Selected Cell
Cell:
Value:
Project
Investigation
Study
ObservationUnit
Sample
Assay
AmpliconAssay
AmpliconLibraryAssay
DNAseqAssay
MetabolomicsAssay
ProteomicsAssay
RNAseqAssay
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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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# Package | Structured comment name | Requirement | Value syntax | Example | Preferred unit | URL | Definition | ||
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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water | alkalinity_method | X | {text} | titration | Method used for alkalinity measurement | ||||
water | alkyl_diethers | X | {float} {unit} | 0.005 mole per liter | mole per liter, microgram per gram sample | Concentration of alkyl diethers | |||
water | aminopept_act | X | {float} {unit} | 0.269 mole per liter per hour | mole per liter per hour | Measurement of aminopeptidase activity | |||
water | ammonium | X | {float} {unit} | 1.5 milligram per liter | micromole per liter, milligram per liter, parts per million | Concentration of ammonium in the sample | |||
water | atmospheric_data | X | {text};{float} {unit} | wind speed;9 knots | Measurement of atmospheric data; can include multiple data | ||||
water | bacteria_carb_prod | X | {float} {unit} | 2.53 microgram per liter per hour | nanogram per hour, microgram per liter per hour | Measurement of bacterial carbon production | |||
water | bac_prod | X | {float} {unit} | 5 milligram per cubic meter per day | milligram per cubic meter per day | Bacterial production in the water column measured by isotope uptake | |||
water | bac_resp | X | {float} {unit} | 300 micromole oxygen per liter per hour | milligram per cubic meter per day, micromole oxygen per liter per hour | Measurement of bacterial respiration in the water column | |||
water | biomass | X | {text};{float} {unit} | total;20 gram | ton, kilogram, gram | Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements | |||
water | bishomohopanol | X | {float} {unit} | 14 microgram per liter | microgram per liter, microgram per gram | Concentration of bishomohopanol | |||
water | bromide | X | {float} {unit} | 0.05 parts per million | parts per million | Concentration of bromide | |||
water | calcium | X | {float} {unit} | 0.2 micromole per liter | milligram per liter, micromole per liter, parts per million | Concentration of calcium in the sample | |||
water | carb_nitro_ratio | X | {float}:{float} | 0.417361111 | Ratio of amount or concentrations of carbon to nitrogen | ||||
water | 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 | ||||
water | chloride | X | {float} {unit} | 5000 milligram per liter | milligram per liter, parts per million | Concentration of chloride in the sample | |||
water | chlorophyll | X | {float} {unit} | 5 milligram per cubic meter | milligram per cubic meter, microgram per liter | Concentration of chlorophyll | |||
water | conduc | X | {float} {unit} | 10 milliSiemens per centimeter | milliSiemens per centimeter | Electrical conductivity of water | |||
water | density | X | {float} {unit} | 1000 kilogram per cubic meter | gram per cubic meter, gram per cubic centimeter, kilogram per cubic meter | Density of the sample, which is its mass per unit volume (aka volumetric mass density) | |||
water | diether_lipids | X | {text};{float} {unit} | 0.2 nanogram per liter | nanogram per liter | Concentration of diether lipids; can include multiple types of diether lipids | |||
water | diss_carb_dioxide | X | {float} {unit} | 5 milligram per liter | micromole per liter, milligram per liter | Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample | |||
water | diss_hydrogen | X | {float} {unit} | 0.3 micromole per liter | micromole per liter | Concentration of dissolved hydrogen | |||
water | diss_inorg_carb | X | {float} {unit} | 2059 micromole per kilogram | microgram per liter, milligram per liter, parts per million, micromole per kilogram | Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter | |||
water | diss_inorg_nitro | X | {float} {unit} | 761 micromole per liter | microgram per liter, micromole per liter | Concentration of dissolved inorganic nitrogen | |||
water | diss_inorg_phosp | X | {float} {unit} | 56.5 micromole per liter | microgram per liter, milligram per liter, parts per million, micromole per liter | Concentration of dissolved inorganic phosphorus in the sample | |||
water | diss_org_carb | X | {float} {unit} | 197 micromole per liter | micromole per liter, milligram per liter | Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid | |||
water | diss_org_nitro | X | {float} {unit} | 0.05 micromole per liter | micromole per liter, microgram per liter, milligram per liter | Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 | |||
