Class: MIMS (Mims)

name: Mims
description: Metagenome or Environmental
title: MIMS
from_schema: https://w3id.org/GenomicsStandardsConsortium/mixs-missing-value-sandbox
aliases:
- mims
is_a: Checklist
mixin: true
slots:
- conflicting
- adapters
- alt
- annot
- assembly_name
- assembly_qual
- assembly_software
- associated_resource
- collection_date
- depth
- elev
- env_broad_scale
- env_local_scale
- env_medium
- experimental_factor
- feat_pred
- geo_loc_name
- lat_lon
- lib_layout
- lib_reads_seqd
- lib_screen
- lib_size
- lib_vector
- mid
- neg_cont_type
- nucl_acid_amp
- nucl_acid_ext
- number_contig
- pos_cont_type
- project_name
- ref_biomaterial
- ref_db
- rel_to_oxygen
- samp_collect_device
- samp_collect_method
- samp_mat_process
- samp_name
- samp_size
- samp_taxon_id
- samp_vol_we_dna_ext
- seq_meth
- sim_search_meth
- size_frac
- sop
- source_mat_id
- tax_class
- temp
slot_usage:
  conflicting:
    name: conflicting
    pattern: ^[a-zA-Z]+$
  adapters:
    name: adapters
    recommended: true
  alt:
    name: alt
    recommended: true
  annot:
    name: annot
    recommended: true
  assembly_name:
    name: assembly_name
    recommended: true
  assembly_qual:
    name: assembly_qual
    recommended: true
  assembly_software:
    name: assembly_software
    recommended: true
  depth:
    name: depth
    examples:
    - value: 10 meter
    recommended: true
  elev:
    name: elev
    recommended: true
  experimental_factor:
    name: experimental_factor
    recommended: true
  lib_layout:
    name: lib_layout
    recommended: true
  lib_reads_seqd:
    name: lib_reads_seqd
    recommended: true
  lib_screen:
    name: lib_screen
    recommended: true
  lib_size:
    name: lib_size
    recommended: true
  lib_vector:
    name: lib_vector
    recommended: true
  mid:
    name: mid
    recommended: true
  nucl_acid_amp:
    name: nucl_acid_amp
    recommended: true
  nucl_acid_ext:
    name: nucl_acid_ext
    recommended: true
  number_contig:
    name: number_contig
    recommended: true
  samp_collect_device:
    name: samp_collect_device
    examples:
    - value: swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713]
    recommended: true
  samp_collect_method:
    name: samp_collect_method
    examples:
    - value: swabbing
    recommended: true
  samp_mat_process:
    name: samp_mat_process
    recommended: true
  samp_size:
    name: samp_size
    recommended: true
  sop:
    name: sop
    recommended: true
  source_mat_id:
    name: source_mat_id
    recommended: true
  temp:
    name: temp
    recommended: true
class_uri: MIXS:0010007

name: Mims
description: Metagenome or Environmental
title: MIMS
from_schema: https://w3id.org/GenomicsStandardsConsortium/mixs-missing-value-sandbox
aliases:
- mims
is_a: Checklist
mixin: true
slot_usage:
  conflicting:
    name: conflicting
    pattern: ^[a-zA-Z]+$
  adapters:
    name: adapters
    recommended: true
  alt:
    name: alt
    recommended: true
  annot:
    name: annot
    recommended: true
  assembly_name:
    name: assembly_name
    recommended: true
  assembly_qual:
    name: assembly_qual
    recommended: true
  assembly_software:
    name: assembly_software
    recommended: true
  depth:
    name: depth
    examples:
    - value: 10 meter
    recommended: true
  elev:
    name: elev
    recommended: true
  experimental_factor:
    name: experimental_factor
    recommended: true
  lib_layout:
    name: lib_layout
    recommended: true
  lib_reads_seqd:
    name: lib_reads_seqd
    recommended: true
  lib_screen:
    name: lib_screen
    recommended: true
  lib_size:
    name: lib_size
    recommended: true
  lib_vector:
    name: lib_vector
    recommended: true
  mid:
    name: mid
    recommended: true
  nucl_acid_amp:
    name: nucl_acid_amp
    recommended: true
  nucl_acid_ext:
    name: nucl_acid_ext
    recommended: true
  number_contig:
    name: number_contig
    recommended: true
  samp_collect_device:
    name: samp_collect_device
    examples:
    - value: swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713]
    recommended: true
  samp_collect_method:
    name: samp_collect_method
    examples:
    - value: swabbing
    recommended: true
  samp_mat_process:
    name: samp_mat_process
    recommended: true
  samp_size:
    name: samp_size
    recommended: true
  sop:
    name: sop
    recommended: true
  source_mat_id:
    name: source_mat_id
    recommended: true
  temp:
    name: temp
    recommended: true
attributes:
  conflicting:
    name: conflicting
    description: intentionally set to incompatible states between a Checklist and
      an Extension
    from_schema: https://w3id.org/GenomicsStandardsConsortium/mixs-missing-value-sandbox
    rank: 1000
    alias: conflicting
    owner: Mims
    domain_of:
    - Mims
    - Soil
    range: string
    pattern: ^[a-zA-Z]+$
  adapters:
    name: adapters
    annotations:
      Expected_value:
        tag: Expected_value
        value: adapter A and B sequence
    description: Adapters provide priming sequences for both amplification and sequencing
      of the sample-library fragments. Both adapters should be reported; in uppercase
      letters
    title: adapters
    examples:
    - value: AATGATACGGCGACCACCGAGATCTACACGCT;CAAGCAGAAGACGGCATACGAGAT
    in_subset:
    - sequencing
    from_schema: https://w3id.org/GenomicsStandardsConsortium/mixs-missing-value-sandbox
    rank: 1000
    string_serialization: '{dna};{dna}'
    slot_uri: MIXS:0000048
    alias: adapters
    owner: Mims
    domain_of:
    - Mims
    range: string
    recommended: true
  alt:
    name: alt
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: meter
    description: Heights of objects such as airplanes, space shuttles, rockets, atmospheric
      balloons and heights of places such as atmospheric layers and clouds. It is
      used to measure the height of an object which is above the earth's surface.
