Selected Cell
Cell:
Value:
Project
Investigation
Study
ObservationUnit
Sample
Assay
AmpliconAssay
AmpliconLibraryAssay
DNAseqAssay
MetabolomicsAssay
ProteomicsAssay
RNAseqAssay
A
B
C
D
E
F
G
H
I
J
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
# 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 | |||
A
B
C
D
E
F
G
H
I
J
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
# 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 | |||
A
B
C
D
E
F
G
H
I
J
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
# 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 | |||
A
B
C
D
E
F
G
H
I
J
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
# 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 | |||
A
B
C
D
E
F
G
H
I
J
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
plant-associated | mechanical_damage | X | {text};{text} | pruning;bark | Information about any mechanical damage exerted on the plant; can include multiple damages and sites | ||||
plant-associated | mineral_nutr_regm | X | {text};{float} {unit};{Rn/start_time/end_time/duration} | potassium;15 gram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M | gram, mole per liter, milligram per liter | Information about treatment involving the use of mineral supplements; should include the name of mineral nutrient, 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 mineral nutrient regimens | |||
plant-associated | 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 | ||||
plant-associated | non_mineral_nutr_regm | X | {text};{float} {unit};{Rn/start_time/end_time/duration} | carbon dioxide;10 mole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M | gram, mole per liter, milligram per liter | Information about treatment involving the exposure of plant to non-mineral nutrient such as oxygen, hydrogen or carbon; should include the name of non-mineral nutrient, 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 non-mineral nutrient regimens | |||
plant-associated | 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) | |||
plant-associated | oxy_stat_samp | X | [aerobic|anaerobic|other] | aerobic | Oxygenation status of sample | ||||
plant-associated | ph_regm | X | {float};{Rn/start_time/end_time/duration} | 7.6;R2/2018-05-11:T14:30/2018-05-11T19:30/P1H30M | Information about treatment involving exposure of plants to varying levels of ph of the growth media, 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 regimen | ||||
plant-associated | 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 | ||||
plant-associated | pesticide_regm | X | {text};{float} {unit};{Rn/start_time/end_time/duration} | pyrethrum;0.6 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 insecticides; should include the name of pesticide, 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 pesticide regimens | |||
plant-associated | plant_growth_med | X | {termLabel} {[termID]} or [husk|other artificial liquid medium|other artificial solid medium|peat moss|perlite|pumice|sand|soil|vermiculite|water] | hydroponic plant culture media [EO:0007067] | Specification of the media for growing the plants or tissue cultured samples, e.g. soil, aeroponic, hydroponic, in vitro solid culture medium, in vitro liquid culture medium. Recommended value is a specific value from EO:plant growth medium (follow this link for terms http://purl.obolibrary.org/obo/EO_0007147) or other controlled vocabulary | ||||
plant-associated | plant_product | X | {text} | xylem sap [PO:0025539] | Substance produced by the plant, where the sample was obtained from | ||||
plant-associated | plant_sex | X | [Androdioecious|Androecious|Androgynous|Androgynomonoecious|Andromonoecious|Bisexual|Dichogamous|Diclinous|Dioecious|Gynodioecious|Gynoecious|Gynomonoecious|Hermaphroditic|Imperfect|Monoclinous|Monoecious|Perfect|Polygamodioecious|Polygamomonoecious|Polygamous|Protandrous|Protogynous|Subandroecious|Subdioecious|Subgynoecious|Synoecious|Trimonoecious|Trioecious|Unisexual] | Hermaphroditic | Sex of the reproductive parts on the whole plant, e.g. pistillate, staminate, monoecieous, hermaphrodite. | ||||
plant-associated | plant_struc | X | {termLabel} {[termID]} | epidermis [PO:0005679] | Name of plant structure the sample was obtained from; for Plant Ontology (PO) (v releases/2017-12-14) terms, see http://purl.bioontology.org/ontology/PO, e.g. petiole epidermis (PO_0000051). If an individual flower is sampled, the sex of it can be recorded here. | ||||
plant-associated | radiation_regm | X | {text};{float} {unit};{Rn/start_time/end_time/duration} | gamma radiation;60 gray;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M | rad, gray | Information about treatment involving exposure of plant or a plant part to a particular radiation regimen; should include the radiation type, amount or intensity 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 radiation regimens | |||
