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| # Package | Structured comment name | Requirement | Value syntax | Example | Preferred unit | URL | Definition | ||
| core | ProjectIdentifier | M | {text} | ProjectX | http://schema.org/identifier | Identifier corresponding to the project | |||
| core | ProjectTitle | M | {text} | The title describing project X | http://schema.org/title | Title describing the project | |||
| core | ProjectDescription | M | {text} | A longer description that explains what project X is all about. | http://schema.org/description | Description of the project | |||
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| # Package | Structured comment name | Requirement | Value syntax | Example | Preferred unit | URL | Definition | ||
| core | InvestigationIdentifier | M | {text} | InvestigationID | http://schema.org/identifier | Identifier corresponding to the investigation | |||
| core | InvestigationTitle | M | {text} | Title about the investigation | http://schema.org/title | Title describing the investigation | |||
| core | InvestigationDescription | M | {text} | Description of the investigation | http://schema.org/description | Description of the investigation | |||
| core | FirstName | M | {text} | Jane | http://schema.org/givenName | The given name of a person | |||
| core | LastName | M | {text} | Doe | http://schema.org/familyName | The family name of a person | |||
| core | M | {text} | jane.doe@wur.nl | http://schema.org/email | The email address of a person | ||||
| core | ORCID | M | {integer} | 123456789 | The orcid of a given person | ||||
| core | Organization | M | {text} | Wageningen | http://schema.org/memberOf | Member of an organization | |||
| core | Department | M | {text} | Laboratory of Systems and Synthetic Biology | http://schema.org/department | The department this person belongs to | |||
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| # Package | Structured comment name | Requirement | Value syntax | Example | Preferred unit | URL | Definition | ||
| core | StudyIdentifier | M | {text} | StudyX | http://schema.org/identifier | Identifier corresponding to the study | |||
| core | StudyTitle | M | {text} | Title of the study | http://schema.org/title | Title describing the study | |||
| core | StudyDescription | M | {text} | Description of the study | http://schema.org/description | Description of the study | |||
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| # Package | Structured comment name | Requirement | Value syntax | Example | Preferred unit | URL | Definition | ||
| core | ObservationUnitIdentifier | M | {text} | ObservationX | http://schema.org/identifier | Identifier corresponding to the entity that is being observed | |||
| core | ObservationUnitName | M | {text} | ObservationX Name | http://schema.org/name | Name of the entity being observed | |||
| core | ObservationUnitDescription | M | {text} | ObservationX description | http://schema.org/description | Description of the entity being observed | |||
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| # Package | Structured comment name | Requirement | Value syntax | Example | Preferred unit | URL | Definition | ||
| core | SampleIdentifier | M | {text} | P1S2D3 | http://schema.org/identifier | Identifier corresponding to the sample obtained | |||
| core | SampleDescription | M | {text} | The sample taken from pig 1 in stable 2 on day 3 was more colorless than in general | http://schema.org/description | Description of the sample | |||
| core | SampleName | M | {text} | Pig 1 Stable 2 Day 3 | http://schema.org/name | Readable name of the sample | |||
| core | NCBI taxonomy ID | M | {NCBI taxid} | 1510822 | Taxonomic identifier of the sample according to https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi for example use 2582415 for a blank sample or 1510822 for pig metagenome | ||||
| core | SampleOrganism | M | {text} | Sus scrofa domesticus | Name of the organism | ||||
| core | BioSafetyLevel | M | {integer} | 2 | Biosafety level of the corresponding sample | ||||
| core | SampleSize | X | {float} {unit} | 5 ml | Size of the sample (ml) | ||||
| core | SampleCondition | X | {text} | more coloreless | Condition of the sample | ||||
| core | Material | X | {text} | gut sample | Material the sample is composed of | ||||
| core | SamplingStrategy | X | {text} | strategy X | Strategy used to perform the sampling procedure | ||||
| core | SampleTreatment | X | {text} | treatment X | Treatment applied to the sample | ||||
| core | CollectionTime | X | {timestamp} | 1899-12-31T13:15:0+0000 | The time this sample was collected (24h notation) | ||||
| core | TimePoint | X | {float} {unit} | 3 | When applicable | ||||
| core | CollectionTemperature | X | {float} | 32.4 | The temperature in degrees celcius when this sample was collected | ||||
| core | CollectionPH | X | {float} | 6.1 | The pH when this sample was collected | ||||
| # Package | Structured comment name | Requirement | Value syntax | Example | Preferred unit | URL | Definition | ||
| core | lat_lon | X | {float} {float} | 50.586825 6.408977 | The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system | ||||
| core | depth | X | {float} {unit} | 100 meter | meter | Please refer to the definitions of depth in the environmental packages | |||
