Combination: Miuvig combined with Agriculture (MiuvigAgriculture)
MIxS Data that comply with the Miuvig checklist and the Agriculture Extension
Composition
Miuvig [Checklist] + Agriculture [Extension]
Terms
| MIXS ID | Name | Cardinality and Range | Description |
|---|---|---|---|
| MIXS:0001107 | samp_name | 1 String |
A local identifier or name that for the material sample used for extracting n... |
| MIXS:0000017 | size_frac | 0..1 recommended String |
Filtering pore size used in sample preparation |
| MIXS:0000043 | lib_screen | 1 recommended String |
Specific enrichment or screening methods applied before and/or after creating... |
| MIXS:0000035 | source_uvig | 1 String |
Type of dataset from which the UViG was obtained |
| MIXS:0000062 | ref_db | 0..1 recommended String |
List of database(s) used for ORF annotation, along with version number and re... |
| MIXS:0000038 | nucl_acid_amp | 1 recommended String |
A link to a literature reference, electronic resource or a standard operating... |
| MIXS:0000039 | lib_size | 0..1 recommended Integer |
Total number of clones in the library prepared for the project |
| MIXS:0000047 | mid | 1 recommended String |
Molecular barcodes, called Multiplex Identifiers (MIDs), that are used to spe... |
| MIXS:0000057 | assembly_name | 1 recommended String |
Name/version of the assembly provided by the submitter that is used in the ge... |
| MIXS:0000113 | temp | 1 recommended String |
Temperature of the sample at the time of sampling |
| MIXS:0000069 | compl_score | 0..1 recommended String |
Completeness score is typically based on either the fraction of markers found... |
| MIXS:0000067 | trnas | 0..1 String |
The total number of tRNAs identified from the SAG or MAG |
| MIXS:0000037 | nucl_acid_ext | 1 recommended String |
A link to a literature reference, electronic resource or a standard operating... |
| MIXS:0000001 | samp_size | 1 recommended String |
The total amount or size (volume (ml), mass (g) or area (m2) ) of sample coll... |
| MIXS:0000094 | alt | 0..1 recommended String |
Heights of objects such as airplanes, space shuttles, rockets, atmospheric ba... |
| MIXS:0000024 | estimated_size | 0..1 String |
The estimated size of the genome prior to sequencing |
| MIXS:0000026 | source_mat_id | * recommended String |
A unique identifier assigned to a material sample (as defined by http://rs |
| MIXS:0000111 | samp_vol_we_dna_ext | 1 String |
Volume (ml) or mass (g) of total collected sample processed for DNA extractio... |
| MIXS:0000027 | pathogenicity | 1 String |
To what is the entity pathogenic |
| MIXS:0000040 | lib_reads_seqd | 1 recommended Integer |
Total number of clones sequenced from the library |
| MIXS:0000002 | samp_collect_device | 1 recommended String |
The device used to collect an environmental sample |
| MIXS:0000060 | number_contig | 1 Integer |
Total number of contigs in the cleaned/submitted assembly that makes up a giv... |
| MIXS:0000028 | biotic_relationship | 0..1 recommended BioticRelationshipEnum |
Description of relationship(s) between the subject organism and other organis... |
| MIXS:0000068 | trna_ext_software | 0..1 String |
Tools used for tRNA identification |
| MIXS:0000041 | lib_layout | 0..1 recommended LibLayoutEnum |
Specify whether to expect single, paired, or other configuration of reads |
| MIXS:0000056 | assembly_qual | 1 AssemblyQualEnum |
The assembly quality category is based on sets of criteria outlined for each ... |
| MIXS:0000025 | ref_biomaterial | 0..1 String |
Primary publication if isolated before genome publication; otherwise, primary... |
| MIXS:0000092 | project_name | 1 String |
Name of the project within which the sequencing was organized |
| MIXS:0000042 | lib_vector | 1 recommended String |
Cloning vector type(s) used in construction of libraries |
| MIXS:0000030 | host_spec_range | 1..* String |
The range and diversity of host species that an organism is capable of infect... |
| MIXS:0001321 | neg_cont_type | 0..1 recommended NegContTypeEnum |
The substance or equipment used as a negative control in an investigation |
| MIXS:0000036 | virus_enrich_appr | 1 VirusEnrichApprEnum |
List of approaches used to enrich the sample for viruses, if any |
| MIXS:0000048 | adapters | 1 recommended String |
Adapters provide priming sequences for both amplification and sequencing of t... |
| MIXS:0000058 | assembly_software | 1 String |
Tool(s) used for assembly, including version number and parameters |
| MIXS:0000053 | tax_ident | 0..1 TaxIdentEnum |
The phylogenetic marker(s) used to assign an organism name to the SAG or MAG |
| MIXS:0000059 | annot | 0..1 recommended String |
Tool used for annotation, or for cases where annotation was provided by a com... |
| MIXS:0001322 | pos_cont_type | 0..1 recommended String |
The substance, mixture, product, or apparatus used to verify that a process w... |
| MIXS:0000061 | feat_pred | 0..1 recommended String |
Method used to predict UViGs features such as ORFs, integration site, etc |
| MIXS:0000070 | compl_software | 0..1 String |
Tools used for completion estimate, i |
| MIXS:0000013 | env_local_scale | 1 String |
Report the entity or entities which are in the sample or specimen s local vic... |
| MIXS:0000016 | samp_mat_process | 1 recommended String |
A brief description of any processing applied to the sample during or after r... |
| MIXS:0000063 | sim_search_meth | 0..1 recommended String |
Tool used to compare ORFs with database, along with version and cutoffs used |
| MIXS:0000031 | host_disease_stat | 0..1 recommended String |
List of diseases with which the host has been diagnosed; can include multiple... |
| MIXS:0000018 | depth | 0..1 recommended String |
The vertical distance below local surface |
| MIXS:0001225 | samp_collect_method | 0..1 recommended String |
The method employed for collecting the sample |
| MIXS:0000071 | compl_appr | 0..1 recommended ComplApprEnum |
The approach used to determine the completeness of a given genomic assembly, ... |
| MIXS:0000029 | specific_host | 1 String |
Report the host's taxonomic name and/or NCBI taxonomy ID |
| MIXS:0000014 | env_medium | 1 String |
Report the environmental material(s) immediately surrounding the sample or sp... |
| MIXS:0001320 | samp_taxon_id | 1 String |
NCBI taxon id of the sample |
| MIXS:0000010 | geo_loc_name | 1 String |
The geographical origin of the sample as defined by the country or sea name f... |
| MIXS:0000011 | collection_date | 1 Datetime |
The time of sampling, either as an instance (single point in time) or interva... |
| MIXS:0000050 | seq_meth | 1 String |
Sequencing machine used |
| MIXS:0000009 | lat_lon | 1 String |
The geographical origin of the sample as defined by latitude and longitude |
| MIXS:0000093 | elev | 0..1 recommended String |
Elevation of the sampling site is its height above a fixed reference point, m... |
| MIXS:0000012 | env_broad_scale | 1 String |
Report the major environmental system the sample or specimen came from |
| MIXS:0000064 | tax_class | 0..1 recommended String |
Method used for taxonomic classification, along with reference database used,... |
| MIXS:0000008 | experimental_factor | * recommended String |
Variable aspects of an experiment design that can be used to describe an expe... |
| MIXS:0000075 | sort_tech | 0..1 recommended SortTechEnum |
Method used to sort/isolate cells or particles of interest |
| MIXS:0000076 | sc_lysis_approach | 0..1 recommended ScLysisApproachEnum |
Method used to free DNA from interior of the cell(s) or particle(s) |
| MIXS:0000054 | sc_lysis_method | 0..1 recommended String |
Name of the kit or standard protocol used for cell(s) or particle(s) lysis |
| MIXS:0000055 | wga_amp_appr | 0..1 recommended WgaAmpApprEnum |
Method used to amplify genomic DNA in preparation for sequencing |
| MIXS:0000006 | wga_amp_kit | 0..1 recommended String |
Kit used to amplify genomic DNA in preparation for sequencing |
| MIXS:0000077 | bin_param | 0..1 recommended BinParamEnum |
The parameters that have been applied during the extraction of genomes from m... |
| MIXS:0000078 | bin_software | 0..1 recommended String |
Tool(s) used for the extraction of genomes from metagenomic datasets, where p... |
| MIXS:0000079 | reassembly_bin | 0..1 recommended Boolean |
Has an assembly been performed on a genome bin extracted from a metagenomic a... |
| MIXS:0000080 | mag_cov_software | 0..1 MagCovSoftwareEnum |
Tool(s) used to determine the genome coverage if coverage is used as a binnin... |
| MIXS:0000081 | vir_ident_software | 1 String |
Tool(s) used for the identification of UViG as a viral genome, software or pr... |
| MIXS:0000082 | pred_genome_type | 1 String |
Type of genome predicted for the UViG |
| MIXS:0000083 | pred_genome_struc | 1 PredGenomeStrucEnum |
Expected structure of the viral genome |
| MIXS:0000084 | detec_type | 1 String |
Type of UViG detection |
| MIXS:0000085 | otu_class_appr | 0..1 recommended String |
Cutoffs and approach used when clustering species-level OTUs |
| MIXS:0000086 | otu_seq_comp_appr | 0..1 recommended String |
Tool and thresholds used to compare sequences when computing "species-level" ... |
| MIXS:0000087 | otu_db | 0..1 recommended String |
Reference database (i |
| MIXS:0000088 | host_pred_appr | 0..1 recommended HostPredApprEnum |
Tool or approach used for host prediction |
| MIXS:0000089 | host_pred_est_acc | 0..1 recommended String |
For each tool or approach used for host prediction, estimated false discovery... |
| MIXS:0000091 | associated_resource | * recommended String |
A related resource that is referenced, cited, or otherwise associated to the ... |
| MIXS:0000090 | sop | * recommended String |
Standard operating procedures used in assembly and/or annotation of genomes, ... |
| MIXS:0001057 | plant_growth_med | 0..1 String |
Specification of the media for growing the plants or tissue cultured samples,... |
| MIXS:0001296 | photosynt_activ | 0..1 recommended String |
Measurement of photosythetic activity (i |
| MIXS:0001336 | photosynt_activ_meth | * recommended String |
Reference or method used in measurement of photosythetic activity |
| MIXS:0001177 | enrichment_protocol | 0..1 recommended String |
The microbiological workflow or protocol followed to test for the presence or... |
| MIXS:0001145 | library_prep_kit | 0..1 String |
Packaged kits (containing adapters, indexes, enzymes, buffers etc |
| MIXS:0001156 | sequencing_location | 0..1 String |
The location the sequencing run was performed |
| MIXS:0001163 | soil_temp | 0..1 String |
Temperature of soil at the time of sampling |
| MIXS:0001160 | soil_pH | 0..1 Float |
pH of some soil |
| MIXS:0001158 | soil_conductivity | 0..1 String |
Conductivity of some soil |
| MIXS:0001161 | rel_location | 0..1 recommended String |
Location of sampled soil to other parts of the farm e |
| MIXS:0001159 | soil_cover | 0..1 recommended String |
Material covering the sampled soil |
| MIXS:0000211 | porosity | 0..1 String |
Porosity of deposited sediment is volume of voids divided by the total volume... |
| MIXS:0000335 | soil_texture | 0..1 String |
The relative proportion of different grain sizes of mineral particles in a so... |
| MIXS:0000336 | soil_texture_meth | 0..1 String |
Reference or method used in determining soil texture |
| MIXS:0001298 | host_symbiont | * String |
The taxonomic name of the organism(s) found living in mutualistic, commensali... |
| MIXS:0000819 | pres_animal_insect | 0..1 String |
The type and number of animals or insects present in the sampling space |
| MIXS:0001111 | plant_water_method | 0..1 recommended String |
Description of the equipment or method used to distribute water to crops |
| MIXS:0001115 | anim_water_method | * String |
Description of the equipment or method used to distribute water to livestock |
| MIXS:0001110 | farm_water_source | 0..1 recommended FarmWaterSourceEnum |
Source of water used on the farm for irrigation of crops or watering of lives... |
| MIXS:0001176 | water_source_shared | * String |
Other users sharing access to the same water source |
| MIXS:0001175 | water_pH | 0..1 Float |
The pH measurement of the sample, or liquid portion of sample, or aqueous pha... |
| MIXS:0000829 | season | 0..1 String |
The season when sampling occurred |
| MIXS:0000112 | solar_irradiance | * String |
The amount of solar energy that arrives at a specific area of a surface durin... |
| MIXS:0001116 | crop_yield | 0..1 String |
Amount of crop produced per unit or area of land |
| MIXS:0001148 | season_humidity | 0..1 Float |
Average humidity of the region throughout the growing season |
| MIXS:0000100 | humidity | 0..1 recommended String |
Amount of water vapour in the air, at the time of sampling |
| MIXS:0001121 | adjacent_environment | * String |
Description of the environmental system or features that are adjacent to the ... |
| MIXS:0000751 | chem_administration | 1..* String |
List of chemical compounds administered to the host or site where sampling oc... |
| MIXS:0001211 | food_prod | * String |
Descriptors of the food production system or of the agricultural environment ... |
| MIXS:0001147 | lot_number | * String |
A distinctive alpha-numeric identification code assigned by the manufacturer ... |
| MIXS:0001127 | fertilizer_admin | 0..1 String |
Type of fertilizer or amendment added to the soil or water for the purpose of... |
| MIXS:0000110 | samp_store_temp | 0..1 String |
Temperature at which sample was stored, e |
| MIXS:0001137 | food_trav_mode | * String |
A descriptor for the method of movement of food commodity along the food dist... |
| MIXS:0001138 | food_trav_vehic | * String |
A descriptor for the mobile machine which is used to transport food commoditi... |
| MIXS:0001124 | farm_equip_san | * String |
Method used to sanitize growing and harvesting equipment |
| MIXS:0001126 | farm_equip | * String |
List of equipment used for planting, fertilization, harvesting, irrigation, l... |
| MIXS:0001123 | farm_equip_shared | * String |
List of planting, growing or harvesting equipment shared with other farms |
| MIXS:0001133 | food_harvest_proc | * String |
A harvesting process is a process which takes in some food material from an i... |
| MIXS:0001060 | plant_struc | 0..1 recommended String |
Name of plant structure the sample was obtained from; for Plant Ontology (PO)... |
| MIXS:0000257 | host_dry_mass | 0..1 String |
Measurement of dry mass |
| MIXS:0000247 | ances_data | 0..1 String |
Information about either pedigree or other ancestral information description ... |
| MIXS:0000859 | genetic_mod | 0..1 String |
Genetic modifications of the genome of an organism, which may occur naturally... |
| MIXS:0001184 | food_product_type | 0..1 String |
A food product type is a class of food products that is differentiated by its... |
| MIXS:0001139 | food_source | 1 String |
Type of plant or animal from which the food product or its major ingredient i... |
| MIXS:0001170 | spikein_strain | * String |
Taxonomic information about the spike-in organism(s) at the strain level |
| MIXS:0000103 | organism_count | * recommended String |
Total cell count of any organism (or group of organisms) per gram, volume or ... |
| MIXS:0000735 | size_frac_low | 0..1 String |
Refers to the mesh/pore size used to pre-filter/pre-sort the sample |
| MIXS:0000736 | size_frac_up | 0..1 String |
Mesh or pore size of the device used to retain the sample |
| MIXS:0001181 | cult_isol_date | 0..1 Datetime |
The datetime marking the end of a process in which a sample yields a positive... |
| MIXS:0001153 | samp_pooling | * recommended String |
Physical combination of several instances of like material, e |
| MIXS:0000578 | root_med_macronutr | 0..1 String |
Measurement of the culture rooting medium macronutrients (N,P, K, Ca, Mg, S);... |
| MIXS:0000577 | root_med_carbon | 0..1 String |
Source of organic carbon in the culture rooting medium; e |
| MIXS:0001062 | root_med_ph | 0..1 Float |
pH measurement of the culture rooting medium; e |
| MIXS:0000590 | water_temp_regm | * recommended String |
Information about treatment involving an exposure to water with varying degre... |
| MIXS:0000591 | watering_regm | * recommended String |
Information about treatment involving an exposure to watering frequencies, tr... |
| MIXS:0001069 | standing_water_regm | * recommended String |
Treatment involving an exposure to standing water during a plant's life span,... |
| MIXS:0000558 | gaseous_environment | * recommended String |
Use of conditions with differing gaseous environments; should include the nam... |
| MIXS:0000557 | fungicide_regm | * recommended String |
Information about treatment involving use of fungicides; should include the n... |
| MIXS:0001040 | climate_environment | * recommended String |
Treatment involving an exposure to a particular climate; treatment regimen in... |
| MIXS:0000561 | herbicide_regm | * recommended String |
Information about treatment involving use of herbicides; information about tr... |
| MIXS:0000571 | non_min_nutr_regm | * recommended String |
Information about treatment involving the exposure of plant to non-mineral nu... |
| MIXS:0000573 | pesticide_regm | * recommended String |
Information about treatment involving use of insecticides; should include the... |
| MIXS:0001056 | ph_regm | * recommended String |
Information about treatment involving exposure of plants to varying levels of... |
| MIXS:0000582 | salt_regm | * recommended String |
Information about treatment involving use of salts as supplement to liquid an... |
| MIXS:0001068 | season_environment | * recommended String |
Treatment involving an exposure to a particular season (e |
| MIXS:0000754 | perturbation | * recommended String |
Type of perturbation, e |
| MIXS:0000003 | isol_growth_condt | 0..1 String |
Publication reference in the form of pubmed ID (pmid), digital object identif... |
| MIXS:0000116 | samp_store_dur | 1 String |
Duration for which the sample was stored |
| MIXS:0000755 | samp_store_loc | 1 String |
Location at which sample was stored, usually name of a specific freezer/room |
| MIXS:0000255 | host_age | 1 String |
Age of host at the time of sampling; relevant scale depends on species and st... |
| MIXS:0000248 | host_common_name | 1 String |
Common name of the host |
| MIXS:0000365 | host_genotype | 1 String |
Observed genotype |
| MIXS:0000264 | host_height | 1 String |
The height of subject |
| MIXS:0001318 | host_subspecf_genlin | * String |
Information about the genetic distinctness of the host organism below the sub... |
| MIXS:0000256 | host_length | 1 String |
The length of subject |
| MIXS:0000251 | host_life_stage | 1 String |
Description of life stage of host |
| MIXS:0000874 | host_phenotype | 1 String |
Phenotype of human or other host |
| MIXS:0000250 | host_taxid | 1 String |
NCBI taxon id of the host, e |
| MIXS:0000263 | host_tot_mass | 1 String |
Total mass of the host at collection, the unit depends on host |
| MIXS:0000032 | trophic_level | 0..1 recommended TrophicLevelEnum |
Trophic levels are the feeding position in a food chain |
| MIXS:0001058 | plant_product | 0..1 recommended String |