      In this context, the altitude measurement is the vertical distance between the
      earth's surface above sea level and the sampled position in the air
    title: altitude
    examples:
    - value: 100 meter
    in_subset:
    - environment
    from_schema: https://w3id.org/GenomicsStandardsConsortium/mixs-missing-value-sandbox
    rank: 1000
    slot_uri: MIXS:0000094
    alias: alt
    owner: Mims
    domain_of:
    - Mims
    range: string
    recommended: true
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  annot:
    name: annot
    annotations:
      Expected_value:
        tag: Expected_value
        value: name of tool or pipeline used, or annotation source description
    description: Tool used for annotation, or for cases where annotation was provided
      by a community jamboree or model organism database rather than by a specific
      submitter
    title: annotation
    examples:
    - value: prokka
    in_subset:
    - sequencing
    from_schema: https://w3id.org/GenomicsStandardsConsortium/mixs-missing-value-sandbox
    rank: 1000
    string_serialization: '{text}'
    slot_uri: MIXS:0000059
    alias: annot
    owner: Mims
    domain_of:
    - Mims
    range: string
    recommended: true
  assembly_name:
    name: assembly_name
    annotations:
      Expected_value:
        tag: Expected_value
        value: name and version of assembly
    description: Name/version of the assembly provided by the submitter that is used
      in the genome browsers and in the community
    title: assembly name
    examples:
    - value: HuRef, JCVI_ISG_i3_1.0
    in_subset:
    - sequencing
    from_schema: https://w3id.org/GenomicsStandardsConsortium/mixs-missing-value-sandbox
    rank: 1000
    string_serialization: '{text} {text}'
    slot_uri: MIXS:0000057
    alias: assembly_name
    owner: Mims
    domain_of:
    - Mims
    range: string
    recommended: true
  assembly_qual:
    name: assembly_qual
    annotations:
      Expected_value:
        tag: Expected_value
        value: enumeration
    description: 'The assembly quality category is based on sets of criteria outlined
      for each assembly quality category. For MISAG/MIMAG; Finished: Single, validated,
      contiguous sequence per replicon without gaps or ambiguities with a consensus
      error rate equivalent to Q50 or better. High Quality Draft:Multiple fragments
      where gaps span repetitive regions. Presence of the large subunit (LSU) RNA,
      small subunit (SSU) and the presence of 5.8S rRNA or 5S rRNA depending on whether
      it is a eukaryotic or prokaryotic genome, respectively. Medium Quality Draft:Many
      fragments with little to no review of assembly other than reporting of standard
      assembly statistics. Low Quality Draft:Many fragments with little to no review
      of assembly other than reporting of standard assembly statistics. Assembly statistics
      include, but are not limited to total assembly size, number of contigs, contig
      N50/L50, and maximum contig length. For MIUVIG; Finished: Single, validated,
      contiguous sequence per replicon without gaps or ambiguities, with extensive
      manual review and editing to annotate putative gene functions and transcriptional
      units. High-quality draft genome: One or multiple fragments, totaling   90%
      of the expected genome or replicon sequence or predicted complete. Genome fragment(s):
      One or multiple fragments, totalling < 90% of the expected genome or replicon
      sequence, or for which no genome size could be estimated'
    title: assembly quality
    examples:
    - value: High-quality draft genome
    in_subset:
    - sequencing
    from_schema: https://w3id.org/GenomicsStandardsConsortium/mixs-missing-value-sandbox
    rank: 1000
    keywords:
    - quality
    string_serialization: '[Finished genome|High-quality draft genome|Medium-quality
      draft genome|Low-quality draft genome|Genome fragment(s)]'
    slot_uri: MIXS:0000056
    alias: assembly_qual
    owner: Mims
    domain_of:
    - Mims
    range: string
    recommended: true
  assembly_software:
    name: assembly_software
    description: Tool(s) used for assembly, including version number and parameters
    title: assembly software
    examples:
    - value: metaSPAdes;3.11.0;kmer set 21,33,55,77,99,121, default parameters otherwise
    in_subset:
    - sequencing
    from_schema: https://w3id.org/GenomicsStandardsConsortium/mixs-missing-value-sandbox
    rank: 1000
    keywords:
    - software
    slot_uri: MIXS:0000058
    alias: assembly_software
    owner: Mims
    domain_of:
    - Mims
    range: string
    recommended: true
    pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+);([^\s-]{1,2}|[^\s-]+.+[^\s-]+);([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{software};{version};{parameters}$
