Class: built environment MISAG

Combinatorial checklist Minimum Information About a Single Amplified Genome with environmental package built environment

URI: mixs.vocab:BuiltEnvironmentMISAG

img

Parents

Uses Mixin

  • mixin: MISAG - Minimum Information About a Single Amplified Genome

Attributes

Inherited from built environment:

Mixed in from MISAG:

  • MISAG➞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 MISAG:

  • MISAG➞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 MISAG:

  • MISAG➞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 MISAG:

  • MISAG➞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 MISAG:

Mixed in from MISAG:

  • MISAG➞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 MISAG:

  • MISAG➞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 MISAG:

  • MISAG➞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 MISAG:

  • MISAG➞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 MISAG:

  • MISAG➞rel_to_oxygen 0..1
    • Description: Is this organism an aerobe, anaerobe? Please note that aerobic and anaerobic are valid descriptors for microbial environments
    • Range: rel_to_oxygen_enum
    • Example: aerobe None

Mixed in from MISAG:

  • MISAG➞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 MISAG:

Mixed in from MISAG:

  • MISAG➞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 MISAG:

  • MISAG➞size_frac 0..1
    • Description: Filtering pore size used in sample preparation
    • Range: String
    • Example: 0-0.22 micrometer None

Mixed in from MISAG:

  • MISAG➞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 MISAG:

  • MISAG➞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 MISAG:

  • MISAG➞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 MISAG:

  • MISAG➞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 MISAG:

  • MISAG➞lib_size 0..1
    • Description: Total number of clones in the library prepared for the project
    • Range: Integer
    • Example: 50 None

Mixed in from MISAG:

Mixed in from MISAG:

Mixed in from MISAG:

  • MISAG➞lib_vector 0..1
    • Description: Cloning vector type(s) used in construction of libraries
    • Range: String
    • Example: Bacteriophage P1 None

Mixed in from MISAG:

  • MISAG➞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 MISAG:

  • MISAG➞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 MISAG:

  • MISAG➞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 MISAG:

  • MISAG➞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 MISAG:

  • MISAG➞tax_ident 1..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 MISAG:

  • MISAG➞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 MISAG:

  • MISAG➞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 MISAG:

  • MISAG➞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 MISAG:

  • MISAG➞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 MISAG:

  • MISAG➞number_contig 0..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 MISAG:

  • MISAG➞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 MISAG:

  • MISAG➞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 MISAG:

  • MISAG➞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 MISAG:

  • MISAG➞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 MISAG:

Mixed in from MISAG:

Mixed in from MISAG:

  • MISAG➞trnas 0..1
    • Description: The total number of tRNAs identified from the SAG or MAG
    • Range: Integer
    • Example: 18 None

Mixed in from MISAG:

Mixed in from MISAG:

  • MISAG➞compl_score 1..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 MISAG:

  • MISAG➞compl_software 1..1
    • Description: Tools used for completion estimate, i.e. checkm, anvi'o, busco
    • Range: String
    • Example: checkm None

Mixed in from MISAG:

  • MISAG➞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 MISAG:

  • MISAG➞contam_score 1..1
    • Description: 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
    • Range: String
    • Example: 1% None

Mixed in from MISAG:

Mixed in from MISAG:

  • MISAG➞contam_screen_param 0..1
    • Description: 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
    • Range: contam_screen_param_enum
    • Example: kmer None

Mixed in from MISAG:

Mixed in from MISAG:

Mixed in from MISAG:

Mixed in from MISAG:

  • MISAG➞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 MISAG:

  • MISAG➞wga_amp_appr 1..1
    • Description: Method used to amplify genomic DNA in preparation for sequencing
    • Range: String
    • Example: mda based None

Mixed in from MISAG:

  • MISAG➞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 MISAG:

  • MISAG➞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 MISAG:

  • MISAG➞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