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AgricultureMIGSPlant

Combinatorial checklist Minimal Information about a Genome Sequence: plant with environmental package agriculture

URI: mixs.vocab:AgricultureMIGSPlant

Inheritance

Slots

MIxS ID Name Multiplicity Description Pattern Info
MIXS:0001107 samp_name 1..1 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. None .
MIXS:0001320 samp_taxon_id 1..1 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. None .
MIXS:0000092 project_name 1..1 Name of the project within which the sequencing was organized None .
MIXS:0000008 experimental_factor 0..1 Experimental factors are essentially the variable aspects of an experiment design which 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). For a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO; for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI None .
MIXS:0000009 lat_lon 1..1 The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system None .
MIXS:0000018 depth 0..1 The vertical distance below local surface, e.g. for sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. None .
MIXS:0000094 alt 0..1 Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air None .
MIXS:0000093 elev 0..1 Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit. None .
MIXS:0000113 temp 1..1 Temperature of the sample at the time of sampling. None .
MIXS:0000010 geo_loc_name 1..1 The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (http://purl.bioontology.org/ontology/GAZ) None .
MIXS:0000011 collection_date 1..1 The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant None .
MIXS:0001321 neg_cont_type 0..1 recommended RECOMMENDED The substance or equipment used as a negative control in an investigation None .
MIXS:0001322 pos_cont_type 0..1 recommended RECOMMENDED The substance, mixture, product, or apparatus used to verify that a process which is part of an investigation delivers a true positive. None .
MIXS:0000012 env_broad_scale 1..1 Report the major environmental system the sample or specimen came from. The system(s) identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. in the desert or a rainforest). We recommend using subclasses of EnvO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS None .
MIXS:0000013 env_local_scale 1..1 Report the entity or entities which are in the sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. We recommend using EnvO terms which are of smaller spatial grain than your entry for env_broad_scale. Terms, such as anatomical sites, from other OBO Library ontologies which interoperate with EnvO (e.g. UBERON) are accepted in this field. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS. None .
MIXS:0000014 env_medium 1..1 Report the environmental material(s) immediately surrounding the sample or specimen at the time of sampling. We recommend using subclasses of 'environmental material' (http://purl.obolibrary.org/obo/ENVO_00010483). EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS . Terms from other OBO ontologies are permissible as long as they reference mass/volume nouns (e.g. air, water, blood) and not discrete, countable entities (e.g. a tree, a leaf, a table top). None .
MIXS:0000020 subspecf_gen_lin 0..1 recommended RECOMMENDED Information about the genetic distinctness of the sequenced organism below the subspecies level, e.g., serovar, serotype, biotype, ecotype, or any relevant genetic typing schemes like Group I plasmid. Subspecies should not be recorded in this term, but in the NCBI taxonomy. Supply both the lineage name and the lineage rank separated by a colon, e.g., biovar:abc123. None .
MIXS:0000021 ploidy 0..1 The ploidy level of the genome (e.g. allopolyploid, haploid, diploid, triploid, tetraploid). It has implications for the downstream study of duplicated gene and regions of the genomes (and perhaps for difficulties in assembly). For terms, please select terms listed under class ploidy (PATO:001374) of Phenotypic Quality Ontology (PATO), and for a browser of PATO (v 2018-03-27) please refer to http://purl.bioontology.org/ontology/PATO None .
MIXS:0000022 num_replicons 0..1 Reports the number of replicons in a nuclear genome of eukaryotes, in the genome of a bacterium or archaea or the number of segments in a segmented virus. Always applied to the haploid chromosome count of a eukaryote None .
MIXS:0000023 extrachrom_elements 0..1 Do plasmids exist of significant phenotypic consequence (e.g. ones that determine virulence or antibiotic resistance). Megaplasmids? Other plasmids (borrelia has 15+ plasmids) None .
MIXS:0000024 estimated_size 0..1 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. None .
MIXS:0000025 ref_biomaterial 0..1 Primary publication if isolated before genome publication; otherwise, primary genome report. None .
