source plant

No description specified

SEEK ID: https://datahub-test.elixir-belgium.org/templates/20

Submitter: System

Projects: Default Project

Version: 1.1.1

Group: ena

2 Sample types are referencing this Experiment Sample Template

ISA Level: study source

Organism: plant

Parent Template: None

Child Templates:

Attributes

NameTypeDescriptionPID helpISA Tag helpUnit
Source Name*StringSources are considered as the starting biological material used in a study.-source-
Title*StringShort text that can be used to call out sample records in search results or in displays.-source_characteristic-
Description*StringFree-form text describing the sample, its origin, and its method of isolation.-source_characteristic-
tax_id*StringNCBI Taxonomy Identifier number ID. This is appropriate for individual organisms and some environmental samples.-source_characteristic-
organismStringScientific name of sample that distinguishes its taxonomy. Please use a name or synonym that is tracked in the INSDC Taxonomy database. Also, this field can be used to confirm the TAXON_ID setting.-source_characteristic-
ploidy*Controlled Vocabulary - ploidyThe ploidy level of the genome (e.g. allopolyploid, haploid, diploid, triploid, tetraploid). It has implications for the downstream study of duplicated gene and regions of the genomes (and perhaps for difficulties in assembly). For terms, please select terms listed under class ploidy (PATO:001374) of Phenotypic Quality Ontology (PATO), and for a browser of PATO (v 2013-10-28) please refer to http://purl.bioontology.org/ontology/PATO. Mandatory for MIGS of eukaryotes.-source_characteristic-
number of replicons*IntegerReports the number of replicons in a nuclear genome of eukaryotes, in the genome of a bacterium or archaea or the number of segments in a segmented virus. Always applied to the haploid chromosome count of a eukaryote. Mandatory for MIGS of eukaryotes, bacteria, archaea and segmented virus.-source_characteristic-
extrachromosomal elementsIntegerDo plasmids exist of significant phenotypic consequence (e.g. ones that determine virulence or antibiotic resistance). Megaplasmids? Other plasmids (borrelia has 15+ plasmids).-source_characteristic-
estimated size*IntegerThe estimated size of the genome (in bp) prior to sequencing. Of particular importance in the sequencing of (eukaryotic) genome which could remain in draft form for a long or unspecified period. Mandatory for MIGS of eukaryotes.-source_characteristic-
collected_byStringname of persons or institute who collected the specimen-source_characteristic-
collection date*StringThe date 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 ISO8601 compliant times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008.-source_characteristic-
geographic location (altitude)StringThe altitude of the sample is the vertical distance between Earth's surface above Sea Level and the sampled position in the air.-source_characteristic-
geographic location (country and/or sea)*Controlled Vocabulary - geographic location (country and/or sea)The geographical origin of the sample as defined by the country or sea. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html).-source_characteristic-
geographic location (latitude)*StringThe geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system-source_characteristic-
geographic location (longitude)*StringThe geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system-source_characteristic-
geographic location (region and locality)StringThe geographical origin of the sample as defined by the specific region name followed by the locality name.-source_characteristic-
identified_byStringname of the expert who identified the specimen taxonomically-source_characteristic-
geographic location (depth)StringDepth is defined as the vertical distance below surface, e.g. for sediment or soil samples depth is measured from sediment or soil surface, respectivly. Depth can be reported as an interval for subsurface samples.-source_characteristic-
environment (biome)Controlled Vocabulary - environment (biome)Biomes are defined based on factors such as plant structures, leaf types, plant spacing, and other factors like climate. Biome should be treated as the descriptor of the broad ecological context of a sample. Examples include: desert, taiga, deciduous woodland, or coral reef. EnvO (v 2013-06-14) terms can be found via the link: www.environmentontology.org/Browse-EnvO-source_characteristic-
environment (feature)StringEnvironmental feature level includes geographic environmental features. Compared to biome, feature is a descriptor of the more local environment. Examples include: harbor, cliff, or lake. EnvO (v 2013-06-14) terms can be found via the link: www.environmentontology.org/Browse-EnvO-source_characteristic-
geographic location (elevation)StringThe elevation of the sampling site as measured by the vertical distance from mean sea level.---