water | diss_oxygen | X | {float} {unit} | 175 micromole per kilogram | micromole per kilogram, milligram per liter | Concentration of dissolved oxygen | |||
water | down_par | X | {float} {unit} | 28.71 microEinstein per square meter per second | microEinstein per square meter per second, microEinstein per square centimeter per second | Visible waveband radiance and irradiance measurements in the water column | |||
water | fluor | X | {float} {unit} | 2.5 volts | milligram chlorophyll a per cubic meter, volts | Raw or converted fluorescence of water | |||
water | glucosidase_act | X | {float} {unit} | 5 mol per liter per hour | mol per liter per hour | Measurement of glucosidase activity | |||
water | light_intensity | X | {float} {unit} | 0.3 lux | lux | Measurement of light intensity | |||
water | magnesium | X | {float} {unit} | 52.8 micromole per kilogram | mole per liter, milligram per liter, parts per million, micromole per kilogram | Concentration of magnesium in the sample | |||
water | mean_frict_vel | X | {float} {unit} | 0.5 meter per second | meter per second | Measurement of mean friction velocity | |||
water | mean_peak_frict_vel | X | {float} {unit} | 1 meter per second | meter per second | Measurement of mean peak friction velocity | |||
water | 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 | ||||
water | n_alkanes | X | {text};{float} {unit} | n-hexadecane;100 milligram per liter | micromole per liter, milligram per liter | Concentration of n-alkanes; can include multiple n-alkanes | |||
water | nitrate | X | {float} {unit} | 65 micromole per liter | micromole per liter, milligram per liter, parts per million, micromole per kilogram | Concentration of nitrate in the sample | |||
water | nitrite | X | {float} {unit} | 0.5 micromole per liter | micromole per liter, milligram per liter, parts per million, micromole per kilogram | Concentration of nitrite in the sample | |||
water | nitro | X | {float} {unit} | 4.2 micromole per liter | micromole per liter | Concentration of nitrogen (total) | |||
water | org_carb | X | {float} {unit} | 1.5 microgram per liter | micromole per liter, microgram per liter | Concentration of organic carbon | |||
water | org_matter | X | {float} {unit} | 1.75 milligram per cubic meter | microgram per liter, milligram per cubic meter | Concentration of organic matter | |||
water | org_nitro | X | {float} {unit} | 4 micromole per liter | microgram per liter, micromole per liter | Concentration of organic nitrogen | |||
water | 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) | |||
water | oxy_stat_samp | X | [aerobic|anaerobic|other] | aerobic | Oxygenation status of sample | ||||
water | ph | X | {float} | 7.2 | Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid | ||||
water | part_org_carb | X | {float} {unit} | 1.92 micromole per liter | microgram per liter, micromole per liter | Concentration of particulate organic carbon | |||
water | part_org_nitro | X | {float} {unit} | 0.3 micromole per liter | microgram per liter, micromole per liter | Concentration of particulate organic nitrogen | |||
water | 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 | ||||
water | petroleum_hydrocarb | X | {float} {unit} | 0.05 micromole per liter | micromole per liter | Concentration of petroleum hydrocarbon | |||
water | phaeopigments | X | {text};{float} {unit} | 2.5 milligram per cubic meter | milligram per cubic meter | Concentration of phaeopigments; can include multiple phaeopigments | |||
water | phosphate | X | {float} {unit} | 0.7 micromole per liter | micromole per liter | Concentration of phosphate | |||
water | phosplipid_fatt_acid | X | {text};{float} {unit} | 2.98 milligram per liter | mole per gram, mole per liter, milligram per liter | Concentration of phospholipid fatty acids; can include multiple values | |||
water | photon_flux | X | {float} {unit} | 3.926 micromole photons per second per square meter | number of photons per second per unit area | Measurement of photon flux | |||
water | potassium | X | {float} {unit} | 463 milligram per liter | milligram per liter, parts per million | Concentration of potassium in the sample | |||
water | pressure | X | {float} {unit} | 50 atmosphere | atmosphere | Pressure to which the sample is subject to, in atmospheres | |||
water | primary_prod | X | {float} {unit} | 100 milligram per cubic meter per day | milligram per cubic meter per day, gram per square meter per day | Measurement of primary production, generally measured as isotope uptake | |||
water | redox_potential | X | {float} {unit} | 300 millivolt | millivolt | Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential | |||