Substance produced by the plant, where the sample was obtained from |
| MIXS:0000753 | oxy_stat_samp | 0..1 recommended OxyStatSampEnum |
Oxygenation status of sample |
| MIXS:0000046 | pcr_primers | 1 String |
PCR primers that were used to amplify the sequence of the targeted gene, locu... |
| MIXS:0000044 | target_gene | 1 String |
Targeted gene or locus name for marker gene studies |
| MIXS:0000045 | target_subfragment | 1 String |
Name of subfragment of a gene or locus |
| MIXS:0000049 | pcr_cond | 1 String |
Description of reaction conditions and components of polymerase chain reactio... |
| MIXS:0000051 | seq_quality_check | 0..1 SeqQualityCheckEnum |
Indicate if the sequence has been called by automatic systems (none) or under... |
| MIXS:0000052 | chimera_check | 1 String |
Tool(s) used for chimera checking, including version number and parameters, t... |
| MIXS:0001083 | fao_class | 0..1 recommended FaoClassEnum |
Soil classification from the FAO World soil distribution from International S... |
| MIXS:0000330 | local_class | 0..1 recommended String |
Soil classification based on local soil classification system |
| MIXS:0000331 | local_class_meth | 0..1 recommended String |
Reference or method used in determining the local soil classification |
| MIXS:0000332 | soil_type | 1 String |
Description of the soil type or classification |
| MIXS:0000334 | soil_type_meth | 1 String |
Reference or method used in determining soil series name or other lower-level... |
| MIXS:0001082 | soil_horizon | 0..1 recommended SoilHorizonEnum |
Specific layer in the land area which measures parallel to the soil surface a... |
| MIXS:0000321 | horizon_meth | 0..1 recommended String |
Reference or method used in determining the horizon |
| MIXS:0000329 | link_class_info | 0..1 String |
Link to digitized soil maps or other soil classification information |
| MIXS:0000315 | previous_land_use | 0..1 recommended String |
Previous land use and dates |
| MIXS:0000316 | prev_land_use_meth | 0..1 recommended String |
Reference or method used in determining previous land use and dates |
| MIXS:0000318 | crop_rotation | 0..1 recommended String |
Whether or not crop is rotated, and if yes, rotation schedule |
| MIXS:0000639 | agrochem_addition | * String |
Addition of fertilizers, pesticides, etc |
| MIXS:0001081 | tillage | * recommended TillageEnum |
Note method(s) used for tilling |
| MIXS:0001086 | fire | 0..1 recommended Datetime |
Historical and/or physical evidence of fire |
| MIXS:0000319 | flooding | 0..1 recommended Datetime |
Historical and/or physical evidence of flooding |
| MIXS:0000320 | extreme_event | 0..1 recommended Datetime |
Unusual physical events that may have affected microbial populations |
| MIXS:0000328 | link_climate_info | 0..1 String |
Link to climate resource |
| MIXS:0000642 | annual_temp | 0..1 String |
Mean annual temperature |
| MIXS:0000643 | season_temp | 0..1 String |
Mean seasonal temperature |
| MIXS:0000644 | annual_precpt | 0..1 String |
The average of all annual precipitation values known, or an estimated equival... |
| MIXS:0000645 | season_precpt | 0..1 String |
The average of all seasonal precipitation values known, or an estimated equiv... |
| MIXS:0001080 | cur_land_use | 0..1 String |
Present state of sample site |
| MIXS:0000646 | slope_gradient | 0..1 recommended String |
Commonly called 'slope' |
| MIXS:0000647 | slope_aspect | 0..1 recommended String |
The direction a slope faces |
| MIXS:0001084 | profile_position | 0..1 recommended ProfilePositionEnum |
Cross-sectional position in the hillslope where sample was collected |
| MIXS:0001085 | drainage_class | 0..1 recommended DrainageClassEnum |
Drainage classification from a standard system such as the USDA system |
| MIXS:0000327 | store_cond | 1 String |
Explain how and for how long the soil sample was stored before DNA extraction... |
| MIXS:0001106 | ph_meth | 0..1 recommended String |
Reference or method used in determining pH |
| MIXS:0000312 | cur_vegetation | 0..1 recommended String |
Vegetation classification from one or more standard classification systems, o... |
| MIXS:0000314 | cur_vegetation_meth | 0..1 recommended String |
Reference or method used in vegetation classification |
| MIXS:0000533 | tot_org_carb | 0..1 recommended String |
Total organic carbon content |
| MIXS:0000337 | tot_org_c_meth | 0..1 recommended String |
Reference or method used in determining total organic carbon |
| MIXS:0000530 | tot_nitro_content | 0..1 recommended String |
Total nitrogen content of the sample |
| MIXS:0000338 | tot_nitro_cont_meth | 0..1 recommended String |
Reference or method used in determining the total nitrogen |
| MIXS:0000650 | microbial_biomass | 1 String |
The part of the organic matter in the soil that constitutes living microorgan... |
| MIXS:0000339 | micro_biomass_meth | 1 String |
Reference or method used in determining microbial biomass |
| MIXS:0000343 | heavy_metals_meth | 0..1 recommended String |
Reference or method used in determining heavy metals |
| MIXS:0000525 | tot_carb | 0..1 recommended String |
Total carbon content |
| MIXS:0000689 | tot_phosphate | 0..1 recommended String |
Total amount or concentration of phosphate |
| MIXS:0000322 | sieving | 1 String |
Collection design of pooled samples and/or sieve size and amount of sample si... |
| MIXS:0000325 | pool_dna_extracts | 1 String |
Indicate whether multiple DNA extractions were mixed |
| MIXS:0000752 | misc_param | * String |
Any other measurement performed or parameter collected, that is not listed he... |
LinkML Source
Direct
name: MiuvigAgriculture
description: MIxS Data that comply with the Miuvig checklist and the Agriculture Extension
title: Miuvig combined with Agriculture
in_subset:
- combination_classes
from_schema: https://w3id.org/mixs
is_a: Agriculture
mixins:
- Miuvig
class_uri: MIXS:0010012_0016018
Induced
name: MiuvigAgriculture
description: MIxS Data that comply with the Miuvig checklist and the Agriculture Extension
title: Miuvig combined with Agriculture
in_subset:
- combination_classes
from_schema: https://w3id.org/mixs
is_a: Agriculture
mixins:
- Miuvig
attributes:
samp_name:
name: samp_name
annotations:
Preferred_unit:
tag: Preferred_unit
value: ''
description: A local identifier or name that for the material sample used for
extracting nucleic acids, and subsequent sequencing. It can refer either to
the original material collected or to any derived sub-samples. It can have any
format, but we suggest that you make it concise, unique and consistent within
your lab, and as informative as possible. INSDC requires every sample name from
a single Submitter to be unique. Use of a globally unique identifier for the
field source_mat_id is recommended in addition to sample_name
title: sample name
examples:
- value: ISDsoil1
in_subset:
- investigation
from_schema: https://w3id.org/mixs
keywords:
- sample
slot_uri: MIXS:0001107
alias: samp_name
owner: MiuvigAgriculture
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Air
- BuiltEnvironment
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodFoodProductionFacility
- FoodHumanFoods
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- HydrocarbonResourcesCores
- HydrocarbonResourcesFluidsSwabs
- MicrobialMatBiofilm
- MiscellaneousNaturalOrArtificialEnvironment
- PlantAssociated
- Sediment
- Soil
- SymbiontAssociated
- WastewaterSludge
- Water
range: string
required: true
size_frac:
name: size_frac
annotations:
Expected_value:
tag: Expected_value
value: filter size value range
description: Filtering pore size used in sample preparation
title: size fraction selected
examples:
- value: 0-0.22 micrometer
in_subset:
- nucleic acid sequence source
from_schema: https://w3id.org/mixs
keywords:
- fraction
- size
string_serialization: '{float}-{float} {unit}'
slot_uri: MIXS:0000017
alias: size_frac
owner: MiuvigAgriculture
domain_of:
- Mimag
- MimarksS
- Mims
- Misag
- Miuvig
range: string
recommended: true
lib_screen:
name: lib_screen
annotations:
Expected_value:
tag: Expected_value
value: screening strategy name
description: Specific enrichment or screening methods applied before and/or after
creating libraries
title: library screening strategy
examples:
- value: enriched, screened, normalized
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
keywords:
- library
slot_uri: MIXS:0000043
alias: lib_screen
owner: MiuvigAgriculture
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
range: string
required: true
recommended: true
source_uvig:
name: source_uvig
annotations:
Expected_value:
tag: Expected_value
value: enumeration
description: Type of dataset from which the UViG was obtained
title: source of UViGs
examples:
- value: viral fraction metagenome (virome)
in_subset:
- nucleic acid sequence source
from_schema: https://w3id.org/mixs
keywords:
- source
string_serialization: '[metagenome (not viral targeted)|viral fraction metagenome
(virome)|sequence-targeted metagenome|metatranscriptome (not viral targeted)|viral
fraction RNA metagenome (RNA virome)|sequence-targeted RNA metagenome|microbial
single amplified genome (SAG)|viral single amplified genome (vSAG)|isolate microbial
genome|other]'
slot_uri: MIXS:0000035
alias: source_uvig
owner: MiuvigAgriculture
domain_of:
- Miuvig
range: string
required: true
ref_db:
name: ref_db
annotations:
Expected_value:
tag: Expected_value
value: names, versions, and references of databases
description: List of database(s) used for ORF annotation, along with version number
and reference to website or publication
title: reference database(s)
examples:
- value: pVOGs;5;http://dmk-brain.ecn.uiowa.edu/pVOGs/ Grazziotin et al. 2017
doi:10.1093/nar/gkw975
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
keywords:
- database
string_serialization: '{database};{version};{reference}'
slot_uri: MIXS:0000062
alias: ref_db
owner: MiuvigAgriculture
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- Mims
- Misag
- Miuvig
range: string
recommended: true
nucl_acid_amp:
name: nucl_acid_amp
description: A link to a literature reference, electronic resource or a standard
operating procedure (SOP), that describes the enzymatic amplification (PCR,
TMA, NASBA) of specific nucleic acids
title: nucleic acid amplification
examples:
- value: https://phylogenomics.me/protocols/16s-pcr-protocol/
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
slot_uri: MIXS:0000038
alias: nucl_acid_amp
owner: MiuvigAgriculture
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
range: string
required: true
recommended: true
pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$
structured_pattern:
syntax: ^{PMID}|{DOI}|{URL}$
interpolated: true
partial_match: true
lib_size:
name: lib_size
description: Total number of clones in the library prepared for the project
title: library size
examples:
- value: '50'
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
keywords:
- library
- size
slot_uri: MIXS:0000039
alias: lib_size
owner: MiuvigAgriculture
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
range: integer
recommended: true
mid:
name: mid
description: Molecular barcodes, called Multiplex Identifiers (MIDs), that are
used to specifically tag unique samples in a sequencing run. Sequence should
be reported in uppercase letters
title: multiplex identifiers
examples:
- value: GTGAATAT
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
keywords:
- identifier
slot_uri: MIXS:0000047
alias: mid
owner: MiuvigAgriculture
domain_of:
- Mimag
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
range: string
required: true
recommended: true
pattern: ^[ACGTRKSYMWBHDVN]+$
structured_pattern:
syntax: ^{ambiguous_nucleotides}$
interpolated: true
partial_match: true
assembly_name:
name: assembly_name
annotations:
Expected_value:
tag: Expected_value
value: name and version of assembly
description: Name/version of the assembly provided by the submitter that is used
in the genome browsers and in the community
title: assembly name
examples:
- value: HuRef, JCVI_ISG_i3_1.0
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
string_serialization: '{text} {text}'
slot_uri: MIXS:0000057
alias: assembly_name
owner: MiuvigAgriculture
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- Mims
- Misag
- Miuvig
- Agriculture
range: string
required: true
recommended: true
temp:
name: temp
annotations:
Preferred_unit:
tag: Preferred_unit
value: degree Celsius
description: Temperature of the sample at the time of sampling
title: temperature
examples:
- value: 25 degree Celsius
in_subset:
- environment
from_schema: https://w3id.org/mixs
keywords:
- temperature
slot_uri: MIXS:0000113
alias: temp
owner: MiuvigAgriculture
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
- Air
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodHumanFoods
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- HydrocarbonResourcesCores
- HydrocarbonResourcesFluidsSwabs
- MicrobialMatBiofilm
- MiscellaneousNaturalOrArtificialEnvironment
- PlantAssociated
- Sediment
- Soil
- SymbiontAssociated
- WastewaterSludge
- Water
range: string
required: true
recommended: true
pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
*([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
structured_pattern:
syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
interpolated: true
partial_match: true
compl_score:
name: compl_score
annotations:
Expected_value:
tag: Expected_value
value: quality;percent completeness
description: 'Completeness score is typically based on either the fraction of
markers found as compared to a database or the percent of a genome found as
compared to a closely related reference genome. High Quality Draft: >90%, Medium
Quality Draft: >50%, and Low Quality Draft: < 50% should have the indicated
completeness scores'
title: completeness score
examples:
- value: med;60%
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
keywords:
- score
string_serialization: '[high|med|low];{percentage}'
slot_uri: MIXS:0000069
alias: compl_score
owner: MiuvigAgriculture
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- Misag
- Miuvig
range: string
recommended: true
trnas:
name: trnas
annotations:
Expected_value:
tag: Expected_value
value: value from 0-21
description: The total number of tRNAs identified from the SAG or MAG
title: number of standard tRNAs extracted
examples:
- value: '18'
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
keywords:
- number
string_serialization: '{integer}'
slot_uri: MIXS:0000067
alias: trnas
owner: MiuvigAgriculture
domain_of:
- Mimag
- Misag
- Miuvig
range: string
nucl_acid_ext:
name: nucl_acid_ext
description: A link to a literature reference, electronic resource or a standard
operating procedure (SOP), that describes the material separation to recover
the nucleic acid fraction from a sample
title: nucleic acid extraction
examples:
- value: https://mobio.com/media/wysiwyg/pdfs/protocols/12888.pdf
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
slot_uri: MIXS:0000037
alias: nucl_acid_ext
owner: MiuvigAgriculture
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodFoodProductionFacility
- FoodHumanFoods
range: string
required: true
recommended: true
pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$
structured_pattern:
syntax: ^{PMID}|{DOI}|{URL}$
interpolated: true
partial_match: true
samp_size:
name: samp_size
description: The total amount or size (volume (ml), mass (g) or area (m2) ) of
sample collected
title: amount or size of sample collected
examples:
- value: 5 liter
in_subset:
- nucleic acid sequence source
from_schema: https://w3id.org/mixs
keywords:
- sample
- size
slot_uri: MIXS:0000001
alias: samp_size
owner: MiuvigAgriculture
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodFoodProductionFacility
- FoodHumanFoods
range: string
required: true
recommended: true
pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
*([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
structured_pattern:
syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
interpolated: true
partial_match: true
alt:
name: alt
annotations:
Preferred_unit:
tag: Preferred_unit
value: meter
description: 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
title: altitude
examples:
- value: 100 meter
in_subset:
- environment
from_schema: https://w3id.org/mixs
slot_uri: MIXS:0000094
alias: alt
owner: MiuvigAgriculture
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Air
- HostAssociated
- MiscellaneousNaturalOrArtificialEnvironment
- SymbiontAssociated
range: string
recommended: true
pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
*([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
structured_pattern:
syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
interpolated: true
partial_match: true
estimated_size:
name: estimated_size
annotations:
Expected_value:
tag: Expected_value
value: number of base pairs
description: The estimated size of the genome prior to sequencing. Of particular
importance in the sequencing of (eukaryotic) genome which could remain in draft
form for a long or unspecified period
title: estimated size
examples:
- value: 300000 bp
in_subset:
- nucleic acid sequence source
from_schema: https://w3id.org/mixs
keywords:
- size
string_serialization: '{integer} bp'
slot_uri: MIXS:0000024
alias: estimated_size
owner: MiuvigAgriculture
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Miuvig
range: string
source_mat_id:
name: source_mat_id
annotations:
Expected_value:
tag: Expected_value
value: 'for cultures of microorganisms: identifiers for two culture collections;
for other material a unique arbitrary identifer'
description: A 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)
title: source material identifiers
examples:
- value: MPI012345
in_subset:
- nucleic acid sequence source
from_schema: https://w3id.org/mixs
keywords:
- identifier
- material
- source
slot_uri: MIXS:0000026
alias: source_mat_id
owner: MiuvigAgriculture
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
- SymbiontAssociated
range: string
recommended: true
multivalued: true
samp_vol_we_dna_ext:
name: samp_vol_we_dna_ext
annotations:
Preferred_unit:
tag: Preferred_unit
value: milliliter, gram, milligram, square centimeter
description: 'Volume (ml) or mass (g) of total collected sample processed for
DNA extraction. Note: total sample collected should be entered under the term
Sample Size (MIXS:0000001)'
title: sample volume or weight for DNA extraction
examples:
- value: 1500 milliliter
in_subset:
- nucleic acid sequence source
from_schema: https://w3id.org/mixs
keywords:
- dna
- sample
- volume
- weight
slot_uri: MIXS:0000111
alias: samp_vol_we_dna_ext
owner: MiuvigAgriculture
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
- Air
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodFoodProductionFacility
- FoodHumanFoods
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- HydrocarbonResourcesCores
- HydrocarbonResourcesFluidsSwabs
- MicrobialMatBiofilm
- MiscellaneousNaturalOrArtificialEnvironment
- PlantAssociated
- Sediment
- Soil
- SymbiontAssociated
- WastewaterSludge
- Water
range: string
required: true
pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
*([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
