Class: miscellaneous natural or artificial environment MIUVIG
Combinatorial checklist Minimum Information About an Uncultivated Virus Genome with environmental package miscellaneous natural or artificial environment
URI: mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMIUVIG
Parents
- is_a: MiscellaneousNaturalOrArtificialEnvironment - miscellaneous natural or artificial environment
Uses Mixin
- mixin: MIUVIG - Minimum Information About an Uncultivated Virus Genome
Attributes
Inherited from miscellaneous natural or artificial environment:
- lat_lon 0..1
- Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system
- Range: String
- Example: 50.586825 6.408977 None
- miscellaneous natural or artificial environment➞depth 0..1
- Description: 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.
- Range: QuantityValue
- Example: 10 meter None
- miscellaneous natural or artificial environment➞alt 0..1
- Description: 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
- Range: QuantityValue
- Example: 100 meter None
- miscellaneous natural or artificial environment➞elev 0..1
- 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.
- Range: QuantityValue
- Example: 100 meter None
- miscellaneous natural or artificial environment➞temp 0..1
- Description: Temperature of the sample at the time of sampling.
- Range: QuantityValue
- Example: 25 degree Celsius None
- geo_loc_name 0..1
- 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)
- Range: String
- Example: USA: Maryland, Bethesda None
- collection_date 0..1
- 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
- Range: Date
- Example: 2018-05-11T10:00:00+01:00; 2018-05-11 None
- env_broad_scale 0..1
- 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
- Range: String
- Example: oceanic epipelagic zone biome [ENVO:01000033] for annotating a water sample from the photic zone in middle of the Atlantic Ocean None
- env_local_scale 0..1
- 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.
- Range: String
- Example: litter layer [ENVO:01000338]; Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. None
- env_medium 0..1
- 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).
- Range: String
- Example: soil [ENVO:00001998]; Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air [ENVO_00002005] None
- miscellaneous natural or artificial environment➞alkalinity 0..1
- Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate
- Range: QuantityValue
- Example: 50 milligram per liter None
- miscellaneous natural or artificial environment➞ammonium 0..1
- Description: Concentration of ammonium in the sample
- Range: QuantityValue
- Example: 1.5 milligram per liter None
- miscellaneous natural or artificial environment➞biomass 0..*
- Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements
- Range: String
- Example: total;20 gram None
- miscellaneous natural or artificial environment➞bromide 0..1
- Description: Concentration of bromide
- Range: QuantityValue
- Example: 0.05 parts per million None
- miscellaneous natural or artificial environment➞calcium 0..1
- Description: Concentration of calcium in the sample
- Range: QuantityValue
- Example: 0.2 micromole per liter None
- miscellaneous natural or artificial environment➞chem_administration 0..*
- 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
- Range: String
- Example: agar [CHEBI:2509];2018-05-11T20:00Z None
- miscellaneous natural or artificial environment➞chloride 0..1
- Description: Concentration of chloride in the sample
- Range: QuantityValue
- Example: 5000 milligram per liter None
- miscellaneous natural or artificial environment➞chlorophyll 0..1
- Description: Concentration of chlorophyll
- Range: QuantityValue
- Example: 5 milligram per cubic meter None
- miscellaneous natural or artificial environment➞density 0..1
- Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density)
- Range: QuantityValue
- Example: 1000 kilogram per cubic meter None
- miscellaneous natural or artificial environment➞diether_lipids 0..*
- Description: Concentration of diether lipids; can include multiple types of diether lipids
- Range: String
- Example: 0.2 nanogram per liter None
- miscellaneous natural or artificial environment➞diss_carb_dioxide 0..1
- Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample
- Range: QuantityValue
- Example: 5 milligram per liter None
- miscellaneous natural or artificial environment➞diss_hydrogen 0..1
- Description: Concentration of dissolved hydrogen
- Range: QuantityValue
- Example: 0.3 micromole per liter None
- miscellaneous natural or artificial environment➞diss_inorg_carb 0..1
- Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter
- Range: QuantityValue
- Example: 2059 micromole per kilogram None
- miscellaneous natural or artificial environment➞diss_org_nitro 0..1
- Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2
- Range: QuantityValue
