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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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hydrocarbon resources-fluids/swabs | samp_loc_corr_rate | C | {float} - {float} {unit} | 3 - 5 units | millimeter per year | Metal corrosion rate is the speed of metal deterioration due to environmental conditions. As environmental conditions change corrosion rates change accordingly. Therefore, long term corrosion rates are generally more informative than short term rates and for that reason they are preferred during reporting. In the case of suspected MIC, corrosion rate measurements at the time of sampling might provide insights into the involvement of certain microbial community members in MIC as well as potential microbial interplays | |||
hydrocarbon resources-fluids/swabs | samp_well_name | C | {text} | BXA1123 | Name of the well (e.g. BXA1123) where sample was taken | ||||
hydrocarbon resources-fluids/swabs | win | C | {text} | XAP4524 | A unique identifier of a well or wellbore. This is part of the Global Framework for Well Identification initiative which is compiled by the Professional Petroleum Data Management Association (PPDM) in an effort to improve well identification systems. (Supporting information: https://ppdm.org/ and http://dl.ppdm.org/dl/690) | ||||
hydrocarbon resources-fluids/swabs | samp_type | M | [core|rock trimmings|drill cuttings|piping section|coupon|pigging debris|solid deposit|produced fluid|produced water|injected water|water from treatment plant|fresh water|sea water|drilling fluid|procedural blank|positive control|negative control|other] | solid deposit | Type of material (i.e. sample) collected. Includes types like core, rock trimmings, drill cuttings, piping section, coupon, pigging debris, solid deposit, produced fluid, produced water, injected water, swabs, etc. If "other" is specified, please propose entry in "additional info" field | ||||
hydrocarbon resources-fluids/swabs | samp_subtype | C | [oil phase|water phase|biofilm|not applicable|other] | biofilm | Name of sample sub-type. For example if "sample type" is "Produced Water" then subtype could be "Oil Phase" or "Water Phase". If "other" is specified, please propose entry in "additional info" field | ||||
hydrocarbon resources-fluids/swabs | samp_collection_point | M | [well|test well|drilling rig|wellhead|separator|storage tank|other] | well | Sampling point on the asset were sample was collected (e.g. Wellhead, storage tank, separator, etc). If "other" is specified, please propose entry in "additional info" field | ||||
hydrocarbon resources-fluids/swabs | temp | M | {float} {unit} | 25 degree Celsius | degree Celsius | Temperature of the sample at the time of sampling | |||
hydrocarbon resources-fluids/swabs | pressure | X | {float} {unit} | 50 atmosphere | atmosphere | Pressure to which the sample is subject to, in atmospheres | |||
hydrocarbon resources-fluids/swabs | oxy_stat_samp | X | [aerobic|anaerobic|other] | aerobic | Oxygenation status of sample | ||||
hydrocarbon resources-fluids/swabs | samp_preserv | X | {text};{float} {unit} | Rnalater; 2 ml | milliliter | Preservative added to the sample (e.g. Rnalater, alcohol, formaldehyde, etc.). Where appropriate include volume added (e.g. Rnalater; 2 ml) | |||
hydrocarbon resources-fluids/swabs | samp_transport_cond | X | {float} {unit};{float} {unit} | 5 days;-20 degree Celsius | days;degree Celsius | Sample transport duration (in days or hrs) and temperature the sample was exposed to (e.g. 5.5 days; 20 °C) | |||
hydrocarbon resources-fluids/swabs | samp_store_temp | X | {float} {unit} | -80 degree Celsius | degree Celsius | Temperature at which sample was stored, e.g. -80 degree Celsius | |||
hydrocarbon resources-fluids/swabs | samp_store_dur | X | {duration} | P1Y6M | Duration for which the sample was stored | ||||
hydrocarbon resources-fluids/swabs | samp_store_loc | X | {text} | Freezer no:5 | Location at which sample was stored, usually name of a specific freezer/room | ||||
hydrocarbon resources-fluids/swabs | samp_vol_we_dna_ext | C | {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 | |||
hydrocarbon resources-fluids/swabs | organism_count | C | {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) | |||