MIXS:0000026 source_mat_id 0..1 recommended RECOMMENDED 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). None .
MIXS:0000027 pathogenicity 1..1 To what is the entity pathogenic None .
MIXS:0000028 biotic_relationship 0..1 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 None .
MIXS:0000029 specific_host 1..1 recommended RECOMMENDED Report the host's taxonomic name and/or NCBI taxonomy ID. None .
MIXS:0000030 host_spec_range 1..1 The range and diversity of host species that an organism is capable of infecting, defined by NCBI taxonomy identifier. None .
MIXS:0000031 host_disease_stat 0..1 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 None .
MIXS:0000032 trophic_level 0..1 Trophic levels are the feeding position in a food chain. Microbes can be a range of producers (e.g. chemolithotroph) None .
MIXS:0000033 propagation 1..1 The type of reproduction from the parent stock. Values for this field is specific to different taxa. For phage or virus: lytic/lysogenic/temperate/obligately lytic. For plasmids: incompatibility group. For eukaryotes: sexual/asexual. None .
MIXS:0000034 encoded_traits 0..1 recommended RECOMMENDED Should include key traits like antibiotic resistance or xenobiotic degradation phenotypes for plasmids, converting genes for phage None .
MIXS:0000015 rel_to_oxygen 0..1 Is this organism an aerobe, anaerobe? Please note that aerobic and anaerobic are valid descriptors for microbial environments None .
MIXS:0000003 isol_growth_condt 1..1 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 None .
MIXS:0000002 samp_collec_device 0..1 The device used to collect an environmental sample. This field accepts terms listed under environmental sampling device (http://purl.obolibrary.org/obo/ENVO). This field also accepts terms listed under specimen collection device (http://purl.obolibrary.org/obo/GENEPIO_0002094). None .
MIXS:0001225 samp_collec_method 0..1 The method employed for collecting the sample. None .
MIXS:0000016 samp_mat_process 1..1 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. None .
MIXS:0000017 size_frac 0..1 Filtering pore size used in sample preparation None .
MIXS:0000001 samp_size 1..1 The total amount or size (volume (ml), mass (g) or area (m2) ) of sample collected. None .
MIXS:0000111 samp_vol_we_dna_ext 1..1 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). None .
MIXS:0000035 source_uvig 0..1 Type of dataset from which the UViG was obtained None .
MIXS:0000036 virus_enrich_appr 0..1 List of approaches used to enrich the sample for viruses, if any None .
MIXS:0000037 nucl_acid_ext 1..1 recommended RECOMMENDED 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 None .
MIXS:0000038 nucl_acid_amp 1..1 recommended RECOMMENDED 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 None .
MIXS:0000039 lib_size 0..1 Total number of clones in the library prepared for the project None .
MIXS:0000040 lib_reads_seqd 1..1 Total number of clones sequenced from the library None .
MIXS:0000041 lib_layout 0..1 Specify whether to expect single, paired, or other configuration of reads None .
MIXS:0000042 lib_vector 1..1 Cloning vector type(s) used in construction of libraries None .
MIXS:0000043 lib_screen 1..1 Specific enrichment or screening methods applied before and/or after creating libraries None .
MIXS:0000044 target_gene 1..1 Targeted gene or locus name for marker gene studies None .
MIXS:0000045 target_subfragment 1..1 Name of subfragment of a gene or locus. Important to e.g. identify special regions on marker genes like V6 on 16S rRNA None .
MIXS:0000046 pcr_primers 1..1 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 None .
MIXS:0000047 mid 1..1 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 None .
MIXS:0000048 adapters 1..1 recommended RECOMMENDED Adapters provide priming sequences for both amplification and sequencing of the sample-library fragments. Both adapters should be reported; in uppercase letters None .
MIXS:0000049 pcr_cond 1..1 Description of reaction conditions and components of PCR in the form of 'initial denaturation:94degC_1.5min; annealing=...' None .
MIXS:0000050 seq_meth 1..1 Sequencing machine used. Where possible the term should be taken from the OBI list of DNA sequencers (http://purl.obolibrary.org/obo/OBI_0400103). None .