- Example: 0.05 micromole per liter None
- miscellaneous natural or artificial environment➞diss_oxygen 0..1
- Description: Concentration of dissolved oxygen
- Range: QuantityValue
- Example: 175 micromole per kilogram None
- miscellaneous natural or artificial environment➞misc_param 0..*
- Description: Any other measurement performed or parameter collected, that is not listed here
- Range: String
- Example: Bicarbonate ion concentration;2075 micromole per kilogram None
- miscellaneous natural or artificial environment➞nitrate 0..1
- Description: Concentration of nitrate in the sample
- Range: QuantityValue
- Example: 65 micromole per liter None
- miscellaneous natural or artificial environment➞nitrite 0..1
- Description: Concentration of nitrite in the sample
- Range: QuantityValue
- Example: 0.5 micromole per liter None
- miscellaneous natural or artificial environment➞nitro 0..1
- Description: Concentration of nitrogen (total)
- Range: QuantityValue
- Example: 4.2 micromole per liter None
- miscellaneous natural or artificial environment➞org_carb 0..1
- Description: Concentration of organic carbon
- Range: QuantityValue
- Example: 1.5 microgram per liter None
- miscellaneous natural or artificial environment➞org_matter 0..1
- Description: Concentration of organic matter
- Range: QuantityValue
- Example: 1.75 milligram per cubic meter None
- miscellaneous natural or artificial environment➞org_nitro 0..1
- Description: Concentration of organic nitrogen
- Range: QuantityValue
- Example: 4 micromole per liter None
- miscellaneous natural or artificial environment➞organism_count 0..*
- 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)
- Range: organism_count_enum
- Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None
- miscellaneous natural or artificial environment➞oxy_stat_samp 0..1
- Description: Oxygenation status of sample
- Range: oxy_stat_samp_enum
- Example: aerobic None
- miscellaneous natural or artificial environment➞ph 0..1
- Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid
- Range: Double
- Example: 7.2 None
- miscellaneous natural or artificial environment➞perturbation 0..*
- 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
- Range: String
- Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None
- miscellaneous natural or artificial environment➞phosphate 0..1
- Description: Concentration of phosphate
- Range: QuantityValue
- Example: 0.7 micromole per liter None
- miscellaneous natural or artificial environment➞phosplipid_fatt_acid 0..*
- Description: Concentration of phospholipid fatty acids; can include multiple values
- Range: String
- Example: 2.98 milligram per liter None
- miscellaneous natural or artificial environment➞potassium 0..1
- Description: Concentration of potassium in the sample
- Range: QuantityValue
- Example: 463 milligram per liter None
- miscellaneous natural or artificial environment➞pressure 0..1
- Description: Pressure to which the sample is subject to, in atmospheres
- Range: QuantityValue
- Example: 50 atmosphere None
- miscellaneous natural or artificial environment➞salinity 0..1
- Description: The total concentration of all dissolved salts in a liquid or solid sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater.
- Range: QuantityValue
- Example: 25 practical salinity unit None
- miscellaneous natural or artificial environment➞samp_store_dur 0..1
- Description: Duration for which the sample was stored
- Range: String
- Example: P1Y6M None
- miscellaneous natural or artificial environment➞samp_store_loc 0..1
- Description: Location at which sample was stored, usually name of a specific freezer/room
- Range: String
- Example: Freezer no:5 None
- miscellaneous natural or artificial environment➞samp_store_temp 0..1
- Description: Temperature at which sample was stored, e.g. -80 degree Celsius
- Range: QuantityValue
- Example: -80 degree Celsius None
- miscellaneous natural or artificial environment➞silicate 0..1
- Description: Concentration of silicate
- Range: QuantityValue
- Example: 0.05 micromole per liter None
- miscellaneous natural or artificial environment➞sodium 0..1
- Description: Sodium concentration in the sample
- Range: QuantityValue
- Example: 10.5 milligram per liter None
- miscellaneous natural or artificial environment➞sulfate 0..1
- Description: Concentration of sulfate in the sample
- Range: QuantityValue
- Example: 5 micromole per liter None
- miscellaneous natural or artificial environment➞sulfide 0..1
- Description: Concentration of sulfide in the sample
- Range: QuantityValue
- Example: 2 micromole per liter None
- miscellaneous natural or artificial environment➞water_current 0..1
- Description: Measurement of magnitude and direction of flow within a fluid
- Range: QuantityValue
- Example: 10 cubic meter per second None
- miscellaneous natural or artificial environment➞samp_name 1..1
- 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.
