Selected Cell
Cell:
Value:
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ObservationUnit
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AmpliconAssay
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DNAseqAssay
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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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microbial mat/biofilm | phosphate | X | {float} {unit} | 0.7 micromole per liter | micromole per liter | Concentration of phosphate | |||
microbial mat/biofilm | phosplipid_fatt_acid | X | {text};{float} {unit} | 2.98 milligram per liter | mole per gram, mole per liter | Concentration of phospholipid fatty acids; can include multiple values | |||
microbial mat/biofilm | potassium | X | {float} {unit} | 463 milligram per liter | milligram per liter, parts per million | Concentration of potassium in the sample | |||
microbial mat/biofilm | pressure | X | {float} {unit} | 50 atmosphere | atmosphere | Pressure to which the sample is subject to, in atmospheres | |||
microbial mat/biofilm | redox_potential | X | {float} {unit} | 300 millivolt | millivolt | Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential | |||
microbial mat/biofilm | 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 | |||
microbial mat/biofilm | samp_store_dur | X | {duration} | P1Y6M | Duration for which the sample was stored | ||||
microbial mat/biofilm | samp_store_loc | X | {text} | Freezer no:5 | Location at which sample was stored, usually name of a specific freezer/room | ||||
microbial mat/biofilm | samp_store_temp | X | {float} {unit} | -80 degree Celsius | degree Celsius | Temperature at which sample was stored, e.g. -80 degree Celsius | |||
microbial mat/biofilm | 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 | |||
microbial mat/biofilm | silicate | X | {float} {unit} | 0.05 micromole per liter | micromole per liter | Concentration of silicate | |||
microbial mat/biofilm | sodium | X | {float} {unit} | 10.5 milligram per liter | milligram per liter, parts per million | Sodium concentration in the sample | |||
microbial mat/biofilm | sulfate | X | {float} {unit} | 5 micromole per liter | micromole per liter, milligram per liter, parts per million | Concentration of sulfate in the sample | |||
microbial mat/biofilm | sulfide | X | {float} {unit} | 2 micromole per liter | micromole per liter, milligram per liter, parts per million | Concentration of sulfide in the sample | |||
microbial mat/biofilm | temp | X | {float} {unit} | 25 degree Celsius | degree Celsius | Temperature of the sample at the time of sampling | |||
microbial mat/biofilm | tot_carb | X | {float} {unit} | 5 gram | microgram per liter | Total carbon content | |||
microbial mat/biofilm | tot_nitro_content | X | {float} {unit} | 2 milligram | microgram per liter, micromole per liter, milligram per liter | Total nitrogen content of the sample | |||
microbial mat/biofilm | tot_org_carb | X | {float} {unit} | 2 milligram | gram Carbon per kilogram sample material | Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content | |||
microbial mat/biofilm | 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 | |||
microbial mat/biofilm | water_content | X | {float} {unit} | 2 gram per liter | gram per gram or cubic centimeter per cubic centimeter | Water content measurement | |||
miscellaneous natural or artificial environment | alt | C | {float} {unit} | 100 meter | meter | Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth’s surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air | |||
miscellaneous natural or artificial environment | 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 | |||
miscellaneous natural or artificial environment | 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 | |||
miscellaneous natural or artificial environment | 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 | |||
miscellaneous natural or artificial environment | ammonium | X | {float} {unit} | 1.5 milligram per liter | micromole per liter, milligram per liter, parts per million | Concentration of ammonium in the sample | |||
miscellaneous natural or artificial environment | 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 | |||
miscellaneous natural or artificial environment | bromide | X | {float} {unit} | 0.05 parts per million | parts per million | Concentration of bromide | |||
miscellaneous natural or artificial environment | calcium | X | {float} {unit} | 0.2 micromole per liter | milligram per liter, micromole per liter, parts per million | Concentration of calcium in the sample | |||
miscellaneous natural or artificial environment | 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 | ||||
