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AmpliconLibraryAssay
DNAseqAssay
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# Package | Structured comment name | Requirement | Value syntax | Example | Preferred unit | URL | Definition | ||
core | ProjectIdentifier | M | {text} | ProjectX | http://schema.org/identifier | Identifier corresponding to the project | |||
core | ProjectTitle | M | {text} | The title describing project X | http://schema.org/title | Title describing the project | |||
core | ProjectDescription | M | {text} | A longer description that explains what project X is all about. | http://schema.org/description | Description of the project | |||
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# Package | Structured comment name | Requirement | Value syntax | Example | Preferred unit | URL | Definition | ||
core | InvestigationIdentifier | M | {text} | InvestigationID | http://schema.org/identifier | Identifier corresponding to the investigation | |||
core | InvestigationTitle | M | {text} | Title about the investigation | http://schema.org/title | Title describing the investigation | |||
core | InvestigationDescription | M | {text} | Description of the investigation | http://schema.org/description | Description of the investigation | |||
core | FirstName | M | {text} | Jane | http://schema.org/givenName | The given name of a person | |||
core | LastName | M | {text} | Doe | http://schema.org/familyName | The family name of a person | |||
core | M | {text} | jane.doe@wur.nl | http://schema.org/email | The email address of a person | ||||
core | ORCID | M | {integer} | 123456789 | The orcid of a given person | ||||
core | Organization | M | {text} | Wageningen | http://schema.org/memberOf | Member of an organization | |||
core | Department | M | {text} | Laboratory of Systems and Synthetic Biology | http://schema.org/department | The department this person belongs to | |||
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# 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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host-associated | samp_store_loc | X | {text} | Freezer no:5 | Location at which sample was stored, usually name of a specific freezer/room | ||||
host-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 | ||||
human-associated | host_subject_id | X | {text} | MPI123 | A unique identifier by which each subject can be referred to, de-identified, e.g. #131 | ||||
human-associated | host_age | X | {float} {unit} | 30 years | 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 | |||
human-associated | host_sex | X | [male|female|neuter|hermaphrodite|not determined] | female | Physical sex of the host | ||||
human-associated | host_disease_stat | X | {termLabel} {[termID]} | measles [DOID:8622] | List of diseases with which the host has been diagnosed; can include multiple diagnoses. The terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org. | ||||
human-associated | ihmc_medication_code | X | {integer} | 810 | Can include multiple medication codes | ||||
human-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 | ||||
human-associated | host_body_site | X | {termLabel} {[termID]} | Lung parenchyma [fma27360] | 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 | ||||
human-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 | ||||
human-associated | host_tot_mass | X | {float} {unit} | 65 kilogram | kilogram, gram | Total mass of the host at collection, the unit depends on host | |||
human-associated | host_height | X | {float} {unit} | 1.75 meter | centimeter, millimeter, meter | The height of subject | |||
human-associated | host_diet | X | {text} | high-fat | Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types | ||||
human-associated | host_last_meal | X | {text};{duration} | french fries;P5H30M | Content of last meal and time since feeding; can include multiple values | ||||
human-associated | host_family_relationship | X | {text};{text} | mother;ID298 | Relationships to other hosts in the same study; can include multiple relationships | ||||
human-associated | host_genotype | X | {text} | ST1 | Observed genotype | ||||
human-associated | host_phenotype | X | {termLabel} {[termID]} | Tinnitus [HP:0000360] | 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 | ||||
human-associated | host_body_temp | X | {float} {unit} | 36.5 degree Celsius | degree Celsius | Core body temperature of the host when sample was collected | |||
human-associated | smoker | X | {boolean} | yes | Specification of smoking status | ||||
human-associated | host_hiv_stat | X | {boolean};{boolean} | yes;yes | HIV status of subject, if yes HAART initiation status should also be indicated as [YES or NO] | ||||
human-associated | drug_usage | X | {text};{integer}/[year|month|week|day|hour] | Lipitor;2/day | Any drug used by subject and the frequency of usage; can include multiple drugs used | ||||
human-associated | host_body_mass_index | X | {float} {unit} | 22 kilogram per square meter | kilogram per square meter | Body mass index, calculated as weight/(height)squared | |||
human-associated | diet_last_six_month | X | {boolean};{text} | yes;vegetarian diet | Specification of major diet changes in the last six months, if yes the change should be specified | ||||
human-associated | weight_loss_3_month | X | {boolean};{float} {unit} | yes;5 kilogram | kilogram, gram | Specification of weight loss in the last three months, if yes should be further specified to include amount of weight loss | |||