| core | alt | X | {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 | |||
| core | elev | X | {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 | |||
| core | geo_loc_name | X | {term};{term};{text} | Germany;North Rhine-Westphalia;Eifel National Park | The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) | ||||
| core | collection_date | M | {timestamp} | 2018-05-11T10:00:00 | yyyy-mm-ddThh:mm:ss | The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant | |||
| core | env_broad_scale | X | {termLabel} {[termID]} | forest biome [ENVO:01000174] | In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html | ||||
| core | env_local_scale | X | {termLabel} {[termID]} | litter layer [ENVO:01000338] | In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html | ||||
| core | env_medium | X | {termLabel} {[termID]} | soil [ENVO:00001998] | In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html | ||||
| # Package | Structured comment name | Requirement | Value syntax | Example | Preferred unit | URL | Definition | ||
| air | alt | M | {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 | |||
| air | 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 | |||
| air | barometric_press | X | {float} {unit} | 5 millibar | millibar | Force per unit area exerted against a surface by the weight of air above that surface | |||
| air | carb_dioxide | X | {float} {unit} | 410 parts per million | micromole per liter, parts per million | Carbon dioxide (gas) amount or concentration at the time of sampling | |||
| air | carb_monoxide | X | {float} {unit} | 0.1 parts per million | micromole per liter, parts per million | Carbon monoxide (gas) amount or concentration at the time of sampling | |||
| air | 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 | ||||
| air | humidity | X | {float} {unit} | 25 gram per cubic meter | gram per cubic meter | Amount of water vapour in the air, at the time of sampling | |||
| air | methane | X | {float} {unit} | 1800 parts per billion | micromole per liter, parts per billion, parts per million | Methane (gas) amount or concentration at the time of sampling | |||
| air | 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 | ||||
| air | 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) | |||
| air | oxygen | X | {float} {unit} | 600 parts per million | milligram per liter, parts per million | Oxygen (gas) amount or concentration at the time of sampling | |||
| air | oxy_stat_samp | X | [aerobic|anaerobic|other] | aerobic | Oxygenation status of sample | ||||
| air | 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 | ||||
| air | pollutants | X | {text};{float} {unit} | lead;0.15 microgram per cubic meter | gram, mole per liter, milligram per liter, microgram per cubic meter | Pollutant types and, amount or concentrations measured at the time of sampling; can report multiple pollutants by entering numeric values preceded by name of pollutant | |||
| air | resp_part_matter | X | {text};{float} {unit} | PM2.5;10 microgram per cubic meter | microgram per cubic meter | Concentration of substances that remain suspended in the air, and comprise mixtures of organic and inorganic substances (PM10 and PM2.5); can report multiple PM's by entering numeric values preceded by name of PM | |||
| air | 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 | |||
| air | samp_store_dur | X | {duration} | P1Y6M | Duration for which the sample was stored | ||||
| air | samp_store_loc | X | {text} | Freezer no:5 | Location at which sample was stored, usually name of a specific freezer/room | ||||
| air | samp_store_temp | X | {float} {unit} | -80 degree Celsius | degree Celsius | Temperature at which sample was stored, e.g. -80 degree Celsius | |||
| air | 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 | |||
| air | solar_irradiance | X | {float} {unit} | 1.36 kilowatts per square meter per day | kilowatts per square meter per day, ergs per square centimeter per second | The amount of solar energy that arrives at a specific area of a surface during a specific time interval | |||
| air | temp | X | {float} {unit} | 25 degree Celsius | degree Celsius | Temperature of the sample at the time of sampling | |||
| air | ventilation_rate | X | {float} {unit} | 750 cubic meter per minute | cubic meter per minute, liters per second | Ventilation rate of the system in the sampled premises | |||
| air | ventilation_type | X | {text} | Operable windows | Ventilation system used in the sampled premises | ||||
| air | volatile_org_comp | X | {text};{float} {unit} | formaldehyde;500 nanogram per liter | microgram per cubic meter, parts per million, nanogram per liter | Concentration of carbon-based chemicals that easily evaporate at room temperature; can report multiple volatile organic compounds by entering numeric values preceded by name of compound | |||
| air | wind_direction | X | {text} | Northwest | Wind direction is the direction from which a wind originates | ||||
| air | wind_speed | X | {float} {unit} | 21 kilometer per hour | meter per second, kilometer per hour | Speed of wind measured at the time of sampling | |||
| host-associated | 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 | |||
| host-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 | |||
| host-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 | |||
