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# Package | Structured comment name | Requirement | Value syntax | Example | Preferred unit | URL | Definition | ||
core | ProjectIdentifier | M | {text} | ProjectX | http://schema.org/identifier | Identifier corresponding to the project | |||
core | ProjectTitle | M | {text} | The title describing project X | http://schema.org/title | Title describing the project | |||
core | ProjectDescription | M | {text} | A longer description that explains what project X is all about. | http://schema.org/description | Description of the project | |||
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# Package | Structured comment name | Requirement | Value syntax | Example | Preferred unit | URL | Definition | ||
core | InvestigationIdentifier | M | {text} | InvestigationID | http://schema.org/identifier | Identifier corresponding to the investigation | |||
core | InvestigationTitle | M | {text} | Title about the investigation | http://schema.org/title | Title describing the investigation | |||
core | InvestigationDescription | M | {text} | Description of the investigation | http://schema.org/description | Description of the investigation | |||
core | FirstName | M | {text} | Jane | http://schema.org/givenName | The given name of a person | |||
core | LastName | M | {text} | Doe | http://schema.org/familyName | The family name of a person | |||
core | M | {text} | jane.doe@wur.nl | http://schema.org/email | The email address of a person | ||||
core | ORCID | M | {integer} | 123456789 | The orcid of a given person | ||||
core | Organization | M | {text} | Wageningen | http://schema.org/memberOf | Member of an organization | |||
core | Department | M | {text} | Laboratory of Systems and Synthetic Biology | http://schema.org/department | The department this person belongs to | |||
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core | StudyIdentifier | M | {text} | StudyX | http://schema.org/identifier | Identifier corresponding to the study | |||
core | StudyTitle | M | {text} | Title of the study | http://schema.org/title | Title describing the study | |||
core | StudyDescription | M | {text} | Description of the study | http://schema.org/description | Description of the study | |||
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# Package | Structured comment name | Requirement | Value syntax | Example | Preferred unit | URL | Definition | ||
core | ObservationUnitIdentifier | M | {text} | ObservationX | http://schema.org/identifier | Identifier corresponding to the entity that is being observed | |||
core | ObservationUnitName | M | {text} | ObservationX Name | http://schema.org/name | Name of the entity being observed | |||
core | ObservationUnitDescription | M | {text} | ObservationX description | http://schema.org/description | Description of the entity being observed | |||
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sediment | tot_depth_water_col | X | {float} {unit} | 500 meter | meter | Measurement of total depth of water column | |||
sediment | tot_nitro_content | X | {float} {unit} | 5 microgram per liter | microgram per liter, micromole per liter, milligram per liter | Total nitrogen content of the sample | |||
sediment | tot_org_carb | X | {float} {unit} | 6 gram Carbon per kilogram sample material | gram Carbon per kilogram sample material | Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content | |||
sediment | turbidity | X | {float} {unit} | 0.3 nephelometric turbidity units | formazin turbidity unit, formazin nephelometric units | Measure of the amount of cloudiness or haziness in water caused by individual particles | |||
sediment | water_content | X | {float} {unit} | 3 gram per gram | gram per gram or cubic centimeter per cubic centimeter | Water content measurement | |||
soil | depth | M | {float} {unit} | 10 meter | meter | Depth is defined as the vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples | |||
soil | elev | M | {float} {unit} | 100 meter | meter | Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit | |||