structured_pattern:
syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
interpolated: true
partial_match: true
pathogenicity:
name: pathogenicity
annotations:
Expected_value:
tag: Expected_value
value: names of organisms that the entity is pathogenic to
description: To what is the entity pathogenic
title: known pathogenicity
examples:
- value: human, animal, plant, fungi, bacteria
in_subset:
- nucleic acid sequence source
from_schema: https://w3id.org/mixs
slot_uri: MIXS:0000027
alias: pathogenicity
owner: MiuvigAgriculture
domain_of:
- MigsBa
- MigsEu
- MigsVi
- Miuvig
- Agriculture
range: string
required: true
lib_reads_seqd:
name: lib_reads_seqd
description: Total number of clones sequenced from the library
title: library reads sequenced
examples:
- value: '20'
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
keywords:
- library
slot_uri: MIXS:0000040
alias: lib_reads_seqd
owner: MiuvigAgriculture
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
range: integer
required: true
recommended: true
samp_collect_device:
name: samp_collect_device
annotations:
Expected_value:
tag: Expected_value
value: device name
description: 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)
title: sample collection device
examples:
- value: swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713]
in_subset:
- nucleic acid sequence source
from_schema: https://w3id.org/mixs
keywords:
- device
- sample
string_serialization: '{termLabel} [{termID}]|{text}'
slot_uri: MIXS:0000002
alias: samp_collect_device
owner: MiuvigAgriculture
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodFoodProductionFacility
- FoodHumanFoods
range: string
required: true
recommended: true
number_contig:
name: number_contig
description: Total number of contigs in the cleaned/submitted assembly that makes
up a given genome, SAG, MAG, or UViG
title: number of contigs
examples:
- value: '40'
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
keywords:
- number
slot_uri: MIXS:0000060
alias: number_contig
owner: MiuvigAgriculture
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- Mims
- Misag
- Miuvig
range: integer
required: true
biotic_relationship:
name: biotic_relationship
description: Description of relationship(s) between the subject organism and other
organism(s) it is associated 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
title: observed biotic relationship
examples:
- value: free living
in_subset:
- nucleic acid sequence source
from_schema: https://w3id.org/mixs
keywords:
- observed
- relationship
slot_uri: MIXS:0000028
alias: biotic_relationship
owner: MiuvigAgriculture
domain_of:
- MigsBa
- MigsEu
- MigsVi
- MimarksC
- Miuvig
- Agriculture
range: BioticRelationshipEnum
recommended: true
trna_ext_software:
name: trna_ext_software
description: Tools used for tRNA identification
title: tRNA extraction software
examples:
- value: infernal;v2;default parameters
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
keywords:
- software
slot_uri: MIXS:0000068
alias: trna_ext_software
owner: MiuvigAgriculture
domain_of:
- Mimag
- Misag
- Miuvig
range: string
pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+);([^\s-]{1,2}|[^\s-]+.+[^\s-]+);([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
structured_pattern:
syntax: ^{software};{version};{parameters}$
interpolated: true
partial_match: true
lib_layout:
name: lib_layout
description: Specify whether to expect single, paired, or other configuration
of reads
title: library layout
examples:
- value: paired
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
keywords:
- library
slot_uri: MIXS:0000041
alias: lib_layout
owner: MiuvigAgriculture
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
range: LibLayoutEnum
recommended: true
assembly_qual:
name: assembly_qual
description: 'The assembly quality category is based on sets of criteria outlined
for each assembly quality category. For MISAG/MIMAG; Finished: Single, validated,
contiguous sequence per replicon without gaps or ambiguities with a consensus
error rate equivalent to Q50 or better. High Quality Draft:Multiple fragments
where gaps span repetitive regions. Presence of the large subunit (LSU) RNA,
small subunit (SSU) and the presence of 5.8S rRNA or 5S rRNA depending on whether
it is a eukaryotic or prokaryotic genome, respectively. Medium Quality Draft:Many
fragments with little to no review of assembly other than reporting of standard
assembly statistics. Low Quality Draft:Many fragments with little to no review
of assembly other than reporting of standard assembly statistics. Assembly statistics
include, but are not limited to total assembly size, number of contigs, contig
N50/L50, and maximum contig length. For MIUVIG; Finished: Single, validated,
contiguous sequence per replicon without gaps or ambiguities, with extensive
manual review and editing to annotate putative gene functions and transcriptional
units. High-quality draft genome: One or multiple fragments, totaling 90%
of the expected genome or replicon sequence or predicted complete. Genome fragment(s):
One or multiple fragments, totalling < 90% of the expected genome or replicon
sequence, or for which no genome size could be estimated'
title: assembly quality
examples:
- value: High-quality draft genome
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
keywords:
- quality
slot_uri: MIXS:0000056
alias: assembly_qual
owner: MiuvigAgriculture
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- Mims
- Misag
- Miuvig
- Agriculture
range: AssemblyQualEnum
required: true
ref_biomaterial:
name: ref_biomaterial
description: Primary publication if isolated before genome publication; otherwise,
primary genome report
title: reference for biomaterial
examples:
- value: doi:10.1016/j.syapm.2018.01.009
in_subset:
- nucleic acid sequence source
from_schema: https://w3id.org/mixs
slot_uri: MIXS:0000025
alias: ref_biomaterial
owner: MiuvigAgriculture
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- Mims
- Misag
- Miuvig
range: string
pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$
structured_pattern:
syntax: ^{PMID}|{DOI}|{URL}$
interpolated: true
partial_match: true
project_name:
name: project_name
description: Name of the project within which the sequencing was organized
title: project name
examples:
- value: Forest soil metagenome
in_subset:
- investigation
from_schema: https://w3id.org/mixs
keywords:
- project
slot_uri: MIXS:0000092
alias: project_name
owner: MiuvigAgriculture
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Air
- BuiltEnvironment
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodFoodProductionFacility
- FoodHumanFoods
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- HydrocarbonResourcesCores
- HydrocarbonResourcesFluidsSwabs
- MicrobialMatBiofilm
- MiscellaneousNaturalOrArtificialEnvironment
- PlantAssociated
- Sediment
- Soil
- SymbiontAssociated
- WastewaterSludge
- Water
range: string
required: true
lib_vector:
name: lib_vector
annotations:
Expected_value:
tag: Expected_value
value: vector
description: Cloning vector type(s) used in construction of libraries
title: library vector
examples:
- value: Bacteriophage P1
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
keywords:
- library
slot_uri: MIXS:0000042
alias: lib_vector
owner: MiuvigAgriculture
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
range: string
required: true
recommended: true
host_spec_range:
name: host_spec_range
annotations:
Expected_value:
tag: Expected_value
value: NCBI taxid
description: The range and diversity of host species that an organism is capable
of infecting, defined by NCBI taxonomy identifier
title: host specificity or range
examples:
- value: '9606'
in_subset:
- nucleic acid sequence source
from_schema: https://w3id.org/mixs
keywords:
- host
- host.
- range
string_serialization: '{integer}'
slot_uri: MIXS:0000030
alias: host_spec_range
owner: MiuvigAgriculture
domain_of:
- MigsBa
- MigsEu
- MigsPl
- MigsVi
- Miuvig
- Agriculture
range: string
required: true
multivalued: true
neg_cont_type:
name: neg_cont_type
annotations:
Expected_value:
tag: Expected_value
value: enumeration or text
description: The substance or equipment used as a negative control in an investigation
title: negative control type
in_subset:
- investigation
from_schema: https://w3id.org/mixs
keywords:
- type
slot_uri: MIXS:0001321
alias: neg_cont_type
owner: MiuvigAgriculture
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
range: NegContTypeEnum
recommended: true
virus_enrich_appr:
name: virus_enrich_appr
description: List of approaches used to enrich the sample for viruses, if any
title: virus enrichment approach
examples:
- value: filtration
description: was filtration + FeCl Precipitation + ultracentrifugation + DNAse
- value: FeCl Precipitation
description: was filtration + FeCl Precipitation + ultracentrifugation + DNAse
- value: ultracentrifugation
description: was filtration + FeCl Precipitation + ultracentrifugation + DNAse
- value: DNAse
description: was filtration + FeCl Precipitation + ultracentrifugation + DNAse
in_subset:
- nucleic acid sequence source
from_schema: https://w3id.org/mixs
keywords:
- enrichment
slot_uri: MIXS:0000036
alias: virus_enrich_appr
owner: MiuvigAgriculture
domain_of:
- MigsVi
- Miuvig
range: VirusEnrichApprEnum
required: true
adapters:
name: adapters
description: Adapters provide priming sequences for both amplification and sequencing
of the sample-library fragments. Both adapters should be reported; in uppercase
letters
title: adapters
examples:
- value: AATGATACGGCGACCACCGAGATCTACACGCT;CAAGCAGAAGACGGCATACGAGAT
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
slot_uri: MIXS:0000048
alias: adapters
owner: MiuvigAgriculture
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
range: string
required: true
recommended: true
structured_pattern:
syntax: ^{adapter_A_DNA_sequence};{adapter_B_DNA_sequence}$
interpolated: true
partial_match: true
assembly_software:
name: assembly_software
description: Tool(s) used for assembly, including version number and parameters
title: assembly software
examples:
- value: metaSPAdes;3.11.0;kmer set 21,33,55,77,99,121, default parameters otherwise
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
keywords:
- software
slot_uri: MIXS:0000058
alias: assembly_software
owner: MiuvigAgriculture
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
range: string
required: true
pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+);([^\s-]{1,2}|[^\s-]+.+[^\s-]+);([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
structured_pattern:
syntax: ^{software};{version};{parameters}$
interpolated: true
partial_match: true
tax_ident:
name: tax_ident
description: The phylogenetic marker(s) used to assign an organism name to the
SAG or MAG
title: taxonomic identity marker
examples:
- value: other
description: was other <colon> rpoB gene
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
keywords:
- identifier
- marker
- taxon
slot_uri: MIXS:0000053
alias: tax_ident
owner: MiuvigAgriculture
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- Misag
- Miuvig
range: TaxIdentEnum
annot:
name: annot
annotations:
Expected_value:
tag: Expected_value
value: name of tool or pipeline used, or annotation source description
description: Tool used for annotation, or for cases where annotation was provided
by a community jamboree or model organism database rather than by a specific
submitter
title: annotation
examples:
- value: prokka
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
slot_uri: MIXS:0000059
alias: annot
owner: MiuvigAgriculture
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- Mims
- Misag
- Miuvig
- Agriculture
range: string
recommended: true
pos_cont_type:
name: pos_cont_type
description: The substance, mixture, product, or apparatus used to verify that
a process which is part of an investigation delivers a true positive
title: positive control type
in_subset:
- investigation
from_schema: https://w3id.org/mixs
keywords:
- type
string_serialization: '{term} or {text}'
slot_uri: MIXS:0001322
alias: pos_cont_type
owner: MiuvigAgriculture
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
range: string
recommended: true
feat_pred:
name: feat_pred
description: Method used to predict UViGs features such as ORFs, integration site,
etc
title: feature prediction
examples:
- value: Prodigal;2.6.3;default parameters
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
keywords:
- feature
- predict
slot_uri: MIXS:0000061
alias: feat_pred
owner: MiuvigAgriculture
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- Mims
- Misag
- Miuvig
range: string
recommended: true
pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+);([^\s-]{1,2}|[^\s-]+.+[^\s-]+);([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
structured_pattern:
syntax: ^{software};{version};{parameters}$
interpolated: true
partial_match: true
compl_software:
name: compl_software
annotations:
Expected_value:
tag: Expected_value
value: names and versions of software(s) used
description: Tools used for completion estimate, i.e. checkm, anvi'o, busco
title: completeness software
examples:
- value: checkm
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
keywords:
- software
string_serialization: '{software};{version}'
slot_uri: MIXS:0000070
alias: compl_software
owner: MiuvigAgriculture
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- Misag
- Miuvig
range: string
env_local_scale:
name: env_local_scale
annotations:
Expected_value:
tag: Expected_value
value: Environmental entities having causal influences upon the entity at
time of sampling
description: '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'
title: local environmental context
examples:
- value: hillside [ENVO:01000333]
in_subset:
- environment
from_schema: https://w3id.org/mixs
keywords:
- context
- environmental
slot_uri: MIXS:0000013
alias: env_local_scale
owner: MiuvigAgriculture
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
range: string
required: true
structured_pattern:
syntax: ^{termLabel} \[{termID}\]$
interpolated: true
partial_match: true
samp_mat_process:
name: samp_mat_process
description: A brief description of any processing applied to the sample during
or after retrieving the sample from environment, or a link to the relevant protocol(s)
performed
title: sample material processing
examples:
- value: filtering of seawater, storing samples in ethanol
in_subset:
- nucleic acid sequence source
from_schema: https://w3id.org/mixs
keywords:
- material
- process
- sample
slot_uri: MIXS:0000016
alias: samp_mat_process
owner: MiuvigAgriculture
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
range: string
required: true
recommended: true
sim_search_meth:
name: sim_search_meth
description: Tool used to compare ORFs with database, along with version and cutoffs
used
title: similarity search method
examples:
- value: HMMER3;3.1b2;hmmsearch, cutoff of 50 on score
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
keywords:
- method
slot_uri: MIXS:0000063
alias: sim_search_meth
owner: MiuvigAgriculture
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- Mims
- Misag
- Miuvig
range: string
recommended: true
pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+);([^\s-]{1,2}|[^\s-]+.+[^\s-]+);([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
structured_pattern:
syntax: ^{software};{version};{parameters}$
interpolated: true
partial_match: true
host_disease_stat:
name: host_disease_stat
annotations:
Expected_value:
tag: Expected_value
value: disease name or Disease Ontology term
description: List of diseases with which the host has been diagnosed; can include
multiple diagnoses. The value of the field depends on host; for humans the terms
should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org,
non-human host diseases are free text
title: host disease status
examples:
- value: rabies [DOID:11260]
in_subset:
- nucleic acid sequence source
from_schema: https://w3id.org/mixs
keywords:
- disease
- host
- host.
- status
string_serialization: '{termLabel} [{termID}]|{text}'
slot_uri: MIXS:0000031
alias: host_disease_stat
owner: MiuvigAgriculture
domain_of:
- MigsBa
- MigsEu
- MigsVi
- Miuvig
- Agriculture
- FoodFarmEnvironment
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- PlantAssociated
range: string
recommended: true
depth:
name: depth
annotations:
Preferred_unit:
tag: Preferred_unit
value: meter
description: The vertical distance below local surface. For sediment or soil samples
depth is measured from sediment or soil surface, respectively. Depth can be
reported as an interval for subsurface samples
title: depth
examples:
- value: 10 meter
in_subset:
- environment
from_schema: https://w3id.org/mixs
keywords:
- depth
slot_uri: MIXS:0000018
alias: depth
owner: MiuvigAgriculture
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
- FoodFarmEnvironment
- HostAssociated
- MicrobialMatBiofilm
- MiscellaneousNaturalOrArtificialEnvironment
- PlantAssociated
- Sediment
- Soil
- SymbiontAssociated
- WastewaterSludge
- Water
range: string
recommended: true
pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
*([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
structured_pattern:
syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
interpolated: true
partial_match: true
samp_collect_method:
name: samp_collect_method
description: The method employed for collecting the sample
title: sample collection method
examples:
- value: swabbing
in_subset:
- nucleic acid sequence source
from_schema: https://w3id.org/mixs
keywords:
- method
- sample
slot_uri: MIXS:0001225
alias: samp_collect_method
owner: MiuvigAgriculture
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
- FoodAnimalAndAnimalFeed
- FoodFoodProductionFacility
- FoodHumanFoods
range: string
recommended: true
pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$|([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
structured_pattern:
syntax: ^{PMID}|{DOI}|{URL}|{text}$
interpolated: true
partial_match: true
compl_appr:
name: compl_appr
annotations:
Expected_value:
tag: Expected_value
value: text
description: The approach used to determine the completeness of a given genomic
assembly, which would typically make use of a set of conserved marker genes
or a closely related reference genome. For UViG completeness, include reference
genome or group used, and contig feature suggesting a complete genome
title: completeness approach
examples:
- value: other
description: was other <colon> UViG length compared to the average length of
reference genomes from the P22virus genus (NCBI RefSeq v83)
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
slot_uri: MIXS:0000071
alias: compl_appr
owner: MiuvigAgriculture
domain_of:
- Mimag
- Misag
- Miuvig
range: ComplApprEnum
recommended: true
specific_host:
name: specific_host
annotations:
Expected_value:
tag: Expected_value
value: host scientific name, taxonomy ID
description: Report the host's taxonomic name and/or NCBI taxonomy ID
title: host scientific name
examples:
- value: Homo sapiens and/or 9606
in_subset:
- nucleic acid sequence source
from_schema: https://w3id.org/mixs
keywords:
- host
- host.