MIXS:0000051 seq_quality_check 0..1 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 None .
MIXS:0000052 chimera_check 1..1 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. None .
MIXS:0000053 tax_ident 0..1 recommended RECOMMENDED The phylogenetic marker(s) used to assign an organism name to the SAG or MAG None .
MIXS:0000056 assembly_qual 0..1 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 23S, 16S and 5S rRNA genes and at least 18 tRNAs. 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 None .
MIXS:0000057 assembly_name 1..1 recommended RECOMMENDED Name/version of the assembly provided by the submitter that is used in the genome browsers and in the community None .
MIXS:0000058 assembly_software 1..1 Tool(s) used for assembly, including version number and parameters None .
MIXS:0000059 annot 0..1 recommended RECOMMENDED 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 None .
MIXS:0000060 number_contig 0..1 Total number of contigs in the cleaned/submitted assembly that makes up a given genome, SAG, MAG, or UViG None .
MIXS:0000061 feat_pred 0..1 Method used to predict UViGs features such as ORFs, integration site, etc. None .
MIXS:0000062 ref_db 0..1 List of database(s) used for ORF annotation, along with version number and reference to website or publication None .
MIXS:0000063 sim_search_meth 0..1 Tool used to compare ORFs with database, along with version and cutoffs used None .
MIXS:0000064 tax_class 0..1 Method used for taxonomic classification, along with reference database used, classification rank, and thresholds used to classify new genomes None .
MIXS:0000065 x_16s_recover 0..1 Can a 16S gene be recovered from the submitted SAG or MAG? None .
MIXS:0000066 x_16s_recover_software 0..1 Tools used for 16S rRNA gene extraction None .
MIXS:0000067 trnas 0..1 The total number of tRNAs identified from the SAG or MAG None .
MIXS:0000068 trna_ext_software 0..1 Tools used for tRNA identification None .
MIXS:0000069 compl_score 0..1 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 None .
MIXS:0000070 compl_software 0..1 Tools used for completion estimate, i.e. checkm, anvi'o, busco None .
MIXS:0000071 compl_appr 0..1 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 None .
MIXS:0000072 contam_score 0..1 The contamination score is based on the fraction of single-copy genes that are observed more than once in a query genome. The following scores are acceptable for; High Quality Draft: < 5%, Medium Quality Draft: < 10%, Low Quality Draft: < 10%. Contamination must be below 5% for a SAG or MAG to be deposited into any of the public databases None .
MIXS:0000005 contam_screen_input 0..1 The type of sequence data used as input None .
MIXS:0000073 contam_screen_param 0..1 Specific parameters used in the decontamination sofware, such as reference database, coverage, and kmers. Combinations of these parameters may also be used, i.e. kmer and coverage, or reference database and kmer None .
MIXS:0000074 decontam_software 0..1 Tool(s) used in contamination screening None .
MIXS:0000075 sort_tech 0..1 Method used to sort/isolate cells or particles of interest None .
MIXS:0000076 single_cell_lysis_appr 0..1 Method used to free DNA from interior of the cell(s) or particle(s) None .
MIXS:0000054 single_cell_lysis_prot 0..1 Name of the kit or standard protocol used for cell(s) or particle(s) lysis None .
MIXS:0000055 wga_amp_appr 0..1 Method used to amplify genomic DNA in preparation for sequencing None .
MIXS:0000006 wga_amp_kit 0..1 Kit used to amplify genomic DNA in preparation for sequencing None .
MIXS:0000077 bin_param 0..1 The parameters that have been applied during the extraction of genomes from metagenomic datasets None .
MIXS:0000078 bin_software 0..1 Tool(s) used for the extraction of genomes from metagenomic datasets, where possible include a product ID (PID) of the tool(s) used. None .
MIXS:0000079 reassembly_bin 0..1 Has an assembly been performed on a genome bin extracted from a metagenomic assembly? None .
MIXS:0000080 mag_cov_software 0..1 Tool(s) used to determine the genome coverage if coverage is used as a binning parameter in the extraction of genomes from metagenomic datasets None .
