Skip to content

Agriculture

agriculture

URI: mixs.vocab:Agriculture

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 1..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:0000753 oxy_stat_samp 0..1 Oxygenation status of sample. None .
MIXS:0000819 pres_animal_insect 0..1 The type and number of animals or insects present in the sampling space. None .
MIXS:0001080 cur_land_use 0..1 Present state of sample site None .
MIXS:0001081 tillage 0..* Note method(s) used for tilling None .
MIXS:0001110 farm_water_source 0..* Source of water used on the farm for irrigation of crops or watering of livestock. None .
MIXS:0001176 water_source_shared 0..* Other users sharing access to the same water source. Multiple terms can be separated by one or more pipes. None .
MIXS:0001082 horizon 0..1 Specific layer in the land area which measures parallel to the soil surface and possesses physical characteristics which differ from the layers above and beneath None .
MIXS:0001084 profile_position 0..1 Cross-sectional position in the hillslope where sample was collected.sample area position in relation to surrounding areas None .
MIXS:0001085 drainage_class 0..1 Drainage classification from a standard system such as the USDA system None .
MIXS:0000322 sieving 1..1 Collection design of pooled samples and/or sieve size and amount of sample sieved None .
MIXS:0000325 pool_dna_extracts 1..* Indicate whether multiple DNA extractions were mixed. If the answer yes, the number of extracts that were pooled should be given. None .
MIXS:0000318 crop_rotation 0..1 Whether or not crop is rotated, and if yes, rotation schedule None .
MIXS:0001062 root_med_ph 0..1 pH measurement of the culture rooting medium; e.g. 5.5. None .
MIXS:0001175 water_pH 0..1 pH measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid. None .
MIXS:0000211 porosity 0..1 Porosity of deposited sediment is volume of voids divided by the total volume of sample None .
MIXS:0000644 annual_precpt 0..1 The average of all annual precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps. None .
MIXS:0000642 annual_temp 0..1 Mean annual temperature None .
MIXS:0000255 host_age 1..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 1..1 The height of subject None .
MIXS:0000256 host_length 1..1 The length of subject None .
MIXS:0000263 host_tot_mass 1..1 Total mass of the host at collection, the unit depends on host None .
MIXS:0000100 humidity 0..1 Amount of water vapour in the air, at the time of sampling None .
MIXS:0000650 microbial_biomass 1..1 The part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer. If you keep this, you would need to have correction factors used for conversion to the final units None .
MIXS:0001296 photosynt_activ 0..* Measurement of photosythetic activity (i.e. leaf gas exchange / chlorophyll fluorescence emissions / reflectance / transpiration) Please also include the term method term detailing the method of activity measurement. None .
MIXS:0000110 samp_stor_temp 0..1 Temperature at which sample was stored, e.g. -80 degree Celsius. None .
MIXS:0001148 season_humidity 0..1 Average humidity of the region throughout the growing season. None .
MIXS:0000645 season_precpt 0..1 The average of all seasonal precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps. None .
MIXS:0000643 season_temp 0..1 Mean seasonal temperature None .
MIXS:0000735 size_frac_low 0..1 Refers to the mesh/pore size used to pre-filter/pre-sort the sample. Materials larger than the size threshold are excluded from the sample None .
MIXS:0000736 size_frac_up 0..1 Refers to the mesh/pore size used to retain the sample. Materials smaller than the size threshold are excluded from the sample None .
MIXS:0000647 slope_aspect 0..1 The direction a slope faces. While looking down a slope use a compass to record the direction you are facing (direction or degrees); e.g., nw or 315 degrees. This measure provides an indication of sun and wind exposure that will influence soil temperature and evapotranspiration. None .
MIXS:0000646 slope_gradient 0..1 Commonly called 'slope'. The angle between ground surface and a horizontal line (in percent). This is the direction that overland water would flow. This measure is usually taken with a hand level meter or clinometer None .
MIXS:0000018 soil_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:0000112 solar_irradiance 0..1 The amount of solar energy that arrives at a specific area of a surface during a specific time interval None .
MIXS:0000335 texture 0..1 The 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. None .
MIXS:0000525 tot_car 0..1 Total carbon content None .
MIXS:0000102 tot_nitro 0..1 Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen None .
MIXS:0000533 tot_org_carb 0..1 Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content None .
MIXS:0000689 tot_phos 0..1 Total amount or concentration of phosphate 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:0001116 crop_yield 0..1 Amount of crop produced per unit or area of land. None .
MIXS:0001163 soil_temp 0..* Temperature of soil at the time of sampling. None .
MIXS:0000250 host_taxid 1..1 NCBI taxon id of the host. None .
MIXS:0001147 lot_number 0..* A distinctive alpha-numeric identification code assigned by the manufacturer or distributor to a specific quantity of manufactured material or product within a batch. Synonym: Batch Number. The submitter should provide lot number of the item followed by the item name for which the lot number was provided. None .