- Range: String
- Example: ISDsoil1 None
- miscellaneous natural or artificial environment➞project_name 1..1
- Description: Name of the project within which the sequencing was organized
- Range: String
- Example: Forest soil metagenome None
- miscellaneous natural or artificial environment➞samp_vol_we_dna_ext 0..1
- 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).
- Range: QuantityValue
- Example: 1500 milliliter None
Mixed in from MIUVIG:
- MIUVIG➞submitted_to_insdc 1..1
- Description: Depending on the study (large-scale e.g. done with next generation sequencing technology, or small-scale) sequences have to be submitted to SRA (Sequence Read Archive), DRA (DDBJ Read Archive) or via the classical Webin/Sequin systems to Genbank, ENA and DDBJ. Although this field is mandatory, it is meant as a self-test field, therefore it is not necessary to include this field in contextual data submitted to databases
- Range: String
- Example: yes None
Mixed in from MIUVIG:
- MIUVIG➞investigation_type 1..1
- Description: Nucleic Acid Sequence Report is the root element of all MIGS/MIMS compliant reports as standardized by Genomic Standards Consortium. This field is either eukaryote,bacteria,virus,plasmid,organelle, metagenome,mimarks-survey, mimarks-specimen, metatranscriptome, single amplified genome, metagenome-assembled genome, or uncultivated viral genome
- Range: investigation_type_enum
- Example: metagenome None
Mixed in from MIUVIG:
- MIUVIG➞samp_taxon_id 1..1
- 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.
- Range: String
- Example: Gut Metagenome [NCBI:txid749906] None
Mixed in from MIUVIG:
- MIUVIG➞experimental_factor 0..1
- Description: 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
- Range: String
- Example: time series design [EFO:EFO_0001779] None
Mixed in from MIUVIG:
- MIUVIG➞neg_cont_type 0..1
- Description: The substance or equipment used as a negative control in an investigation
- Range: neg_cont_type_enum
- Example: None
Mixed in from MIUVIG:
- MIUVIG➞pos_cont_type 0..1
- Description: The substance, mixture, product, or apparatus used to verify that a process which is part of an investigation delivers a true positive.
- Range: String
- Example: None
Mixed in from MIUVIG:
- MIUVIG➞env_package 0..1
- Description: MIxS extension for reporting of measurements and observations obtained from one or more of the environments where the sample was obtained. All environmental packages listed here are further defined in separate subtables. By giving the name of the environmental package, a selection of fields can be made from the subtables and can be reported
- Range: env_package_enum
- Example: soil None
Mixed in from MIUVIG:
- MIUVIG➞estimated_size 0..1
- 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.
- Range: String
- Example: 300000 bp None
Mixed in from MIUVIG:
- MIUVIG➞ref_biomaterial 0..1
- Description: Primary publication if isolated before genome publication; otherwise, primary genome report.
- Range: String
- Example: doi:10.1016/j.syapm.2018.01.009 None
Mixed in from MIUVIG:
- MIUVIG➞source_mat_id 0..1
- 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).
- Range: String
- Example: MPI012345 None
Mixed in from MIUVIG:
- MIUVIG➞pathogenicity 0..1
- Description: To what is the entity pathogenic
- Range: String
- Example: human, animal, plant, fungi, bacteria None
Mixed in from MIUVIG:
- MIUVIG➞biotic_relationship 0..1
- 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
- Range: biotic_relationship_enum
- Example: free living None
Mixed in from MIUVIG:
- MIUVIG➞specific_host 0..1
- Description: Report the host's taxonomic name and/or NCBI taxonomy ID.