hydrocarbon resources-fluids/swabs | organism_count_qpcr_info | X | {text};FWD:{dna};REV:{dna};initial denaturation:degrees_minutes;denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final elongation:degrees_minutes; total cycles | 16S rrna; FWD:ACGTAGCTATGACGT REV:GTGCTAGTCGAGTAC; initial denaturation:90C_5min; denaturation:90C_2min; annealing:52C_30 sec; elongation:72C_30 sec; 90 C for 1 min; final elongation:72C_5min; 30 cycles | number of cells per gram (or ml or cm^2) | If qpcr was used for the cell count, the target gene name, the primer sequence and the cycling conditions should also be provided. (Example: 16S rrna; FWD:ACGTAGCTATGACGT REV:GTGCTAGTCGAGTAC; initial denaturation:90C_5min; denaturation:90C_2min; annealing:52C_30 sec; elongation:72C_30 sec; 90 C for 1 min; final elongation:72C_5min; 30 cycles) | |||
hydrocarbon resources-fluids/swabs | ph | C | {float} | 7.2 | Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid | ||||
hydrocarbon resources-fluids/swabs | samp_salinity | M | {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 | |||
hydrocarbon resources-fluids/swabs | 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 | |||
hydrocarbon resources-fluids/swabs | alkalinity_method | X | {text} | titration | Method used for alkalinity measurement | ||||
hydrocarbon resources-fluids/swabs | sulfate | M | {float} {unit} | 5 micromole per liter | micromole per liter, milligram per liter, parts per million | Concentration of sulfate in the sample | |||
hydrocarbon resources-fluids/swabs | sulfide | M | {float} {unit} | 2 micromole per liter | micromole per liter, milligram per liter, parts per million | Concentration of sulfide in the sample | |||
hydrocarbon resources-fluids/swabs | tot_sulfur | C | {float} {unit} | 2 micromole per liter | milligram per liter, parts per million | Concentration of total sulfur in the sample | |||
hydrocarbon resources-fluids/swabs | nitrate | M | {float} {unit} | 65 micromole per liter | micromole per liter, milligram per liter, parts per million | Concentration of nitrate in the sample | |||
hydrocarbon resources-fluids/swabs | nitrite | C | {float} {unit} | 0.5 micromole per liter | micromole per liter, milligram per liter, parts per million | Concentration of nitrite in the sample | |||
hydrocarbon resources-fluids/swabs | ammonium | C | {float} {unit} | 1.5 milligram per liter | micromole per liter, milligram per liter, parts per million | Concentration of ammonium in the sample | |||
hydrocarbon resources-fluids/swabs | 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 | |||
hydrocarbon resources-fluids/swabs | diss_iron | C | {float} {unit} | 2 micromole per liter | milligram per liter | Concentration of dissolved iron in the sample | |||
hydrocarbon resources-fluids/swabs | sodium | X | {float} {unit} | 10.5 milligram per liter | milligram per liter, parts per million | Sodium concentration in the sample | |||
hydrocarbon resources-fluids/swabs | chloride | X | {float} {unit} | 5000 milligram per liter | milligram per liter, parts per million | Concentration of chloride in the sample | |||
hydrocarbon resources-fluids/swabs | potassium | X | {float} {unit} | 463 milligram per liter | milligram per liter, parts per million | Concentration of potassium in the sample | |||
hydrocarbon resources-fluids/swabs | 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 | |||
hydrocarbon resources-fluids/swabs | calcium | X | {float} {unit} | 0.2 micromole per liter | milligram per liter, micromole per liter, parts per million | Concentration of calcium in the sample | |||
hydrocarbon resources-fluids/swabs | tot_iron | C | {float} {unit} | 2 micromole per liter | milligram per liter, milligram per kilogram | Concentration of total iron in the sample | |||
hydrocarbon resources-fluids/swabs | 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 | |||
hydrocarbon resources-fluids/swabs | 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 | |||
hydrocarbon resources-fluids/swabs | diss_inorg_phosp | C | {float} {unit} | 56.5 micromole per liter | microgram per liter, milligram per liter, parts per million | Concentration of dissolved inorganic phosphorus in the sample | |||
hydrocarbon resources-fluids/swabs | 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 | |||
hydrocarbon resources-fluids/swabs | suspend_solids | X | {text};{float} {unit} | oxyen;2 micromole per liter | gram, microgram, milligram per liter, mole per liter, gram per liter, part per million | Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances | |||
hydrocarbon resources-fluids/swabs | 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) | |||
hydrocarbon resources-fluids/swabs | 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 | |||
hydrocarbon resources-fluids/swabs | diss_oxygen_fluid | X | {float} {unit} | 5 milligram per liter | micromole per kilogram, milligram per liter | Concentration of dissolved oxygen in the oil field produced fluids as it contributes to oxgen-corrosion and microbial activity (e.g. Mic). | |||