soil | cur_land_use | X | [cities|farmstead|industrial areas|roads/railroads|rock|sand|gravel|mudflats|salt flats|badlands|permanent snow or ice|saline seeps|mines/quarries|oil waste areas|small grains|row crops|vegetable crops|horticultural plants (e.g. tulips)|marshlands (grass,sedges,rushes)|tundra (mosses,lichens)|rangeland|pastureland (grasslands used for livestock grazing)|hayland|meadows (grasses,alfalfa,fescue,bromegrass,timothy)|shrub land (e.g. mesquite,sage-brush,creosote bush,shrub oak,eucalyptus)|successional shrub land (tree saplings,hazels,sumacs,chokecherry,shrub dogwoods,blackberries)|shrub crops (blueberries,nursery ornamentals,filberts)|vine crops (grapes)|conifers (e.g. pine,spruce,fir,cypress)|hardwoods (e.g. oak,hickory,elm,aspen)|intermixed hardwood and conifers|tropical (e.g. mangrove,palms)|rainforest (evergreen forest receiving >406 cm annual rainfall)|swamp (permanent or semi-permanent water body dominated by woody plants)|crop trees (nuts,fruit,christmas trees,nursery trees)] | conifers | Present state of sample site | ||||
soil | cur_vegetation | X | {text} | vegetation classififer | Vegetation classification from one or more standard classification systems, or agricultural crop | ||||
soil | cur_vegetation_meth | X | {PMID}|{DOI}|{URL} | http://dx.doi.org/10.1594/PANGAEA.726855|https://doi.pangaea.de/10.1594/PANGAEA.726855 | Reference or method used in vegetation classification | ||||
soil | previous_land_use | X | {text};{timestamp} | landuse; 2018-06-21 | Previous land use and dates | ||||
soil | previous_land_use_meth | X | {PMID}|{DOI}|{URL} | http://dx.doi.org/10.1594/PANGAEA.726855|https://doi.pangaea.de/10.1594/PANGAEA.726855 | Reference or method used in determining previous land use and dates | ||||
soil | crop_rotation | X | {boolean};{Rn/start_time/end_time/duration} | yes;R2/2017-01-01/2018-12-31/P6M | Whether or not crop is rotated, and if yes, rotation schedule | ||||
soil | agrochem_addition | X | {text};{float} {unit};{timestamp} | roundup;5 milligram per liter;2018-06-21 | gram, mole per liter, milligram per liter | Addition of fertilizers, pesticides, etc. - amount and time of applications | |||
soil | tillage | X | [drill|cutting disc|ridge till|strip tillage|zonal tillage|chisel|tined|mouldboard|disc plough] | chisel | Note method(s) used for tilling | ||||
soil | fire | X | {timestamp} | 2018-06-21T0:0:0+0000 | Historical and/or physical evidence of fire | ||||
soil | flooding | X | {timestamp} | 2018-06-21T0:0:0+0000 | Historical and/or physical evidence of flooding | ||||
soil | extreme_event | X | {timestamp} | 2018-06-21T0:0:0+0000 | Unusual physical events that may have affected microbial populations | ||||
soil | horizon | X | [O horizon|A horizon|E horizon|B horizon|C horizon|R layer|Permafrost] | A horizon | Specific layer in the land area which measures parallel to the soil surface and possesses physical characteristics which differ from the layers above and beneath | ||||
soil | horizon_meth | X | {PMID}|{DOI}|{URL} | http://dx.doi.org/10.1594/PANGAEA.726855|https://doi.pangaea.de/10.1594/PANGAEA.726855 | Reference or method used in determining the horizon | ||||
soil | sieving | H | {{text}|{float} {unit}};{float} {unit} | Collection design of pooled samples and/or sieve size and amount of sample sieved | |||||
soil | water_content | X | {float} | 5 gram per gram | gram per gram or cubic centimeter per cubic centimeter | Water content measurement | |||
soil | water_content_soil_meth | X | {PMID}|{DOI}|{URL} | http://dx.doi.org/10.1594/PANGAEA.726855|https://doi.pangaea.de/10.1594/PANGAEA.726855 | Reference or method used in determining the water content of soil | ||||
soil | samp_vol_we_dna_ext | X | {float} {unit} | 1500 milliliter | millliter, gram, milligram, square centimeter | Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction | |||
soil | pool_dna_extracts | X | {boolean};{integer} | yes;5 | Indicate whether multiple DNA extractions were mixed. If the answer yes, the number of extracts that were pooled should be given | ||||