miscellaneous natural or artificial environment | chloride | X | {float} {unit} | 5000 milligram per liter | milligram per liter, parts per million | Concentration of chloride in the sample | |||
miscellaneous natural or artificial environment | chlorophyll | X | {float} {unit} | 5 milligram per cubic meter | milligram per cubic meter, microgram per liter | Concentration of chlorophyll | |||
miscellaneous natural or artificial environment | density | X | {float} {unit} | 1000 kilogram per cubic meter | gram per cubic meter, gram per cubic centimeter | Density of the sample, which is its mass per unit volume (aka volumetric mass density) | |||
miscellaneous natural or artificial environment | 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 | |||
miscellaneous natural or artificial environment | 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 | |||
miscellaneous natural or artificial environment | diss_hydrogen | X | {float} {unit} | 0.3 micromole per liter | micromole per liter | Concentration of dissolved hydrogen | |||
miscellaneous natural or artificial environment | diss_inorg_carb | X | {float} {unit} | 2059 micromole per kilogram | microgram per liter, milligram per liter, parts per million | Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter | |||
miscellaneous natural or artificial environment | diss_org_nitro | X | {float} {unit} | 0.05 micromole per liter | microgram per liter, milligram per liter | Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 | |||
miscellaneous natural or artificial environment | diss_oxygen | X | {float} {unit} | 175 micromole per kilogram | micromole per kilogram, milligram per liter | Concentration of dissolved oxygen | |||
miscellaneous natural or artificial environment | 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 | ||||
miscellaneous natural or artificial environment | nitrate | X | {float} {unit} | 65 micromole per liter | micromole per liter, milligram per liter, parts per million | Concentration of nitrate in the sample | |||
miscellaneous natural or artificial environment | nitrite | X | {float} {unit} | 0.5 micromole per liter | micromole per liter, milligram per liter, parts per million | Concentration of nitrite in the sample | |||
miscellaneous natural or artificial environment | nitro | X | {float} {unit} | 4.2 micromole per liter | micromole per liter | Concentration of nitrogen (total) | |||
miscellaneous natural or artificial environment | org_carb | X | {float} {unit} | 1.5 microgram per liter | micromole per liter | Concentration of organic carbon | |||
miscellaneous natural or artificial environment | org_matter | X | {float} {unit} | 1.75 milligram per cubic meter | microgram per liter | Concentration of organic matter | |||
miscellaneous natural or artificial environment | org_nitro | X | {float} {unit} | 4 micromole per liter | microgram per liter | Concentration of organic nitrogen | |||
miscellaneous natural or artificial environment | 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) | |||
miscellaneous natural or artificial environment | oxy_stat_samp | X | [aerobic|anaerobic|other] | aerobic | Oxygenation status of sample | ||||
miscellaneous natural or artificial environment | ph | X | {float} | 7.2 | Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid | ||||
miscellaneous natural or artificial environment | 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 | ||||
miscellaneous natural or artificial environment | phosphate | X | {float} {unit} | 0.7 micromole per liter | micromole per liter | Concentration of phosphate | |||
miscellaneous natural or artificial environment | phosplipid_fatt_acid | X | {text};{float} {unit} | 2.98 milligram per liter | mole per gram, mole per liter | Concentration of phospholipid fatty acids; can include multiple values | |||
miscellaneous natural or artificial environment | potassium | X | {float} {unit} | 463 milligram per liter | milligram per liter, parts per million | Concentration of potassium in the sample | |||
miscellaneous natural or artificial environment | pressure | X | {float} {unit} | 50 atmosphere | atmosphere | Pressure to which the sample is subject to, in atmospheres | |||
miscellaneous natural or artificial environment | 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 | |||
miscellaneous natural or artificial environment | samp_store_dur | X | {duration} | P1Y6M | Duration for which the sample was stored | ||||
miscellaneous natural or artificial environment | samp_store_loc | X | {text} | Freezer no:5 | Location at which sample was stored, usually name of a specific freezer/room | ||||
miscellaneous natural or artificial environment | samp_store_temp | X | {float} {unit} | -80 degree Celsius | degree Celsius | Temperature at which sample was stored, e.g. -80 degree Celsius | |||
miscellaneous natural or artificial environment | 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 | |||