      interpolated: true
      partial_match: true
  associated_resource:
    name: associated_resource
    annotations:
      Expected_value:
        tag: Expected_value
        value: reference to resource
    description: A related resource that is referenced, cited, or otherwise associated
      to the sequence
    title: relevant electronic resources
    examples:
    - value: http://www.earthmicrobiome.org/
    in_subset:
    - sequencing
    from_schema: https://w3id.org/GenomicsStandardsConsortium/mixs-missing-value-sandbox
    rank: 1000
    keywords:
    - resource
    string_serialization: '{PMID}|{DOI}|{URL}'
    slot_uri: MIXS:0000091
    alias: associated_resource
    owner: Mims
    domain_of:
    - Mims
    range: string
    recommended: true
    multivalued: true
  collection_date:
    name: collection_date
    description: 'The time of sampling, either as an instance (single point in time)
      or interval. In case no exact time is available, the date/time can be right
      truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10;
      2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant'
    title: collection date
    examples:
    - value: '2013-03-25T12:42:31+01:00'
    in_subset:
    - environment
    from_schema: https://w3id.org/GenomicsStandardsConsortium/mixs-missing-value-sandbox
    rank: 1000
    keywords:
    - date
    slot_uri: MIXS:0000011
    alias: collection_date
    owner: Mims
    domain_of:
    - Mims
    range: datetime
    required: true
  depth:
    name: depth
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: meter
    description: The vertical distance below local surface. For sediment or soil samples
      depth is measured from sediment or soil surface, respectively. Depth can be
      reported as an interval for subsurface samples
    title: depth
    examples:
    - value: 10 meter
    in_subset:
    - environment
    from_schema: https://w3id.org/GenomicsStandardsConsortium/mixs-missing-value-sandbox
    rank: 1000
    keywords:
    - depth
    slot_uri: MIXS:0000018
    alias: depth
    owner: Mims
    domain_of:
    - Mims
    - Soil
    range: string
    recommended: true
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  elev:
    name: elev
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: meter
    description: Elevation of the sampling site is its height above a fixed reference
      point, most commonly the mean sea level. Elevation is mainly used when referring
      to points on the earth's surface, while altitude is used for points above the
      surface, such as an aircraft in flight or a spacecraft in orbit
    title: elevation
    examples:
    - value: 100 meter
    in_subset:
    - environment
    from_schema: https://w3id.org/GenomicsStandardsConsortium/mixs-missing-value-sandbox
    rank: 1000
    keywords:
    - elevation
    slot_uri: MIXS:0000093
    alias: elev
    owner: Mims
    domain_of:
    - Mims
    - Soil
    range: string
    recommended: true
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  env_broad_scale:
    name: env_broad_scale
    description: 'Report the major environmental system the sample or specimen came
      from. The system(s) identified should have a coarse spatial grain, to provide
      the general environmental context of where the sampling was done (e.g. in the
      desert or a rainforest). We recommend using subclasses of EnvO s biome class:  http://purl.obolibrary.org/obo/ENVO_00000428.
      EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS'
    title: broad-scale environmental context
    examples:
    - value: rangeland biome [ENVO:01000247]
    in_subset:
    - environment
    from_schema: https://w3id.org/GenomicsStandardsConsortium/mixs-missing-value-sandbox
    rank: 1000
    keywords:
    - context
    - environmental
    slot_uri: MIXS:0000012
    alias: env_broad_scale
    owner: Mims
    domain_of:
    - Mims
    range: string
    required: true
    pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\]$
    structured_pattern:
      syntax: ^{termLabel} \[{termID}\]$
      interpolated: true
      partial_match: true
  env_local_scale:
    name: env_local_scale
    annotations:
      Expected_value:
        tag: Expected_value
        value: Environmental entities having causal influences upon the entity at
          time of sampling
    description: 'Report the entity or entities which are in the sample or specimen
      s local vicinity and which you believe have significant causal influences on
      your sample or specimen. We recommend using EnvO terms which are of smaller
      spatial grain than your entry for env_broad_scale. Terms, such as anatomical
      sites, from other OBO Library ontologies which interoperate with EnvO (e.g.