plant-associated | rainfall_regm | X | {float} {unit};{Rn/start_time/end_time/duration} | 15 millimeter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M | millimeter | Information about treatment involving an exposure to a given amount of rainfall, 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 | root_cond | X | {PMID}|{DOI}|{URL}|{text} | http://himedialabs.com/TD/PT158.pdf | Relevant rooting conditions such as field plot size, sowing density, container dimensions, number of plants per container. | ||||
plant-associated | root_med_carbon | X | {text};{float} {unit} | sucrose | milligram per liter | Source of organic carbon in the culture rooting medium; e.g. sucrose. | |||
plant-associated | root_med_macronutr | X | {text};{float} {unit} | KH2PO4;170 milligram per liter | milligram per liter | Measurement of the culture rooting medium macronutrients (N,P, K, Ca, Mg, S); e.g. KH2PO4 (170 mg/L). | |||
plant-associated | root_med_micronutr | X | {text};{float} {unit} | H3BO3;6.2 milligram per liter | milligram per liter | Measurement of the culture rooting medium micronutrients (Fe, Mn, Zn, B, Cu, Mo); e.g. H3BO3 (6.2 mg/L). | |||
plant-associated | root_med_suppl | X | {text};{float} {unit} | nicotinic acid;0.5 milligram per liter | milligram per liter | Organic supplements of the culture rooting medium, such as vitamins, amino acids, organic acids, antibiotics activated charcoal; e.g. nicotinic acid (0.5 mg/L). | |||
plant-associated | root_med_ph | X | {float} | 7.5 | pH measurement of the culture rooting medium; e.g. 5.5. | ||||
plant-associated | root_med_regl | X | {text};{float} {unit} | abscisic acid;0.75 milligram per liter | milligram per liter | Growth regulators in the culture rooting medium such as cytokinins, auxins, gybberellins, abscisic acid; e.g. 0.5 mg/L NAA. | |||
plant-associated | root_med_solid | X | {text} | agar | Specification of the solidifying agent in the culture rooting medium; e.g. agar. | ||||
plant-associated | salt_regm | X | {text};{float} {unit};{Rn/start_time/end_time/duration} | NaCl;5 gram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M | gram, microgram, mole per liter, gram per liter | Information about treatment involving use of salts as supplement to liquid and soil growth media; should include the name of salt, 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 salt regimens | |||
plant-associated | samp_capt_status | X | [active surveillance in response to an outbreak|active surveillance not initiated by an outbreak|farm sample|market sample|other] | farm sample | Reason for the sample | ||||
plant-associated | samp_dis_stage | X | {text} | infection | Stage of the disease at the time of sample collection, e.g. inoculation, penetration, infection, growth and reproduction, dissemination of pathogen. | ||||
plant-associated | 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 | |||
plant-associated | samp_store_dur | X | {duration} | P1Y6M | Duration for which the sample was stored | ||||
plant-associated | samp_store_loc | X | {text} | Freezer no:5 | Location at which sample was stored, usually name of a specific freezer/room | ||||
plant-associated | samp_store_temp | X | {float} {unit} | -80 degree Celsius | degree Celsius | Temperature at which sample was stored, e.g. -80 degree Celsius | |||
plant-associated | 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 | |||
plant-associated | season_environment | X | {text};{Rn/start_time/end_time/duration} | rainy;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M | Treatment involving an exposure to a particular season (e.g. Winter, summer, rabi, rainy etc.), 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 | ||||
plant-associated | standing_water_regm | X | {text};{Rn/start_time/end_time/duration} | standing water;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M | Treatment involving an exposure to standing water during a plant's life span, types can be flood water or standing water, 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 | temp | X | {float} {unit} | 25 degree Celsius | degree Celsius | Temperature of the sample at the time of sampling | |||
plant-associated | tiss_cult_growth_med | X | {PMID}|{DOI}|{URL}|{text} | https://link.springer.com/content/pdf/10.1007/BF02796489.pdf | Description of plant tissue culture growth media used | ||||
plant-associated | water_temp_regm | X | {float} {unit};{Rn/start_time/end_time/duration} | 15 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M | degree Celsius | Information about treatment involving an exposure to water with varying degree of 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 multiple regimens | |||