MIXS:0000081 vir_ident_software 0..1 Tool(s) used for the identification of UViG as a viral genome, software or protocol name including version number, parameters, and cutoffs used None .
MIXS:0000082 pred_genome_type 0..1 Type of genome predicted for the UViG None .
MIXS:0000083 pred_genome_struc 0..1 Expected structure of the viral genome None .
MIXS:0000084 detec_type 0..1 Type of UViG detection None .
MIXS:0000085 otu_class_appr 0..1 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 None .
MIXS:0000086 otu_seq_comp_appr 0..1 Tool and thresholds used to compare sequences when computing "species-level" OTUs None .
MIXS:0000087 otu_db 0..1 Reference database (i.e. sequences not generated as part of the current study) used to cluster new genomes in "species-level" OTUs, if any None .
MIXS:0000088 host_pred_appr 0..1 Tool or approach used for host prediction None .
MIXS:0000089 host_pred_est_acc 0..1 For each tool or approach used for host prediction, estimated false discovery rates should be included, either computed de novo or from the literature None .
MIXS:0000091 associated_resource 0..1 recommended RECOMMENDED A related resource that is referenced, cited, or otherwise associated to the sequence. None .
MIXS:0000090 sop 0..1 recommended RECOMMENDED Standard operating procedures used in assembly and/or annotation of genomes, metagenomes or environmental sequences None .
MIXS:0000753 oxy_stat_samp 0..1 Oxygenation status of sample. None .
MIXS:0000819 pres_animal_insect 0..1 The type and number of animals or insects present in the sampling space. None .
MIXS:0001080 cur_land_use 0..1 Present state of sample site None .
MIXS:0001081 tillage 0..* Note method(s) used for tilling None .
MIXS:0001110 farm_water_source 0..* Source of water used on the farm for irrigation of crops or watering of livestock. None .
MIXS:0001176 water_source_shared 0..* Other users sharing access to the same water source. Multiple terms can be separated by one or more pipes. None .
MIXS:0001082 horizon 0..1 Specific layer in the land area which measures parallel to the soil surface and possesses physical characteristics which differ from the layers above and beneath None .
MIXS:0001084 profile_position 0..1 Cross-sectional position in the hillslope where sample was collected.sample area position in relation to surrounding areas None .
MIXS:0001085 drainage_class 0..1 Drainage classification from a standard system such as the USDA system None .
MIXS:0000322 sieving 1..1 Collection design of pooled samples and/or sieve size and amount of sample sieved None .
MIXS:0000325 pool_dna_extracts 1..* Indicate whether multiple DNA extractions were mixed. If the answer yes, the number of extracts that were pooled should be given. None .
MIXS:0000318 crop_rotation 0..1 Whether or not crop is rotated, and if yes, rotation schedule None .
MIXS:0001062 root_med_ph 0..1 pH measurement of the culture rooting medium; e.g. 5.5. None .
MIXS:0001175 water_pH 0..1 pH measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid. None .
MIXS:0000211 porosity 0..1 Porosity of deposited sediment is volume of voids divided by the total volume of sample None .
MIXS:0000644 annual_precpt 0..1 The average of all annual precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps. None .
MIXS:0000642 annual_temp 0..1 Mean annual temperature None .
MIXS:0000255 host_age 1..1 Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees None .
MIXS:0000257 host_dry_mass 0..1 Measurement of dry mass None .
MIXS:0000264 host_height 1..1 The height of subject None .
MIXS:0000256 host_length 1..1 The length of subject None .
MIXS:0000263 host_tot_mass 1..1 Total mass of the host at collection, the unit depends on host None .
MIXS:0000100 humidity 0..1 Amount of water vapour in the air, at the time of sampling None .
MIXS:0000650 microbial_biomass 1..1 The part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer. If you keep this, you would need to have correction factors used for conversion to the final units None .
MIXS:0001296 photosynt_activ 0..* Measurement of photosythetic activity (i.e. leaf gas exchange / chlorophyll fluorescence emissions / reflectance / transpiration) Please also include the term method term detailing the method of activity measurement. None .
