Plant-associated
plant-associated
URI: mixs.vocab:Plant-associated
Combinations
- Plant-associated
- Plant-associatedMIGSEukaryote [ MIGS eukaryote]
- Plant-associatedMIGSBacteria [ MIGS bacteria]
- Plant-associatedMIGSPlant [ MIGS plant]
- Plant-associatedMIGSVirus [ MIGS virus]
- Plant-associatedMIGSOrg [ MIGS org]
- Plant-associatedMIMS [ MIMS]
- Plant-associatedMIMARKSSpecimen [ MIMARKS specimen]
- Plant-associatedMIMARKSSurvey [ MIMARKS survey]
- Plant-associatedMISAG [ MISAG]
- Plant-associatedMIMAG [ MIMAG]
- Plant-associatedMIUVIG [ MIUVIG]
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 | . |