source material identifiersStringA unique identifier assigned to a material sample (as defined by http://rs.tdwg.org/dwc/terms/materialSampleID, and as opposed to a particular digital record of a material sample) used for extracting nucleic acids, and subsequent sequencing. The identifier can refer either to the original material collected or to any derived sub-samples. The INSDC qualifiers /specimen_voucher, /bio_material, or /culture_collection may or may not share the same value as the source_mat_id field. For instance, the /specimen_voucher qualifier and source_mat_id may both contain 'UAM:Herps:14' , referring to both the specimen voucher and sampled tissue with the same identifier. However, the /culture_collection qualifier may refer to a value from an initial culture (e.g. ATCC:11775) while source_mat_id would refer to an identifier from some derived culture from which the nucleic acids were extracted (e.g. xatc123 or ark:/2154/R2).-source_characteristic-
isolation and growth condition*StringPublication reference in the form of pubmed ID (pmid), digital object identifier (doi) or url for isolation and growth condition specifications of the organism/material. Mandatory for MIGS and MIMARKS Specimen.-source_characteristic-
propagationStringThis field is specific to different taxa. For plants: sexual/asexual, for phages: lytic/lysogenic, for plasmids: incompatibility group (Note: there is the strong opinion to name phage propagation obligately lytic or temperate, therefore we also give this choice. Mandatory for MIGS of eukaryotes, plasmids and viruses.-source_characteristic-
plant structure*Controlled Vocabulary - plant structurename of plant structure that the sample was obtained from; for Plant Ontology (PO) terms see http://purl.bioontology.org/ontology/PO, e.g. petiole epidermis (PO_0000051); if an individual flower is sampled the sex of it can be recorded here-source_characteristic-
plant developmental stage*Controlled Vocabulary - plant developmental stagedevelopmental stage at the time of sample collection; for Plant Ontology (PO) (v 20) terms, see http://purl.bioontology.org/ontology/PO, e.g. hypocotyl emergence stage (PO_0007043)-source_characteristic-
sampled ageStringage of subject at the time of sample collection; relevant scale depends on species and study; e.g. 2 weeks old-source_characteristic-
sample phenotypeStringphenotype of the plant from which the sample was obtained, such as colour of corolla, fruit diameter, circular leaf shape; Plant Trait Ontology (TO), Phenotypic Quality Ontology (PATO), or other ontology is recommended; e.g. stem epidermis colour (TO:1000018)-source_characteristic-
sample health stateControlled Vocabulary - sample health statehealth status of the subject at the time of sample collection-source_characteristic-
sample disease statusStringlist of diseases with which the subject has been diagnosed at the time of sample collection; can include multiple diagnoses; the value of the field depends on subject; e.g. Charcoal rot (Macrophomina phaseolina), Late wilt (Cephalosporium maydis)-source_characteristic-
sample disease stageStringstage of the disease at the time of sample collection, e.g. inoculation, penetration, infection, growth and reproduction, dissemination of pathogen-source_characteristic-
sample wet massStringmeasurement of wet mass at the time of sample collection; e.g. 0.23 g-source_characteristic-
sample dry massStringmeasurement of dry mass at the time of sample collection; e.g. 0.05g-source_characteristic-
sample heightStringheight of subject at the time of sampling, if different from the length; e.g. 0.75m-source_characteristic-
sample lengthStringlength of subject at the time of sampling, if different from the height; e.g. 2m-source_characteristic-
growth facilityControlled Vocabulary - growth facilitytype of facility where the sampled plant was grown-source_characteristic-
sample capture statusControlled Vocabulary - sample capture statusReason for the sample collection.-source_characteristic-
genotypeStringname or code for genotype of organism-source_characteristic-
genetic modificationStringA genetic modification of the genome of an organism which may occur naturally by spontaneous mutation, or be introduced by some experimental means. Examples of genetic modification include specification of a transgene or the gene knocked-out or details of transient transfection.-source_characteristic-
organism common nameStringcommon name of the subject organism, e.g. maize-source_characteristic-
subspecific genetic lineage rankStringfurther information about the genetic distinctness of this lineage by recording additional information i.e. variety, cultivar, ecotype, inbred line,; it can also contain alternative taxonomic information-source_characteristic-
subspecific genetic lineage nameStringname of the infraspecific rank, e.g ecotype Col-0-source_characteristic-
biological statusStringthe level of genome modification; controlled vocabulary: wild, natural, semi-natural, inbred line, breeder's line, hybrid, clonal selection, mutant-source_characteristic-
organism phenotypeStringmost relevant phenotypic traits of the subject; for Phenotypic quality Ontology (PATO) (v 2013-10-28) terms, please see http://purl.bioontology.org/ontology/PATO, e.g. bifurcated (PATO_0001784); terms from Trait Ontology (TO), Plant Ontology (PO) or Crop Ontology (CO) are also accepted; include name/method/scale for each trait; can include multiple traits-source_characteristic-
ancestral dataStringinformation about either pedigree or other description of ancestral information (e.g. parental variety in case of mutant or selection), e.g. A/3*B (meaning [(A x B) x B] x B)-source_characteristic-
source material descriptionStringfurther information to clarify the nature of the specimen or population used that is not collected elsewhere, e.g. if source was derived from accessioned stock, describe how it links to the original material-source_characteristic-