      UBERON) are accepted in this field. EnvO documentation about how to use the
      field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS'
    title: local environmental context
    examples:
    - value: hillside [ENVO:01000333]
    in_subset:
    - environment
    from_schema: https://w3id.org/GenomicsStandardsConsortium/mixs-missing-value-sandbox
    rank: 1000
    keywords:
    - context
    - environmental
    string_serialization: '{termLabel} [{termID}]'
    slot_uri: MIXS:0000013
    alias: env_local_scale
    owner: Mims
    domain_of:
    - Mims
    range: string
    required: true
  env_medium:
    name: env_medium
    description: 'Report the environmental material(s) immediately surrounding the
      sample or specimen at the time of sampling. We recommend using subclasses of
      ''environmental material'' (http://purl.obolibrary.org/obo/ENVO_00010483). EnvO
      documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS
      . Terms from other OBO ontologies are permissible as long as they reference
      mass/volume nouns (e.g. air, water, blood) and not discrete, countable entities
      (e.g. a tree, a leaf, a table top)'
    title: environmental medium
    examples:
    - value: bluegrass field soil [ENVO:00005789]
    in_subset:
    - environment
    from_schema: https://w3id.org/GenomicsStandardsConsortium/mixs-missing-value-sandbox
    rank: 1000
    keywords:
    - environmental
    slot_uri: MIXS:0000014
    alias: env_medium
    owner: Mims
    domain_of:
    - Mims
    range: string
    required: true
    pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\]$
    structured_pattern:
      syntax: ^{termLabel} \[{termID}\]$
      interpolated: true
      partial_match: true
  experimental_factor:
    name: experimental_factor
    annotations:
      Expected_value:
        tag: Expected_value
        value: text or EFO and/or OBI
    description: Variable aspects of an experiment design that can be used to describe
      an experiment, or set of experiments, in an increasingly detailed manner. This
      field accepts ontology terms from Experimental Factor Ontology (EFO) and/or
      Ontology for Biomedical Investigations (OBI)
    title: experimental factor
    examples:
    - value: time series design [EFO:0001779]
    in_subset:
    - investigation
    from_schema: https://w3id.org/GenomicsStandardsConsortium/mixs-missing-value-sandbox
    rank: 1000
    keywords:
    - experimental
    - factor
    string_serialization: '{termLabel} [{termID}]|{text}'
    slot_uri: MIXS:0000008
    alias: experimental_factor
    owner: Mims
    domain_of:
    - Mims
    range: string
    recommended: true
    multivalued: true
    pattern: ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$
  feat_pred:
    name: feat_pred
    description: Method used to predict UViGs features such as ORFs, integration site,
      etc
    title: feature prediction
    examples:
    - value: Prodigal;2.6.3;default parameters
    in_subset:
    - sequencing
    from_schema: https://w3id.org/GenomicsStandardsConsortium/mixs-missing-value-sandbox
    rank: 1000
    keywords:
    - feature
    - predict
    slot_uri: MIXS:0000061
    alias: feat_pred
    owner: Mims
    domain_of:
    - Mims
    range: string
    pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+);([^\s-]{1,2}|[^\s-]+.+[^\s-]+);([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{software};{version};{parameters}$
      interpolated: true
      partial_match: true
  geo_loc_name:
    name: geo_loc_name
    description: The geographical origin of the sample as defined by the country or
      sea name followed by specific region name. Country or sea names should be chosen
      from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology
      (http://purl.bioontology.org/ontology/GAZ)
    title: geographic location (country and/or sea,region)
    examples:
    - value: 'USA: Maryland, Bethesda'
    in_subset:
    - environment
    from_schema: https://w3id.org/GenomicsStandardsConsortium/mixs-missing-value-sandbox
    rank: 1000
    keywords:
    - geographic
    - location
    slot_uri: MIXS:0000010
    alias: geo_loc_name
    owner: Mims
    domain_of:
    - Mims
    range: string
    required: true
    pattern: '^([^\s-]{1,2}|[^\s-]+.+[^\s-]+): ([^\s-]{1,2}|[^\s-]+.+[^\s-]+), ([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$'
    structured_pattern:
      syntax: '^{text}: {text}, {text}$'
      interpolated: true
      partial_match: true
  lat_lon:
    name: lat_lon
    annotations:
      Expected_value:
        tag: Expected_value
        value: decimal degrees,  limit to 8 decimal points
    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
    title: geographic location (latitude and longitude)
    examples:
    - value: 50.586825 6.408977
    in_subset:
    - environment
    from_schema: https://w3id.org/GenomicsStandardsConsortium/mixs-missing-value-sandbox
    rank: 1000
    keywords:
    - geographic