soil | store_cond | X | {text};{duration} | -20 degree Celsius freezer;P2Y10D | Explain how and for how long the soil sample was stored before DNA extraction | ||||
soil | link_climate_info | X | {PMID}|{DOI}|{URL} | http://dx.doi.org/10.1594/PANGAEA.726855|https://doi.pangaea.de/10.1594/PANGAEA.726855 | Link to climate resource | ||||
soil | annual_temp | X | {float} {unit} | 12.5 degree Celsius | degree Celsius | Mean annual temperature | |||
soil | season_temp | X | {float} {unit} | 18 degree Celsius | degree Celsius | Mean seasonal temperature | |||
soil | annual_precpt | X | {float} {unit} | 5 millimeter | millimeter | The average of all annual precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps. | |||
soil | season_precpt | X | {float} {unit} | 5 millimeter | millimeter | The average of all seasonal precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps. | |||
soil | link_class_info | X | {PMID}|{DOI}|{URL} | http://dx.doi.org/10.1594/PANGAEA.726855|https://doi.pangaea.de/10.1594/PANGAEA.726855 | Link to digitized soil maps or other soil classification information | ||||
soil | fao_class | X | [Acrisols|Andosols|Arenosols|Cambisols|Chernozems|Ferralsols|Fluvisols|Gleysols|Greyzems|Gypsisols|Histosols|Kastanozems|Lithosols|Luvisols|Nitosols|Phaeozems|Planosols|Podzols|Podzoluvisols|Rankers|Regosols|Rendzinas|Solonchaks|Solonetz|Vertisols|Yermosols] | Luvisols | Soil classification from the FAO World Reference Database for Soil Resources. The list can be found at http://www.fao.org/nr/land/sols/soil/wrb-soil-maps/reference-groups | ||||
soil | local_class | X | {text} | class x | Soil classification based on local soil classification system | ||||
soil | local_class_meth | X | {PMID}|{DOI}|{URL} | http://dx.doi.org/10.1594/PANGAEA.726855|https://doi.pangaea.de/10.1594/PANGAEA.726855 | Reference or method used in determining the local soil classification | ||||
soil | soil_type | X | {text} | dirt | Soil series name or other lower-level classification | ||||
soil | soil_type_meth | X | {PMID}|{DOI}|{URL} | http://dx.doi.org/10.1594/PANGAEA.726855|https://doi.pangaea.de/10.1594/PANGAEA.726855 | Reference or method used in determining soil series name or other lower-level classification | ||||
soil | slope_gradient | X | {float} {unit} | 10 procent | percentage | Commonly called 'slope'. The angle between ground surface and a horizontal line (in percent). This is the direction that overland water would flow. This measure is usually taken with a hand level meter or clinometer | |||
soil | slope_aspect | X | {float} {unit} | 315 degrees | degree | The direction a slope faces. While looking down a slope use a compass to record the direction you are facing (direction or degrees); e.g., nw or 315 degrees. This measure provides an indication of sun and wind exposure that will influence soil temperature and evapotranspiration. | |||
soil | profile_position | X | [summit|shoulder|backslope|footslope|toeslope] | summit | Cross-sectional position in the hillslope where sample was collected.sample area position in relation to surrounding areas | ||||
soil | drainage_class | X | [very poorly|poorly|somewhat poorly|moderately well|well|excessively drained] | well | Drainage classification from a standard system such as the USDA system | ||||
soil | texture | X | {float} {unit} | 5 mm | The relative proportion of different grain sizes of mineral particles in a soil, as described using a standard system; express as % sand (50 um to 2 mm), silt (2 um to 50 um), and clay (<2 um) with textural name (e.g., silty clay loam) optional. | ||||
soil | texture_meth | X | {PMID}|{DOI}|{URL} | http://dx.doi.org/10.1594/PANGAEA.726855|https://doi.pangaea.de/10.1594/PANGAEA.726855 | Reference or method used in determining soil texture | ||||
soil | ph | X | {float} | 7.2 | Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid | ||||
soil | ph_meth | X | {PMID}|{DOI}|{URL} | http://dx.doi.org/10.1594/PANGAEA.726855|https://doi.pangaea.de/10.1594/PANGAEA.726855 | Reference or method used in determining ph | ||||