human-associated | ihmc_ethnicity | X | {integer}|{text} | caucasian | Ethnicity of the subject | ||||
human-associated | host_occupation | X | {integer} | veterinary | Most frequent job performed by subject | ||||
human-associated | pet_farm_animal | X | {boolean};{text} | yes; 5 cats | Specification of presence of pets or farm animals in the environment of subject, if yes the animals should be specified; can include multiple animals present | ||||
human-associated | travel_out_six_month | X | {text} | 5 times | Specification of the countries travelled in the last six months; can include multiple travels | ||||
human-associated | twin_sibling | X | {boolean} | yes | Specification of twin sibling presence | ||||
human-associated | medic_hist_perform | X | {boolean} | yes | Whether full medical history was collected | ||||
human-associated | study_complt_stat | X | {boolean};[adverse event|non-compliance|lost to follow up|other-specify] | no;non-compliance | Specification of study completion status, if no the reason should be specified | ||||
human-associated | pulmonary_disord | X | {text} | pulmonary tuberculosis | History of pulmonary disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, lung disease (https://disease-ontology.org/?id=DOID:850). | ||||
human-associated | nose_throat_disord | X | {text} | lethal midline granuloma | History of nose-throat disorders; can include multiple disorders, The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, lung disease (https://disease-ontology.org/?id=DOID:850), upper respiratory tract disease (https://disease-ontology.org/?id=DOID:974). | ||||
human-associated | blood_blood_disord | X | {text} | monoclonal gammopathy of uncertain significance | History of blood disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, hematopoietic system disease (https://disease-ontology.org/?id=DOID:74). | ||||
human-associated | host_pulse | X | {float} {unit} | 65 beats per minute | beats per minute | Resting pulse, measured as beats per minute | |||
human-associated | gestation_state | X | {text} | second trimester | Specification of the gestation state | ||||
human-associated | maternal_health_stat | X | {text} | healthy | Specification of the maternal health status | ||||
human-associated | foetal_health_stat | X | {text} | healthy | Specification of foetal health status, should also include abortion | ||||
human-associated | amniotic_fluid_color | X | {text} | clear | Specification of the color of the amniotic fluid sample | ||||
human-associated | History of kidney disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, kidney disease (https://disease-ontology.org/?id=DOID:557). | X | {text} | no | History of kidney disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, kidney disease (https://disease-ontology.org/?id=DOID:557). | ||||
human-associated | urogenit_tract_disor | X | {text} | no | History of urogenital tract disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, urinary system disease (https://disease-ontology.org/?id=DOID:18). | ||||
human-associated | urine_collect_meth | X | [clean catch|catheter] | catheter | Specification of urine collection method | ||||
human-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 | ||||
human-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 | |||
human-associated | oxy_stat_samp | X | [aerobic|anaerobic|other] | aerobic | Oxygenation status of sample | ||||
human-associated | temp | X | {float} {unit} | 25 degree Celsius | degree Celsius | Temperature of the sample at the time of sampling | |||
human-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) | |||
human-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 | |||
human-associated | samp_store_temp | X | {float} {unit} | -80 degree Celsius | degree Celsius | Temperature at which sample was stored, e.g. -80 degree Celsius | |||
human-associated | samp_store_dur | X | {duration} | P1Y6M | Duration for which the sample was stored | ||||
human-associated | samp_store_loc | X | {text} | Freezer no:5 | Location at which sample was stored, usually name of a specific freezer/room | ||||
human-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 | ||||
human-gut | gastrointest_disord | X | {text} | no | History of gastrointestinal tract disorders; can include multiple disorders. History of blood disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, gastrointestinal system disease (https://disease-ontology.org/?id=DOID:77). | ||||
human-gut | liver_disord | X | {text} | no | History of liver disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, liver disease (https://disease-ontology.org/?id=DOID:409). | ||||
human-gut | special_diet | X | [low carb|reduced calorie|vegetarian|other(to be specified)] | other:vegan | Specification of special diet; can include multiple special diets | ||||
human-gut | host_subject_id | X | {text} | MPI123 | A unique identifier by which each subject can be referred to, de-identified, e.g. #131 | ||||
human-gut | host_age | X | {float} {unit} | 30 years | 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 | |||
human-gut | host_sex | X | [male|female|neuter|hermaphrodite|not determined] | female | Physical sex of the host | ||||