| host-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) | ||||
| host-associated | biol_stat | X | [wild|natural|semi-natural|inbred line|breeder's line|hybrid|clonal selection|mutant] | natural | The level of genome modification | ||||
| host-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 | ||||
| host-associated | host_common_name | X | {text} | mussel | Common name of the host, e.g. Human | ||||
| host-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 | ||||
| host-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. | ||||
| host-associated | host_taxid | X | {NCBI taxid} | 7955 | NCBI taxon id of the host, e.g. 9606 | ||||
| host-associated | host_subject_id | X | {text} | MPI123 | A unique identifier by which each subject can be referred to, de-identified, e.g. #131 | ||||
| host-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 | |||
| host-associated | host_life_stage | X | {text} | adult | Description of life stage of host | ||||
| host-associated | host_sex | X | [male|female|neuter|hermaphrodite|not determined] | female | Physical sex of the host | ||||
| host-associated | host_disease_stat | X | {termLabel} {[termID]}|{text} | rabies [DOID:11260] | 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 | ||||
| host-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 | ||||
| host-associated | host_body_habitat | X | {text} | nasopharynx | Original body habitat where the sample was obtained from | ||||
| host-associated | host_body_site | X | {termLabel} {[termID]} | gill [UBERON:0002535] | Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON | ||||
| host-associated | host_body_product | X | {termLabel} {[termID]} | Portion of mucus [fma66938] | Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon | ||||
| host-associated | host_tot_mass | X | {float} {unit} | 2500 gram | kilogram, gram | Total mass of the host at collection, the unit depends on host | |||
| host-associated | host_height | X | {float} {unit} | 0.1 meter | centimeter, millimeter, meter | The height of subject | |||
| host-associated | host_length | X | {float} {unit} | 1 meter | centimeter, millimeter, meter | The length of subject | |||
| host-associated | host_diet | X | {text} | herbivore | Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types | ||||
| host-associated | host_last_meal | X | {text};{duration} | corn feed;P2H | Content of last meal and time since feeding; can include multiple values | ||||
| host-associated | host_growth_cond | X | {PMID}|{DOI}|{URL}|{text} | https://academic.oup.com/icesjms/article/68/2/349/617247 | Literature reference giving growth conditions of the host | ||||
| host-associated | host_substrate | X | {text} | rock | The growth substrate of the host | ||||
| host-associated | host_family_relationship | X | {text};{text} | offspring;Mussel25 | Relationships to other hosts in the same study; can include multiple relationships | ||||
| host-associated | host_infra_specific_name | X | {text} | borealis | Taxonomic information about the host below subspecies level | ||||
| host-associated | host_infra_specific_rank | X | {text} | subspecies | Taxonomic rank information about the host below subspecies level, such as variety, form, rank etc. | ||||
| host-associated | host_genotype | X | {text} | C57BL/6 | Observed genotype | ||||
| host-associated | host_phenotype | X | {termLabel} {[termID]} | elongated [PATO:0001154] | 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 | ||||
| host-associated | host_body_temp | X | {float} {unit} | 15 degree Celsius | degree Celsius | Core body temperature of the host when sample was collected | |||
| host-associated | host_dry_mass | X | {float} {unit} | 500 gram | kilogram, gram | Measurement of dry mass | |||
| host-associated | host_blood_press_diast | X | {float} {unit} | 5.5 mm | millimeter mercury | Resting diastolic blood pressure, measured as mm mercury | |||
| host-associated | host_blood_press_syst | X | {float} {unit} | 4.5 mm | millimeter mercury | Resting systolic blood pressure, measured as mm mercury | |||
| host-associated | host_color | X | {text} | red | The color of host | ||||
| host-associated | host_shape | X | {text} | round | Morphological shape of host | ||||
| host-associated | gravidity | X | {boolean};{timestamp} | yes;due date:2018-05-11 | Whether or not subject is gravid, and if yes date due or date post-conception, specifying which is used | ||||
| host-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 | ||||
| host-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 | |||
| host-associated | oxy_stat_samp | X | [aerobic|anaerobic|other] | aerobic | Oxygenation status of sample | ||||
| host-associated | temp | X | {float} {unit} | 25 degree Celsius | degree Celsius | Temperature of the sample at the time of sampling | |||
| host-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) | |||
| host-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 | |||
| host-associated | samp_store_temp | X | {float} {unit} | -80 degree Celsius | degree Celsius | Temperature at which sample was stored, e.g. -80 degree Celsius | |||
| host-associated | samp_store_dur | X | {duration} | P1Y6M | Duration for which the sample was stored |
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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) | |||