    - location
    string_serialization: '{float} {float}'
    slot_uri: MIXS:0000009
    alias: lat_lon
    owner: Mims
    domain_of:
    - Mims
    range: string
    required: true
    pattern: ^(-?((?:[0-8]?[0-9](?:\.\d{0,8})?)|90)) -?[0-9]+(?:\.[0-9]{0,8})?$|^-?(1[0-7]{1,2})$
    structured_pattern:
      syntax: ^{lat} {lon}$
      interpolated: true
      partial_match: true
  lib_layout:
    name: lib_layout
    description: Specify whether to expect single, paired, or other configuration
      of reads
    title: library layout
    examples:
    - value: paired
    in_subset:
    - sequencing
    from_schema: https://w3id.org/GenomicsStandardsConsortium/mixs-missing-value-sandbox
    rank: 1000
    keywords:
    - library
    slot_uri: MIXS:0000041
    alias: lib_layout
    owner: Mims
    domain_of:
    - Mims
    range: LibLayoutEnum
    recommended: true
  lib_reads_seqd:
    name: lib_reads_seqd
    description: Total number of clones sequenced from the library
    title: library reads sequenced
    examples:
    - value: '20'
    in_subset:
    - sequencing
    from_schema: https://w3id.org/GenomicsStandardsConsortium/mixs-missing-value-sandbox
    rank: 1000
    keywords:
    - library
    slot_uri: MIXS:0000040
    alias: lib_reads_seqd
    owner: Mims
    domain_of:
    - Mims
    range: integer
    recommended: true
  lib_screen:
    name: lib_screen
    annotations:
      Expected_value:
        tag: Expected_value
        value: screening strategy name
    description: Specific enrichment or screening methods applied before and/or after
      creating libraries
    title: library screening strategy
    examples:
    - value: enriched, screened, normalized
    in_subset:
    - sequencing
    from_schema: https://w3id.org/GenomicsStandardsConsortium/mixs-missing-value-sandbox
    rank: 1000
    keywords:
    - library
    string_serialization: '{text}'
    slot_uri: MIXS:0000043
    alias: lib_screen
    owner: Mims
    domain_of:
    - Mims
    range: string
    recommended: true
  lib_size:
    name: lib_size
    description: Total number of clones in the library prepared for the project
    title: library size
    examples:
    - value: '50'
    in_subset:
    - sequencing
    from_schema: https://w3id.org/GenomicsStandardsConsortium/mixs-missing-value-sandbox
    rank: 1000
    keywords:
    - library
    - size
    slot_uri: MIXS:0000039
    alias: lib_size
    owner: Mims
    domain_of:
    - Mims
    range: integer
    recommended: true
  lib_vector:
    name: lib_vector
    annotations:
      Expected_value:
        tag: Expected_value
        value: vector
    description: Cloning vector type(s) used in construction of libraries
    title: library vector
    examples:
    - value: Bacteriophage P1
    in_subset:
    - sequencing
    from_schema: https://w3id.org/GenomicsStandardsConsortium/mixs-missing-value-sandbox
    rank: 1000
    keywords:
    - library
    string_serialization: '{text}'
    slot_uri: MIXS:0000042
    alias: lib_vector
    owner: Mims
    domain_of:
    - Mims
    range: string
    recommended: true
  mid:
    name: mid
    description: Molecular barcodes, called Multiplex Identifiers (MIDs), that are
      used to specifically tag unique samples in a sequencing run. Sequence should
      be reported in uppercase letters
    title: multiplex identifiers
    examples:
    - value: GTGAATAT
    in_subset:
    - sequencing
    from_schema: https://w3id.org/GenomicsStandardsConsortium/mixs-missing-value-sandbox
    rank: 1000
    keywords:
    - identifier
    slot_uri: MIXS:0000047
    alias: mid
    owner: Mims
    domain_of:
    - Mims
    range: string
    recommended: true
    pattern: ^[ACGTRKSYMWBHDVN]+$
    structured_pattern:
      syntax: ^{ambiguous_nucleotides}$
      interpolated: true
      partial_match: true
  neg_cont_type:
    name: neg_cont_type
    annotations:
      Expected_value:
        tag: Expected_value
        value: enumeration or text
    description: The substance or equipment used as a negative control in an investigation
    title: negative control type
    in_subset:
    - investigation
    from_schema: https://w3id.org/GenomicsStandardsConsortium/mixs-missing-value-sandbox
    rank: 1000
    keywords:
    - type
    slot_uri: MIXS:0001321
    alias: neg_cont_type
    owner: Mims
    domain_of:
    - Mims
    range: NegContTypeEnum
    recommended: true
  nucl_acid_amp:
    name: nucl_acid_amp
    description: A link to a literature reference, electronic resource or a standard
      operating procedure (SOP), that describes the enzymatic amplification (PCR,
      TMA, NASBA) of specific nucleic acids
    title: nucleic acid amplification
    examples:
    - value: https://phylogenomics.me/protocols/16s-pcr-protocol/
    in_subset:
    - sequencing
    from_schema: https://w3id.org/GenomicsStandardsConsortium/mixs-missing-value-sandbox
    rank: 1000
    slot_uri: MIXS:0000038
    alias: nucl_acid_amp
    owner: Mims
    domain_of:
    - Mims