biotic relationshipStringfree text description of relationship(s) between the subject organism and other organism(s) it is associate with, e.g., parasite on species X; mutualist with species Y, the target organism is the subject of the relationship, and the other organism(s) is the object-source_characteristic-
growth habitControlled Vocabulary - growth habitcharacteristic shape, appearance or growth form of a plant species-source_characteristic-
plant sexStringsex of the reproductive parts on the whole plant, e.g. pistilate, staminate, monoecieous, hermaphrodite-source_characteristic-
climate environmentStringtreatment involving an exposure to a particular climate; can include multiple climates-source_characteristic-
gaseous environmentStringuse of conditions with differing gaseous environments; should include the name of gaseous compound, amount administered, treatment duration, interval and total experimental duration; can include multiple gaseous environment regimens-source_characteristic-
seasonal environmentStringtreatment involving an exposure to a particular season (e.g. winter, summer, rabi, rainy etc.)-source_characteristic-
soil_taxonomic/FAO classificationStringsoil classification from the FAO World Reference Database for Soil Resources-source_characteristic-
soil_taxonomic/local classificationStringsoil classification based on local soil classification system-source_characteristic-
soil_taxonomic/local classification methodStringreference or method used in determining the local soil classification-source_characteristic-
soil typeControlled Vocabulary - soil typesoil series name or other lower-level classification-source_characteristic-
soil type methodStringreference or method used in determining soil series name or other lower-level classification-source_characteristic-
drainage classificationControlled Vocabulary - drainage classificationdrainage classification from a standard system such as the USDA system-source_characteristic-
textureStringthe relative proportion of different grain sizes of mineral particles in a soil, as described using a standard system; express as % sand (50 um to 2 mm), silt (2 um to 50 um), and clay (<2 um) with textural name (e.g., silty clay loam) optional.-source_characteristic-
texture methodStringreference or method used in determining soil texture-source_characteristic-
soil water contentStringwater content measurement; e.g. 13.6%-source_characteristic-
soil pHStringpH measurement of the soil; e.g. 6.2-source_characteristic-
plant growth medium*Stringspecification of the media for growing the plants or tissue cultured samples, e.g. soil, aeroponic, hydroponic, in vitro solid culture medium, in vitro liquid culture medium, recommended value is a specific value from EO:plant growth medium or other controlled vocabulary-source_characteristic-
rooting conditionsStringrelevant rooting conditions, such as field plot size, sowing density, container dimensions, number of plants per container-source_characteristic-
culture rooting mediumStringname or reference for the hydroponic or in vitro culture rooting medium, can be a name of a commonly used medium or reference to a specific medium; e.g. Murashige and Skoog medium, if the medium has not been formally published, use the rooting medium descriptors-source_characteristic-
rooting medium macronutrientsStringmeasurement of the culture rooting medium macronutrients (N,P, K, Ca, Mg, S); e.g. KH2PO4 (170mg/L)-source_characteristic-
rooting medium micronutrientsStringmeasurement of the culture rooting medium micronutrients (Fe, Mn, Zn, B, Cu, Mo); e.g. H3BO3 (6.2mg/L)-source_characteristic-
rooting medium organic supplementsStringorganic supplements of the culture rooting medium, such as vitaimins, amino acids, organic acids, antibiotics activated charcoal; e.g. Nicotinic acid (0.5mg/L)-source_characteristic-
rooting medium carbonStringsource of organic carbon in the culture rooting medium; e.g. sucrose-source_characteristic-
rooting medium regulatorsStringgrowth regulators in the culture rooting medium, such as cytokinins, auxins, gybberellins, abscisic acid; e.g. 0.5mg/L NAA-source_characteristic-
rooting medium solidifierStringspecification of the solidifying agent in the culture rooting medium; e.g. agar-source_characteristic-
rooting medium pHStringpH measurement of the culture rooting medium; e.g. 5.5-source_characteristic-
air temperature regimenStringinformation about treatment involving an exposure to varying temperatures; should include the temperature, treatment duration, interval and total experimental duration; can include different temperature regimens-source_characteristic-
antibiotic regimenStringinformation about treatment involving antibiotic administration; should include the name of antibiotic, amount administered, treatment duration, interval and total experimental duration; can include multiple antibiotic regimens-source_characteristic-
chemical mutagenStringtreatment involving use of mutagens; should include the name of mutagen, amount administered, treatment duration, interval and total experimental duration; can include multiple mutagen regimens-source_characteristic-