- Range: String
- Example: Homo sapiens and/or 9606 None
Mixed in from MIUVIG:
- MIUVIG➞host_spec_range 0..1
- Description: The range and diversity of host species that an organism is capable of infecting, defined by NCBI taxonomy identifier.
- Range: Integer
- Example: 9606 None
Mixed in from MIUVIG:
- MIUVIG➞host_disease_stat 0..1
- 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
- Range: String
- Example: rabies [DOID:11260] None
Mixed in from MIUVIG:
- MIUVIG➞samp_collec_device 0..1
- 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).
- Range: String
- Example: swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713] None
Mixed in from MIUVIG:
- MIUVIG➞samp_collec_method 0..1
- Description: The method employed for collecting the sample.
- Range: String
- Example: swabbing None
Mixed in from MIUVIG:
- MIUVIG➞samp_mat_process 0..1
- 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.
- Range: String
- Example: filtering of seawater, storing samples in ethanol None
Mixed in from MIUVIG:
- MIUVIG➞size_frac 0..1
- Description: Filtering pore size used in sample preparation
- Range: String
- Example: 0-0.22 micrometer None
Mixed in from MIUVIG:
- MIUVIG➞samp_size 0..1
- Description: The total amount or size (volume (ml), mass (g) or area (m2) ) of sample collected.
- Range: QuantityValue
- Example: 5 liter None
Mixed in from MIUVIG:
- MIUVIG➞source_uvig 1..1
- Description: Type of dataset from which the UViG was obtained
- Range: source_uvig_enum
- Example: viral fraction metagenome (virome) None
Mixed in from MIUVIG:
- MIUVIG➞virus_enrich_appr 1..1
- Description: List of approaches used to enrich the sample for viruses, if any
- Range: virus_enrich_appr_enum
- Example: filtration + FeCl Precipitation + ultracentrifugation + DNAse None
Mixed in from MIUVIG:
- MIUVIG➞nucl_acid_ext 0..1
- 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
- Range: String
- Example: https://mobio.com/media/wysiwyg/pdfs/protocols/12888.pdf None
Mixed in from MIUVIG:
- MIUVIG➞nucl_acid_amp 0..1
- 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
- Range: String
- Example: https://phylogenomics.me/protocols/16s-pcr-protocol/ None
Mixed in from MIUVIG:
- MIUVIG➞lib_size 0..1
- Description: Total number of clones in the library prepared for the project
- Range: Integer
- Example: 50 None
Mixed in from MIUVIG:
- MIUVIG➞lib_reads_seqd 0..1
- Description: Total number of clones sequenced from the library
- Range: Integer
- Example: 20 None
Mixed in from MIUVIG:
- MIUVIG➞lib_layout 0..1
- Description: Specify whether to expect single, paired, or other configuration of reads
- Range: lib_layout_enum
- Example: paired None
Mixed in from MIUVIG:
- MIUVIG➞lib_vector 0..1
- Description: Cloning vector type(s) used in construction of libraries
- Range: String
- Example: Bacteriophage P1 None
Mixed in from MIUVIG:
- MIUVIG➞lib_screen 0..1
- Description: Specific enrichment or screening methods applied before and/or after creating libraries
- Range: String
- Example: enriched, screened, normalized None
Mixed in from MIUVIG:
- MIUVIG➞mid 0..1
- 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
- Range: String
- Example: GTGAATAT None
Mixed in from MIUVIG:
- MIUVIG➞adapters 0..1
- Description: Adapters provide priming sequences for both amplification and sequencing of the sample-library fragments. Both adapters should be reported; in uppercase letters
- Range: String
- Example: AATGATACGGCGACCACCGAGATCTACACGCT;CAAGCAGAAGACGGCATACGAGAT None
Mixed in from MIUVIG:
- MIUVIG➞seq_meth 1..1
- 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).
