Class: built environment MIUVIG

Combinatorial checklist Minimum Information About an Uncultivated Virus Genome with environmental package built environment

URI: mixs.vocab:BuiltEnvironmentMIUVIG

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Parents

Uses Mixin

  • mixin: MIUVIG - Minimum Information About an Uncultivated Virus Genome

Attributes

Inherited from built environment:

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:

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:

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➞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:

Mixed in from MIUVIG:

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:

Mixed in from MIUVIG:

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:

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:

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:

Mixed in from MIUVIG:

Mixed in from MIUVIG:

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:

Mixed in from MIUVIG:

Mixed in from MIUVIG:

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:

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