    range: string
    recommended: true
    pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$
    structured_pattern:
      syntax: ^{PMID}|{DOI}|{URL}$
      interpolated: true
      partial_match: true
  nucl_acid_ext:
    name: nucl_acid_ext
    description: A link to a literature reference, electronic resource or a standard
      operating procedure (SOP), that describes the material separation to recover
      the nucleic acid fraction from a sample
    title: nucleic acid extraction
    examples:
    - value: https://mobio.com/media/wysiwyg/pdfs/protocols/12888.pdf
    in_subset:
    - sequencing
    from_schema: https://w3id.org/GenomicsStandardsConsortium/mixs-missing-value-sandbox
    rank: 1000
    slot_uri: MIXS:0000037
    alias: nucl_acid_ext
    owner: Mims
    domain_of:
    - Mims
    range: string
    recommended: true
    pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$
    structured_pattern:
      syntax: ^{PMID}|{DOI}|{URL}$
      interpolated: true
      partial_match: true
  number_contig:
    name: number_contig
    description: Total number of contigs in the cleaned/submitted assembly that makes
      up a given genome, SAG, MAG, or UViG
    title: number of contigs
    examples:
    - value: '40'
    in_subset:
    - sequencing
    from_schema: https://w3id.org/GenomicsStandardsConsortium/mixs-missing-value-sandbox
    rank: 1000
    keywords:
    - number
    slot_uri: MIXS:0000060
    alias: number_contig
    owner: Mims
    domain_of:
    - Mims
    range: integer
    recommended: true
  pos_cont_type:
    name: pos_cont_type
    description: The substance, mixture, product, or apparatus used to verify that
      a process which is part of an investigation delivers a true positive
    title: positive control type
    in_subset:
    - investigation
    from_schema: https://w3id.org/GenomicsStandardsConsortium/mixs-missing-value-sandbox
    rank: 1000
    keywords:
    - type
    string_serialization: '{term} or {text}'
    slot_uri: MIXS:0001322
    alias: pos_cont_type
    owner: Mims
    domain_of:
    - Mims
    range: string
    recommended: true
  project_name:
    name: project_name
    description: Name of the project within which the sequencing was organized
    title: project name
    examples:
    - value: Forest soil metagenome
    in_subset:
    - investigation
    from_schema: https://w3id.org/GenomicsStandardsConsortium/mixs-missing-value-sandbox
    rank: 1000
    keywords:
    - project
    slot_uri: MIXS:0000092
    alias: project_name
    owner: Mims
    domain_of:
    - Mims
    - Soil
    range: string
    required: true
  ref_biomaterial:
    name: ref_biomaterial
    description: Primary publication if isolated before genome publication; otherwise,
      primary genome report
    title: reference for biomaterial
    examples:
    - value: doi:10.1016/j.syapm.2018.01.009
    in_subset:
    - nucleic acid sequence source
    from_schema: https://w3id.org/GenomicsStandardsConsortium/mixs-missing-value-sandbox
    rank: 1000
    slot_uri: MIXS:0000025
    alias: ref_biomaterial
    owner: Mims
    domain_of:
    - Mims
    range: string
    pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$
    structured_pattern:
      syntax: ^{PMID}|{DOI}|{URL}$
      interpolated: true
      partial_match: true
  ref_db:
    name: ref_db
    annotations:
      Expected_value:
        tag: Expected_value
        value: names, versions, and references of databases
    description: List of database(s) used for ORF annotation, along with version number
      and reference to website or publication
    title: reference database(s)
    examples:
    - value: pVOGs;5;http://dmk-brain.ecn.uiowa.edu/pVOGs/ Grazziotin et al. 2017
        doi:10.1093/nar/gkw975
    in_subset:
    - sequencing
    from_schema: https://w3id.org/GenomicsStandardsConsortium/mixs-missing-value-sandbox
    rank: 1000
    keywords:
    - database
    string_serialization: '{database};{version};{reference}'
    slot_uri: MIXS:0000062
    alias: ref_db
    owner: Mims
    domain_of:
    - Mims
    range: string
  rel_to_oxygen:
    name: rel_to_oxygen
    description: Is this organism an aerobe, anaerobe? Please note that aerobic and
      anaerobic are valid descriptors for microbial environments
    title: relationship to oxygen
    examples:
    - value: aerobe
    in_subset:
    - nucleic acid sequence source
    from_schema: https://w3id.org/GenomicsStandardsConsortium/mixs-missing-value-sandbox
    rank: 1000
    keywords:
    - oxygen
    - relationship
    slot_uri: MIXS:0000015
    alias: rel_to_oxygen
    owner: Mims
    domain_of:
    - Mims
    range: RelToOxygenEnum
  samp_collect_device:
    name: samp_collect_device
    annotations:
      Expected_value:
        tag: Expected_value
        value: device name
    description: The device used to collect an environmental sample. This field accepts
      terms listed under environmental sampling device (http://purl.obolibrary.org/obo/ENVO).