MIXS:0000110 samp_stor_temp 0..1 Temperature at which sample was stored, e.g. -80 degree Celsius. None .
MIXS:0001148 season_humidity 0..1 Average humidity of the region throughout the growing season. None .
MIXS:0000645 season_precpt 0..1 The average of all seasonal precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps. None .
MIXS:0000643 season_temp 0..1 Mean seasonal temperature None .
MIXS:0000735 size_frac_low 0..1 Refers to the mesh/pore size used to pre-filter/pre-sort the sample. Materials larger than the size threshold are excluded from the sample None .
MIXS:0000736 size_frac_up 0..1 Refers to the mesh/pore size used to retain the sample. Materials smaller than the size threshold are excluded from the sample None .
MIXS:0000647 slope_aspect 0..1 The direction a slope faces. While looking down a slope use a compass to record the direction you are facing (direction or degrees); e.g., nw or 315 degrees. This measure provides an indication of sun and wind exposure that will influence soil temperature and evapotranspiration. None .
MIXS:0000646 slope_gradient 0..1 Commonly called 'slope'. The angle between ground surface and a horizontal line (in percent). This is the direction that overland water would flow. This measure is usually taken with a hand level meter or clinometer None .
MIXS:0000018 soil_depth 0..1 The vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. None .
MIXS:0000112 solar_irradiance 0..1 The amount of solar energy that arrives at a specific area of a surface during a specific time interval None .
MIXS:0000335 texture 0..1 The relative proportion of different grain sizes of mineral particles in a soil, as described using a standard system; express as % sand (50 um to 2 mm), silt (2 um to 50 um), and clay (<2 um) with textural name (e.g., silty clay loam) optional. None .
MIXS:0000525 tot_car 0..1 Total carbon content None .
MIXS:0000102 tot_nitro 0..1 Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen None .
MIXS:0000533 tot_org_carb 0..1 Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content None .
MIXS:0000689 tot_phos 0..1 Total amount or concentration of phosphate None .
MIXS:0000590 water_temp_regm 0..* Information about treatment involving an exposure to water with varying degree of temperature, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens None .
MIXS:0000591 watering_regm 0..* Information about treatment involving an exposure to watering frequencies, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens None .
MIXS:0001056 ph_regm 0..* Information about treatment involving exposure of plants to varying levels of ph of the growth media, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimen None .
MIXS:0001116 crop_yield 0..1 Amount of crop produced per unit or area of land. None .
MIXS:0001163 soil_temp 0..* Temperature of soil at the time of sampling. None .
MIXS:0000250 host_taxid 1..1 NCBI taxon id of the host. None .
MIXS:0001147 lot_number 0..* A distinctive alpha-numeric identification code assigned by the manufacturer or distributor to a specific quantity of manufactured material or product within a batch. Synonym: Batch Number. The submitter should provide lot number of the item followed by the item name for which the lot number was provided. None .
MIXS:0000116 samp_store_dur 1..1 Duration for which the sample was stored None .
MIXS:0000336 texture_meth 0..1 Reference or method used in determining soil texture. None .
MIXS:0001177 enrichment_protocol 0..1 The microbiological workflow or protocol followed to test for the presence or enumeration of the target microbial analyte(s). Please provide a PubMed or DOI reference for published protocols. None .
MIXS:0000859 genetic_mod 0..1 Genetic modifications of the genome of an organism, which may occur naturally by spontaneous mutation, or be introduced by some experimental means, e.g. specification of a transgene or the gene knocked-out or details of transient transfection. None .
MIXS:0001336 photosynt_activ_meth 0..* Reference or method used in measurement of photosythetic activity None .
MIXS:0001225 samp_collect_method 0..1 The method employed for collecting the sample. None .
MIXS:0000314 cur_vegetation_meth 0..1 Reference or method used in vegetation classification None .
MIXS:0000343 heavy_metals_meth 0..1 Reference or method used in determining heavy metals None .
MIXS:0000321 horizon_meth 0..1 Reference or method used in determining the horizon None .