string_serialization: '{text}|{NCBI taxid}'
slot_uri: MIXS:0000029
alias: specific_host
owner: MiuvigAgriculture
domain_of:
- MigsBa
- MigsEu
- MigsPl
- MigsVi
- Miuvig
- Agriculture
range: string
required: true
env_medium:
name: env_medium
description: '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)'
title: environmental medium
examples:
- value: bluegrass field soil [ENVO:00005789]
in_subset:
- environment
from_schema: https://w3id.org/mixs
keywords:
- environmental
slot_uri: MIXS:0000014
alias: env_medium
owner: MiuvigAgriculture
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
range: string
required: true
pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\]$
structured_pattern:
syntax: ^{termLabel} \[{termID}\]$
interpolated: true
partial_match: true
samp_taxon_id:
name: samp_taxon_id
description: NCBI taxon id of the sample. Maybe be a single taxon or mixed taxa
sample. Use 'synthetic metagenome for mock community/positive controls, or
'blank sample' for negative controls
title: taxonomy ID of DNA sample
examples:
- value: Gut Metagenome [NCBITaxon:749906]
in_subset:
- investigation
from_schema: https://w3id.org/mixs
keywords:
- dna
- identifier
- sample
- taxon
slot_uri: MIXS:0001320
alias: samp_taxon_id
owner: MiuvigAgriculture
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
range: string
required: true
pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[NCBITaxon:\d+\]$
structured_pattern:
syntax: ^{text} \[{NCBItaxon_id}\]$
interpolated: true
partial_match: true
geo_loc_name:
name: geo_loc_name
description: 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)
title: geographic location (country and/or sea,region)
examples:
- value: 'USA: Maryland, Bethesda'
in_subset:
- environment
from_schema: https://w3id.org/mixs
keywords:
- geographic
- location
slot_uri: MIXS:0000010
alias: geo_loc_name
owner: MiuvigAgriculture
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodFoodProductionFacility
- FoodHumanFoods
- SymbiontAssociated
range: string
required: true
pattern: '^([^\s-]{1,2}|[^\s-]+.+[^\s-]+): ([^\s-]{1,2}|[^\s-]+.+[^\s-]+), ([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$'
structured_pattern:
syntax: '^{text}: {text}, {text}$'
interpolated: true
partial_match: true
collection_date:
name: collection_date
description: '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'
title: collection date
examples:
- value: '2013-03-25T12:42:31+01:00'
in_subset:
- environment
from_schema: https://w3id.org/mixs
keywords:
- date
slot_uri: MIXS:0000011
alias: collection_date
owner: MiuvigAgriculture
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodFoodProductionFacility
- FoodHumanFoods
- SymbiontAssociated
range: datetime
required: true
seq_meth:
name: seq_meth
description: Sequencing machine used. Where possible the term should be taken
from the OBI list of DNA sequencers (http://purl.obolibrary.org/obo/OBI_0400103)
title: sequencing method
examples:
- value: 454 Genome Sequencer FLX [OBI:0000702]
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
keywords:
- method
slot_uri: MIXS:0000050
alias: seq_meth
owner: MiuvigAgriculture
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodFoodProductionFacility
- FoodHumanFoods
range: string
required: true
pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+)|(([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\])$
structured_pattern:
syntax: ^{text}|({termLabel} \[{termID}\])$
interpolated: true
partial_match: true
lat_lon:
name: lat_lon
description: The geographical origin of the sample as defined by latitude and
longitude. The values should be reported in decimal degrees, limited to 8 decimal
points, and in WGS84 system
title: geographic location (latitude and longitude)
examples:
- value: 50.586825 6.408977
in_subset:
- environment
from_schema: https://w3id.org/mixs
keywords:
- geographic
- location
slot_uri: MIXS:0000009
alias: lat_lon
owner: MiuvigAgriculture
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodFoodProductionFacility
- FoodHumanFoods
- SymbiontAssociated
range: string
required: true
pattern: ^(-?((?:[0-8]?[0-9](?:\.\d{0,8})?)|90)) -?[0-9]+(?:\.[0-9]{0,8})?$|^-?(1[0-7]{1,2})$
structured_pattern:
syntax: ^{lat} {lon}$
interpolated: true
partial_match: true
elev:
name: elev
annotations:
Preferred_unit:
tag: Preferred_unit
value: meter
description: 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
title: elevation
examples:
- value: 100 meter
in_subset:
- environment
from_schema: https://w3id.org/mixs
keywords:
- elevation
slot_uri: MIXS:0000093
alias: elev
owner: MiuvigAgriculture
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
- Air
- HostAssociated
- HydrocarbonResourcesCores
- MicrobialMatBiofilm
- MiscellaneousNaturalOrArtificialEnvironment
- PlantAssociated
- Sediment
- Soil
- SymbiontAssociated
- Water
range: string
recommended: true
pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
*([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
structured_pattern:
syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
interpolated: true
partial_match: true
env_broad_scale:
name: env_broad_scale
description: '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'
title: broad-scale environmental context
examples:
- value: rangeland biome [ENVO:01000247]
in_subset:
- environment
from_schema: https://w3id.org/mixs
keywords:
- context
- environmental
slot_uri: MIXS:0000012
alias: env_broad_scale
owner: MiuvigAgriculture
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
range: string
required: true
pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\]$
structured_pattern:
syntax: ^{termLabel} \[{termID}\]$
interpolated: true
partial_match: true
tax_class:
name: tax_class
description: Method used for taxonomic classification, along with reference database
used, classification rank, and thresholds used to classify new genomes
title: taxonomic classification
examples:
- value: vConTACT vContact2 (references from NCBI RefSeq v83, genus rank classification,
default parameters)
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
keywords:
- classification
- taxon
slot_uri: MIXS:0000064
alias: tax_class
owner: MiuvigAgriculture
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- Mims
- Misag
- Miuvig
range: string
recommended: true
experimental_factor:
name: experimental_factor
annotations:
Expected_value:
tag: Expected_value
value: text or EFO and/or OBI
description: Variable aspects of an experiment design that can be used to describe
an experiment, or set of experiments, in an increasingly detailed manner. This
field accepts ontology terms from Experimental Factor Ontology (EFO) and/or
Ontology for Biomedical Investigations (OBI)
title: experimental factor
examples:
- value: time series design [EFO:0001779]
in_subset:
- investigation
from_schema: https://w3id.org/mixs
keywords:
- experimental
- factor
string_serialization: '{termLabel} [{termID}]|{text}'
slot_uri: MIXS:0000008
alias: experimental_factor
owner: MiuvigAgriculture
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- FoodAnimalAndAnimalFeed
- FoodFoodProductionFacility
- FoodHumanFoods
range: string
recommended: true
multivalued: true
pattern: ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$
sort_tech:
name: sort_tech
description: Method used to sort/isolate cells or particles of interest
title: sorting technology
examples:
- value: optical manipulation
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
slot_uri: MIXS:0000075
alias: sort_tech
owner: MiuvigAgriculture
domain_of:
- Misag
- Miuvig
range: SortTechEnum
recommended: true
sc_lysis_approach:
name: sc_lysis_approach
description: Method used to free DNA from interior of the cell(s) or particle(s)
title: single cell or viral particle lysis approach
examples:
- value: enzymatic
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
keywords:
- particle
- single
slot_uri: MIXS:0000076
alias: sc_lysis_approach
owner: MiuvigAgriculture
domain_of:
- Misag
- Miuvig
range: ScLysisApproachEnum
recommended: true
sc_lysis_method:
name: sc_lysis_method
annotations:
Expected_value:
tag: Expected_value
value: kit, protocol name
description: Name of the kit or standard protocol used for cell(s) or particle(s)
lysis
title: single cell or viral particle lysis kit protocol
examples:
- value: ambion single cell lysis kit
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
keywords:
- kit
- particle
- protocol
- single
slot_uri: MIXS:0000054
alias: sc_lysis_method
owner: MiuvigAgriculture
domain_of:
- Misag
- Miuvig
range: string
recommended: true
wga_amp_appr:
name: wga_amp_appr
description: Method used to amplify genomic DNA in preparation for sequencing
title: WGA amplification approach
examples:
- value: mda based
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
slot_uri: MIXS:0000055
alias: wga_amp_appr
owner: MiuvigAgriculture
domain_of:
- Misag
- Miuvig
range: WgaAmpApprEnum
recommended: true
wga_amp_kit:
name: wga_amp_kit
annotations:
Expected_value:
tag: Expected_value
value: kit name
description: Kit used to amplify genomic DNA in preparation for sequencing
title: WGA amplification kit
examples:
- value: qiagen repli-g
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
keywords:
- kit
slot_uri: MIXS:0000006
alias: wga_amp_kit
owner: MiuvigAgriculture
domain_of:
- Misag
- Miuvig
range: string
recommended: true
bin_param:
name: bin_param
description: The parameters that have been applied during the extraction of genomes
from metagenomic datasets
title: binning parameters
examples:
- value: coverage
description: was 'coverage and kmer'
- value: kmer
description: was coverage and kmer
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
keywords:
- parameter
slot_uri: MIXS:0000077
alias: bin_param
owner: MiuvigAgriculture
domain_of:
- Mimag
- Miuvig
range: BinParamEnum
recommended: true
bin_software:
name: bin_software
annotations:
Expected_value:
tag: Expected_value
value: names and versions of software(s) used
description: Tool(s) used for the extraction of genomes from metagenomic datasets,
where possible include a product ID (PID) of the tool(s) used
title: binning software
examples:
- value: MetaCluster-TA (RRID:SCR_004599), MaxBin (biotools:maxbin)
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
keywords:
- software
string_serialization: '{software};{version}{PID}'
slot_uri: MIXS:0000078
alias: bin_software
owner: MiuvigAgriculture
domain_of:
- Mimag
- Miuvig
range: string
recommended: true
reassembly_bin:
name: reassembly_bin
description: Has an assembly been performed on a genome bin extracted from a metagenomic
assembly?
title: reassembly post binning
examples:
- value: 'no'
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
keywords:
- post
slot_uri: MIXS:0000079
alias: reassembly_bin
owner: MiuvigAgriculture
domain_of:
- Mimag
- Miuvig
range: boolean
recommended: true
mag_cov_software:
name: mag_cov_software
description: Tool(s) used to determine the genome coverage if coverage is used
as a binning parameter in the extraction of genomes from metagenomic datasets
title: MAG coverage software
examples:
- value: bbmap
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
keywords:
- software
slot_uri: MIXS:0000080
alias: mag_cov_software
owner: MiuvigAgriculture
domain_of:
- Mimag
- Miuvig
range: MagCovSoftwareEnum
vir_ident_software:
name: vir_ident_software
annotations:
Expected_value:
tag: Expected_value
value: software name, version and relevant parameters
description: Tool(s) used for the identification of UViG as a viral genome, software
or protocol name including version number, parameters, and cutoffs used
title: viral identification software
examples:
- value: VirSorter; 1.0.4; Virome database, category 2
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
keywords:
- identifier
- software
string_serialization: '{software};{version};{parameters}'
slot_uri: MIXS:0000081
alias: vir_ident_software
owner: MiuvigAgriculture
domain_of:
- Miuvig
range: string
required: true
pred_genome_type:
name: pred_genome_type
annotations:
Expected_value:
tag: Expected_value
value: enumeration
description: Type of genome predicted for the UViG
title: predicted genome type
examples:
- value: dsDNA
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
keywords:
- predict
- type
string_serialization: '[DNA|dsDNA|ssDNA|RNA|dsRNA|ssRNA|ssRNA (+)|ssRNA (-)|mixed|uncharacterized]'
slot_uri: MIXS:0000082
alias: pred_genome_type
owner: MiuvigAgriculture
domain_of:
- Miuvig
range: string
required: true
pred_genome_struc:
name: pred_genome_struc
description: Expected structure of the viral genome
title: predicted genome structure
examples:
- value: non-segmented
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
keywords:
- predict
slot_uri: MIXS:0000083
alias: pred_genome_struc
owner: MiuvigAgriculture
domain_of:
- Miuvig
range: PredGenomeStrucEnum
required: true
detec_type:
name: detec_type
annotations:
Expected_value:
tag: Expected_value
value: enumeration
description: Type of UViG detection
title: detection type
examples:
- value: independent sequence (UViG)
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
keywords:
- type
string_serialization: '[independent sequence (UViG)|provirus (UpViG)]'
slot_uri: MIXS:0000084
alias: detec_type
owner: MiuvigAgriculture
domain_of:
- Miuvig
range: string
required: true
otu_class_appr:
name: otu_class_appr
annotations:
Expected_value:
tag: Expected_value
value: cutoffs and method used
description: Cutoffs and approach used when clustering species-level OTUs. Note
that results from standard 95% ANI / 85% AF clustering should be provided alongside
OTUS defined from another set of thresholds, even if the latter are the ones
primarily used during the analysis
title: OTU classification approach
examples:
- value: 95% ANI;85% AF; greedy incremental clustering
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
keywords:
- classification
- otu
string_serialization: '{ANI cutoff};{AF cutoff};{clustering method}'
slot_uri: MIXS:0000085
alias: otu_class_appr
owner: MiuvigAgriculture
domain_of:
- Miuvig
range: string
recommended: true
otu_seq_comp_appr:
name: otu_seq_comp_appr
annotations:
Expected_value:
tag: Expected_value
value: software name, version and relevant parameters
description: Tool and thresholds used to compare sequences when computing "species-level"
OTUs
title: OTU sequence comparison approach
examples:
- value: 'blastn;2.6.0+;e-value cutoff: 0.001'
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
keywords:
- otu
string_serialization: '{software};{version};{parameters}'
slot_uri: MIXS:0000086
alias: otu_seq_comp_appr
owner: MiuvigAgriculture
domain_of:
- Miuvig
range: string
recommended: true
otu_db:
name: otu_db
annotations:
Expected_value:
tag: Expected_value
value: database and version
description: Reference database (i.e. sequences not generated as part of the current
study) used to cluster new genomes in "species-level" OTUs, if any
title: OTU database
examples:
- value: NCBI Viral RefSeq;83
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
keywords:
- database
- otu
string_serialization: '{database};{version}'
slot_uri: MIXS:0000087
alias: otu_db
owner: MiuvigAgriculture
domain_of:
- Miuvig
range: string
recommended: true
host_pred_appr:
name: host_pred_appr
description: Tool or approach used for host prediction
title: host prediction approach
examples:
- value: CRISPR spacer match
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
keywords:
- host
- host.
- predict
slot_uri: MIXS:0000088
alias: host_pred_appr
owner: MiuvigAgriculture
domain_of:
- Miuvig
range: HostPredApprEnum
recommended: true
host_pred_est_acc:
name: host_pred_est_acc
description: For each tool or approach used for host prediction, estimated false
discovery rates should be included, either computed de novo or from the literature
title: host prediction estimated accuracy
examples:
- value: 'CRISPR spacer match: 0 or 1 mismatches, estimated 8% FDR at the host
genus rank (Edwards et al. 2016 doi:10.1093/femsre/fuv048)'
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
keywords:
- host
- host.
- predict
slot_uri: MIXS:0000089
alias: host_pred_est_acc
owner: MiuvigAgriculture
domain_of:
- Miuvig
range: string
recommended: true
associated_resource:
name: associated_resource
annotations:
Expected_value:
tag: Expected_value
value: reference to resource
description: A related resource that is referenced, cited, or otherwise associated
to the sequence
title: relevant electronic resources
examples:
- value: http://www.earthmicrobiome.org/
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
keywords:
- resource
string_serialization: '{PMID}|{DOI}|{URL}'
slot_uri: MIXS:0000091
alias: associated_resource
owner: MiuvigAgriculture
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
range: string
recommended: true
multivalued: true
sop:
name: sop
annotations:
Expected_value:
tag: Expected_value
value: reference to SOP
description: Standard operating procedures used in assembly and/or annotation
of genomes, metagenomes or environmental sequences
title: relevant standard operating procedures
examples:
- value: http://press.igsb.anl.gov/earthmicrobiome/protocols-and-standards/its/
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
keywords:
- procedures
string_serialization: '{PMID}|{DOI}|{URL}'
slot_uri: MIXS:0000090
alias: sop
owner: MiuvigAgriculture
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
range: string
recommended: true
multivalued: true
plant_growth_med:
name: plant_growth_med
annotations:
Expected_value:
tag: Expected_value
value: EO or enumeration
description: 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
title: plant growth medium
examples:
- value: hydroponic plant culture media [EO:0007067]
from_schema: https://w3id.org/mixs
keywords:
- growth
- plant
string_serialization: '{termLabel} [{termID}] or [husk|other artificial liquid
medium|other artificial solid medium|peat moss|perlite|pumice|sand|soil|vermiculite|water]'
slot_uri: MIXS:0001057
alias: plant_growth_med
owner: MiuvigAgriculture
domain_of:
- Agriculture
- FoodFarmEnvironment
- PlantAssociated
range: string
photosynt_activ:
name: photosynt_activ
annotations:
Preferred_unit:
tag: Preferred_unit
value: mol m-2 s-1
description: 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
title: photosynthetic activity
examples:
- value: 0.1 mol CO2 m-2 s-1
description: added a magnitude to the example from the XLSX file, " mol CO2
m-2 s-1"
from_schema: https://w3id.org/mixs
slot_uri: MIXS:0001296
alias: photosynt_activ
owner: MiuvigAgriculture
domain_of:
- Agriculture
range: string
recommended: true
pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
*([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
structured_pattern:
syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
interpolated: true
partial_match: true
photosynt_activ_meth:
name: photosynt_activ_meth
description: Reference or method used in measurement of photosythetic activity
title: photosynthetic activity method
from_schema: https://w3id.org/mixs
keywords:
- method
slot_uri: MIXS:0001336
alias: photosynt_activ_meth
owner: MiuvigAgriculture
domain_of:
- Agriculture
range: string
recommended: true
multivalued: true
pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$|([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
structured_pattern:
syntax: ^{PMID}|{DOI}|{URL}|{text}$
interpolated: true
partial_match: true
enrichment_protocol:
name: enrichment_protocol
description: 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
title: enrichment protocol
examples:
- value: 'BAM Chapter 4: Enumeration of Escherichia coli and the Coliform Bacteria'
from_schema: https://w3id.org/mixs
keywords:
- enrichment
- protocol
slot_uri: MIXS:0001177
alias: enrichment_protocol
owner: MiuvigAgriculture
domain_of:
- Agriculture
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodFoodProductionFacility
- FoodHumanFoods
range: string
recommended: true
pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$|([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
structured_pattern:
syntax: ^{PMID}|{DOI}|{URL}|{text}$
interpolated: true
partial_match: true
library_prep_kit:
name: library_prep_kit
annotations:
Expected_value:
tag: Expected_value
value: name of library preparation kit
description: 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
title: library preparation kit
examples:
- value: llumina DNA Prep, (M) Tagmentation
from_schema: https://w3id.org/mixs
keywords:
- kit
- library
- preparation
slot_uri: MIXS:0001145
alias: library_prep_kit
owner: MiuvigAgriculture
domain_of:
- Agriculture
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodFoodProductionFacility
- FoodHumanFoods
range: string
sequencing_location:
name: sequencing_location
description: The location the sequencing run was performed. Indicate the name
of the lab or core facility where samples were sequenced
title: sequencing location
examples:
- value: University of Maryland Genomics Resource Center
from_schema: https://w3id.org/mixs
keywords:
- location
slot_uri: MIXS:0001156
alias: sequencing_location
owner: MiuvigAgriculture
domain_of:
- Agriculture
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodFoodProductionFacility
- FoodHumanFoods
range: string
soil_temp:
name: soil_temp
annotations:
Preferred_unit:
tag: Preferred_unit
value: degree Celsius
description: Temperature of soil at the time of sampling
title: soil temperature
examples:
- value: 25 degrees Celsius
from_schema: https://w3id.org/mixs
keywords:
- soil
- temperature
slot_uri: MIXS:0001163
alias: soil_temp
owner: MiuvigAgriculture
domain_of:
- Agriculture
- FoodFarmEnvironment
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
*([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
structured_pattern:
syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
interpolated: true
partial_match: true
soil_pH:
name: soil_pH
description: pH of some soil.