human-gut | host_disease_stat | X | {termLabel} {[termID]} | measles [DOID:8622] | List of diseases with which the host has been diagnosed; can include multiple diagnoses. The terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org. | ||||
human-gut | ihmc_medication_code | X | {integer} | 810 | Can include multiple medication codes | ||||
human-gut | 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 | ||||
human-gut | host_body_site | X | {termLabel} {[termID]} | Wall of gut [fma45653] | 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 | ||||
human-gut | 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 | ||||
human-gut | host_tot_mass | X | {float} {unit} | 65 kilogram | kilogram, gram | Total mass of the host at collection, the unit depends on host | |||
human-gut | host_height | X | {float} {unit} | 1.75 meter | centimeter, millimeter, meter | The height of subject | |||
human-gut | host_diet | X | {text} | high-fat | Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types | ||||
human-gut | host_last_meal | X | {text};{duration} | french fries;P5H30M | Content of last meal and time since feeding; can include multiple values | ||||
human-gut | host_family_relationship | X | {text};{text} | mother;ID298 | Relationships to other hosts in the same study; can include multiple relationships | ||||
human-gut | host_genotype | X | {text} | ST1 | Observed genotype | ||||
human-gut | host_phenotype | X | {termLabel} {[termID]} | Tinnitus [HP:0000360] | 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 | ||||
human-gut | host_body_temp | X | {float} {unit} | 36.5 degree Celsius | degree Celsius | Core body temperature of the host when sample was collected | |||
human-gut | host_body_mass_index | X | {float} {unit} | 22 kilogram per square meter | kilogram per square meter | Body mass index, calculated as weight/(height)squared | |||
human-gut | ihmc_ethnicity | X | {integer}|{text} | caucasian | Ethnicity of the subject | ||||
human-gut | host_occupation | X | {integer} | veterinary | Most frequent job performed by subject | ||||
human-gut | medic_hist_perform | X | {boolean} | yes | Whether full medical history was collected | ||||
human-gut | host_pulse | X | {float} {unit} | 65 beats per minute | beats per minute | Resting pulse, measured as beats per minute | |||
human-gut | 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 | ||||
human-gut | 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 | |||
human-gut | oxy_stat_samp | X | [aerobic|anaerobic|other] | aerobic | Oxygenation status of sample | ||||
human-gut | temp | X | {float} {unit} | 25 degree Celsius | degree Celsius | Temperature of the sample at the time of sampling | |||
human-gut | 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) | |||
human-gut | samp_store_temp | X | {float} {unit} | -80 degree Celsius | degree Celsius | Temperature at which sample was stored, e.g. -80 degree Celsius | |||
human-gut | 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 | |||
human-gut | samp_store_dur | X | {duration} | P1Y6M | Duration for which the sample was stored | ||||
human-gut | samp_store_loc | X | {text} | Freezer no:5 | Location at which sample was stored, usually name of a specific freezer/room | ||||
human-gut | 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 | ||||
human-oral | nose_mouth_teeth_throat_disord | X | {text} | no | History of nose/mouth/teeth/throat disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, nose disease (https://disease-ontology.org/?id=DOID:2825), mouth disease (https://disease-ontology.org/?id=DOID:403), tooth disease (https://disease-ontology.org/?id=DOID:1091), or upper respiratory tract disease (https://disease-ontology.org/?id=DOID:974). | ||||
human-oral | time_last_toothbrush | X | {duration} | P2H45M | Specification of the time since last toothbrushing | ||||
human-oral | host_subject_id | X | {text} | MPI123 | A unique identifier by which each subject can be referred to, de-identified, e.g. #131 | ||||
human-oral | host_age | X | {float} {unit} | 30 years | 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 | |||
human-oral | host_sex | X | [male|female|neuter|hermaphrodite|not determined] | female | Physical sex of the host | ||||
human-oral | host_disease_stat | X | {termLabel} {[termID]} | measles [DOID:8622] | List of diseases with which the host has been diagnosed; can include multiple diagnoses. The terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org. | ||||
human-oral | ihmc_medication_code | X | {integer} | 810 | Can include multiple medication codes | ||||
human-oral | 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 | ||||
human-oral | host_body_site | X | {termLabel} {[termID]} | Epithelium of tongue [fma284658] | 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 | ||||
human-oral | 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 | ||||
human-oral | host_tot_mass | X | {float} {unit} | 65 kilogram | kilogram, gram | Total mass of the host at collection, the unit depends on host | |||
human-oral | host_height | X | {float} {unit} | 1.75 meter | centimeter, millimeter, meter | The height of subject | |||
human-oral | host_diet | X | {text} | high-fat | Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types | ||||
human-oral | host_last_meal | X | {text};{duration} | french fries;P5H30M | Content of last meal and time since feeding; can include multiple values |
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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) | |||