plant-associated | watering_regm | X | {float} {unit};{Rn/start_time/end_time/duration} | 1 liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M | milliliter, liter | Information about treatment involving an exposure to watering frequencies, 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 | |||
sediment | 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 | |||
sediment | 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 | |||
sediment | 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 | |||
sediment | alkyl_diethers | X | {float} {unit} | 0.005 mole per liter | mole per liter | Concentration of alkyl diethers | |||
sediment | aminopept_act | X | {float} {unit} | 0.269 mole per liter per hour | mole per liter per hour | Measurement of aminopeptidase activity | |||
sediment | ammonium | X | {float} {unit} | 1.5 milligram per liter | micromole per liter, milligram per liter, parts per million | Concentration of ammonium in the sample | |||
sediment | bacteria_carb_prod | X | {float} {unit} | 2.53 microgram per liter per hour | nanogram per hour | Measurement of bacterial carbon production | |||
sediment | 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 | |||
sediment | bishomohopanol | X | {float} {unit} | 14 microgram per liter | microgram per liter, microgram per gram | Concentration of bishomohopanol | |||
sediment | bromide | X | {float} {unit} | 0.05 parts per million | parts per million | Concentration of bromide | |||
sediment | calcium | X | {float} {unit} | 0.2 micromole per liter | milligram per liter, micromole per liter, parts per million | Concentration of calcium in the sample | |||
sediment | carb_nitro_ratio | X | {float} {unit} | 0.417361111 | Ratio of amount or concentrations of carbon to nitrogen | ||||
sediment | 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 | ||||
sediment | chloride | X | {float} {unit} | 5000 milligram per liter | milligram per liter, parts per million | Concentration of chloride in the sample | |||
sediment | chlorophyll | X | {float} {unit} | 5 milligram per cubic meter | milligram per cubic meter, microgram per liter | Concentration of chlorophyll | |||
sediment | 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) | |||
sediment | 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 | |||
sediment | 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 | |||
sediment | diss_hydrogen | X | {float} {unit} | 0.3 micromole per liter | micromole per liter | Concentration of dissolved hydrogen | |||
sediment | 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 | |||
sediment | 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 | |||
sediment | 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 | |||
sediment | diss_oxygen | X | {float} {unit} | 175 micromole per kilogram | micromole per kilogram, milligram per liter | Concentration of dissolved oxygen | |||
sediment | glucosidase_act | X | {float} {unit} | 5 mol per liter per hour | mol per liter per hour | Measurement of glucosidase activity | |||
sediment | 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 | |||
sediment | mean_frict_vel | X | {float} {unit} | 0.5 meter per second | meter per second | Measurement of mean friction velocity | |||
sediment | mean_peak_frict_vel | X | {float} {unit} | 1 meter per second | meter per second | Measurement of mean peak friction velocity | |||
sediment | methane | X | {float} {unit} | 0.15 micromole per liter | micromole per liter, parts per billion, parts per million | Methane (gas) amount or concentration at the time of sampling | |||
sediment | 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 | ||||
sediment | n_alkanes | X | {text};{float} {unit} | n-hexadecane;100 milligram per liter | micromole per liter | Concentration of n-alkanes; can include multiple n-alkanes | |||
sediment | nitrate | X | {float} {unit} | 65 micromole per liter | micromole per liter, milligram per liter, parts per million | Concentration of nitrate in the sample | |||
sediment | nitrite | X | {float} {unit} | 0.5 micromole per liter | micromole per liter, milligram per liter, parts per million | Concentration of nitrite in the sample | |||
sediment | nitro | X | {float} {unit} | 4.2 micromole per liter | micromole per liter | Concentration of nitrogen (total) | |||
sediment | org_carb | X | {float} {unit} | 1.5 microgram per liter | micromole per liter | Concentration of organic carbon | |||
sediment | org_matter | X | {float} {unit} | 1.75 milligram per cubic meter | microgram per liter | Concentration of organic matter | |||