soil | tot_org_carb | X | {float} {unit} | 5 gram | gram Carbon per kilogram sample material | Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content | |||
soil | tot_org_c_meth | X | {PMID}|{DOI}|{URL} | http://dx.doi.org/10.1594/PANGAEA.726855|https://doi.pangaea.de/10.1594/PANGAEA.726855 | Reference or method used in determining total organic carbon | ||||
soil | tot_nitro_content | X | {float} {unit} | 5 micromole per liter | microgram per liter, micromole per liter, milligram per liter | Total nitrogen content of the sample | |||
soil | tot_nitro_content_meth | X | {PMID}|{DOI}|{URL} | http://dx.doi.org/10.1594/PANGAEA.726855|https://doi.pangaea.de/10.1594/PANGAEA.726855 | Reference or method used in determining the total nitrogen | ||||
soil | microbial_biomass | X | {float} {unit} | 5 gram | ton, kilogram, gram per kilogram soil | The part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer. If you keep this, you would need to have correction factors used for conversion to the final units | |||
soil | microbial_biomass_meth | X | {PMID}|{DOI}|{URL} | http://dx.doi.org/10.1594/PANGAEA.726855|https://doi.pangaea.de/10.1594/PANGAEA.726855 | Reference or method used in determining microbial biomass | ||||
soil | link_addit_analys | X | {PMID}|{DOI}|{URL} | http://dx.doi.org/10.1594/PANGAEA.726855|https://doi.pangaea.de/10.1594/PANGAEA.726855 | Link to additional analysis results performed on the sample | ||||
soil | extreme_salinity | X | {float} {unit} | 55 procent | millisiemens per meter | Measured salinity | |||
soil | salinity_meth | X | {PMID}|{DOI}|{URL} | http://dx.doi.org/10.1594/PANGAEA.726855|https://doi.pangaea.de/10.1594/PANGAEA.726855 | Reference or method used in determining salinity | ||||
soil | heavy_metals | X | {text};{float} {unit} | particle; 5 milligram per liter | microgram per gram | Heavy metals present and concentrationsany drug used by subject and the frequency of usage; can include multiple heavy metals and concentrations | |||
soil | heavy_metals_meth | X | {PMID}|{DOI}|{URL} | http://dx.doi.org/10.1594/PANGAEA.726855|https://doi.pangaea.de/10.1594/PANGAEA.726855 | Reference or method used in determining heavy metals | ||||
soil | al_sat | X | {float} {unit} | 5.5 % | percentage | Aluminum saturation (esp. For tropical soils) | |||
soil | al_sat_meth | X | {PMID}|{DOI}|{URL} | http://dx.doi.org/10.1594/PANGAEA.726855|https://doi.pangaea.de/10.1594/PANGAEA.726855 | Reference or method used in determining Al saturation | ||||
soil | misc_param | X | {text};{float} {unit} | Bicarbonate ion concentration;2075 micromole per kilogram | Any other measurement performed or parameter collected, that is not listed here | ||||
wastewater/sludge | depth | C | {float} {unit} | 10 meter | meter | Depth is defined as the vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples | |||
wastewater/sludge | alkalinity | X | {float} {unit} | 50 milligram per liter | milliequivalent per liter, milligram per liter | Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate | |||
wastewater/sludge | biochem_oxygen_dem | X | {float} {unit} | 5 micromole per liter | milligram per liter | Amount of dissolved oxygen needed by aerobic biological organisms in a body of water to break down organic material present in a given water sample at certain temperature over a specific time period | |||
wastewater/sludge | chem_administration | X | {termLabel} {[termID]}; {timestamp} | agar [CHEBI:2509];2018-05-11T20:00Z | List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi | ||||
wastewater/sludge | chem_oxygen_dem | X | {float} {unit} | 5 micromole per liter | milligram per liter | A measure of the capacity of water to consume oxygen during the decomposition of organic matter and the oxidation of inorganic chemicals such as ammonia and nitrite | |||
wastewater/sludge | efficiency_percent | X | {float} {unit} | 65 procent | micromole per liter | Percentage of volatile solids removed from the anaerobic digestor | |||