      This field also accepts terms listed under specimen collection device (http://purl.obolibrary.org/obo/GENEPIO_0002094)
    title: sample collection device
    examples:
    - value: swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713]
    in_subset:
    - nucleic acid sequence source
    from_schema: https://w3id.org/GenomicsStandardsConsortium/mixs-missing-value-sandbox
    rank: 1000
    keywords:
    - device
    - sample
    string_serialization: '{termLabel} [{termID}]|{text}'
    slot_uri: MIXS:0000002
    alias: samp_collect_device
    owner: Mims
    domain_of:
    - Mims
    range: string
    recommended: true
  samp_collect_method:
    name: samp_collect_method
    description: The method employed for collecting the sample
    title: sample collection method
    examples:
    - value: swabbing
    in_subset:
    - nucleic acid sequence source
    from_schema: https://w3id.org/GenomicsStandardsConsortium/mixs-missing-value-sandbox
    rank: 1000
    keywords:
    - method
    - sample
    slot_uri: MIXS:0001225
    alias: samp_collect_method
    owner: Mims
    domain_of:
    - Mims
    range: string
    recommended: true
    pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$|([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{PMID}|{DOI}|{URL}|{text}$
      interpolated: true
      partial_match: true
  samp_mat_process:
    name: samp_mat_process
    description: A brief description of any processing applied to the sample during
      or after retrieving the sample from environment, or a link to the relevant protocol(s)
      performed
    title: sample material processing
    examples:
    - value: filtering of seawater, storing samples in ethanol
    in_subset:
    - nucleic acid sequence source
    from_schema: https://w3id.org/GenomicsStandardsConsortium/mixs-missing-value-sandbox
    rank: 1000
    keywords:
    - material
    - process
    - sample
    slot_uri: MIXS:0000016
    alias: samp_mat_process
    owner: Mims
    domain_of:
    - Mims
    range: string
    recommended: true
  samp_name:
    name: samp_name
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: ''
    description: A local identifier or name that for the material sample used for
      extracting nucleic acids, and subsequent sequencing. It can refer either to
      the original material collected or to any derived sub-samples. It can have any
      format, but we suggest that you make it concise, unique and consistent within
      your lab, and as informative as possible. INSDC requires every sample name from
      a single Submitter to be unique. Use of a globally unique identifier for the
      field source_mat_id is recommended in addition to sample_name
    title: sample name
    examples:
    - value: ISDsoil1
    in_subset:
    - investigation
    from_schema: https://w3id.org/GenomicsStandardsConsortium/mixs-missing-value-sandbox
    rank: 1000
    keywords:
    - sample
    slot_uri: MIXS:0001107
    alias: samp_name
    owner: Mims
    domain_of:
    - Mims
    - Soil
    range: string
    required: true
  samp_size:
    name: samp_size
    description: The total amount or size (volume (ml), mass (g) or area (m2) ) of
      sample collected
    title: amount or size of sample collected
    examples:
    - value: 5 liter
    in_subset:
    - nucleic acid sequence source
    from_schema: https://w3id.org/GenomicsStandardsConsortium/mixs-missing-value-sandbox
    rank: 1000
    keywords:
    - sample
    - size
    slot_uri: MIXS:0000001
    alias: samp_size
    owner: Mims
    domain_of:
    - Mims
    range: string
    recommended: true
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  samp_taxon_id:
    name: samp_taxon_id
    description: NCBI taxon id of the sample.  Maybe be a single taxon or mixed taxa
      sample. Use 'synthetic metagenome  for mock community/positive controls, or
      'blank sample' for negative controls
    title: taxonomy ID of DNA sample
    examples:
    - value: Gut Metagenome [NCBITaxon:749906]
    in_subset:
    - investigation
    from_schema: https://w3id.org/GenomicsStandardsConsortium/mixs-missing-value-sandbox
    rank: 1000
    keywords:
    - dna
    - identifier
    - sample
    - taxon
    slot_uri: MIXS:0001320
    alias: samp_taxon_id
    owner: Mims
    domain_of:
    - Mims
    range: string
    required: true
    pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[NCBITaxon:\d+\]$
    structured_pattern:
      syntax: ^{text} \[{NCBItaxon_id}\]$
      interpolated: true
      partial_match: true
  samp_vol_we_dna_ext:
    name: samp_vol_we_dna_ext
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: milliliter, gram, milligram, square centimeter
    description: 'Volume (ml) or mass (g) of total collected sample processed for
      DNA extraction. Note: total sample collected should be entered under the term
      Sample Size (MIXS:0000001)'
    title: sample volume or weight for DNA extraction
    examples:
    - value: 1500 milliliter
    in_subset:
    - nucleic acid sequence source
    from_schema: https://w3id.org/GenomicsStandardsConsortium/mixs-missing-value-sandbox
    rank: 1000
    keywords:
    - dna
    - sample
    - volume
    - weight
    slot_uri: MIXS:0000111
    alias: samp_vol_we_dna_ext
    owner: Mims
    domain_of:
    - Mims
    - Soil
    range: string
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  seq_meth:
    name: seq_meth
    description: Sequencing machine used. Where possible the term should be taken
      from the OBI list of DNA sequencers (http://purl.obolibrary.org/obo/OBI_0400103)
    title: sequencing method
    examples:
    - value: 454 Genome Sequencer FLX [OBI:0000702]