fertilizer regimenStringinformation about treatment involving the use of fertilizers; should include the name fertilizer, amount administered, treatment duration, interval and total experimental duration; can include multiple fertilizer regimens-source_characteristic-
fungicide regimenStringinformation about treatment involving use of fungicides; should include the name of fungicide, amount administered, treatment duration, interval and total experimental duration; can include multiple fungicide regimens-source_characteristic-
gravityStringinformation about treatment involving use of gravity factor to study various types of responses in presence, absence or modified levels of gravity; can include multiple treatments-source_characteristic-
growth hormone regimenStringinformation about treatment involving use of growth hormones; should include the name of growth hormone, amount administered, treatment duration, interval and total experimental duration; can include multiple growth hormone regimens-source_characteristic-
herbicide regimenStringinformation about treatment involving use of herbicides; information about treatment involving use of growth hormones; should include the name of herbicide, amount administered, treatment duration, interval and total experimental duration; can include multiple regimens-source_characteristic-
humidity regimenStringinformation about treatment involving an exposure to varying degree of humidity; information about treatment involving use of growth hormones; should include amount of humidity administered, treatment duration, interval and total experimental duration; can include multiple regimens-source_characteristic-
mineral nutrient regimenStringinformation about treatment involving the use of mineral supplements; should include the name of mineral nutrient, amount administered, treatment duration, interval and total experimental duration; can include multiple mineral nutrient regimens-source_characteristic-
non-mineral nutrient regimenStringinformation about treatment involving the exposure of plant to non-mineral nutrient such as oxygen, hydrogen or carbon; should include the name of non-mineral nutrient, amount administered, treatment duration, interval and total experimental duration; can include multiple non-mineral nutrient regimens-source_characteristic-
pesticide regimenStringinformation about treatment involving use of insecticides; should include the name of pesticide, amount administered, treatment duration, interval and total experimental duration; can include multiple pesticide regimens-source_characteristic-
pH regimenStringinformation about treatment involving exposure of plants to varying levels of pH of the growth media; can include multiple regimen-source_characteristic-
radiation regimenStringinformation about treatment involving exposure of plant or a plant part to a particular radiation regimen; should include the radiation type, amount or intensity administered, treatment duration, interval and total experimental duration; can include multiple radiation regimens-source_characteristic-
rainfall regimenStringinformation about treatment involving an exposure to a given amount of rainfall; can include multiple regimens-source_characteristic-
salt regimenStringinformation about treatment involving use of salts as supplement to liquid and soil growth media; should include the name of salt, amount administered, treatment duration, interval and total experimental duration; can include multiple salt regimens-source_characteristic-
standing water regimenStringtreatment involving an exposure to standing water during a plant's life span, types can be flood water or standing water; can include multiple regimens-source_characteristic-
watering regimenStringinformation about treatment involving an exposure to watering frequencies; can include multiple regimens-source_characteristic-
water temperature regimenStringinformation about treatment involving an exposure to water with varying degree of temperature; can include multiple regimens-source_characteristic-
plant treatmentStringontology term(s) that describes the plant treatment or relevant environmental conditions, recommend use of Plant Environment Ontology (EO) or other ontology, such as XEML Environment Ontology (XEO) or Crop Ontology (CO), more specific fields in the treatment section can be used in addition to or in place of this field-source_characteristic-
light regimenStringinformation about treatment involving an exposure to light, this includes both light intensity and quality---
biotic regimenStringinformation about treatment involving use of biotic factors, such as bacteria, viruses or fungi-source_characteristic-
mechanical damageStringinformation about any mechanical damage exerted on the plant; can include multiple damages and sites-source_characteristic-
chemical administrationStringlist 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) (v111), please see http://purl.bioontology.org/ontology/CHEBI-source_characteristic-
perturbationStringtype of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with time that perturbation occurred; can include multiple perturbation types-source_characteristic-
submission dateStringDate in which sample was submitted to ENA.-source_characteristic-
statusControlled Vocabulary - statusStatus of submission to ENA.-source_characteristic-
accessionStringENA sample accession code. Provided by ENA after submission.-source_characteristic-
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