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Submitter: System

Projects: Default Project

Version: 1.2.0

Group: arrayexpress

11 Sample types are referencing this Template

ISA Level: study source

Organism: plant

Parent Template: None

Child Templates:


NameTypeDescriptionPID helpISA Tag helpUnit
Source Name*StringSources are considered as the starting biological material used in a study.-source-
organism*Controlled Vocabulary - organismA material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs. E.g Drosophila melanogaster.
organism part*Controlled Vocabulary - organism partThe part of organism's anatomy or substance arising from an organism from which the biomaterial was derived, excludes cells. E.g. tissue, organ, system, sperm, blood or body location (arm).
developmental stage*Controlled Vocabulary - developmental stageA developmental stage is spatiotemporal region encompassing some part of the life cycle of an organism, e.g. blastula stage
age*Controlled Vocabulary - ageA temporal measurement of the time period elapsed since an identifiable point in the life cycle of an organism. If a developmental stage is specified, the identifiable point would be the beginning of that stage. Otherwise the identifiable point must be specified such as planting (e.g. 3 days post planting).
genotype*Controlled Vocabulary - genotypeThe total sum of the genetic information of an organism that is known and relevant to the experiment being performed, including chromosomal, plasmid, viral or other genetic material which has been introduced into the organism either prior to or during the experiment.
cultivar*StringA cultivated plant variety selected and given a name because it has desirable characteristics that distinguish it from otherwise similar plants of the same species.
cultured cellControlled Vocabulary - cultured cellA cell in vitro that is or has been maintained or propagated as part of a cell culture.
cell typeControlled Vocabulary - cell typeA cell type is a distinct morphological or functional form of cell. Examples are epithelial, glial etc.
clinical historyControlled Vocabulary - clinical historyIs an information entity about the material's (i.e., the patient's) medical record as background information relevant to the experiment.
chemical entityControlled Vocabulary - chemical entityA drug, solvent, chemical, etc., with a property that can be measured such as concentration. A molecular entity consisting of two or more chemical elements.
dietControlled Vocabulary - dietThe customary allowance of food and drink taken by a person or an animal from day to day, particularly one especially planned to meet specific requirements of the individual, including or excluding certain items of food; a prescribed course of eating and drinking in which the amount and kind of food, as well as the times at which it is to be taken, are regulated for therapeutic purposes or selected with reference to a particular state of health. Regular course of eating and drinking adopted by a person or animal. This does not include DIET THERAPY, a specific diet prescribed in the treatment of a disease.
disease stagingControlled Vocabulary - disease stagingThe stage or progression of a disease in an organism. Includes pathological staging of cancers and other disease progression. E.g. Dukes C stage describing colon cancer.
doseStringThe total quantity or strength of a substance administered at one time.
ecotypeControlled Vocabulary - ecotypeA biotype resulting from selection in a particular habitat, e.g. the A. thaliana Ecotype Ler.
enviromental historyStringInformation concerning the envinonrment a material entity has been exposed to, such as an organism from a lake.
enviromental stress treatmentStringEnvironmental stress is a treatment where some aspect of the environment is perturbed in order to stress the organism or culture, e.g. change in temperature, change in watering regime.
fractionStringDefinition: A dimensionless ratio unit which relates the part (the numerator) to the whole (the denominator). [Wikipedia]
genetic modificationControlled Vocabulary - genetic modificationA 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.
growth conditionControlled Vocabulary - growth conditionA role that a material entity can play which enables particular conditions used to grow organisms or parts of the organism. This includes isolated environments such as cultures and open environments such as field studies.
immunoprecipitateControlled Vocabulary - immunoprecipitateThe precipitate antibody bound target molecules generated when precipitating an antigen out of a solution during the process of immunoprecipitation.
individualStringAn individual used a specimen in an experiment, from which a material sample was derived.
infectionStringThe state of being infected such as from the introduction of a foreign agent such as serum, vaccine, antigenic substance or organism.
inferred cell typeStringA cell type classification that is determined as result of a single-cell analysis, such as cell clustering or trajectory analysis.
injuryControlled Vocabulary - injuryDamage inflicted on the body as the direct or indirect result of an external force, with or without disruption of structural continuity. [ NCIT:C3671 ]
irradiateStringThe process of treating a material with radiation.
karyotypeStringA karyotype is the number and appearance of chromosomes in the nucleus of a eukaryotic cell.
phenotypeControlled Vocabulary - phenotypeThe observable form taken by some character (or group of characters) in an individual or an organism, excluding pathology and disease. The detectable outward manifestations of a specific genotype.
RNA interferenceStringThe process in which double-stranded RNAs silence cognate genes. Involves posttranscriptional gene inactivation ('silencing') both of transgenes or dsRNA introduced into a germline, and of the host gene(s) homologous to the transgenes or dsRNA. This silencing is triggered by the introduction of transgenes or double-stranded RNA (dsRNA), and can occur through a specific decrease in the level of mRNA, or by negative regulation of translation, of both host genes and transgenes.
replicateControlled Vocabulary - replicateA role played by a a biological sample in the context of an experiment where the intent is that biological or technical variation is measured.
sexControlled Vocabulary - sexThe assemblage of physical properties or qualities by which male is distinguished from female; the physical difference between male and female; the distinguishing peculiarity of male or female. An organismal quality inhering in a bearer by virtue of the bearer's ability to undergo sexual reproduction in order to differentiate the individuals or types involved. Term applied to any organism able to undergo sexual reproduction in order to differentiate the individuals or types involved. Sexual reproduction is defined as the ability to exchange genetic material with the potential of recombinant progeny.
single cell identifierStringA unique identifier for a single cell specimen.
specimen with known storage stateControlled Vocabulary - specimen with known storage stateA specimen for which it is known whether it has been subjected to storage of a specified type.
strainStringA population of organisms that is geneticaly different from others of the same species and possessing a set of defined characteristics.
timeStringNot specified
tumor gradingControlled Vocabulary - tumor gradingAn assay that determines the grade (severity/stage) of a tumor sample, used in cancer biology to describe abnormalities/qualities of tumor cells or tissues. Values can be described by terms from NCI Thesaurus. Determination of the grade (severity/stage) of a tumor sample, used in cancer biology to describe abnormalities/qualities of tumor cells or tissues. Values can be described by terms from NCI Thesaurus.
material type*Controlled Vocabulary - material typeUsed as an attribute column following Source Name, Sample Name, Extract Name, or Labeled Extract Name. This column contains terms describing the type of each material, for examples: whole organism, organism part, cell, total RNA.-source_characteristic-
help Creators and Submitter
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  • The JERM Harvester JERM

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Created: 18th Jul 2022 at 12:45

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