MIXS:0000329 link_class_info 0..1 Link to digitized soil maps or other soil classification information None .
MIXS:0000328 link_climate_info 0..1 Link to climate resource None .
MIXS:0000331 local_class_meth 0..1 Reference or method used in determining the local soil classification None .
MIXS:0000339 microbial_biomass_meth 1..1 Reference or method used in determining microbial biomass None .
MIXS:0001106 ph_meth 0..1 Reference or method used in determining ph None .
MIXS:0000316 previous_land_use_meth 0..1 Reference or method used in determining previous land use and dates None .
MIXS:0000334 soil_type_meth 1..1 Reference or method used in determining soil series name or other lower-level classification None .
MIXS:0000338 tot_n_meth 0..1 Reference or method used in determining the total nitrogen None .
MIXS:0000337 tot_org_c_meth 0..1 Reference or method used in determining total organic carbon None .
MIXS:0001318 host_subspecf_genlin 0..* Information about the genetic distinctness of the host organism below the subspecies level e.g., serovar, serotype, biotype, ecotype, variety, cultivar, or any relevant genetic typing schemes like Group I plasmid. Subspecies should not be recorded in this term, but in the NCBI taxonomy. Supply both the lineage name and the lineage rank separated by a colon, e.g., biovar:abc123. None .
MIXS:0000058 assembly_quality 0..1 Tool(s) used for assembly, including version number and parameters None .
MIXS:0001083 fao_class 0..1 Soil classification from the FAO World Reference Database for Soil Resources. The list can be found at http://www.fao.org/nr/land/sols/soil/wrb-soil-maps/reference-groups None .
MIXS:0000874 host_phenotype 1..1 Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP. None .
MIXS:0001115 anim_water_method 0..* Description of the equipment or method used to distribute water to livestock. This field accepts termed listed under water delivery equipment (http://opendata.inra.fr/EOL/EOL_0001653). Multiple terms can be separated by pipes. None .
MIXS:0001126 farm_equip 0..* List of equipment used for planting, fertilization, harvesting, irrigation, land levelling, residue management, weeding or transplanting during the growing season. This field accepts terms listed under agricultural implement (http://purl.obolibrary.org/obo/AGRO_00000416). Multiple terms can be separated by pipes. None .
MIXS:0001127 fertilizer_admin 0..1 Type of fertilizer or amendment added to the soil or water for the purpose of improving substrate health and quality for plant growth. This field accepts terms listed under agronomic fertilizer (http://purl.obolibrary.org/obo/AGRO_00002062). Multiple terms may apply and can be separated by pipes, listing in reverse chronological order. None .
MIXS:0001211 food_prod 0..* Descriptors of the food production system or of the agricultural environment and growing conditions related to the farm production system, such as wild caught, organic, free-range, industrial, dairy, beef, domestic or cultivated food production. This field accepts terms listed under food production (http://purl.obolibrary.org/obo/FOODON_03530206). Multiple terms may apply and can be separated by pipes. None .
MIXS:0001137 food_trav_mode 0..* A descriptor for the method of movement of food commodity along the food distribution system. This field accepts terms listed under travel mode (http://purl.obolibrary.org/obo/GENEPIO_0001064). If the proper descrptor is not listed please use text to describe the mode of travel. Multiple terms can be separated by one or more pipes. None .
MIXS:0001060 plant_struc 0..1 Name of plant structure the sample was obtained from; for Plant Ontology (PO) (v releases/2017-12-14) terms, see http://purl.bioontology.org/ontology/PO, e.g. petiole epidermis (PO_0000051). If an individual flower is sampled, the sex of it can be recorded here. None .
MIXS:0001111 plant_water_method 0..1 Description of the equipment or method used to distribute water to crops. This field accepts termed listed under irrigation process (http://purl.obolibrary.org/obo/AGRO_00000006). Multiple terms can be separated by pipes. None .
MIXS:0000829 season 0..1 The season when sampling occurred. Any of the four periods into which the year is divided by the equinoxes and solstices. This field accepts terms listed under season (http://purl.obolibrary.org/obo/NCIT_C94729). None .