hydrocarbon resources-fluids/swabs | vfa | C | {float} {unit} | 5 milligram per liter | milligram per liter, parts per million | Concentration of Volatile Fatty Acids in the sample | |||
hydrocarbon resources-fluids/swabs | benzene | C | {float} {unit} | 5 milligram per liter | milligram per liter, parts per million | Concentration of benzene in the sample | |||
hydrocarbon resources-fluids/swabs | toluene | C | {float} {unit} | 5 milligram per liter | milligram per liter, parts per million | Concentration of toluene in the sample | |||
hydrocarbon resources-fluids/swabs | ethylbenzene | C | {float} {unit} | 5 milligram per liter | milligram per liter, parts per million | Concentration of ethylbenzene in the sample | |||
hydrocarbon resources-fluids/swabs | xylene | C | {float} {unit} | 5 milligram per liter | milligram per liter, parts per million | Concentration of xylene in the sample | |||
hydrocarbon resources-fluids/swabs | api | M | {float} {unit} | 31.1 API | degrees API | API gravity is a measure of how heavy or light a petroleum liquid is compared to water (source: https://en.wikipedia.org/wiki/API_gravity) (e.g. 31.1° API) | |||
hydrocarbon resources-fluids/swabs | tan | C | {float} {unit} | 5.2 TAN | milligram per liter | Total Acid Number (TAN) is a measurement of acidity that is determined by the amount of potassium hydroxide in milligrams that is needed to neutralize the acids in one gram of oil. It is an important quality measurement of crude oil. (source: https://en.wikipedia.org/wiki/Total_acid_number) | |||
hydrocarbon resources-fluids/swabs | viscosity | X | {float} {unit};{float} {unit} | 3.5 cp; 100 C | cP at degree Celsius | A measure of oil's resistance to gradual deformation by shear stress or tensile stress (e.g. 3.5 cp; 100 °C) | |||
hydrocarbon resources-fluids/swabs | pour_point | X | {float} {unit} | 35 c | degree Celsius | Temperature at which a liquid becomes semi solid and loses its flow characteristics. In crude oil a high pour point is generally associated with a high paraffin content, typically found in crude deriving from a larger proportion of plant material. (soure: https://en.wikipedia.org/wiki/pour_point) | |||
hydrocarbon resources-fluids/swabs | saturates_pc | C | {text};{float} {unit} | Bicarbonate ion concentration;2075 micromole per kilogram | percent | Saturate, Aromatic, Resin and Asphaltene (SARA) is an analysis method that divides crude oil components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) | |||
hydrocarbon resources-fluids/swabs | aromatics_pc | C | {text};{float} {unit} | Bicarbonate ion concentration;2075 micromole per kilogram | percent | Saturate, Aromatic, Resin and Asphaltene (SARA) is an analysis method that divides crude oil components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) | |||
hydrocarbon resources-fluids/swabs | resins_pc | C | {text};{float} {unit} | Bicarbonate ion concentration;2075 micromole per kilogram | percent | Saturate, Aromatic, Resin and Asphaltene (SARA) is an analysis method that divides crude oil components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) | |||
hydrocarbon resources-fluids/swabs | asphaltenes_pc | C | {text};{float} {unit} | Bicarbonate ion concentration;2075 micromole per kilogram | percent | Saturate, Aromatic, Resin and Asphaltene (SARA) is an analysis method that divides crude oil components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene) | |||
hydrocarbon resources-fluids/swabs | 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 | ||||
hydrocarbon resources-fluids/swabs | additional_info | X | {text} | additional information field | Information that doesn't fit anywhere else. Can also be used to propose new entries for fields with controlled vocabulary | ||||
microbial mat/biofilm | 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 | |||
microbial mat/biofilm | 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 | |||
microbial mat/biofilm | 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 | |||
microbial mat/biofilm | alkyl_diethers | X | {float} {unit} | 0.005 mole per liter | mole per liter | Concentration of alkyl diethers | |||
microbial mat/biofilm | aminopept_act | X | {float} {unit} | 0.269 mole per liter per hour | mole per liter per hour | Measurement of aminopeptidase activity | |||
microbial mat/biofilm | ammonium | X | {float} {unit} | 1.5 milligram per liter | micromole per liter, milligram per liter, parts per million | Concentration of ammonium in the sample | |||
microbial mat/biofilm | bacteria_carb_prod | X | {float} {unit} | 2.53 microgram per liter per hour | nanogram per hour | Measurement of bacterial carbon production | |||
microbial mat/biofilm | 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 | |||