    in_subset:
    - sequencing
    from_schema: https://w3id.org/GenomicsStandardsConsortium/mixs-missing-value-sandbox
    rank: 1000
    keywords:
    - method
    slot_uri: MIXS:0000050
    alias: seq_meth
    owner: Mims
    domain_of:
    - Mims
    range: string
    required: true
    pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+)|(([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\])$
    structured_pattern:
      syntax: ^{text}|({termLabel} \[{termID}\])$
      interpolated: true
      partial_match: true
  sim_search_meth:
    name: sim_search_meth
    description: Tool used to compare ORFs with database, along with version and cutoffs
      used
    title: similarity search method
    examples:
    - value: HMMER3;3.1b2;hmmsearch, cutoff of 50 on score
    in_subset:
    - sequencing
    from_schema: https://w3id.org/GenomicsStandardsConsortium/mixs-missing-value-sandbox
    rank: 1000
    keywords:
    - method
    slot_uri: MIXS:0000063
    alias: sim_search_meth
    owner: Mims
    domain_of:
    - Mims
    range: string
    pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+);([^\s-]{1,2}|[^\s-]+.+[^\s-]+);([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{software};{version};{parameters}$
      interpolated: true
      partial_match: true
  size_frac:
    name: size_frac
    annotations:
      Expected_value:
        tag: Expected_value
        value: filter size value range
    description: Filtering pore size used in sample preparation
    title: size fraction selected
    examples:
    - value: 0-0.22 micrometer
    in_subset:
    - nucleic acid sequence source
    from_schema: https://w3id.org/GenomicsStandardsConsortium/mixs-missing-value-sandbox
    rank: 1000
    keywords:
    - fraction
    - size
    string_serialization: '{float}-{float} {unit}'
    slot_uri: MIXS:0000017
    alias: size_frac
    owner: Mims
    domain_of:
    - Mims
    range: string
  sop:
    name: sop
    annotations:
      Expected_value:
        tag: Expected_value
        value: reference to SOP
    description: Standard operating procedures used in assembly and/or annotation
      of genomes, metagenomes or environmental sequences
    title: relevant standard operating procedures
    examples:
    - value: http://press.igsb.anl.gov/earthmicrobiome/protocols-and-standards/its/
    in_subset:
    - sequencing
    from_schema: https://w3id.org/GenomicsStandardsConsortium/mixs-missing-value-sandbox
    rank: 1000
    keywords:
    - procedures
    string_serialization: '{PMID}|{DOI}|{URL}'
    slot_uri: MIXS:0000090
    alias: sop
    owner: Mims
    domain_of:
    - Mims
    range: string
    recommended: true
    multivalued: true
  source_mat_id:
    name: source_mat_id
    annotations:
      Expected_value:
        tag: Expected_value
        value: 'for cultures of microorganisms: identifiers for two culture collections;
          for other material a unique arbitrary identifer'
    description: A unique identifier assigned to a material sample (as defined by
      http://rs.tdwg.org/dwc/terms/materialSampleID, and as opposed to a particular
      digital record of a material sample) used for extracting nucleic acids, and
      subsequent sequencing. The identifier can refer either to the original material
      collected or to any derived sub-samples. The INSDC qualifiers /specimen_voucher,
      /bio_material, or /culture_collection may or may not share the same value as
      the source_mat_id field. For instance, the /specimen_voucher qualifier and source_mat_id
      may both contain 'UAM:Herps:14' , referring to both the specimen voucher and
      sampled tissue with the same identifier. However, the /culture_collection qualifier
      may refer to a value from an initial culture (e.g. ATCC:11775) while source_mat_id
      would refer to an identifier from some derived culture from which the nucleic
      acids were extracted (e.g. xatc123 or ark:/2154/R2)
    title: source material identifiers
    examples:
    - value: MPI012345
    in_subset:
    - nucleic acid sequence source
    from_schema: https://w3id.org/GenomicsStandardsConsortium/mixs-missing-value-sandbox
    rank: 1000
    keywords:
    - identifier
    - material
    - source
    string_serialization: '{text}'
    slot_uri: MIXS:0000026
    alias: source_mat_id
    owner: Mims
    domain_of:
    - Mims
    range: string
    recommended: true
    multivalued: true
  tax_class:
    name: tax_class
    description: Method used for taxonomic classification, along with reference database
      used, classification rank, and thresholds used to classify new genomes
    title: taxonomic classification
    examples:
    - value: vConTACT vContact2 (references from NCBI RefSeq v83, genus rank classification,
        default parameters)
    in_subset:
    - sequencing
    from_schema: https://w3id.org/GenomicsStandardsConsortium/mixs-missing-value-sandbox
    rank: 1000
    keywords:
    - classification
    - taxon
    slot_uri: MIXS:0000064
    alias: tax_class
    owner: Mims
    domain_of:
    - Mims
    range: string
  temp:
    name: temp
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: degree Celsius
    description: Temperature of the sample at the time of sampling
    title: temperature
    examples:
    - value: 25 degree Celsius
    in_subset:
    - environment
    from_schema: https://w3id.org/GenomicsStandardsConsortium/mixs-missing-value-sandbox
    rank: 1000
    keywords:
    - temperature
    slot_uri: MIXS:0000113
    alias: temp
    owner: Mims
    domain_of:
    - Mims
    - Soil
    range: string
    recommended: true
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
class_uri: MIXS:0010007