sediment | org_nitro | X | {float} {unit} | 4 micromole per liter | microgram per liter | Concentration of organic nitrogen | |||
sediment | 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) | |||
sediment | oxy_stat_samp | X | [aerobic|anaerobic|other] | aerobic | Oxygenation status of sample | ||||
sediment | ph | X | {float} | 7.2 | Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid | ||||
sediment | particle_class | X | {text};{float} {unit} | particle; 5 milligram per liter | micrometer | Particles are classified, based on their size, into six general categories:clay, silt, sand, gravel, cobbles, and boulders; should include amount of particle preceded by the name of the particle type; can include multiple values | |||
sediment | part_org_carb | X | {float} {unit} | 1.92 micromole per liter | microgram per liter | Concentration of particulate organic carbon | |||
sediment | 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 | ||||
sediment | petroleum_hydrocarb | X | {float} {unit} | 0.05 micromole per liter | micromole per liter | Concentration of petroleum hydrocarbon | |||
sediment | phaeopigments | X | {text};{float} {unit} | 2.5 milligram per cubic meter | milligram per cubic meter | Concentration of phaeopigments; can include multiple phaeopigments | |||
sediment | phosphate | X | {float} {unit} | 0.7 micromole per liter | micromole per liter | Concentration of phosphate | |||
sediment | 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 | |||
sediment | porosity | X | {float} - {float} {unit} | 0.05 | percentage | Porosity of deposited sediment is volume of voids divided by the total volume of sample | |||
sediment | potassium | X | {float} {unit} | 463 milligram per liter | milligram per liter, parts per million | Concentration of potassium in the sample | |||
sediment | pressure | X | {float} {unit} | 50 atmosphere | atmosphere | Pressure to which the sample is subject to, in atmospheres | |||
sediment | redox_potential | X | {float} {unit} | 300 millivolt | millivolt | Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential | |||
sediment | 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 | |||
sediment | samp_store_dur | X | {duration} | P1Y6M | Duration for which the sample was stored | ||||
sediment | samp_store_loc | X | {text} | Freezer no:5 | Location at which sample was stored, usually name of a specific freezer/room | ||||
sediment | samp_store_temp | X | {float} {unit} | -80 degree Celsius | degree Celsius | Temperature at which sample was stored, e.g. -80 degree Celsius | |||
sediment | 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 | |||
sediment | sediment_type | X | [biogenous|cosmogenous|hydrogenous|lithogenous] | biogenous | Information about the sediment type based on major constituents | ||||
sediment | silicate | X | {float} {unit} | 0.05 micromole per liter | micromole per liter | Concentration of silicate | |||
sediment | sodium | X | {float} {unit} | 10.5 milligram per liter | milligram per liter, parts per million | Sodium concentration in the sample | |||
sediment | sulfate | X | {float} {unit} | 5 micromole per liter | micromole per liter, milligram per liter, parts per million | Concentration of sulfate in the sample | |||
sediment | sulfide | X | {float} {unit} | 2 micromole per liter | micromole per liter, milligram per liter, parts per million | Concentration of sulfide in the sample | |||
sediment | temp | X | {float} {unit} | 25 degree Celsius | degree Celsius | Temperature of the sample at the time of sampling | |||
sediment | tidal_stage | X | [low tide|ebb tide|flood tide|high tide] | high tide | Stage of tide | ||||
sediment | tot_carb | X | {float} {unit} | 5 microgram per liter | microgram per liter | Total carbon content |
A
B
C
D
E
F
G
H
I
J
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
# 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 | |||
A
B
C
D
E
F
G
H
I
J
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
# 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 | |||
A
B
C
D
E
F
G
H
I
J
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
# 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 | |||
A
B
C
D
E
F
G
H
I
J
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
# 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 | |||
A
B
C
D
E
F
G
H
I
J
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
# 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 | |||
A
B
C
D
E
F
G
H
I
J
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
# 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) | |||
A
B
C
D
E
F
G
H
I
J
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
# 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) | |||