MIXS:0001057 plant_growth_med 0..1 Specification of the media for growing the plants or tissue cultured samples, e.g. soil, aeroponic, hydroponic, in vitro solid culture medium, in vitro liquid culture medium. Recommended value is a specific value from EO:plant growth medium (follow this link for terms http://purl.obolibrary.org/obo/EO_0007147) or other controlled vocabulary None .
MIXS:0000751 chem_administration 1..* List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi None .
MIXS:0001170 spikein_strain 0..* Taxonomic information about the spike-in organism(s) at the strain level. This field accepts terms under organism (http://purl.obolibrary.org/obo/NCIT_C14250). This field also accepts identification numbers from NCBI under https://www.ncbi.nlm.nih.gov/taxonomy. Multiple terms can be separated by pipes. None .
MIXS:0001121 adjacent_environment 0..* Description of the environmental system or features that are adjacent to the sampling site. This field accepts terms under ecosystem (http://purl.obolibrary.org/obo/ENVO_01001110) and human construction (http://purl.obolibrary.org/obo/ENVO_00000070). Multiple terms can be separated by pipes. None .
MIXS:0000247 ances_data 0..1 Information about either pedigree or other ancestral information description (e.g. parental variety in case of mutant or selection), e.g. A/3*B (meaning [(A x B) x B] x B) None .
MIXS:0000312 cur_vegetation 0..1 Vegetation classification from one or more standard classification systems, or agricultural crop None .
MIXS:0001184 Food_Product_type 0..1 new food product categories and food products themselves None .
MIXS:0001139 Food_source 1..1 Type of plant or animal from which the food product or its major ingredient is derived or a chemical food source [FDA CFSAN 1995]. None .
MIXS:0000248 host_common_name 1..1 Common name of the host. None .
MIXS:0000365 host_genotype 1..1 Observed genotype None .
MIXS:0000251 host_life_stage 1..1 Description of life stage of host None .
MIXS:0001298 host_symbiont 0..* The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. None .
MIXS:0001145 library_prep_kit 0..1 Packaged kits (containing adapters, indexes, enzymes, buffers etc.), tailored for specific sequencing workflows, which allow the simplified preparation of sequencing-ready libraries for small genomes, amplicons, and plasmids. None .
MIXS:0000330 local_class 0..1 Soil classification based on local soil classification system None .
MIXS:0001058 plant_product 0..1 Substance produced by the plant, where the sample was obtained from None .
MIXS:0000002 samp_collect_device 1..1 The device used to collect an environmental sample. This field accepts terms listed under environmental sampling device (http://purl.obolibrary.org/obo/ENVO). This field also accepts terms listed under specimen collection device (http://purl.obolibrary.org/obo/GENEPIO_0002094). None .
MIXS:0000755 samp_store_loc 1..1 Location at which sample was stored, usually name of a specific freezer/room None .
MIXS:0001156 sequencing_location 0..1 The location the sequencing run was performed. Indicate the name of the lab or core facility where samples were sequenced. None .
MIXS:0000332 soil_type 1..* Description of the soil type or classification. This field accepts terms under soil (http://purl.obolibrary.org/obo/ENVO_00001998). Multiple terms can be separated by pipes. None .
MIXS:0000752 misc_param 0..* Any other measurement performed or parameter collected, that is not listed here None .
MIXS:0000577 root_med_carbon 0..1 Source of organic carbon in the culture rooting medium; e.g. sucrose. None .
MIXS:0000578 root_med_macronutr 0..1 Measurement of the culture rooting medium macronutrients (N,P, K, Ca, Mg, S); e.g. KH2PO4 (170 mg/L). None .
MIXS:0000103 organism_count 0..* Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr). None .
MIXS:0000557 fungicide_regm 0..* Information about treatment involving use of fungicides; should include the name of fungicide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple fungicide regimens None .
MIXS:0000558 gaseous_environment 0..* Use of conditions with differing gaseous environments; should include the name of gaseous compound, amount administered, treatment duration, interval and total experimental duration; can include multiple gaseous environment regimens None .