- Range: String
- Example: 454 Genome Sequencer FLX [OBI:0000702] None
Mixed in from MIUVIG:
- MIUVIG➞tax_ident 0..1
- Description: The phylogenetic marker(s) used to assign an organism name to the SAG or MAG
- Range: tax_ident_enum
- Example: other: rpoB gene None
Mixed in from MIUVIG:
- MIUVIG➞assembly_qual 1..1
- 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 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
- Range: assembly_qual_enum
- Example: High-quality draft genome None
Mixed in from MIUVIG:
- MIUVIG➞assembly_name 0..1
- Description: Name/version of the assembly provided by the submitter that is used in the genome browsers and in the community
- Range: String
- Example: HuRef, JCVI_ISG_i3_1.0 None
Mixed in from MIUVIG:
- MIUVIG➞assembly_software 1..1
- Description: Tool(s) used for assembly, including version number and parameters
- Range: String
- Example: metaSPAdes;3.11.0;kmer set 21,33,55,77,99,121, default parameters otherwise None
Mixed in from MIUVIG:
- MIUVIG➞annot 0..1
- 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
- Range: String
- Example: prokka None
Mixed in from MIUVIG:
- MIUVIG➞number_contig 1..1
- Description: Total number of contigs in the cleaned/submitted assembly that makes up a given genome, SAG, MAG, or UViG
- Range: Integer
- Example: 40 None
Mixed in from MIUVIG:
- MIUVIG➞feat_pred 0..1
- Description: Method used to predict UViGs features such as ORFs, integration site, etc.
- Range: String
- Example: Prodigal;2.6.3;default parameters None
Mixed in from MIUVIG:
- MIUVIG➞ref_db 0..1
- Description: List of database(s) used for ORF annotation, along with version number and reference to website or publication
- Range: String
- Example: pVOGs;5;http://dmk-brain.ecn.uiowa.edu/pVOGs/ Grazziotin et al. 2017 doi:10.1093/nar/gkw975 None
Mixed in from MIUVIG:
- MIUVIG➞sim_search_meth 0..1
- Description: Tool used to compare ORFs with database, along with version and cutoffs used
- Range: String
- Example: HMMER3;3.1b2;hmmsearch, cutoff of 50 on score None
Mixed in from MIUVIG:
- MIUVIG➞tax_class 0..1
- Description: Method used for taxonomic classification, along with reference database used, classification rank, and thresholds used to classify new genomes
- Range: String
- Example: vConTACT vContact2 (references from NCBI RefSeq v83, genus rank classification, default parameters) None
Mixed in from MIUVIG:
- MIUVIG➞trnas 0..1
- Description: The total number of tRNAs identified from the SAG or MAG
- Range: Integer
- Example: 18 None
Mixed in from MIUVIG:
- MIUVIG➞trna_ext_software 0..1
- Description: Tools used for tRNA identification
- Range: String
- Example: infernal;v2;default parameters None
Mixed in from MIUVIG:
- MIUVIG➞compl_score 0..1
- 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
- Range: compl_score_enum
- Example: med;60% None
Mixed in from MIUVIG:
- MIUVIG➞compl_software 0..1
- Description: Tools used for completion estimate, i.e. checkm, anvi'o, busco
- Range: String
- Example: checkm None
Mixed in from MIUVIG:
- MIUVIG➞compl_appr 0..1
- 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
- Range: compl_appr_enum
- Example: other: UViG length compared to the average length of reference genomes from the P22virus genus (NCBI RefSeq v83) None
Mixed in from MIUVIG:
- MIUVIG➞sort_tech 0..1
- Description: Method used to sort/isolate cells or particles of interest
- Range: sort_tech_enum
- Example: optical manipulation None
Mixed in from MIUVIG:
- MIUVIG➞single_cell_lysis_appr 0..1
- Description: Method used to free DNA from interior of the cell(s) or particle(s)
- Range: single_cell_lysis_appr_enum
- Example: enzymatic None
Mixed in from MIUVIG:
- MIUVIG➞single_cell_lysis_prot 0..1
- Description: Name of the kit or standard protocol used for cell(s) or particle(s) lysis
- Range: String
- Example: ambion single cell lysis kit None
Mixed in from MIUVIG:
- MIUVIG➞wga_amp_appr 0..1
- Description: Method used to amplify genomic DNA in preparation for sequencing
- Range: String
- Example: mda based None
Mixed in from MIUVIG:
- MIUVIG➞wga_amp_kit 0..1
- Description: Kit used to amplify genomic DNA in preparation for sequencing
- Range: String
- Example: qiagen repli-g None
Mixed in from MIUVIG:
- MIUVIG➞bin_param 0..1
- Description: The parameters that have been applied during the extraction of genomes from metagenomic datasets
- Range: bin_param_enum
- Example: coverage and kmer None
Mixed in from MIUVIG:
- MIUVIG➞bin_software 0..1
- Description: Tool(s) used for the extraction of genomes from metagenomic datasets, where possible include a product ID (PID) of the tool(s) used.