title: soil pH
examples:
- value: '7.2'
from_schema: https://w3id.org/mixs
keywords:
- ph
- soil
slot_uri: MIXS:0001160
alias: soil_pH
owner: MiuvigAgriculture
domain_of:
- Agriculture
- FoodFarmEnvironment
range: float
soil_conductivity:
name: soil_conductivity
annotations:
Preferred_unit:
tag: Preferred_unit
value: milliSiemens per centimeter
description: Conductivity of some soil.
title: soil conductivity
examples:
- value: 10 milliSiemens per centimeter
from_schema: https://w3id.org/mixs
keywords:
- soil
slot_uri: MIXS:0001158
alias: soil_conductivity
owner: MiuvigAgriculture
domain_of:
- Agriculture
- FoodFarmEnvironment
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
*([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
structured_pattern:
syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
interpolated: true
partial_match: true
rel_location:
name: rel_location
description: Location of sampled soil to other parts of the farm e.g. under crop
plant, near irrigation ditch, from the dirt road
title: relative location of sample
examples:
- value: furrow
from_schema: https://w3id.org/mixs
keywords:
- location
- relative
- sample
slot_uri: MIXS:0001161
alias: rel_location
owner: MiuvigAgriculture
domain_of:
- Agriculture
- FoodFarmEnvironment
range: string
recommended: true
soil_cover:
name: soil_cover
annotations:
Expected_value:
tag: Expected_value
value: subclass of 'environmental material', http://purl.obolibrary.org/obo/ENVO_00010483
description: Material covering the sampled soil. This field accepts terms under
ENVO:00010483, environmental material
title: soil cover
examples:
- value: bare soil [ENVO01001616]
from_schema: https://w3id.org/mixs
keywords:
- soil
string_serialization: bare soil [ENVO:01001616]
slot_uri: MIXS:0001159
alias: soil_cover
owner: MiuvigAgriculture
domain_of:
- Agriculture
- FoodFarmEnvironment
range: string
recommended: true
porosity:
name: porosity
annotations:
Expected_value:
tag: Expected_value
value: measurement value or range
Preferred_unit:
tag: Preferred_unit
value: percentage
description: Porosity of deposited sediment is volume of voids divided by the
total volume of sample
title: porosity
from_schema: https://w3id.org/mixs
keywords:
- porosity
string_serialization: '{float} - {float} {unit}'
slot_uri: MIXS:0000211
alias: porosity
owner: MiuvigAgriculture
domain_of:
- Agriculture
- HydrocarbonResourcesCores
- Sediment
range: string
soil_texture:
name: soil_texture
description: 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
title: soil texture
from_schema: https://w3id.org/mixs
keywords:
- soil
- texture
slot_uri: MIXS:0000335
alias: soil_texture
owner: MiuvigAgriculture
domain_of:
- Agriculture
- Soil
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
*([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
structured_pattern:
syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
interpolated: true
partial_match: true
soil_texture_meth:
name: soil_texture_meth
description: Reference or method used in determining soil texture
title: soil texture method
examples:
- value: https://uwlab.soils.wisc.edu/wp-content/uploads/sites/17/2015/09/particle_size.pdf
from_schema: https://w3id.org/mixs
keywords:
- method
- soil
- texture
slot_uri: MIXS:0000336
alias: soil_texture_meth
owner: MiuvigAgriculture
domain_of:
- Agriculture
- FoodFarmEnvironment
- Soil
range: string
pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$
structured_pattern:
syntax: ^{PMID}|{DOI}|{URL}$
interpolated: true
partial_match: true
host_symbiont:
name: host_symbiont
annotations:
Expected_value:
tag: Expected_value
value: species name or common name
description: The taxonomic name of the organism(s) found living in mutualistic,
commensalistic, or parasitic symbiosis with the specific host. The sampled symbiont
can have its own symbionts. For example, parasites may have hyperparasites (=parasites
of the parasite)
title: observed host symbionts
examples:
- value: Paragordius varius
from_schema: https://w3id.org/mixs
keywords:
- host
- host.
- observed
- symbiosis
slot_uri: MIXS:0001298
alias: host_symbiont
owner: MiuvigAgriculture
domain_of:
- Agriculture
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- PlantAssociated
- SymbiontAssociated
range: string
multivalued: true
pres_animal_insect:
name: pres_animal_insect
annotations:
Expected_value:
tag: Expected_value
value: enumeration;count
description: The type and number of animals or insects present in the sampling
space
title: presence of pets, animals, or insects
examples:
- value: cat;5
from_schema: https://w3id.org/mixs
keywords:
- animal
- presence
string_serialization: '[cat|dog|rodent|snake|other];{integer}'
slot_uri: MIXS:0000819
alias: pres_animal_insect
owner: MiuvigAgriculture
domain_of:
- Agriculture
- BuiltEnvironment
range: string
plant_water_method:
name: plant_water_method
description: 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
title: plant water delivery method
examples:
- value: drip irrigation process [AGRO:00000056]
from_schema: https://w3id.org/mixs
keywords:
- delivery
- method
- plant
- water
slot_uri: MIXS:0001111
alias: plant_water_method
owner: MiuvigAgriculture
domain_of:
- Agriculture
- FoodFarmEnvironment
range: string
recommended: true
pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\]$
structured_pattern:
syntax: ^{termLabel} \[{termID}\]$
interpolated: true
partial_match: true
anim_water_method:
name: anim_water_method
description: 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
title: animal water delivery method
examples:
- value: water trough [EOL:0001618]
from_schema: https://w3id.org/mixs
keywords:
- animal
- delivery
- method
- water
slot_uri: MIXS:0001115
alias: anim_water_method
owner: MiuvigAgriculture
domain_of:
- Agriculture
- FoodFarmEnvironment
range: string
multivalued: true
pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\]$
structured_pattern:
syntax: ^{termLabel} \[{termID}\]$
interpolated: true
partial_match: true
farm_water_source:
name: farm_water_source
description: Source of water used on the farm for irrigation of crops or watering
of livestock
title: farm watering water source
examples:
- value: well
description: was water well (ENVO:01000002)
from_schema: https://w3id.org/mixs
keywords:
- farm
- source
- water
slot_uri: MIXS:0001110
alias: farm_water_source
owner: MiuvigAgriculture
domain_of:
- Agriculture
- FoodFarmEnvironment
range: FarmWaterSourceEnum
recommended: true
water_source_shared:
name: water_source_shared
annotations:
Expected_value:
tag: Expected_value
value: enumeration
description: Other users sharing access to the same water source. Multiple terms
can be separated by one or more pipes
title: water source shared
examples:
- value: no sharing
from_schema: https://w3id.org/mixs
keywords:
- source
- water
string_serialization: '[multiple users, agricutural|multiple users, other|no sharing]'
slot_uri: MIXS:0001176
alias: water_source_shared
owner: MiuvigAgriculture
domain_of:
- Agriculture
- FoodFarmEnvironment
range: string
multivalued: true
water_pH:
name: water_pH
description: The pH measurement of the sample, or liquid portion of sample, or
aqueous phase of the fluid.
title: water pH
examples:
- value: '7.2'
from_schema: https://w3id.org/mixs
keywords:
- ph
- water
slot_uri: MIXS:0001175
alias: water_pH
owner: MiuvigAgriculture
domain_of:
- Agriculture
- FoodFarmEnvironment
range: float
season:
name: season
annotations:
Expected_value:
tag: Expected_value
value: autumn [NCIT:C94733], spring [NCIT:C94731], summer [NCIT:C94732], winter
[NCIT:C94730]
description: 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)
title: season
comments:
- autumn [NCIT:C94733] does not match ^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$
- would require ^\\S+.*\\S+ \\[[a-zA-Z]{2,}:[a-zA-Z0-9]\\]$
examples:
- value: autumn [NCIT:C94733]
from_schema: https://w3id.org/mixs
keywords:
- season
string_serialization: '{termLabel} [{termID}]'
slot_uri: MIXS:0000829
alias: season
owner: MiuvigAgriculture
domain_of:
- Agriculture
- BuiltEnvironment
- FoodFarmEnvironment
range: string
pattern: ^\S+.*\S+ \[[a-zA-Z]{2,}:[a-zA-Z0-9]+\]$
solar_irradiance:
name: solar_irradiance
annotations:
Preferred_unit:
tag: Preferred_unit
value: kilowatts per square meter per day, ergs per square centimeter per
second
description: The amount of solar energy that arrives at a specific area of a surface
during a specific time interval
title: solar irradiance
examples:
- value: 1.36 kilowatts per square meter per day
from_schema: https://w3id.org/mixs
slot_uri: MIXS:0000112
alias: solar_irradiance
owner: MiuvigAgriculture
domain_of:
- Agriculture
- Air
- FoodFarmEnvironment
range: string
multivalued: true
pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
*([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
structured_pattern:
syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
interpolated: true
partial_match: true
crop_yield:
name: crop_yield
annotations:
Preferred_unit:
tag: Preferred_unit
value: kilogram per metre square
description: Amount of crop produced per unit or area of land
title: crop yield
examples:
- value: 570 kilogram per metre square
from_schema: https://w3id.org/mixs
keywords:
- crop
slot_uri: MIXS:0001116
alias: crop_yield
owner: MiuvigAgriculture
domain_of:
- Agriculture
- FoodFarmEnvironment
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
*([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
structured_pattern:
syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
interpolated: true
partial_match: true
season_humidity:
name: season_humidity
description: Average humidity of the region throughout the growing season
title: mean seasonal humidity
comments:
- percent or float?
examples:
- value: '0.25'
from_schema: https://w3id.org/mixs
keywords:
- humidity
- mean
- season
slot_uri: MIXS:0001148
alias: season_humidity
owner: MiuvigAgriculture
domain_of:
- Agriculture
- FoodFarmEnvironment
range: float
pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
*([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
structured_pattern:
syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
interpolated: true
partial_match: true
humidity:
name: humidity
description: Amount of water vapour in the air, at the time of sampling
title: humidity
examples:
- value: 30% relative humidity
from_schema: https://w3id.org/mixs
keywords:
- humidity
slot_uri: MIXS:0000100
alias: humidity
owner: MiuvigAgriculture
domain_of:
- Agriculture
- Air
- FoodFarmEnvironment
range: string
recommended: true
pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
*([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
structured_pattern:
syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
interpolated: true
partial_match: true
adjacent_environment:
name: adjacent_environment
annotations:
Expected_value:
tag: Expected_value
value: ENVO_01001110 or ENVO_00000070
description: 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
title: environment adjacent to site
examples:
- value: estuarine biome [ENVO:01000020]
from_schema: https://w3id.org/mixs
keywords:
- adjacent
- environment
- site
string_serialization: '{termLabel}{[termID]}'
slot_uri: MIXS:0001121
alias: adjacent_environment
owner: MiuvigAgriculture
domain_of:
- Agriculture
- FoodFarmEnvironment
range: string
multivalued: true
chem_administration:
name: chem_administration
annotations:
Expected_value:
tag: Expected_value
value: CHEBI;timestamp
description: 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
title: chemical administration
examples:
- value: agar [CHEBI:2509];2018-05-11T20:00Z
from_schema: https://w3id.org/mixs
keywords:
- administration
string_serialization: '{termLabel} [{termID}];{timestamp}'
slot_uri: MIXS:0000751
alias: chem_administration
owner: MiuvigAgriculture
domain_of:
- Agriculture
- Air
- FoodFarmEnvironment
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- MicrobialMatBiofilm
- MiscellaneousNaturalOrArtificialEnvironment
- PlantAssociated
- Sediment
- SymbiontAssociated
- WastewaterSludge
- Water
range: string
required: true
multivalued: true
food_prod:
name: food_prod
description: 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
title: food production system characteristics
examples:
- value: organic plant cultivation [FOODON:03530253]
from_schema: https://w3id.org/mixs
keywords:
- food
- production
slot_uri: MIXS:0001211
alias: food_prod
owner: MiuvigAgriculture
domain_of:
- Agriculture
- FoodAnimalAndAnimalFeed
- FoodFoodProductionFacility
- FoodHumanFoods
range: string
multivalued: true
pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\]$
structured_pattern:
syntax: ^{termLabel} \[{termID}\]$
interpolated: true
partial_match: true
lot_number:
name: lot_number
annotations:
Expected_value:
tag: Expected_value
value: lot number, item
description: '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'
title: lot number
examples:
- value: 1239ABC01A, split Cornish hens
from_schema: https://w3id.org/mixs
keywords:
- number
string_serialization: '{integer}, {text}'
slot_uri: MIXS:0001147
alias: lot_number
owner: MiuvigAgriculture
domain_of:
- Agriculture
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodFoodProductionFacility
- FoodHumanFoods
range: string
multivalued: true
fertilizer_admin:
name: fertilizer_admin
description: 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
title: fertilizer administration
examples:
- value: fish emulsion [AGRO:00000082]
from_schema: https://w3id.org/mixs
keywords:
- administration
slot_uri: MIXS:0001127
alias: fertilizer_admin
owner: MiuvigAgriculture
domain_of:
- Agriculture
- FoodFarmEnvironment
range: string
pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\]$
structured_pattern:
syntax: ^{termLabel} \[{termID}\]$
interpolated: true
partial_match: true
samp_store_temp:
name: samp_store_temp
annotations:
Preferred_unit:
tag: Preferred_unit
value: degree Celsius
description: Temperature at which sample was stored, e.g. -80 degree Celsius
title: sample storage temperature
examples:
- value: -80 degree Celsius
from_schema: https://w3id.org/mixs
keywords:
- sample
- storage
- temperature
slot_uri: MIXS:0000110
alias: samp_store_temp
owner: MiuvigAgriculture
domain_of:
- Agriculture
- Air
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodFoodProductionFacility
- FoodHumanFoods
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- HydrocarbonResourcesCores
- HydrocarbonResourcesFluidsSwabs
- MicrobialMatBiofilm
- MiscellaneousNaturalOrArtificialEnvironment
- PlantAssociated
- Sediment
- SymbiontAssociated
- WastewaterSludge
- Water
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
*([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
structured_pattern:
syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
interpolated: true
partial_match: true
food_trav_mode:
name: food_trav_mode
description: 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
title: food shipping transportation method
examples:
- value: train travel [GENEPIO:0001060]
from_schema: https://w3id.org/mixs
keywords:
- food
- method
- transport
slot_uri: MIXS:0001137
alias: food_trav_mode
owner: MiuvigAgriculture
domain_of:
- Agriculture
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodFoodProductionFacility
- FoodHumanFoods
range: string
multivalued: true
pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\]$
structured_pattern:
syntax: ^{termLabel} \[{termID}\]$
interpolated: true
partial_match: true
food_trav_vehic:
name: food_trav_vehic
annotations:
Expected_value:
tag: Expected_value
value: ENVO:01000604
description: 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
title: food shipping transportation vehicle
examples:
- value: aircraft [ENVO:01001488]|car [ENVO:01000605]
from_schema: https://w3id.org/mixs
keywords:
- food
- transport
string_serialization: '{text}|{termLabel} [{termID}]'
slot_uri: MIXS:0001138
alias: food_trav_vehic
owner: MiuvigAgriculture
domain_of:
- Agriculture
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodFoodProductionFacility
- FoodHumanFoods
range: string
multivalued: true
farm_equip_san:
name: farm_equip_san
annotations:
Expected_value:
tag: Expected_value
value: text or commercial name of sanitizer or class of sanitizer or active
ingredient in sanitizer
Preferred_unit:
tag: Preferred_unit
value: parts per million
description: 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
title: farm equipment sanitization
examples:
- value: hot water pressure wash, hypochlorite solution, 50 parts per million
from_schema: https://w3id.org/mixs
keywords:
- equipment
- farm
string_serialization: '{text} {float} {unit}'
slot_uri: MIXS:0001124
alias: farm_equip_san
owner: MiuvigAgriculture
domain_of:
- Agriculture
- FoodFarmEnvironment
range: string
multivalued: true
farm_equip:
name: farm_equip
description: 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
title: farm equipment used
examples:
- value: combine harvester [AGRO:00000473]
from_schema: https://w3id.org/mixs
keywords:
- equipment
- farm
- use
slot_uri: MIXS:0001126
alias: farm_equip
owner: MiuvigAgriculture
domain_of:
- Agriculture
- FoodFarmEnvironment
range: string
multivalued: true
pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\]$
structured_pattern:
syntax: ^{termLabel} \[{termID}\]$
interpolated: true
partial_match: true
farm_equip_shared:
name: farm_equip_shared
description: 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
title: equipment shared with other farms
examples:
- value: combine harvester [AGRO:00000473]
from_schema: https://w3id.org/mixs
keywords:
- equipment
- farm
slot_uri: MIXS:0001123
alias: farm_equip_shared
owner: MiuvigAgriculture
domain_of:
- Agriculture
- FoodFarmEnvironment
range: string
multivalued: true
pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\]$
structured_pattern:
syntax: ^{termLabel} \[{termID}\]$
interpolated: true
partial_match: true
food_harvest_proc:
name: food_harvest_proc
description: 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
title: Food harvesting process
examples:
- value: hand-picked
from_schema: https://w3id.org/mixs
keywords:
- food
- process
slot_uri: MIXS:0001133
alias: food_harvest_proc
owner: MiuvigAgriculture
domain_of:
- Agriculture
- FoodFarmEnvironment
range: string
multivalued: true
plant_struc:
name: plant_struc
description: 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
title: plant structure
examples:
- value: epidermis [PO:0005679]
from_schema: https://w3id.org/mixs
keywords:
- plant
slot_uri: MIXS:0001060
alias: plant_struc
owner: MiuvigAgriculture
domain_of:
- Agriculture
- PlantAssociated
range: string
recommended: true
pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\]$
structured_pattern:
syntax: ^{termLabel} \[{termID}\]$
interpolated: true
partial_match: true
host_dry_mass:
name: host_dry_mass
annotations:
Preferred_unit:
tag: Preferred_unit
value: kilogram, gram
description: Measurement of dry mass
title: host dry mass
examples:
- value: 500 gram
from_schema: https://w3id.org/mixs
keywords:
- dry
- host
- host.