microbial mat/biofilm | bishomohopanol | X | {float} {unit} | 14 microgram per liter | microgram per liter, microgram per gram | Concentration of bishomohopanol | |||
microbial mat/biofilm | bromide | X | {float} {unit} | 0.05 parts per million | parts per million | Concentration of bromide | |||
microbial mat/biofilm | calcium | X | {float} {unit} | 0.2 micromole per liter | milligram per liter, micromole per liter, parts per million | Concentration of calcium in the sample | |||
microbial mat/biofilm | carb_nitro_ratio | X | {float} {unit} | 0.417361111 | Ratio of amount or concentrations of carbon to nitrogen | ||||
microbial mat/biofilm | 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 | ||||
microbial mat/biofilm | chloride | X | {float} {unit} | 5000 milligram per liter | milligram per liter, parts per million | Concentration of chloride in the sample | |||
microbial mat/biofilm | chlorophyll | X | {float} {unit} | 5 milligram per cubic meter | milligram per cubic meter, microgram per liter | Concentration of chlorophyll | |||
microbial mat/biofilm | 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 | |||
microbial mat/biofilm | 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 | |||
microbial mat/biofilm | diss_hydrogen | X | {float} {unit} | 0.3 micromole per liter | micromole per liter | Concentration of dissolved hydrogen | |||
microbial mat/biofilm | 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 | |||
microbial mat/biofilm | 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 | |||
microbial mat/biofilm | 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 | |||
microbial mat/biofilm | diss_oxygen | X | {float} {unit} | 175 micromole per kilogram | micromole per kilogram, milligram per liter | Concentration of dissolved oxygen | |||
microbial mat/biofilm | glucosidase_act | X | {float} {unit} | 5 mol per liter per hour | mol per liter per hour | Measurement of glucosidase activity | |||
microbial mat/biofilm | 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 | |||
microbial mat/biofilm | mean_frict_vel | X | {float} {unit} | 0.5 meter per second | meter per second | Measurement of mean friction velocity | |||
microbial mat/biofilm | mean_peak_frict_vel | X | {float} {unit} | 1 meter per second | meter per second | Measurement of mean peak friction velocity | |||
microbial mat/biofilm | 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 | |||
microbial mat/biofilm | 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 | ||||
microbial mat/biofilm | n_alkanes | X | {text};{float} {unit} | n-hexadecane;100 milligram per liter | micromole per liter | Concentration of n-alkanes; can include multiple n-alkanes | |||
microbial mat/biofilm | nitrate | X | {float} {unit} | 65 micromole per liter | micromole per liter, milligram per liter, parts per million | Concentration of nitrate in the sample | |||
microbial mat/biofilm | nitrite | X | {float} {unit} | 0.5 micromole per liter | micromole per liter, milligram per liter, parts per million | Concentration of nitrite in the sample | |||
microbial mat/biofilm | nitro | X | {float} {unit} | 4.2 micromole per liter | micromole per liter | Concentration of nitrogen (total) | |||
microbial mat/biofilm | org_carb | X | {float} {unit} | 1.5 microgram per liter | micromole per liter | Concentration of organic carbon | |||
microbial mat/biofilm | org_matter | X | {float} {unit} | 1.75 milligram per cubic meter | microgram per liter | Concentration of organic matter | |||
microbial mat/biofilm | org_nitro | X | {float} {unit} | 4 micromole per liter | microgram per liter | Concentration of organic nitrogen | |||
microbial mat/biofilm | 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) | |||
microbial mat/biofilm | oxy_stat_samp | X | [aerobic|anaerobic|other] | aerobic | Oxygenation status of sample | ||||
microbial mat/biofilm | ph | X | {float} | 7.2 | Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid | ||||
microbial mat/biofilm | part_org_carb | X | {float} {unit} | 1.92 micromole per liter | microgram per liter | Concentration of particulate organic carbon | |||
microbial mat/biofilm | 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 | ||||
microbial mat/biofilm | petroleum_hydrocarb | X | {float} {unit} | 0.05 micromole per liter | micromole per liter | Concentration of petroleum hydrocarbon | |||
microbial mat/biofilm | phaeopigments | X | {text};{float} {unit} | 2.5 milligram per cubic meter | milligram per cubic meter | Concentration of phaeopigments; can include multiple phaeopigments |
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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) | |||