wastewater/sludge | emulsions | X | {text};{float} {unit} | particle; 5 milligram per liter | gram per liter | Amount or concentration of substances such as paints, adhesives, mayonnaise, hair colorants, emulsified oils, etc.; can include multiple emulsion types | |||
wastewater/sludge | gaseous_substances | X | {text};{float} {unit} | particle; 5 milligram per liter | micromole per liter | Amount or concentration of substances such as hydrogen sulfide, carbon dioxide, methane, etc.; can include multiple substances | |||
wastewater/sludge | indust_eff_percent | X | {float} {unit} | 5 procent | percentage | Percentage of industrial effluents received by wastewater treatment plant | |||
wastewater/sludge | inorg_particles | X | {text};{float} {unit} | particle; 5 milligram per liter | mole per liter, milligram per liter | Concentration of particles such as sand, grit, metal particles, ceramics, etc.; can include multiple particles | |||
wastewater/sludge | misc_param | X | {text};{float} {unit} | Bicarbonate ion concentration;2075 micromole per kilogram | Any other measurement performed or parameter collected, that is not listed here | ||||
wastewater/sludge | nitrate | X | {float} {unit} | 65 micromole per liter | micromole per liter, milligram per liter, parts per million | Concentration of nitrate in the sample | |||
wastewater/sludge | org_particles | X | {text};{float} {unit} | particle; 5 milligram per liter | gram per liter | Concentration of particles such as faeces, hairs, food, vomit, paper fibers, plant material, humus, etc. | |||
wastewater/sludge | organism_count | X | {text};{float} {unit};[qPCR|ATP|MPN|other] | total prokaryotes;3.5e7 cells per milliliter;qPCR | number of cells per cubic meter, number of cells per milliliter, number of cells per cubic centimeter | Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr) | |||
wastewater/sludge | oxy_stat_samp | X | [aerobic|anaerobic|other] | aerobic | Oxygenation status of sample | ||||
wastewater/sludge | ph | X | {float} | 7.2 | Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid | ||||
wastewater/sludge | perturbation | X | {text};{Rn/start_time/end_time/duration} | antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M | Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types | ||||
wastewater/sludge | phosphate | X | {float} {unit} | 0.7 micromole per liter | micromole per liter | Concentration of phosphate | |||
wastewater/sludge | pre_treatment | X | {text} | pre treatment x | The process of pre-treatment removes materials that can be easily collected from the raw wastewater | ||||
wastewater/sludge | primary_treatment | X | {text} | treatment x | The process to produce both a generally homogeneous liquid capable of being treated biologically and a sludge that can be separately treated or processed | ||||
wastewater/sludge | reactor_type | X | {text} | single stage reactor | Anaerobic digesters can be designed and engineered to operate using a number of different process configurations, as batch or continuous, mesophilic, high solid or low solid, and single stage or multistage | ||||
wastewater/sludge | samp_salinity | X | {float} {unit} | 1 milligram per liter | milligram per liter, practical salinity unit, percentage | Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater | |||
wastewater/sludge | samp_store_dur | X | {duration} | P1Y6M | Duration for which the sample was stored | ||||
wastewater/sludge | samp_store_loc | X | {text} | Freezer no:5 | Location at which sample was stored, usually name of a specific freezer/room | ||||
wastewater/sludge | samp_store_temp | X | {float} {unit} | -80 degree Celsius | degree Celsius | Temperature at which sample was stored, e.g. -80 degree Celsius | |||
wastewater/sludge | samp_vol_we_dna_ext | X | {float} {unit} | 1500 milliliter | millliter, gram, milligram, square centimeter | Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction | |||
wastewater/sludge | secondary_treatment | X | {text} | secondary treatment | The process for substantially degrading the biological content of the sewage | ||||