- mass
slot_uri: MIXS:0000257
alias: host_dry_mass
owner: MiuvigAgriculture
domain_of:
- Agriculture
- FoodFarmEnvironment
- HostAssociated
- PlantAssociated
- SymbiontAssociated
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
*([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
structured_pattern:
syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
interpolated: true
partial_match: true
ances_data:
name: ances_data
description: 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)
title: ancestral data
examples:
- value: A/3*B
from_schema: https://w3id.org/mixs
slot_uri: MIXS:0000247
alias: ances_data
owner: MiuvigAgriculture
domain_of:
- Agriculture
- FoodFarmEnvironment
- HostAssociated
- PlantAssociated
range: string
genetic_mod:
name: genetic_mod
annotations:
Expected_value:
tag: Expected_value
value: PMID, DOI, URL or text
description: 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
title: genetic modification
examples:
- value: aox1A transgenic
from_schema: https://w3id.org/mixs
string_serialization: '{PMID}|{DOI}|{URL}'
slot_uri: MIXS:0000859
alias: genetic_mod
owner: MiuvigAgriculture
domain_of:
- Agriculture
- FoodFarmEnvironment
- FoodFoodProductionFacility
- FoodHumanFoods
- HostAssociated
- PlantAssociated
range: string
food_product_type:
name: food_product_type
annotations:
Expected_value:
tag: Expected_value
value: FOODON:00001002 or FOODON:03309997
description: A food product type is a class of food products that is differentiated
by its food composition (e.g., single- or multi-ingredient), processing and/or
consumption characteristics. This does not include brand name products but it
may include generic food dish categories. This field accepts terms under food
product type (http://purl.obolibrary.org/obo/FOODON:03400361). For terms related
to food product for an animal, consult food product for animal (http://purl.obolibrary.org/obo/FOODON_03309997).
If the proper descriptor is not listed please use text to describe the food
type. Multiple terms can be separated by one or more pipes
title: food product type
examples:
- value: delicatessen salad; FOODON:03316276
from_schema: https://w3id.org/mixs
keywords:
- food
- product
- type
string_serialization: '{text}|{termLabel} [{termID}]'
slot_uri: MIXS:0001184
alias: food_product_type
owner: MiuvigAgriculture
domain_of:
- Agriculture
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodFoodProductionFacility
- FoodHumanFoods
range: string
food_source:
name: food_source
annotations:
Expected_value:
tag: Expected_value
value: FOODON term
description: Type of plant or animal from which the food product or its major
ingredient is derived or a chemical food source [FDA CFSAN 1995]
title: food source
examples:
- value: red swamp crayfish; FOODON:03412231
from_schema: https://w3id.org/mixs
keywords:
- food
- source
string_serialization: '{termLabel} [{termID}]'
slot_uri: MIXS:0001139
alias: food_source
owner: MiuvigAgriculture
domain_of:
- Agriculture
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodFoodProductionFacility
- FoodHumanFoods
range: string
required: true
spikein_strain:
name: spikein_strain
annotations:
Expected_value:
tag: Expected_value
value: NCIT:C14250 or NCBI taxid or text
description: 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
title: spike-in microbial strain
examples:
- value: '169963'
from_schema: https://w3id.org/mixs
keywords:
- microbial
- spike
string_serialization: '{termLabel} [{termID}]|{integer}'
slot_uri: MIXS:0001170
alias: spikein_strain
owner: MiuvigAgriculture
domain_of:
- Agriculture
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodHumanFoods
range: string
multivalued: true
organism_count:
name: organism_count
annotations:
Expected_value:
tag: Expected_value
value: organism name;measurement value;enumeration
description: '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)'
title: organism count
examples:
- value: total prokaryotes;3.5e7 cells per milliliter;qPCR
from_schema: https://w3id.org/mixs
keywords:
- count
- organism
string_serialization: '{text};{float} {unit};[ATP|MPN|qPCR|other]'
slot_uri: MIXS:0000103
alias: organism_count
owner: MiuvigAgriculture
domain_of:
- Agriculture
- Air
- BuiltEnvironment
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodFoodProductionFacility
- FoodHumanFoods
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- HydrocarbonResourcesCores
- HydrocarbonResourcesFluidsSwabs
- MicrobialMatBiofilm
- MiscellaneousNaturalOrArtificialEnvironment
- PlantAssociated
- Sediment
- SymbiontAssociated
- WastewaterSludge
- Water
range: string
recommended: true
multivalued: true
size_frac_low:
name: size_frac_low
annotations:
Preferred_unit:
tag: Preferred_unit
value: micrometer
description: Refers to the mesh/pore size used to pre-filter/pre-sort the sample.
Materials smaller than the size threshold are excluded from the sample
title: size-fraction lower threshold
examples:
- value: 0.2 micrometer
from_schema: https://w3id.org/mixs
keywords:
- lower
slot_uri: MIXS:0000735
alias: size_frac_low
owner: MiuvigAgriculture
domain_of:
- Agriculture
- FoodFarmEnvironment
- Water
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
*([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
structured_pattern:
syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
interpolated: true
partial_match: true
size_frac_up:
name: size_frac_up
annotations:
Preferred_unit:
tag: Preferred_unit
value: micrometer
description: Mesh or pore size of the device used to retain the sample. Materials
larger than the size threshold are excluded from the sample.
title: size-fraction upper threshold
examples:
- value: 20 micrometer
from_schema: https://w3id.org/mixs
keywords:
- upper
slot_uri: MIXS:0000736
alias: size_frac_up
owner: MiuvigAgriculture
domain_of:
- Agriculture
- FoodFarmEnvironment
- Water
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
*([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
structured_pattern:
syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
interpolated: true
partial_match: true
cult_isol_date:
name: cult_isol_date
description: The datetime 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
title: culture isolation date
examples:
- value: '2018-05-11T10:00:00+01:00'
from_schema: https://w3id.org/mixs
keywords:
- culture
- date
- isolation
slot_uri: MIXS:0001181
alias: cult_isol_date
owner: MiuvigAgriculture
domain_of:
- Agriculture
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodFoodProductionFacility
- FoodHumanFoods
range: datetime
samp_pooling:
name: samp_pooling
description: 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
title: sample pooling
examples:
- value: 5uL of extracted genomic DNA from 5 leaves were pooled
from_schema: https://w3id.org/mixs
keywords:
- pooling
- sample
slot_uri: MIXS:0001153
alias: samp_pooling
owner: MiuvigAgriculture
domain_of:
- Agriculture
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodFoodProductionFacility
- FoodHumanFoods
range: string
recommended: true
multivalued: true
root_med_macronutr:
name: root_med_macronutr
annotations:
Expected_value:
tag: Expected_value
value: macronutrient name;measurement value
Preferred_unit:
tag: Preferred_unit
value: milligram per liter
description: Measurement of the culture rooting medium macronutrients (N,P, K,
Ca, Mg, S); e.g. KH2PO4 (170 mg/L)
title: rooting medium macronutrients
examples:
- value: KH2PO4;170 milligram per liter
from_schema: https://w3id.org/mixs
keywords:
- macronutrients
string_serialization: '{text};{float} {unit}'
slot_uri: MIXS:0000578
alias: root_med_macronutr
owner: MiuvigAgriculture
domain_of:
- Agriculture
- FoodFarmEnvironment
- PlantAssociated
range: string
root_med_carbon:
name: root_med_carbon
annotations:
Expected_value:
tag: Expected_value
value: carbon source name;measurement value
Preferred_unit:
tag: Preferred_unit
value: milligram per liter
description: Source of organic carbon in the culture rooting medium; e.g. sucrose
title: rooting medium carbon
examples:
- value: sucrose
from_schema: https://w3id.org/mixs
keywords:
- carbon
string_serialization: '{text};{float} {unit}'
slot_uri: MIXS:0000577
alias: root_med_carbon
owner: MiuvigAgriculture
domain_of:
- Agriculture
- FoodFarmEnvironment
- PlantAssociated
range: string
root_med_ph:
name: root_med_ph
description: pH measurement of the culture rooting medium; e.g. 5.5
title: rooting medium pH
examples:
- value: '7.5'
from_schema: https://w3id.org/mixs
keywords:
- ph
slot_uri: MIXS:0001062
alias: root_med_ph
owner: MiuvigAgriculture
domain_of:
- Agriculture
- FoodFarmEnvironment
- PlantAssociated
range: float
water_temp_regm:
name: water_temp_regm
annotations:
Preferred_unit:
tag: Preferred_unit
value: degree Celsius
description: 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
title: water temperature regimen
examples:
- value: 15 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M
from_schema: https://w3id.org/mixs
keywords:
- regimen
- temperature
- water
string_serialization: '{float} {unit};{period};{interval};{period}'
slot_uri: MIXS:0000590
alias: water_temp_regm
owner: MiuvigAgriculture
domain_of:
- Agriculture
- PlantAssociated
range: string
recommended: true
multivalued: true
watering_regm:
name: watering_regm
annotations:
Preferred_unit:
tag: Preferred_unit
value: milliliter, liter
description: 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
title: watering regimen
examples:
- value: 1 liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M
from_schema: https://w3id.org/mixs
keywords:
- regimen
- water
string_serialization: '{float} {unit};{period};{interval};{period}'
slot_uri: MIXS:0000591
alias: watering_regm
owner: MiuvigAgriculture
domain_of:
- Agriculture
- PlantAssociated
range: string
recommended: true
multivalued: true
standing_water_regm:
name: standing_water_regm
description: 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
title: standing water regimen
examples:
- value: standing water;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M
from_schema: https://w3id.org/mixs
keywords:
- regimen
- water
string_serialization: '{text};{period};{interval};{period}'
slot_uri: MIXS:0001069
alias: standing_water_regm
owner: MiuvigAgriculture
domain_of:
- Agriculture
- PlantAssociated
range: string
recommended: true
multivalued: true
gaseous_environment:
name: gaseous_environment
annotations:
Preferred_unit:
tag: Preferred_unit
value: micromole per liter
description: 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
title: gaseous environment
examples:
- value: nitric oxide;0.5 micromole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M
from_schema: https://w3id.org/mixs
keywords:
- environment
string_serialization: '{text};{float} {unit};{period};{interval};{period}'
slot_uri: MIXS:0000558
alias: gaseous_environment
owner: MiuvigAgriculture
domain_of:
- Agriculture
- PlantAssociated
range: string
recommended: true
multivalued: true
fungicide_regm:
name: fungicide_regm
annotations:
Preferred_unit:
tag: Preferred_unit
value: gram, mole per liter, milligram per liter
description: 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
title: fungicide regimen
examples:
- value: bifonazole;1 mole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M
from_schema: https://w3id.org/mixs
keywords:
- regimen
string_serialization: '{text};{float} {unit};{period};{interval};{period}'
slot_uri: MIXS:0000557
alias: fungicide_regm
owner: MiuvigAgriculture
domain_of:
- Agriculture
- PlantAssociated
range: string
recommended: true
multivalued: true
climate_environment:
name: climate_environment
description: 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
title: climate environment
examples:
- value: tropical climate;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M
from_schema: https://w3id.org/mixs
keywords:
- environment
string_serialization: '{text};{period};{interval};{period}'
slot_uri: MIXS:0001040
alias: climate_environment
owner: MiuvigAgriculture
domain_of:
- Agriculture
- PlantAssociated
range: string
recommended: true
multivalued: true
herbicide_regm:
name: herbicide_regm
annotations:
Preferred_unit:
tag: Preferred_unit
value: gram, mole per liter, milligram per liter
description: 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
title: herbicide regimen
examples:
- value: atrazine;10 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M
from_schema: https://w3id.org/mixs
keywords:
- regimen
string_serialization: '{text};{float} {unit};{period};{interval};{period}'
slot_uri: MIXS:0000561
alias: herbicide_regm
owner: MiuvigAgriculture
domain_of:
- Agriculture
- PlantAssociated
range: string
recommended: true
multivalued: true
non_min_nutr_regm:
name: non_min_nutr_regm
annotations:
Preferred_unit:
tag: Preferred_unit
value: gram, mole per liter, milligram per liter
description: 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
title: non-mineral nutrient regimen
examples:
- value: https://phylogenomics.me/protocols/16s-pcr-protocol/
from_schema: https://w3id.org/mixs
keywords:
- non-mineral
- nutrient
- regimen
string_serialization: '{text};{float} {unit};{period};{interval};{period}'
slot_uri: MIXS:0000571
alias: non_min_nutr_regm
owner: MiuvigAgriculture
domain_of:
- Agriculture
- PlantAssociated
range: string
recommended: true
multivalued: true
pesticide_regm:
name: pesticide_regm
annotations:
Preferred_unit:
tag: Preferred_unit
value: gram, mole per liter, milligram per liter
description: 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
title: pesticide regimen
examples:
- value: pyrethrum;0.6 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M
from_schema: https://w3id.org/mixs
keywords:
- regimen
string_serialization: '{text};{float} {unit};{period};{interval};{period}'
slot_uri: MIXS:0000573
alias: pesticide_regm
owner: MiuvigAgriculture
domain_of:
- Agriculture
- PlantAssociated
range: string
recommended: true
multivalued: true
ph_regm:
name: ph_regm
description: 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
title: pH regimen
examples:
- value: 7.6;R2/2018-05-11:T14:30/2018-05-11T19:30/P1H30M
from_schema: https://w3id.org/mixs
keywords:
- ph
- regimen
string_serialization: '{float};{period};{interval};{period}'
slot_uri: MIXS:0001056
alias: ph_regm
owner: MiuvigAgriculture
domain_of:
- Agriculture
- PlantAssociated
range: string
recommended: true
multivalued: true
salt_regm:
name: salt_regm
annotations:
Preferred_unit:
tag: Preferred_unit
value: gram, microgram, mole per liter, gram per liter
description: 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
title: salt regimen
examples:
- value: NaCl;5 gram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M
from_schema: https://w3id.org/mixs
keywords:
- regimen
- salt
string_serialization: '{text};{float} {unit};{period};{interval};{period}'
slot_uri: MIXS:0000582
alias: salt_regm
owner: MiuvigAgriculture
domain_of:
- Agriculture
- PlantAssociated
range: string
recommended: true
multivalued: true
season_environment:
name: season_environment
description: 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
title: seasonal environment
examples:
- value: rainy;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M
from_schema: https://w3id.org/mixs
keywords:
- environment
- season
string_serialization: '{text};{period};{interval};{period}'
slot_uri: MIXS:0001068
alias: season_environment
owner: MiuvigAgriculture
domain_of:
- Agriculture
- PlantAssociated
range: string
recommended: true
multivalued: true
perturbation:
name: perturbation
annotations:
Expected_value:
tag: Expected_value
value: perturbation type name;perturbation interval and duration
description: 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
title: perturbation
examples:
- value: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M
from_schema: https://w3id.org/mixs
keywords:
- perturbation
string_serialization: '{text};{Rn/start_time/end_time/duration}'
slot_uri: MIXS:0000754
alias: perturbation
owner: MiuvigAgriculture
domain_of:
- Agriculture
- Air
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodHumanFoods
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- MicrobialMatBiofilm
- MiscellaneousNaturalOrArtificialEnvironment
- PlantAssociated
- Sediment
- SymbiontAssociated
- WastewaterSludge
- Water
range: string
recommended: true
multivalued: true
isol_growth_condt:
name: isol_growth_condt
description: Publication reference in the form of pubmed ID (pmid), digital object
identifier (doi) or url for isolation and growth condition specifications of
the organism/material
title: isolation and growth condition
examples:
- value: doi:10.1016/j.syapm.2018.01.009
in_subset:
- nucleic acid sequence source
from_schema: https://w3id.org/mixs
keywords:
- condition
- growth
- isolation
slot_uri: MIXS:0000003
alias: isol_growth_condt
owner: MiuvigAgriculture
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- MimarksC
- Agriculture
range: string
pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$
structured_pattern:
syntax: ^{PMID}|{DOI}|{URL}$
interpolated: true
partial_match: true
samp_store_dur:
name: samp_store_dur
description: Duration for which the sample was stored. Indicate the duration for
which the sample was stored written in ISO 8601 format
title: sample storage duration
examples:
- value: P1Y6M
from_schema: https://w3id.org/mixs
keywords:
- duration
- period
- sample
- storage
slot_uri: MIXS:0000116
alias: samp_store_dur
owner: MiuvigAgriculture
domain_of:
- Agriculture
- Air
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodFoodProductionFacility
- FoodHumanFoods
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- HydrocarbonResourcesCores
- HydrocarbonResourcesFluidsSwabs
- MicrobialMatBiofilm
- MiscellaneousNaturalOrArtificialEnvironment
- PlantAssociated
- Sediment
- SymbiontAssociated
- WastewaterSludge
- Water
range: string
required: true
pattern: ^P(?:(?:\d+D|\d+M(?:\d+D)?|\d+Y(?:\d+M(?:\d+D)?)?)(?:T(?:\d+H(?:\d+M(?:\d+S)?)?|\d+M(?:\d+S)?|\d+S))?|T(?:\d+H(?:\d+M(?:\d+S)?)?|\d+M(?:\d+S)?|\d+S)|\d+W)$
structured_pattern:
syntax: ^{duration}$
interpolated: true
partial_match: true
samp_store_loc:
name: samp_store_loc
annotations:
Expected_value:
tag: Expected_value
value: location name
description: Location at which sample was stored, usually name of a specific freezer/room
title: sample storage location
examples:
- value: Freezer no:5
from_schema: https://w3id.org/mixs
keywords:
- location
- sample
- storage
slot_uri: MIXS:0000755
alias: samp_store_loc
owner: MiuvigAgriculture
domain_of:
- Agriculture
- Air
- FoodAnimalAndAnimalFeed
- FoodFoodProductionFacility
- FoodHumanFoods
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- HydrocarbonResourcesCores
- HydrocarbonResourcesFluidsSwabs
- MicrobialMatBiofilm
- MiscellaneousNaturalOrArtificialEnvironment
- PlantAssociated
- Sediment
- SymbiontAssociated
- WastewaterSludge
- Water
range: string
required: true
host_age:
name: host_age
annotations:
Preferred_unit:
tag: Preferred_unit
value: year, day, hour
description: 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
title: host age
from_schema: https://w3id.org/mixs
keywords:
- age
- host
- host.
