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Plant-associated

plant-associated

URI: mixs.vocab:Plant-associated

Combinations

Slots

MIxS ID Name Multiplicity Description Pattern Info
MIXS:0000009 lat_lon 0..1 The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system None .
MIXS:0000018 depth 0..1 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. None .
MIXS:0000094 alt 0..1 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 None .
MIXS:0000093 elev 0..1 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. None .
MIXS:0000113 temp 0..1 Temperature of the sample at the time of sampling. None .
MIXS:0000010 geo_loc_name 0..1 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 (http://purl.bioontology.org/ontology/GAZ) None .
MIXS:0000011 collection_date 0..1 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 None .
MIXS:0000012 env_broad_scale 0..1 Report the major environmental system the sample or specimen came from. The system(s) identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. in the desert or a rainforest). We recommend using subclasses of EnvO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS None .
MIXS:0000013 env_local_scale 0..1 Report the entity or entities which are in the sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. We recommend using EnvO terms which are of smaller spatial grain than your entry for env_broad_scale. Terms, such as anatomical sites, from other OBO Library ontologies which interoperate with EnvO (e.g. UBERON) are accepted in this field. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS. None .
MIXS:0000014 env_medium 0..1 Report the environmental material(s) immediately surrounding the sample or specimen at the time of sampling. We recommend using subclasses of 'environmental material' (http://purl.obolibrary.org/obo/ENVO_00010483). EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS . Terms from other OBO ontologies are permissible as long as they reference mass/volume nouns (e.g. air, water, blood) and not discrete, countable entities (e.g. a tree, a leaf, a table top). None .
MIXS:0000860 samp_capt_status 0..1 Reason for the sample None .
MIXS:0000753 oxy_stat_samp 0..1 Oxygenation status of sample. None .
MIXS:0001059 plant_sex 0..1 Sex of the reproductive parts on the whole plant, e.g. pistillate, staminate, monoecieous, hermaphrodite. None .
MIXS:0000249 samp_dis_stage 0..1 Stage of the disease at the time of sample collection, e.g. inoculation, penetration, infection, growth and reproduction, dissemination of pathogen. None .
MIXS:0001044 growth_habit 0..1 Characteristic shape, appearance or growth form of a plant species None .
MIXS:0000858 biol_stat 0..1 The level of genome modification. None .
MIXS:0000116 samp_store_dur 0..1 Duration for which the sample was stored None .
MIXS:0001062 root_med_ph 0..1 pH measurement of the culture rooting medium; e.g. 5.5. None .
MIXS:0000255 host_age 0..1 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 None .
MIXS:0000257 host_dry_mass 0..1 Measurement of dry mass None .
MIXS:0000264 host_height 0..1 The height of subject None .
MIXS:0000256 host_length 0..1 The length of subject None .
MIXS:0000263 host_tot_mass 0..1 Total mass of the host at collection, the unit depends on host None .
MIXS:0000567 host_wet_mass 0..1 Measurement of wet mass None .
MIXS:0000183 salinity 0..1 The total concentration of all dissolved salts in a liquid or solid 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. None .
MIXS:0000110 samp_store_temp 0..1 Temperature at which sample was stored, e.g. -80 degree Celsius None .
MIXS:0000551 air_temp_regm 0..* Information about treatment involving an exposure to varying temperatures; should include the temperature, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include different temperature regimens None .
MIXS:0000559 gravity 0..* Information about treatment involving use of gravity factor to study various types of responses in presence, absence or modified levels of gravity; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple treatments None .
MIXS:0000568 humidity_regm 0..* Information 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 regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens None .
MIXS:0000576 rainfall_regm 0..* Information about treatment involving an exposure to a given amount of rainfall, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens None .
MIXS:0000590 water_temp_regm 0..* Information about treatment involving an exposure to water with varying degree of temperature, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens None .
MIXS:0000591 watering_regm 0..* Information about treatment involving an exposure to watering frequencies, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens None .
MIXS:0001056 ph_regm 0..* Information about treatment involving exposure of plants to varying levels of ph of the growth media, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimen None .
MIXS:0000250 host_taxid 0..1 NCBI taxon id of the host. None .
MIXS:0000859 genetic_mod 0..1 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. None .
MIXS:0001061 root_cond 0..1 Relevant rooting conditions such as field plot size, sowing density, container dimensions, number of plants per container. None .
MIXS:0001070 tiss_cult_growth_med 0..1 Description of plant tissue culture growth media used None .
MIXS:0001318 host_subspecf_genlin 0..* Information about the genetic distinctness of the host organism below the subspecies level e.g., serovar, serotype, biotype, ecotype, variety, cultivar, or any relevant genetic typing schemes like Group I plasmid. Subspecies should not be recorded in this term, but in the NCBI taxonomy. Supply both the lineage name and the lineage rank separated by a colon, e.g., biovar:abc123. None .
MIXS:0001060 plant_struc 0..1 Name of plant structure the sample was obtained from; for Plant Ontology (PO) (v releases/2017-12-14) 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. None .
