The R^2 value of the model used to calculate flux over sampling period. | dimensionless |
| n2o_flux_notes | Any user submitted notes about N2O during the sampling period. | |
| air_temperature_inside_chamber | Air temperature inside chamber measured over the sampling time. | degreesCelsius |
| air_temperature_outside_chamber | Air temperature outside chamber measured over the sampling time. | degreesCelsius |
| soil_temperature | Soil temperature inside chamber measured over the sampling time. | degreesCelsius |
| soil_temperature_depth | Soil temperature probe depth. | centimeter |
| soil_water_content | Soil water content (volumetric) inside chamber, range 0-100 | Percent |
| soil_water_content_depth | Soil depth at which water content/maisture has been measured | centimeter |
| par_inside_chamber | Photosynthetically active raditation, incoming, inside the chamber | micromolPhotonPerSquareMeterPerSecond |
| par_outside_chamber | Photosynthetically active raditation, incoming, outside the chamber | micromolPhotonPerSquareMeterPerSecond |
| conductivity | Temperature corrected electrical conductivity (EC) | milliSiemensPerMeter |
| salinity | Salinity measured during the sampling interval | ppt |
| conductivity_salinity_media | Indicate whether conductivity and salinity where measured in surface, porewaters or bulk soil. | surface; porewater; soil |
| conductivity_salinity_depth | Conductivity and salinity probe depth. Negative values indicate depths below soil surface. | centimeter |
| water_table_depth | water table depth (negative values belowground surface) | meter |
| sampling_interval_notes | Any other relevant user submitted notes. | free text |
Porewater Level
| attribute_name | definition | unit, format, or codes |
|---|---|---|
| study_id | Unique identifier for the study made up of the first author's family name, as well as the second author's or 'et al' if more than three, then publication year seperated by underscores. | |
| site_id | Site identification code unique to each study. | |
| chamber_id | Chamber identification code unique to each site. | |
| sample_id | Unique identifier for samples if there are more than one replicate per sampling event. | |
| porewater_method | Method used to collect porewater samples | sippers; peepers; piezometer; centrifugation; core |
| sample_year | Year of the sampling event. | YYYY |
| sample_month | Month of the sampling event. | MM |
| sample_day | Day of sampling event. If day was not recorded please use NA | DD |
| sample_start_time | Start of measurement period, local time, no DST | HH:mm:ss |
| sample_end_time | End of measurement period, local time, no DST | HH:mm:ss |
| porewater_depth | Depth of the porewater draw | centimeter |
| porewater_depth_min | If porewaters integrate several centimeters, min (upper) depth of the porewater draw | centimeter |
| porewater_depth_max | If porewaters integrate several centimeters, maximum (bottom) depth of the porewater draw | centimeter |
| porewater_temperature | Temperature of porewaters at chamber or site location | degreesCelcious |
| porewater_conductivity | Porewater conductivity at chamber or site location | milliSiemens |
| porewater_conductivity_depth | Depth of the porewater draw | centimeter |
| porewater_salinity | Salinity measured in porewater at chamber or site location | partsPerThousand |
| porewater_salinity_depth | Porewater salinity probe depth | centimeter |
| porewater_pH | soil porewater pH | numeric |
| porewater_O2_concentration | Dissolved oxygen measured in porewater at sampling time. | microMolar |
| porewater_SO4_concentration | Sulfate measured in porewater at sampling time. | milliMolar |
| porewater_H2S_concentration | Sulfide measured in porewater at sampling time. | microMolar |
| porewater_FeIII_concentration | Ferric iron measured in porewater at sampling time. | microMolar |
| porewater_FeII_concentration | Ferrous iron measured in porewater at sampling time | microMolar |
| porewater_NH4+ | Ammonium measured in porewater at sampling time | microMolar |
| porewater_NO3+NO2 | Nitrate-Nitrite measured in porewater at sampling time | microMolar |
| porewater_CH4_concentration | Methane measured in porewater at sampling time. | microMolar |
| porewater_DOC_concentration | Dissolved organic carbon measured in porewater at sampling time | microMolar |
| porewater_DIC_concentration | Dissolved inorganic carbon measured in porewater at sampling time | microMolar |