miscellaneous natural or artificial environment | silicate | X | {float} {unit} | 0.05 micromole per liter | micromole per liter | Concentration of silicate | |||
miscellaneous natural or artificial environment | sodium | X | {float} {unit} | 10.5 milligram per liter | milligram per liter, parts per million | Sodium concentration in the sample | |||
miscellaneous natural or artificial environment | sulfate | X | {float} {unit} | 5 micromole per liter | micromole per liter, milligram per liter, parts per million | Concentration of sulfate in the sample | |||
miscellaneous natural or artificial environment | sulfide | X | {float} {unit} | 2 micromole per liter | micromole per liter, milligram per liter, parts per million | Concentration of sulfide in the sample | |||
miscellaneous natural or artificial environment | temp | X | {float} {unit} | 25 degree Celsius | degree Celsius | Temperature of the sample at the time of sampling | |||
miscellaneous natural or artificial environment | 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 | |||
plant-associated | 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 | |||
plant-associated | 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 | |||
plant-associated | air_temp_regm | X | {float} {unit};{Rn/start_time/end_time/duration} | 25 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M | degree Celsius | Information about treatment involving an exposure to varying temperatures; should include the temperature, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include different temperature regimens | |||
plant-associated | ances_data | X | {text} | A/3*B | Information about either pedigree or other ancestral information description (e.g. parental variety in case of mutant or selection), e.g. A/3*B (meaning [(A x B) x B] x B) | ||||
plant-associated | antibiotic_regm | X | {text};{float} {unit};{Rn/start_time/end_time/duration} | penicillin;5 milligram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M | milligram | Information about treatment involving antibiotic administration; should include the name of antibiotic, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple antibiotic regimens | |||
plant-associated | biol_stat | X | [wild|natural|semi-natural|inbred line|breeder's line|hybrid|clonal selection|mutant] | natural | The level of genome modification | ||||
plant-associated | biotic_regm | X | {text} | sample inoculated with Rhizobium spp. Culture | Information about treatment(s) involving use of biotic factors, such as bacteria, viruses or fungi. | ||||
plant-associated | 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 | ||||
plant-associated | chem_mutagen | X | {text};{float} {unit};{Rn/start_time/end_time/duration} | nitrous acid;0.5 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M | milligram per liter | Treatment involving use of mutagens; should include the name of mutagen, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple mutagen regimens | |||
plant-associated | climate_environment | X | {text};{Rn/start_time/end_time/duration} | tropical climate;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M | Treatment involving an exposure to a particular climate; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple climates | ||||
plant-associated | cult_root_med | X | {text}|{PMID}|{DOI}|{URL} | http://himedialabs.com/TD/PT158.pdf | Name or reference for the hydroponic or in vitro culture rooting medium; can be the name of a commonly used medium or reference to a specific medium, e.g. Murashige and Skoog medium. If the medium has not been formally published, use the rooting medium descriptors. | ||||
plant-associated | fertilizer_regm | X | {text};{float} {unit};{Rn/start_time/end_time/duration} | urea;0.6 milligram per liter;R2/2018-05-11:T14:30/2018-05-11T19:30/P1H30M | gram, mole per liter, milligram per liter | Information about treatment involving the use of fertilizers; should include the name of fertilizer, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple fertilizer regimens | |||
plant-associated | fungicide_regm | X | {text};{float} {unit};{Rn/start_time/end_time/duration} | bifonazole;1 mole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M | gram, mole per liter, milligram per liter | Information about treatment involving use of fungicides; should include the name of fungicide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple fungicide regimens | |||
plant-associated | gaseous_environment | X | {text};{float} {unit};{Rn/start_time/end_time/duration} | nitric oxide;0.5 micromole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M | micromole per liter | Use of conditions with differing gaseous environments; should include the name of gaseous compound, amount administered, treatment duration, interval and total experimental duration; can include multiple gaseous environment regimens | |||