MIXS:0000561 herbicide_regm 0..* Information about treatment involving use of herbicides; information about treatment involving use of growth hormones; should include the name of herbicide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens None .
MIXS:0000571 non_mineral_nutr_regm 0..* Information about treatment involving the exposure of plant to non-mineral nutrient such as oxygen, hydrogen or carbon; should include the name of non-mineral nutrient, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple non-mineral nutrient regimens None .
MIXS:0000573 pesticide_regm 0..* Information about treatment involving use of insecticides; should include the name of pesticide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple pesticide regimens None .
MIXS:0000582 salt_regm 0..* Information about treatment involving use of salts as supplement to liquid and soil growth media; should include the name of salt, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple salt regimens None .
MIXS:0000639 agrochem_addition 0..* Addition of fertilizers, pesticides, etc. - amount and time of applications None .
MIXS:0000754 perturbation 0..* Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types None .
MIXS:0000327 store_cond 1..1 Explain how and for how long the soil sample was stored before DNA extraction (fresh/frozen/other). None .
MIXS:0001040 climate_environment 0..* Treatment involving an exposure to a particular climate; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple climates None .
MIXS:0001068 season_environment 0..* Treatment involving an exposure to a particular season (e.g. Winter, summer, rabi, rainy etc.), treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment None .
MIXS:0001069 standing_water_regm 0..* Treatment involving an exposure to standing water during a plant's life span, types can be flood water or standing water, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens None .
MIXS:0000315 previous_land_use 0..1 Previous land use and dates None .
MIXS:0001138 food_trav_vehic 0..* A descriptor for the mobile machine which is used to transport food commodities along the food distribution system. This field accepts terms listed under vehicle (http://purl.obolibrary.org/obo/ENVO_01000604). If the proper descrptor is not listed please use text to describe the mode of travel. Multiple terms can be separated by one or more pipes. None .
MIXS:0000320 extreme_event 0..1 Unusual physical events that may have affected microbial populations None .
MIXS:0001086 fire 0..1 Historical and/or physical evidence of fire None .
MIXS:0000319 flooding 0..1 Historical and/or physical evidence of flooding None .
MIXS:0000091 url 0..* A related resource that is referenced, cited, or otherwise associated to the sequence. None .
MIXS:0001082 soil_horizon 0..1 Specific layer in the land area which measures parallel to the soil surface and possesses physical characteristics which differ from the layers above and beneath None .
MIXS:0001181 cult_isol_date 0..1 A culture isolation date is a date-time entity marking the end of a process in which a sample yields a positive result for the target microbial analyte(s) in the form of an isolated colony or colonies. None .
MIXS:0001124 farm_equip_san 0..* Method used to sanitize growing and harvesting equipment. This can including type and concentration of sanitizing solution. Multiple terms can be separated by one or more pipes. None .
MIXS:0001123 farm_equip_shared 0..* List of planting, growing or harvesting equipment shared with other farms. This field accepts terms listed under agricultural implement (http://purl.obolibrary.org/obo/AGRO_00000416). Multiple terms can be separated by pipes. None .
MIXS:0001133 food_harvest_proc 0..* A harvesting process is a process which takes in some food material from an individual or community of plant or animal organisms in a given context and time, and outputs a precursor or consumable food product. This may include a part of an organism or the whole, and may involve killing the organism. None .
MIXS:0001161 rel_location 0..1 Location of sampled soil to other parts of the farm e.g. under crop plant, near irrigation ditch, from the dirt road. None .
MIXS:0001153 samp_pooling 0..* Physical combination of several instances of like material, e.g. RNA extracted from samples or dishes of cell cultures into one big aliquot of cells. Please provide a short description of the samples that were pooled. None .
MIXS:0001158 soil_conductivity 0..1 Conductivity of soil at time of sampling. None .
MIXS:0001159 soil_cover 0..1 Description of the material covering the sampled soil. This field accepts terms under ENVO:00010483, environmental material. None .
MIXS:0001160 soil_pH 0..1 The pH of soil at time of sampling. None .

Usages

Identifier and Mapping Information