water | salinity | X | {float} {unit} | 25 practical salinity unit | practical salinity unit, percentage | Salinity is the total concentration of all dissolved salts in a water 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 | |||
water | samp_store_dur | X | {duration} | P1Y6M | Duration for which the sample was stored | ||||
water | samp_store_loc | X | {text} | Freezer no:5 | Location at which sample was stored, usually name of a specific freezer/room | ||||
water | samp_store_temp | X | {float} {unit} | -80 degree Celsius | degree Celsius | Temperature at which sample was stored, e.g. -80 degree Celsius | |||
water | 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 | |||
water | silicate | X | {float} {unit} | 0.05 micromole per liter | micromole per liter | Concentration of silicate | |||
water | size_frac_low | X | {float} {unit} | 0.2 micrometer | micrometer | Refers to the mesh/pore size used to pre-filter/pre-sort the sample. Materials larger than the size threshold are excluded from the sample | |||
water | size_frac_up | X | {float} {unit} | 20 micrometer | micrometer | Refers to the mesh/pore size used to retain the sample. Materials smaller than the size threshold are excluded from the sample | |||
water | sodium | X | {float} {unit} | 10.5 milligram per liter | milligram per liter, parts per million | Sodium concentration in the sample | |||
water | soluble_react_phosp | X | {float} {unit} | 0.1 milligram per liter | micromole per liter, milligram per liter, parts per million | Concentration of soluble reactive phosphorus | |||
water | sulfate | X | {float} {unit} | 5 micromole per liter | micromole per liter, milligram per liter, parts per million | Concentration of sulfate in the sample | |||
water | sulfide | X | {float} {unit} | 2 micromole per liter | micromole per liter, milligram per liter, parts per million | Concentration of sulfide in the sample | |||
water | suspend_part_matter | X | {float} {unit} | 0.5 milligram per liter | milligram per liter | Concentration of suspended particulate matter | |||
water | temp | X | {float} {unit} | 25 degree Celsius | degree Celsius | Temperature of the sample at the time of sampling | |||
water | tidal_stage | X | [low tide|ebb tide|flood tide|high tide] | high tide | Stage of tide | ||||
water | tot_depth_water_col | X | {float} {unit} | 500 meter | meter | Measurement of total depth of water column | |||
water | tot_diss_nitro | X | {float} {unit} | 40 microgram per liter | microgram per liter | Total dissolved nitrogen concentration, reported as nitrogen, measured by: total dissolved nitrogen = NH4 + NO3NO2 + dissolved organic nitrogen | |||
water | tot_inorg_nitro | X | {float} {unit} | 40 microgram per liter | microgram per liter | Total inorganic nitrogen content | |||
water | 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 | |||
water | tot_part_carb | X | {float} {unit} | 35 micromole per liter | microgram per liter, micromole per liter | Total particulate carbon content | |||
water | tot_phosp | X | {float} {unit} | 0.03 milligram per liter | micromole per liter, milligram per liter, parts per million | Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus | |||
water | turbidity | X | {float} {unit} | 0.3 nephelometric turbidity units | formazin turbidity unit, formazin nephelometric units, nephelometric turbidity units | Measure of the amount of cloudiness or haziness in water caused by individual particles | |||
water | water_current | X | {float} {unit} | 10 cubic meter per second | cubic meter per second, knots | Measurement of magnitude and direction of flow within a fluid | |||
# http://cropnet.pl/phenotypes/wp-content/uploads/2016/04/MIAPPE.pdf | decimal degrees | ||||||||
- | |||||||||
measurement value | |||||||||
measurement value | |||||||||
country or sea name (INSDC or GAZ);region(GAZ);specific location name | |||||||||
date and time | |||||||||
Add terms that identify the major environment type(s) where your sample was collected. Recommend subclasses of biome [ENVO:00000428]. Multiple terms can be separated by one or more pipes e.g.: mangrove biome [ENVO:01000181]|estuarine biome [ENVO:01000020] | |||||||||
Add terms that identify environmental entities having causal influences upon the entity at time of sampling, multiple terms can be separated by pipes, e.g.: shoreline [ENVO:00000486]|intertidal zone [ENVO:00000316] | |||||||||
Add terms that identify the material displaced by the entity at time of sampling. Recommend subclasses of environmental material [ENVO:00010483]. Multiple terms can be separated by pipes e.g.: estuarine water [ENVO:01000301]|estuarine mud [ENVO:00002160] |
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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) | |||