plant-associated | genetic_mod | X | {PMID}|{DOI}|{URL}|{text} | aox1A transgenic | Genetic modifications of the genome of an organism, which may occur naturally by spontaneous mutation, or be introduced by some experimental means, e.g. specification of a transgene or the gene knocked-out or details of transient transfection | ||||
plant-associated | gravity | X | {float} {unit};{Rn/start_time/end_time/duration} | 12 g;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M | meter per square second, g | Information about treatment involving use of gravity factor to study various types of responses in presence, absence or modified levels of gravity; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple treatments | |||
plant-associated | growth_facil | X | {text}|{termLabel} {[termID]} | Growth chamber [CO_715:0000189] | Type of facility where the sampled plant was grown; controlled vocabulary: growth chamber, open top chamber, glasshouse, experimental garden, field. Alternatively use Crop Ontology (CO) terms, see http://www.cropontology.org/ontology/CO_715/Crop%20Research | ||||
plant-associated | growth_habit | X | [erect|semi-erect|spreading|prostrate] | spreading | Characteristic shape, appearance or growth form of a plant species | ||||
plant-associated | growth_hormone_regm | X | {text};{float} {unit};{Rn/start_time/end_time/duration} | abscisic acid;0.5 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M | gram, mole per liter, milligram per liter | Information about treatment involving use of growth hormones; should include the name of growth hormone, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple growth hormone regimens | |||
plant-associated | herbicide_regm | X | {text};{float} {unit};{Rn/start_time/end_time/duration} | atrazine;10 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M | gram, mole per liter, milligram per liter | Information about treatment involving use of herbicides; information about treatment involving use of growth hormones; should include the name of herbicide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens | |||
plant-associated | host_age | X | {float} {unit} | 10 days | year, day, hour | Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees | |||
plant-associated | host_common_name | X | {text} | rice | Common name of the host, e.g. Human | ||||
plant-associated | host_disease_stat | X | {text}|{termLabel} {[termID]} | downy mildew | List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text. | ||||
plant-associated | host_dry_mass | X | {float} {unit} | 500 gram | kilogram, gram | Measurement of dry mass | |||
plant-associated | host_genotype | X | {text} | Ts | Observed genotype | ||||
plant-associated | host_height | X | {float} {unit} | 1 meter | centimeter, millimeter, meter | The height of subject | |||
plant-associated | host_infra_specific_name | X | {text} | glabrum | Taxonomic information about the host below subspecies level | ||||
plant-associated | host_infra_specific_rank | X | {text} | subvariety | Taxonomic rank information about the host below subspecies level, such as variety, form, rank etc. | ||||
plant-associated | host_length | X | {float} {unit} | 1 meter | centimeter, millimeter, meter | The length of subject | |||
plant-associated | host_life_stage | X | {text} | adult | Description of life stage of host | ||||
plant-associated | host_phenotype | X | {text};{termLabel} {[termID]} | seed pod; green [PATO:0000320] | Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP | ||||
plant-associated | host_taxid | X | {NCBI taxid} | 4530 | NCBI taxon id of the host, e.g. 9606 | ||||
plant-associated | host_tot_mass | X | {float} {unit} | 2500 gram | kilogram, gram | Total mass of the host at collection, the unit depends on host | |||
plant-associated | host_wet_mass | X | {float} {unit} | 1500 gram | kilogram, gram | Measurement of wet mass | |||
plant-associated | humidity_regm | X | {float} {unit};{Rn/start_time/end_time/duration} | 25 gram per cubic meter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M | gram per cubic meter | Information about treatment involving an exposure to varying degree of humidity; information about treatment involving use of growth hormones; should include amount of humidity administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens | |||
plant-associated | light_regm | X | {text};{float} {unit};{float} {unit} | incandescant light;10 lux;450 nanometer | lux; micrometer, nanometer, angstrom | Information about treatment(s) involving exposure to light, including both light intensity and quality. |
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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) | |||