wastewater/sludge | sewage_type | X | {text} | industrial | Type of wastewater treatment plant as municipial or industrial | ||||
wastewater/sludge | sludge_retent_time | X | {float} {unit} | 5 hours | hours | The time activated sludge remains in reactor | |||
wastewater/sludge | sodium | X | {float} {unit} | 10.5 milligram per liter | milligram per liter, parts per million | Sodium concentration in the sample | |||
wastewater/sludge | soluble_inorg_mat | X | {text};{float} {unit} | substance; 5 milligram per liter | gram, microgram, mole per liter, gram per liter, parts per million | Concentration of substances such as ammonia, road-salt, sea-salt, cyanide, hydrogen sulfide, thiocyanates, thiosulfates, etc. | |||
wastewater/sludge | soluble_org_mat | X | {text};{float} {unit} | substance; 5 milligram per liter | gram, microgram, mole per liter, gram per liter, parts per million | Concentration of substances such as urea, fruit sugars, soluble proteins, drugs, pharmaceuticals, etc. | |||
wastewater/sludge | suspend_solids | X | {text};{float} {unit} | substance; 5 milligram per liter | gram, microgram, milligram per liter, mole per liter, gram per liter, part per million | Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances | |||
wastewater/sludge | temp | X | {float} {unit} | 25 degree Celsius | degree Celsius | Temperature of the sample at the time of sampling | |||
wastewater/sludge | tertiary_treatment | X | {text} | treatment x | The process providing a final treatment stage to raise the effluent quality before it is discharged to the receiving environment | ||||
wastewater/sludge | tot_nitro | X | {float} {unit} | 50 micromole per liter | microgram per liter, micromole per liter, milligram per liter | Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen | |||
wastewater/sludge | tot_phosphate | X | {float} {unit} | 5 micromole per liter | microgram per liter, micromole per liter | Total amount or concentration of phosphate | |||
wastewater/sludge | wastewater_type | X | {text} | rainfall | The origin of wastewater such as human waste, rainfall, storm drains, etc. | ||||
water | depth | M | {float} {unit} | 10 meter | meter | Depth is defined as the vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples | |||
water | elev | C | {float} {unit} | 100 meter | meter | Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit | |||
water | alkalinity | X | {float} {unit} | 50 milligram per liter | milliequivalent per liter, milligram per liter | Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate |
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# Package | Structured comment name | Requirement | Value syntax | Example | URL | Preferred unit | Definition | ||
core | AssayIdentifier | M | {text} | AssayId | http://schema.org/identifier | Identifier that corresponds to this assay | |||
core | AssayName | M | {text} | Assay name | http://schema.org/name | The name of this assay | |||
core | AssayDescription | M | {text} | assay description | http://schema.org/description | The description of this assay | |||
core | IsolationProtocol | M | {text} | http://example.com | The protocol used for isolation (name or url) | ||||
core | Facility | M | {text} | facility name | The facility that was used for generating the data | ||||
core | Platform | M | {text} | Illumina | The platform that was used for generating the data | ||||
core | InstrumentModel | M | {text} | Illumina HiSeq | The instrument model that was used for generating the data | ||||
core | Date | M | {timestamp} | 2018-06-03T0:0:0+0000 | https://schema.org/dateCreated | The date when the data generation took place | |||
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# Package | Structured comment name | Requirement | Value syntax | Example | URL | Preferred unit | Definition | ||
core | FileNameForward | M | {text} | NG-13425_Fyig_005_lib124679_5331_4_1.fastq.gz | http://m-unlock.nl/ontology/file | File name of the forward reads | |||