slot_uri: MIXS:0000255
alias: host_age
owner: MiuvigAgriculture
domain_of:
- Agriculture
- FoodFarmEnvironment
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- PlantAssociated
- SymbiontAssociated
range: string
required: true
pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
*([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
structured_pattern:
syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
interpolated: true
partial_match: true
host_common_name:
name: host_common_name
annotations:
Preferred_unit:
tag: Preferred_unit
value: ''
description: Common name of the host
title: host common name
from_schema: https://w3id.org/mixs
keywords:
- host
- host.
slot_uri: MIXS:0000248
alias: host_common_name
owner: MiuvigAgriculture
domain_of:
- Agriculture
- HostAssociated
- PlantAssociated
- SymbiontAssociated
range: string
required: true
host_genotype:
name: host_genotype
description: Observed genotype
title: host genotype
from_schema: https://w3id.org/mixs
keywords:
- host
- host.
slot_uri: MIXS:0000365
alias: host_genotype
owner: MiuvigAgriculture
domain_of:
- Agriculture
- FoodFarmEnvironment
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- PlantAssociated
- SymbiontAssociated
range: string
required: true
host_height:
name: host_height
annotations:
Preferred_unit:
tag: Preferred_unit
value: centimeter, millimeter, meter
description: The height of subject
title: host height
from_schema: https://w3id.org/mixs
keywords:
- height
- host
- host.
slot_uri: MIXS:0000264
alias: host_height
owner: MiuvigAgriculture
domain_of:
- Agriculture
- FoodFarmEnvironment
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- PlantAssociated
- SymbiontAssociated
range: string
required: true
pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
*([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
structured_pattern:
syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
interpolated: true
partial_match: true
host_subspecf_genlin:
name: host_subspecf_genlin
annotations:
Expected_value:
tag: Expected_value
value: Genetic lineage below lowest rank of NCBI taxonomy, which is subspecies,
e.g. serovar, biotype, ecotype, variety, cultivar
description: 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
title: host subspecific genetic lineage
examples:
- value: 'serovar:Newport, variety:glabrum, cultivar: Red Delicious'
from_schema: https://w3id.org/mixs
keywords:
- host
- host.
- lineage
string_serialization: '{rank name}:{text}'
slot_uri: MIXS:0001318
alias: host_subspecf_genlin
owner: MiuvigAgriculture
domain_of:
- Agriculture
- FoodFarmEnvironment
- HostAssociated
- PlantAssociated
range: string
multivalued: true
host_length:
name: host_length
annotations:
Preferred_unit:
tag: Preferred_unit
value: centimeter, millimeter, meter
description: The length of subject
title: host length
examples:
- value: 1 meter
from_schema: https://w3id.org/mixs
keywords:
- host
- host.
- length
slot_uri: MIXS:0000256
alias: host_length
owner: MiuvigAgriculture
domain_of:
- Agriculture
- FoodFarmEnvironment
- HostAssociated
- PlantAssociated
- SymbiontAssociated
range: string
required: true
pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
*([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
structured_pattern:
syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
interpolated: true
partial_match: true
host_life_stage:
name: host_life_stage
annotations:
Expected_value:
tag: Expected_value
value: stage
description: Description of life stage of host
title: host life stage
from_schema: https://w3id.org/mixs
keywords:
- host
- host.
- life
slot_uri: MIXS:0000251
alias: host_life_stage
owner: MiuvigAgriculture
domain_of:
- Agriculture
- HostAssociated
- PlantAssociated
- SymbiontAssociated
range: string
required: true
host_phenotype:
name: host_phenotype
annotations:
Expected_value:
tag: Expected_value
value: PATO or HP
description: Phenotype of human or other host. Use terms from the phenotypic quality
ontology (pato) or the Human Phenotype Ontology (HP)
title: host phenotype
from_schema: https://w3id.org/mixs
keywords:
- host
- host.
string_serialization: '{termLabel} [{termID}]'
slot_uri: MIXS:0000874
alias: host_phenotype
owner: MiuvigAgriculture
domain_of:
- Agriculture
- FoodFarmEnvironment
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- PlantAssociated
- SymbiontAssociated
range: string
required: true
host_taxid:
name: host_taxid
annotations:
Expected_value:
tag: Expected_value
value: NCBI taxon identifier
description: NCBI taxon id of the host, e.g. 9606
title: host taxid
examples:
- value: '9606'
from_schema: https://w3id.org/mixs
keywords:
- host
- host.
- taxon
string_serialization: '{integer}'
slot_uri: MIXS:0000250
alias: host_taxid
owner: MiuvigAgriculture
domain_of:
- Agriculture
- FoodFarmEnvironment
- HostAssociated
- PlantAssociated
- SymbiontAssociated
range: string
required: true
host_tot_mass:
name: host_tot_mass
annotations:
Preferred_unit:
tag: Preferred_unit
value: kilogram, gram
description: Total mass of the host at collection, the unit depends on host
title: host total mass
from_schema: https://w3id.org/mixs
keywords:
- host
- host.
- mass
- total
slot_uri: MIXS:0000263
alias: host_tot_mass
owner: MiuvigAgriculture
domain_of:
- Agriculture
- FoodFarmEnvironment
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- PlantAssociated
- SymbiontAssociated
range: string
required: true
pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
*([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
structured_pattern:
syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
interpolated: true
partial_match: true
trophic_level:
name: trophic_level
description: Trophic levels are the feeding position in a food chain. Microbes
can be a range of producers (e.g. chemolithotroph)
title: trophic level
examples:
- value: heterotroph
in_subset:
- nucleic acid sequence source
from_schema: https://w3id.org/mixs
keywords:
- level
slot_uri: MIXS:0000032
alias: trophic_level
owner: MiuvigAgriculture
domain_of:
- MigsBa
- MigsEu
- MimarksC
- Agriculture
range: TrophicLevelEnum
recommended: true
plant_product:
name: plant_product
annotations:
Expected_value:
tag: Expected_value
value: product name
description: Substance produced by the plant, where the sample was obtained from
title: plant product
examples:
- value: xylem sap [PO:0025539]
from_schema: https://w3id.org/mixs
keywords:
- plant
- product
slot_uri: MIXS:0001058
alias: plant_product
owner: MiuvigAgriculture
domain_of:
- Agriculture
- PlantAssociated
range: string
recommended: true
oxy_stat_samp:
name: oxy_stat_samp
description: Oxygenation status of sample
title: oxygenation status of sample
examples:
- value: aerobic
from_schema: https://w3id.org/mixs
keywords:
- oxygen
- sample
- status
slot_uri: MIXS:0000753
alias: oxy_stat_samp
owner: MiuvigAgriculture
domain_of:
- Agriculture
- Air
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- HydrocarbonResourcesCores
- HydrocarbonResourcesFluidsSwabs
- MicrobialMatBiofilm
- MiscellaneousNaturalOrArtificialEnvironment
- PlantAssociated
- Sediment
- SymbiontAssociated
- WastewaterSludge
- Water
range: OxyStatSampEnum
recommended: true
pcr_primers:
name: pcr_primers
annotations:
Expected_value:
tag: Expected_value
value: 'FWD: forward primer sequence;REV:reverse primer sequence'
description: PCR primers that were used to amplify the sequence of the targeted
gene, locus or subfragment. This field should contain all the primers used for
a single PCR reaction if multiple forward or reverse primers are present in
a single PCR reaction. The primer sequence should be reported in uppercase letters
title: pcr primers
examples:
- value: FWD:GTGCCAGCMGCCGCGGTAA;REV:GGACTACHVGGGTWTCTAAT
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
keywords:
- pcr
string_serialization: FWD:{dna};REV:{dna}
slot_uri: MIXS:0000046
alias: pcr_primers
owner: MiuvigAgriculture
domain_of:
- MimarksC
- MimarksS
- Agriculture
range: string
required: true
target_gene:
name: target_gene
description: Targeted gene or locus name for marker gene studies
title: target gene
examples:
- value: 16S rRNA, 18S rRNA, nif, amoA, rpo
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
keywords:
- target
slot_uri: MIXS:0000044
alias: target_gene
owner: MiuvigAgriculture
domain_of:
- MimarksC
- MimarksS
- Agriculture
range: string
required: true
target_subfragment:
name: target_subfragment
description: Name of subfragment of a gene or locus. Important to e.g. identify
special regions on marker genes like V6 on 16S rRNA
title: target subfragment
examples:
- value: V6, V9, ITS
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
keywords:
- target
slot_uri: MIXS:0000045
alias: target_subfragment
owner: MiuvigAgriculture
domain_of:
- MimarksC
- MimarksS
- Agriculture
range: string
required: true
pcr_cond:
name: pcr_cond
annotations:
Expected_value:
tag: Expected_value
value: initial denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final
elongation:degrees_minutes;total cycles
description: Description of reaction conditions and components of polymerase chain
reaction performed during library preparation.
title: pcr conditions
examples:
- value: initial denaturation:94_3;annealing:50_1;elongation:72_1.5;final elongation:72_10;35
- value: initial denaturation:94degC_1.5min
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
keywords:
- condition
- pcr
string_serialization: initial denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final
elongation:degrees_minutes;total cycles
slot_uri: MIXS:0000049
alias: pcr_cond
owner: MiuvigAgriculture
domain_of:
- MimarksC
- MimarksS
- Agriculture
range: string
required: true
seq_quality_check:
name: seq_quality_check
annotations:
Expected_value:
tag: Expected_value
value: none or manually edited
description: Indicate if the sequence has been called by automatic systems (none)
or undergone a manual editing procedure (e.g. by inspecting the raw data or
chromatograms). Applied only for sequences that are not submitted to SRA,ENA
or DRA
title: sequence quality check
examples:
- value: none
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
keywords:
- quality
slot_uri: MIXS:0000051
alias: seq_quality_check
owner: MiuvigAgriculture
domain_of:
- MimarksC
- MimarksS
- Agriculture
range: SeqQualityCheckEnum
chimera_check:
name: chimera_check
description: Tool(s) used for chimera checking, including version number and parameters,
to discover and remove chimeric sequences. A chimeric sequence is comprised
of two or more phylogenetically distinct parent sequences
title: chimera check software
examples:
- value: uchime;v4.1;default parameters
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
keywords:
- software
slot_uri: MIXS:0000052
alias: chimera_check
owner: MiuvigAgriculture
domain_of:
- MimarksC
- MimarksS
- Agriculture
range: string
required: true
pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+);([^\s-]{1,2}|[^\s-]+.+[^\s-]+);([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
structured_pattern:
syntax: ^{software};{version};{parameters}$
interpolated: true
partial_match: true
fao_class:
name: fao_class
description: Soil classification from the FAO World soil distribution from International
Soil Reference and Information Centre (ISRIC). The list of available soil classifications
can be found at https://www.isric.org/explore/world-soil-distribution
title: soil_taxonomic/FAO classification
examples:
- value: Luvisols
from_schema: https://w3id.org/mixs
keywords:
- classification
slot_uri: MIXS:0001083
alias: fao_class
owner: MiuvigAgriculture
domain_of:
- Agriculture
- Soil
range: FaoClassEnum
recommended: true
local_class:
name: local_class
annotations:
Expected_value:
tag: Expected_value
value: local classification name
description: Soil classification based on local soil classification system
title: soil_taxonomic/local classification
from_schema: https://w3id.org/mixs
keywords:
- classification
slot_uri: MIXS:0000330
alias: local_class
owner: MiuvigAgriculture
domain_of:
- Agriculture
- Soil
range: string
recommended: true
local_class_meth:
name: local_class_meth
description: Reference or method used in determining the local soil classification
title: soil_taxonomic/local classification method
from_schema: https://w3id.org/mixs
keywords:
- classification
- method
slot_uri: MIXS:0000331
alias: local_class_meth
owner: MiuvigAgriculture
domain_of:
- Agriculture
- Soil
range: string
recommended: true
pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$
structured_pattern:
syntax: ^{PMID}|{DOI}|{URL}$
interpolated: true
partial_match: true
soil_type:
name: soil_type
annotations:
Expected_value:
tag: Expected_value
value: ENVO:00001998
description: 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
title: soil type
examples:
- value: plinthosol [ENVO:00002250]
from_schema: https://w3id.org/mixs
keywords:
- soil
- type
slot_uri: MIXS:0000332
alias: soil_type
owner: MiuvigAgriculture
domain_of:
- Agriculture
- FoodFarmEnvironment
- Soil
range: string
required: true
soil_type_meth:
name: soil_type_meth
description: Reference or method used in determining soil series name or other
lower-level classification
title: soil type method
examples:
- value: https://www.lrh.usace.army.mil/Portals/38/docs/PR/BluestoneSFEIS/Appendix%20K-Soil%20Descriptions.pdf
from_schema: https://w3id.org/mixs
keywords:
- method
- soil
- type
slot_uri: MIXS:0000334
alias: soil_type_meth
owner: MiuvigAgriculture
domain_of:
- Agriculture
- FoodFarmEnvironment
- Soil
range: string
required: true
pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$
structured_pattern:
syntax: ^{PMID}|{DOI}|{URL}$
interpolated: true
partial_match: true
soil_horizon:
name: soil_horizon
description: Specific layer in the land area which measures parallel to the soil
surface and possesses physical characteristics which differ from the layers
above and beneath
title: soil horizon
examples:
- value: A horizon
from_schema: https://w3id.org/mixs
keywords:
- horizon
- soil
slot_uri: MIXS:0001082
alias: soil_horizon
owner: MiuvigAgriculture
domain_of:
- Agriculture
- Soil
range: SoilHorizonEnum
recommended: true
horizon_meth:
name: horizon_meth
description: Reference or method used in determining the horizon
title: horizon method
from_schema: https://w3id.org/mixs
keywords:
- horizon
- method
slot_uri: MIXS:0000321
alias: horizon_meth
owner: MiuvigAgriculture
domain_of:
- Agriculture
- Soil
range: string
recommended: true
pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$
structured_pattern:
syntax: ^{PMID}|{DOI}|{URL}$
interpolated: true
partial_match: true
link_class_info:
name: link_class_info
annotations:
Expected_value:
tag: Expected_value
value: PMID,DOI or url
description: Link to digitized soil maps or other soil classification information
title: link to classification information
from_schema: https://w3id.org/mixs
keywords:
- classification
- information
- link
string_serialization: '{termLabel} [{termID}]'
slot_uri: MIXS:0000329
alias: link_class_info
owner: MiuvigAgriculture
domain_of:
- Agriculture
- Soil
range: string
previous_land_use:
name: previous_land_use
annotations:
Expected_value:
tag: Expected_value
value: land use name;date
description: Previous land use and dates
title: history/previous land use
examples:
- value: fallow; 2018-05-11:T14:30Z
from_schema: https://w3id.org/mixs
keywords:
- history
- land
- use
string_serialization: '{text};{timestamp}'
slot_uri: MIXS:0000315
alias: previous_land_use
owner: MiuvigAgriculture
domain_of:
- Agriculture
- FoodFarmEnvironment
- Soil
range: string
recommended: true
prev_land_use_meth:
name: prev_land_use_meth
description: Reference or method used in determining previous land use and dates
title: history/previous land use method
from_schema: https://w3id.org/mixs
keywords:
- history
- land
- method
- use
slot_uri: MIXS:0000316
alias: prev_land_use_meth
owner: MiuvigAgriculture
domain_of:
- Agriculture
- Soil
range: string
recommended: true
pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$
structured_pattern:
syntax: ^{PMID}|{DOI}|{URL}$
interpolated: true
partial_match: true
crop_rotation:
name: crop_rotation
annotations:
Expected_value:
tag: Expected_value
value: crop rotation status;schedule
description: Whether or not crop is rotated, and if yes, rotation schedule
title: history/crop rotation
examples:
- value: yes;R2/2017-01-01/2018-12-31/P6M
from_schema: https://w3id.org/mixs
keywords:
- history
string_serialization: '{boolean};Rn/{timestamp}/{period}'
slot_uri: MIXS:0000318
alias: crop_rotation
owner: MiuvigAgriculture
domain_of:
- Agriculture
- FoodFarmEnvironment
- Soil
range: string
recommended: true
agrochem_addition:
name: agrochem_addition
annotations:
Preferred_unit:
tag: Preferred_unit
value: gram, mole per liter, milligram per liter
description: Addition of fertilizers, pesticides, etc. - amount and time of applications
title: history/agrochemical additions
examples:
- value: roundup;5 milligram per liter;2018-06-21
from_schema: https://w3id.org/mixs
keywords:
- history
slot_uri: MIXS:0000639
alias: agrochem_addition
owner: MiuvigAgriculture
domain_of:
- Agriculture
- Soil
range: string
multivalued: true
structured_pattern:
syntax: ^{agrochemical_name};{amount} {unit};{date_time_stamp}$
interpolated: true
partial_match: true
tillage:
name: tillage
description: Note method(s) used for tilling
title: history/tillage
examples:
- value: chisel