MIXS:0001057 plant_growth_med 0..1 Specification 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 (follow this link for terms http://purl.obolibrary.org/obo/EO_0007147) or other controlled vocabulary None .
MIXS:0000751 chem_administration 0..* 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 None .
MIXS:0000247 ances_data 0..1 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) None .
MIXS:0001038 biotic_regm 0..1 Information about treatment(s) involving use of biotic factors, such as bacteria, viruses or fungi. None .
MIXS:0000248 host_common_name 0..1 Common name of the host. None .
MIXS:0000365 host_genotype 0..1 Observed genotype None .
MIXS:0000251 host_life_stage 0..1 Description of life stage of host None .
MIXS:0001298 host_symbiont 0..* The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. None .
MIXS:0001058 plant_product 0..1 Substance produced by the plant, where the sample was obtained from None .
MIXS:0001063 root_med_solid 0..1 Specification of the solidifying agent in the culture rooting medium; e.g. agar. None .
MIXS:0000755 samp_store_loc 0..1 Location at which sample was stored, usually name of a specific freezer/room None .
MIXS:0000752 misc_param 0..* Any other measurement performed or parameter collected, that is not listed here None .
MIXS:0000577 root_med_carbon 0..1 Source of organic carbon in the culture rooting medium; e.g. sucrose. None .
MIXS:0000578 root_med_macronutr 0..1 Measurement of the culture rooting medium macronutrients (N,P, K, Ca, Mg, S); e.g. KH2PO4 (170 mg/L). None .
MIXS:0000579 root_med_micronutr 0..1 Measurement of the culture rooting medium micronutrients (Fe, Mn, Zn, B, Cu, Mo); e.g. H3BO3 (6.2 mg/L). None .
MIXS:0000581 root_med_regl 0..1 Growth regulators in the culture rooting medium such as cytokinins, auxins, gybberellins, abscisic acid; e.g. 0.5 mg/L NAA. None .
MIXS:0000580 root_med_suppl 0..1 Organic supplements of the culture rooting medium, such as vitamins, amino acids, organic acids, antibiotics activated charcoal; e.g. nicotinic acid (0.5 mg/L). None .
MIXS:0000103 organism_count 0..* 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). None .
MIXS:0000569 light_regm 0..1 Information about treatment(s) involving exposure to light, including both light intensity and quality. None .
MIXS:0000553 antibiotic_regm 0..* Information about treatment involving antibiotic administration; should include the name of antibiotic, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple antibiotic regimens None .
MIXS:0000555 chem_mutagen 0..* Treatment involving use of mutagens; should include the name of mutagen, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple mutagen regimens None .
MIXS:0000556 fertilizer_regm 0..* Information about treatment involving the use of fertilizers; should include the name of fertilizer, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple fertilizer regimens None .
MIXS:0000557 fungicide_regm 0..* Information about treatment involving use of fungicides; should include the name of fungicide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple fungicide regimens None .
MIXS:0000558 gaseous_environment 0..* Use 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 None .
MIXS:0000560 growth_hormone_regm 0..* Information about treatment involving use of growth hormones; should include the name of growth hormone, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple growth hormone regimens None .
MIXS:0000561 herbicide_regm 0..* Information about treatment involving use of herbicides; information about treatment involving use of growth hormones; should include the name of herbicide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens None .
MIXS:0000570 mineral_nutr_regm 0..* Information about treatment involving the use of mineral supplements; should include the name of mineral nutrient, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple mineral nutrient regimens None .
MIXS:0000571 non_min_nutr_regm 0..* Information 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 regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple non-mineral nutrient regimens None .
MIXS:0000573 pesticide_regm 0..* Information about treatment involving use of insecticides; should include the name of pesticide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple pesticide regimens None .
MIXS:0000575 radiation_regm 0..* Information 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 regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple radiation regimens None .
MIXS:0000582 salt_regm 0..* Information about treatment involving use of salts as supplement to liquid and soil growth media; should include the name of salt, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple salt regimens None .
MIXS:0001040 climate_environment 0..* Treatment involving an exposure to a particular climate; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple climates None .
MIXS:0000754 perturbation 0..* 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 None .
MIXS:0001068 season_environment 0..* Treatment involving an exposure to a particular season (e.g. Winter, summer, rabi, rainy etc.), treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment None .
MIXS:0001069 standing_water_regm 0..* Treatment involving an exposure to standing water during a plant's life span, types can be flood water or standing water, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens None .
MIXS:0000874 host_phenotype 0..1 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. None .
MIXS:0001052 mechanical_damage 0..* Information about any mechanical damage exerted on the plant; can include multiple damages and sites None .
MIXS:0001041 cult_root_med 0..1 Name or reference for the hydroponic or in vitro culture rooting medium; can be the 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. None .
MIXS:0001043 growth_facil 0..1 Type of facility where the sampled plant was grown; controlled vocabulary: growth chamber, open top chamber, glasshouse, experimental garden, field. Alternatively use Crop Ontology (CO) terms, see http://www.cropontology.org/ontology/CO_715/Crop%20Research None .

Usages

Identifier and Mapping Information