MIXS:0000116 samp_store_dur 1..1 Duration for which the sample was stored None .
MIXS:0000336 texture_meth 0..1 Reference or method used in determining soil texture. None .
MIXS:0001177 enrichment_protocol 0..1 The microbiological workflow or protocol followed to test for the presence or enumeration of the target microbial analyte(s). Please provide a PubMed or DOI reference for published protocols. 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:0001336 photosynt_activ_meth 0..* Reference or method used in measurement of photosythetic activity None .
MIXS:0001225 samp_collect_method 0..1 The method employed for collecting the sample. None .
MIXS:0000314 cur_vegetation_meth 0..1 Reference or method used in vegetation classification None .
MIXS:0000343 heavy_metals_meth 0..1 Reference or method used in determining heavy metals None .
MIXS:0000321 horizon_meth 0..1 Reference or method used in determining the horizon None .
MIXS:0000329 link_class_info 0..1 Link to digitized soil maps or other soil classification information None .
MIXS:0000328 link_climate_info 0..1 Link to climate resource None .
MIXS:0000331 local_class_meth 0..1 Reference or method used in determining the local soil classification None .
MIXS:0000339 microbial_biomass_meth 1..1 Reference or method used in determining microbial biomass None .
MIXS:0001106 ph_meth 0..1 Reference or method used in determining ph None .
MIXS:0000316 previous_land_use_meth 0..1 Reference or method used in determining previous land use and dates None .
MIXS:0000334 soil_type_meth 1..1 Reference or method used in determining soil series name or other lower-level classification None .
MIXS:0000338 tot_n_meth 0..1 Reference or method used in determining the total nitrogen None .
MIXS:0000337 tot_org_c_meth 0..1 Reference or method used in determining total organic carbon 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:0000058 assembly_quality 0..1 Tool(s) used for assembly, including version number and parameters None .
MIXS:0001083 fao_class 0..1 Soil classification from the FAO World Reference Database for Soil Resources. The list can be found at http://www.fao.org/nr/land/sols/soil/wrb-soil-maps/reference-groups None .
MIXS:0000874 host_phenotype 1..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:0001115 anim_water_method 0..* Description of the equipment or method used to distribute water to livestock. This field accepts termed listed under water delivery equipment (http://opendata.inra.fr/EOL/EOL_0001653). Multiple terms can be separated by pipes. None .
MIXS:0001126 farm_equip 0..* List of equipment used for planting, fertilization, harvesting, irrigation, land levelling, residue management, weeding or transplanting during the growing season. This field accepts terms listed under agricultural implement (http://purl.obolibrary.org/obo/AGRO_00000416). Multiple terms can be separated by pipes. None .
MIXS:0001127 fertilizer_admin 0..1 Type of fertilizer or amendment added to the soil or water for the purpose of improving substrate health and quality for plant growth. This field accepts terms listed under agronomic fertilizer (http://purl.obolibrary.org/obo/AGRO_00002062). Multiple terms may apply and can be separated by pipes, listing in reverse chronological order. None .
MIXS:0001211 food_prod 0..* Descriptors of the food production system or of the agricultural environment and growing conditions related to the farm production system, such as wild caught, organic, free-range, industrial, dairy, beef, domestic or cultivated food production. This field accepts terms listed under food production (http://purl.obolibrary.org/obo/FOODON_03530206). Multiple terms may apply and can be separated by pipes. None .
MIXS:0001137 food_trav_mode 0..* A descriptor for the method of movement of food commodity along the food distribution system. This field accepts terms listed under travel mode (http://purl.obolibrary.org/obo/GENEPIO_0001064). If the proper descrptor is not listed please use text to describe the mode of travel. Multiple terms can be separated by one or more pipes. 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:0001111 plant_water_method 0..1 Description of the equipment or method used to distribute water to crops. This field accepts termed listed under irrigation process (http://purl.obolibrary.org/obo/AGRO_00000006). Multiple terms can be separated by pipes. None .
MIXS:0000829 season 0..1 The season when sampling occurred. Any of the four periods into which the year is divided by the equinoxes and solstices. This field accepts terms listed under season (http://purl.obolibrary.org/obo/NCIT_C94729). 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 1..* 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:0001170 spikein_strain 0..* Taxonomic information about the spike-in organism(s) at the strain level. This field accepts terms under organism (http://purl.obolibrary.org/obo/NCIT_C14250). This field also accepts identification numbers from NCBI under https://www.ncbi.nlm.nih.gov/taxonomy. Multiple terms can be separated by pipes. None .
MIXS:0001121 adjacent_environment 0..* Description of the environmental system or features that are adjacent to the sampling site. This field accepts terms under ecosystem (http://purl.obolibrary.org/obo/ENVO_01001110) and human construction (http://purl.obolibrary.org/obo/ENVO_00000070). Multiple terms can be separated by pipes. 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:0000312 cur_vegetation 0..1 Vegetation classification from one or more standard classification systems, or agricultural crop None .