core | FileNameReverse | X | {text} | NG-13425_Fyig_005_lib124679_5331_4_2.fastq.gz | http://m-unlock.nl/ontology/file | File name of the reverse reads | |||
core | ForwardPrimer | M | {dna} | RGGATTAGATACCC | http://m-unlock.nl/ontology/forwardPrimer | The forward primer | |||
core | ReversePrimer | X | {dna} | CGACRRCCATGCANCACCT | http://m-unlock.nl/ontology/reversePrimer | The reverse primer used | |||
core | PrimerNames | X | {text} | 784F-1064R | http://m-unlock.nl/ontology/primerNames | The primer names corresponding to the primers used | |||
core | target_subfragment | M | {text} | V4 | http://m-unlock.nl/ontology/target_subfragment | Name of subfragment of a gene or locus (e.g. V3-4, V4, V6, V9, ITS). Important to e.g. identify special regions on marker genes like V6 on 16S rRNA | |||
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# Package | Structured comment name | Requirement | Value syntax | Example | URL | Preferred unit | Definition | ||
core | ForwardBarcodeSequence | M | {dna} | GGTACCAA | http://m-unlock.nl/ontology/forwardBarcode | The forward barcode used for this assay | |||
core | ReverseBarcodeSequence | X | {dna} | GGTAGAAT | http://m-unlock.nl/ontology/reverseBarcode | When applicable | |||
core | FileNameForward | M | {text} | NG-13425_Fyig_005_lib124679_5331_4_1.fastq.gz | http://m-unlock.nl/ontology/file | File name of the forward reads | |||
core | FileNameReverse | X | {text} | NG-13425_Fyig_005_lib124679_5331_4_2.fastq.gz | http://m-unlock.nl/ontology/file | When applicable | |||
core | ForwardPrimer | M | {dna} | RGGATTAGATACCC | http://m-unlock.nl/ontology/forwardPrimer | The forward primer | |||
core | ReversePrimer | X | {dna} | CGACRRCCATGCANCACCT | http://m-unlock.nl/ontology/reversePrimer | When applicable the reverse primer used | |||
core | PrimerNames | X | {text} | 784F-1064R | http://m-unlock.nl/ontology/primerNames | The primer names corresponding to the primers used | |||
core | target_subfragment | M | {text} | V4 | http://m-unlock.nl/ontology/target_subfragment | Name of subfragment of a gene or locus (e.g. V3-4, V4, V6, V9, ITS). Important to e.g. identify special regions on marker genes like V6 on 16S rRNA | |||
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# Package | Structured comment name | Requirement | Value syntax | Example | URL | Preferred unit | Definition | ||
core | FileNameForward | M | {text} | NG-13425_Fyig_005_lib124679_5331_4_1.fastq.gz | http://m-unlock.nl/ontology/file | File name of the forward reads | |||
core | FileNameReverse | X | {text} | NG-13425_Fyig_005_lib124679_5331_4_2.fastq.gz | http://m-unlock.nl/ontology/file | When applicable | |||
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# Package | Structured comment name | Requirement | Value syntax | Example | URL | Preferred unit | Definition | ||
core | FileName | M | {text} | filex.gz | http://m-unlock.nl/ontology/file | File name of the forward reads | |||
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# Package | Structured comment name | Requirement | Value syntax | Example | URL | Preferred unit | Definition | ||
core | FileName | M | {text} | file.gz | http://m-unlock.nl/ontology/file | File name of the forward reads | |||
core | Reference | X | {text} | GCA_000007565.2 | http://m-unlock.nl/ontology/reference | Reference genome to which reads can be mapped to (e.g. GCA_... ENA number) | |||
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# Package | Structured comment name | Requirement | Value syntax | Example | URL | Definition | |||
core | FileNameForward | M | {text} | NG-13425_Fyig_005_lib124679_5331_4_1.fastq.gz | http://m-unlock.nl/ontology/file | File name of the forward reads | |||
core | FileNameReverse | X | {text} | NG-13425_Fyig_005_lib124679_5331_4_2.fastq.gz | http://m-unlock.nl/ontology/file | When applicable the file name of the reverse reads | |||
core | Reference | X | {text} | GCA_000007565.2 | http://m-unlock.nl/ontology/reference | Reference genome to which reads can be mapped to (e.g. GCA_... ENA number) | |||