from_schema: https://w3id.org/mixs
keywords:
- history
slot_uri: MIXS:0001081
alias: tillage
owner: MiuvigAgriculture
domain_of:
- Agriculture
- FoodFarmEnvironment
- Soil
range: TillageEnum
recommended: true
multivalued: true
fire:
name: fire
description: Historical and/or physical evidence of fire
title: history/fire
from_schema: https://w3id.org/mixs
keywords:
- history
slot_uri: MIXS:0001086
alias: fire
owner: MiuvigAgriculture
domain_of:
- Agriculture
- Soil
range: datetime
recommended: true
flooding:
name: flooding
description: Historical and/or physical evidence of flooding
title: history/flooding
from_schema: https://w3id.org/mixs
keywords:
- history
slot_uri: MIXS:0000319
alias: flooding
owner: MiuvigAgriculture
domain_of:
- Agriculture
- Soil
range: datetime
recommended: true
extreme_event:
name: extreme_event
description: Unusual physical events that may have affected microbial populations
title: history/extreme events
from_schema: https://w3id.org/mixs
keywords:
- event
- history
slot_uri: MIXS:0000320
alias: extreme_event
owner: MiuvigAgriculture
domain_of:
- Agriculture
- Soil
range: datetime
recommended: true
link_climate_info:
name: link_climate_info
description: Link to climate resource
title: link to climate information
from_schema: https://w3id.org/mixs
keywords:
- information
- link
slot_uri: MIXS:0000328
alias: link_climate_info
owner: MiuvigAgriculture
domain_of:
- Agriculture
- Soil
range: string
pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$
structured_pattern:
syntax: ^{PMID}|{DOI}|{URL}$
interpolated: true
partial_match: true
annual_temp:
name: annual_temp
annotations:
Preferred_unit:
tag: Preferred_unit
value: degree Celsius
description: Mean annual temperature
title: mean annual temperature
examples:
- value: 12.5 degree Celsius
from_schema: https://w3id.org/mixs
keywords:
- mean
- temperature
slot_uri: MIXS:0000642
alias: annual_temp
owner: MiuvigAgriculture
domain_of:
- Agriculture
- Soil
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
*([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
structured_pattern:
syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
interpolated: true
partial_match: true
season_temp:
name: season_temp
annotations:
Preferred_unit:
tag: Preferred_unit
value: degree Celsius
description: Mean seasonal temperature
title: mean seasonal temperature
examples:
- value: 18 degree Celsius
from_schema: https://w3id.org/mixs
keywords:
- mean
- season
- temperature
slot_uri: MIXS:0000643
alias: season_temp
owner: MiuvigAgriculture
domain_of:
- Agriculture
- FoodFarmEnvironment
- Soil
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
*([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
structured_pattern:
syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
interpolated: true
partial_match: true
annual_precpt:
name: annual_precpt
annotations:
Preferred_unit:
tag: Preferred_unit
value: millimeter
description: The average of all annual precipitation values known, or an estimated
equivalent value derived by such methods as regional indexes or Isohyetal maps
title: mean annual precipitation
from_schema: https://w3id.org/mixs
keywords:
- mean
slot_uri: MIXS:0000644
alias: annual_precpt
owner: MiuvigAgriculture
domain_of:
- Agriculture
- Soil
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
*([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
structured_pattern:
syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
interpolated: true
partial_match: true
season_precpt:
name: season_precpt
annotations:
Preferred_unit:
tag: Preferred_unit
value: millimeter
description: The average of all seasonal precipitation values known, or an estimated
equivalent value derived by such methods as regional indexes or Isohyetal maps
title: mean seasonal precipitation
examples:
- value: 75 millimeters
from_schema: https://w3id.org/mixs
keywords:
- mean
- season
slot_uri: MIXS:0000645
alias: season_precpt
owner: MiuvigAgriculture
domain_of:
- Agriculture
- FoodFarmEnvironment
- Soil
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
*([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
structured_pattern:
syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
interpolated: true
partial_match: true
cur_land_use:
name: cur_land_use
annotations:
Expected_value:
tag: Expected_value
value: enumeration
description: Present state of sample site
title: current land use
examples:
- value: conifers
from_schema: https://w3id.org/mixs
keywords:
- land
- use
string_serialization: '[cities|farmstead|industrial areas|roads/railroads|rock|sand|gravel|mudflats|salt
flats|badlands|permanent snow or ice|saline seeps|mines/quarries|oil waste areas|small
grains|row crops|vegetable crops|horticultural plants (e.g. tulips)|marshlands
(grass,sedges,rushes)|tundra (mosses,lichens)|rangeland|pastureland (grasslands
used for livestock grazing)|hayland|meadows (grasses,alfalfa,fescue,bromegrass,timothy)|shrub
land (e.g. mesquite,sage-brush,creosote bush,shrub oak,eucalyptus)|successional
shrub land (tree saplings,hazels,sumacs,chokecherry,shrub dogwoods,blackberries)|shrub
crops (blueberries,nursery ornamentals,filberts)|vine crops (grapes)|conifers
(e.g. pine,spruce,fir,cypress)|hardwoods (e.g. oak,hickory,elm,aspen)|intermixed
hardwood and conifers|tropical (e.g. mangrove,palms)|rainforest (evergreen forest
receiving >406 cm annual rainfall)|swamp (permanent or semi-permanent water
body dominated by woody plants)|crop trees (nuts,fruit,christmas trees,nursery
trees)]'
slot_uri: MIXS:0001080
alias: cur_land_use
owner: MiuvigAgriculture
domain_of:
- Agriculture
- Soil
range: string
slope_gradient:
name: slope_gradient
annotations:
Preferred_unit:
tag: Preferred_unit
value: percentage
description: 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
title: slope gradient
from_schema: https://w3id.org/mixs
keywords:
- slope
slot_uri: MIXS:0000646
alias: slope_gradient
owner: MiuvigAgriculture
domain_of:
- Agriculture
- Soil
range: string
recommended: true
pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
*([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
structured_pattern:
syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
interpolated: true
partial_match: true
slope_aspect:
name: slope_aspect
annotations:
Preferred_unit:
tag: Preferred_unit
value: degree
description: 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
title: slope aspect
from_schema: https://w3id.org/mixs
keywords:
- slope
slot_uri: MIXS:0000647
alias: slope_aspect
owner: MiuvigAgriculture
domain_of:
- Agriculture
- Soil
range: string
recommended: true
pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
*([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
structured_pattern:
syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
interpolated: true
partial_match: true
profile_position:
name: profile_position
description: Cross-sectional position in the hillslope where sample was collected.sample
area position in relation to surrounding areas
title: profile position
examples:
- value: summit
from_schema: https://w3id.org/mixs
slot_uri: MIXS:0001084
alias: profile_position
owner: MiuvigAgriculture
domain_of:
- Agriculture
- Soil
range: ProfilePositionEnum
recommended: true
drainage_class:
name: drainage_class
description: Drainage classification from a standard system such as the USDA system
title: drainage classification
examples:
- value: well
from_schema: https://w3id.org/mixs
keywords:
- classification
slot_uri: MIXS:0001085
alias: drainage_class
owner: MiuvigAgriculture
domain_of:
- Agriculture
- Soil
range: DrainageClassEnum
recommended: true
store_cond:
name: store_cond
annotations:
Expected_value:
tag: Expected_value
value: storage condition type;duration
description: Explain how and for how long the soil sample was stored before DNA
extraction (fresh/frozen/other)
title: storage conditions
examples:
- value: -20 degree Celsius freezer;P2Y10D
from_schema: https://w3id.org/mixs
keywords:
- condition
- storage
string_serialization: '{text};{period}'
slot_uri: MIXS:0000327
alias: store_cond
owner: MiuvigAgriculture
domain_of:
- Agriculture
- Soil
range: string
required: true
ph_meth:
name: ph_meth
description: Reference or method used in determining pH
title: pH method
examples:
- value: https://www.epa.gov/sites/production/files/2015-12/documents/9040c.pdf
from_schema: https://w3id.org/mixs
keywords:
- method
- ph
slot_uri: MIXS:0001106
alias: ph_meth
owner: MiuvigAgriculture
domain_of:
- Agriculture
- FoodFarmEnvironment
- Soil
range: string
recommended: true
pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$
structured_pattern:
syntax: ^{PMID}|{DOI}|{URL}$
interpolated: true
partial_match: true
cur_vegetation:
name: cur_vegetation
annotations:
Expected_value:
tag: Expected_value
value: current vegetation type
description: Vegetation classification from one or more standard classification
systems, or agricultural crop
title: current vegetation
from_schema: https://w3id.org/mixs
keywords:
- vegetation
slot_uri: MIXS:0000312
alias: cur_vegetation
owner: MiuvigAgriculture
domain_of:
- Agriculture
- Soil
range: string
recommended: true
cur_vegetation_meth:
name: cur_vegetation_meth
description: Reference or method used in vegetation classification
title: current vegetation method
from_schema: https://w3id.org/mixs
keywords:
- method
- vegetation
slot_uri: MIXS:0000314
alias: cur_vegetation_meth
owner: MiuvigAgriculture
domain_of:
- Agriculture
- Soil
range: string
recommended: true
pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$
structured_pattern:
syntax: ^{PMID}|{DOI}|{URL}$
interpolated: true
partial_match: true
tot_org_carb:
name: tot_org_carb
annotations:
Preferred_unit:
tag: Preferred_unit
value: gram Carbon per kilogram sample material
description: Total organic carbon content
title: total organic carbon
examples:
- value: '0.02'
from_schema: https://w3id.org/mixs
keywords:
- carbon
- organic
- total
slot_uri: MIXS:0000533
alias: tot_org_carb
owner: MiuvigAgriculture
domain_of:
- Agriculture
- FoodFarmEnvironment
- MicrobialMatBiofilm
- Sediment
- Soil
range: string
recommended: true
pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
*([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
structured_pattern:
syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
interpolated: true
partial_match: true
tot_org_c_meth:
name: tot_org_c_meth
description: Reference or method used in determining total organic carbon
title: total organic carbon method
examples:
- value: https://www.epa.gov/sites/production/files/2015-12/documents/9060a.pdf
from_schema: https://w3id.org/mixs
keywords:
- carbon
- method
- organic
- total
slot_uri: MIXS:0000337
alias: tot_org_c_meth
owner: MiuvigAgriculture
domain_of:
- Agriculture
- FoodFarmEnvironment
- Soil
range: string
recommended: true
pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$
structured_pattern:
syntax: ^{PMID}|{DOI}|{URL}$
interpolated: true
partial_match: true
tot_nitro_content:
name: tot_nitro_content
description: Total nitrogen content of the sample
title: total nitrogen content
examples:
- value: 35 milligrams Nitrogen per kilogram of soil
from_schema: https://w3id.org/mixs
keywords:
- content
- nitrogen
- total
slot_uri: MIXS:0000530
alias: tot_nitro_content
owner: MiuvigAgriculture
domain_of:
- Agriculture
- FoodFarmEnvironment
- MicrobialMatBiofilm
- Sediment
- Soil
range: string
recommended: true
pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
*([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
structured_pattern:
syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
interpolated: true
partial_match: true
tot_nitro_cont_meth:
name: tot_nitro_cont_meth
description: Reference or method used in determining the total nitrogen
title: total nitrogen content method
examples:
- value: https://currentprotocols.onlinelibrary.wiley.com/doi/abs/10.1002/0471142913.fab0102s00
from_schema: https://w3id.org/mixs
keywords:
- content
- method
- nitrogen
- total
slot_uri: MIXS:0000338
alias: tot_nitro_cont_meth
owner: MiuvigAgriculture
domain_of:
- Agriculture
- FoodFarmEnvironment
- Soil
range: string
recommended: true
pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$
structured_pattern:
syntax: ^{PMID}|{DOI}|{URL}$
interpolated: true
partial_match: true
microbial_biomass:
name: microbial_biomass
annotations:
Preferred_unit:
tag: Preferred_unit
value: ton, kilogram, gram per kilogram soil
description: 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
title: microbial biomass
from_schema: https://w3id.org/mixs
keywords:
- biomass
- microbial
slot_uri: MIXS:0000650
alias: microbial_biomass
owner: MiuvigAgriculture
domain_of:
- Agriculture
- Soil
range: string
required: true
pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
*([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
structured_pattern:
syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
interpolated: true
partial_match: true
micro_biomass_meth:
name: micro_biomass_meth
description: Reference or method used in determining microbial biomass
title: microbial biomass method
comments:
- slot name/scn was microbial_biomass_meth
examples:
- value: http://dx.doi.org/10.1016/j.soilbio.2005.01.021
from_schema: https://w3id.org/mixs
keywords:
- biomass
- method
- microbial
slot_uri: MIXS:0000339
alias: micro_biomass_meth
owner: MiuvigAgriculture
domain_of:
- Agriculture
- Soil
range: string
required: true
pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$
structured_pattern:
syntax: ^{PMID}|{DOI}|{URL}$
interpolated: true
partial_match: true
heavy_metals_meth:
name: heavy_metals_meth
description: Reference or method used in determining heavy metals
title: extreme_unusual_properties/heavy metals method
from_schema: https://w3id.org/mixs
keywords:
- extreme
- method
- properties
- unusual
string_serialization: '{PMID|DOI|URL}'
slot_uri: MIXS:0000343
alias: heavy_metals_meth
owner: MiuvigAgriculture
domain_of:
- Agriculture
- Soil
range: string
recommended: true
pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$
structured_pattern:
syntax: ^{PMID}|{DOI}|{URL}$
interpolated: true
partial_match: true
tot_carb:
name: tot_carb
description: Total carbon content
title: total carbon
from_schema: https://w3id.org/mixs
keywords:
- carbon
- total
slot_uri: MIXS:0000525
alias: tot_carb
owner: MiuvigAgriculture
domain_of:
- Agriculture
- MicrobialMatBiofilm
- Sediment
range: string
recommended: true
pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
*([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
structured_pattern:
syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
interpolated: true
partial_match: true
tot_phosphate:
name: tot_phosphate
annotations:
Preferred_unit:
tag: Preferred_unit
value: microgram per liter, micromole per liter
description: Total amount or concentration of phosphate
title: total phosphate
from_schema: https://w3id.org/mixs
keywords:
- phosphate
- total
slot_uri: MIXS:0000689
alias: tot_phosphate
owner: MiuvigAgriculture
domain_of:
- Agriculture
- WastewaterSludge
range: string
recommended: true
pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
*([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
structured_pattern:
syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
interpolated: true
partial_match: true
sieving:
name: sieving
annotations:
Expected_value:
tag: Expected_value
value: design name and/or size;amount
description: Collection design of pooled samples and/or sieve size and amount
of sample sieved
title: sieving
from_schema: https://w3id.org/mixs
string_serialization: '{text};{float} {unit}'
slot_uri: MIXS:0000322
alias: sieving
owner: MiuvigAgriculture
domain_of:
- Agriculture
- Soil
range: string
required: true
pool_dna_extracts:
name: pool_dna_extracts
annotations:
Expected_value:
tag: Expected_value
value: pooling status;number of pooled extracts
Preferred_unit:
tag: Preferred_unit
value: gram, milliliter, microliter
description: Indicate whether multiple DNA extractions were mixed. If the answer
yes, the number of extracts that were pooled should be given
title: pooling of DNA extracts (if done)
examples:
- value: yes, 5
from_schema: https://w3id.org/mixs
keywords:
- dna
- pooling
string_serialization: '{boolean};{float} {unit}'
slot_uri: MIXS:0000325
alias: pool_dna_extracts
owner: MiuvigAgriculture
domain_of:
- Agriculture
- FoodAnimalAndAnimalFeed
- FoodFoodProductionFacility
- FoodHumanFoods
- Soil
range: string
required: true
misc_param:
name: misc_param
annotations:
Expected_value:
tag: Expected_value
value: parameter name;measurement value
description: Any other measurement performed or parameter collected, that is not
listed here
title: miscellaneous parameter
examples:
- value: Bicarbonate ion concentration;2075 micromole per kilogram
from_schema: https://w3id.org/mixs
keywords:
- parameter
string_serialization: '{text};{float} {unit}'
slot_uri: MIXS:0000752
alias: misc_param
owner: MiuvigAgriculture
domain_of:
- Agriculture
- Air
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodFoodProductionFacility
- FoodHumanFoods
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- HydrocarbonResourcesCores
- HydrocarbonResourcesFluidsSwabs
- MicrobialMatBiofilm
- MiscellaneousNaturalOrArtificialEnvironment
- PlantAssociated
- Sediment
- Soil
- SymbiontAssociated
- WastewaterSludge
- Water
range: string
multivalued: true
class_uri: MIXS:0010012_0016018