MIXS:0001184 Food_Product_type 0..1 new food product categories and food products themselves None .
MIXS:0001139 Food_source 1..1 Type of plant or animal from which the food product or its major ingredient is derived or a chemical food source [FDA CFSAN 1995]. None .
MIXS:0000248 host_common_name 1..1 Common name of the host. None .
MIXS:0000365 host_genotype 1..1 Observed genotype None .
MIXS:0000251 host_life_stage 1..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:0001145 library_prep_kit 0..1 Packaged kits (containing adapters, indexes, enzymes, buffers etc.), tailored for specific sequencing workflows, which allow the simplified preparation of sequencing-ready libraries for small genomes, amplicons, and plasmids. None .
MIXS:0000330 local_class 0..1 Soil classification based on local soil classification system None .
MIXS:0001058 plant_product 0..1 Substance produced by the plant, where the sample was obtained from None .
MIXS:0000002 samp_collect_device 1..1 The device used to collect an environmental sample. This field accepts terms listed under environmental sampling device (http://purl.obolibrary.org/obo/ENVO). This field also accepts terms listed under specimen collection device (http://purl.obolibrary.org/obo/GENEPIO_0002094). None .
MIXS:0000755 samp_store_loc 1..1 Location at which sample was stored, usually name of a specific freezer/room None .
MIXS:0001156 sequencing_location 0..1 The location the sequencing run was performed. Indicate the name of the lab or core facility where samples were sequenced. None .
MIXS:0000332 soil_type 1..* Description of the soil type or classification. This field accepts terms under soil (http://purl.obolibrary.org/obo/ENVO_00001998). Multiple terms can be separated by pipes. 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: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: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: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:0000571 non_mineral_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: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:0000639 agrochem_addition 0..* Addition of fertilizers, pesticides, etc. - amount and time of applications 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:0000327 store_cond 1..1 Explain how and for how long the soil sample was stored before DNA extraction (fresh/frozen/other). 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: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:0000315 previous_land_use 0..1 Previous land use and dates None .
MIXS:0001138 food_trav_vehic 0..* A descriptor for the mobile machine which is used to transport food commodities along the food distribution system. This field accepts terms listed under vehicle (http://purl.obolibrary.org/obo/ENVO_01000604). If the proper descrptor is not listed please use text to describe the mode of travel. Multiple terms can be separated by one or more pipes. None .
MIXS:0000320 extreme_event 0..1 Unusual physical events that may have affected microbial populations None .
MIXS:0001086 fire 0..1 Historical and/or physical evidence of fire None .
MIXS:0000319 flooding 0..1 Historical and/or physical evidence of flooding None .
MIXS:0000091 url 0..* A related resource that is referenced, cited, or otherwise associated to the sequence. None .
MIXS:0001082 soil_horizon 0..1 Specific layer in the land area which measures parallel to the soil surface and possesses physical characteristics which differ from the layers above and beneath None .
MIXS:0001181 cult_isol_date 0..1 A culture isolation date is a date-time entity marking the end of a process in which a sample yields a positive result for the target microbial analyte(s) in the form of an isolated colony or colonies. None .
MIXS:0001124 farm_equip_san 0..* Method used to sanitize growing and harvesting equipment. This can including type and concentration of sanitizing solution. Multiple terms can be separated by one or more pipes. None .
MIXS:0001123 farm_equip_shared 0..* List of planting, growing or harvesting equipment shared with other farms. This field accepts terms listed under agricultural implement (http://purl.obolibrary.org/obo/AGRO_00000416). Multiple terms can be separated by pipes. None .
MIXS:0001133 food_harvest_proc 0..* A harvesting process is a process which takes in some food material from an individual or community of plant or animal organisms in a given context and time, and outputs a precursor or consumable food product. This may include a part of an organism or the whole, and may involve killing the organism. None .
MIXS:0001161 rel_location 0..1 Location of sampled soil to other parts of the farm e.g. under crop plant, near irrigation ditch, from the dirt road. None .
MIXS:0001153 samp_pooling 0..* Physical combination of several instances of like material, e.g. RNA extracted from samples or dishes of cell cultures into one big aliquot of cells. Please provide a short description of the samples that were pooled. None .
MIXS:0001158 soil_conductivity 0..1 Conductivity of soil at time of sampling. None .
MIXS:0001159 soil_cover 0..1 Description of the material covering the sampled soil. This field accepts terms under ENVO:00010483, environmental material. None .
MIXS:0001160 soil_pH 0..1 The pH of soil at time of sampling. None .

Usages

Identifier and Mapping Information