- Range: String
- Example: MetaCluster-TA (RRID:SCR_004599), MaxBin (biotools:maxbin) None
Mixed in from MIUVIG:
- MIUVIG➞reassembly_bin 0..1
- Description: Has an assembly been performed on a genome bin extracted from a metagenomic assembly?
- Range: String
- Example: no None
Mixed in from MIUVIG:
- MIUVIG➞mag_cov_software 0..1
- 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
- Range: mag_cov_software_enum
- Example: bbmap None
Mixed in from MIUVIG:
- MIUVIG➞vir_ident_software 1..1
- Description: Tool(s) used for the identification of UViG as a viral genome, software or protocol name including version number, parameters, and cutoffs used
- Range: String
- Example: VirSorter; 1.0.4; Virome database, category 2 None
Mixed in from MIUVIG:
- MIUVIG➞pred_genome_type 1..1
- Description: Type of genome predicted for the UViG
- Range: pred_genome_type_enum
- Example: dsDNA None
Mixed in from MIUVIG:
- MIUVIG➞pred_genome_struc 1..1
- Description: Expected structure of the viral genome
- Range: pred_genome_struc_enum
- Example: non-segmented None
Mixed in from MIUVIG:
- MIUVIG➞detec_type 1..1
- Description: Type of UViG detection
- Range: String
- Example: independent sequence (UViG) None
Mixed in from MIUVIG:
- MIUVIG➞otu_class_appr 0..1
- 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
- Range: String
- Example: 95% ANI;85% AF; greedy incremental clustering None
Mixed in from MIUVIG:
- MIUVIG➞otu_seq_comp_appr 0..1
- Description: Tool and thresholds used to compare sequences when computing "species-level" OTUs
- Range: String
- Example: blastn;2.6.0+;e-value cutoff: 0.001 None
Mixed in from MIUVIG:
- MIUVIG➞otu_db 0..1
- 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
- Range: String
- Example: NCBI Viral RefSeq;83 None
Mixed in from MIUVIG:
- MIUVIG➞host_pred_appr 0..1
- Description: Tool or approach used for host prediction
- Range: host_pred_appr_enum
- Example: CRISPR spacer match None
Mixed in from MIUVIG:
- MIUVIG➞host_pred_est_acc 0..1
- 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
- Range: String
- Example: CRISPR spacer match: 0 or 1 mismatches, estimated 8% FDR at the host genus rank (Edwards et al. 2016 doi:10.1093/femsre/fuv048) None
Mixed in from MIUVIG:
- MIUVIG➞associated resource 0..1
- Description: A related resource that is referenced, cited, or otherwise associated to the sequence.
- Range: String
- Example: http://www.earthmicrobiome.org/ None
Mixed in from MIUVIG:
- MIUVIG➞sop 0..1
- Description: Standard operating procedures used in assembly and/or annotation of genomes, metagenomes or environmental sequences
- Range: String
- Example: http://press.igsb.anl.gov/earthmicrobiome/protocols-and-standards/its/ None