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Class: TraitUnified

Unified trait annotations across samples from multiple sources. Provides consistent trait vocabulary across studies.

STATUS: PLANNED - Not yet implemented in NMDC database.

INTENDED SOURCES: - GOLD organism_phenotype (7,113 curated organism-phenotype mappings) - IMG phenotype_rule_taxons (2M+ predicted trait-taxon mappings) - Literature-derived trait annotations

INTENDED TRAIT CATEGORIES (from available sources): - Phenotype: Acidophile, Alkaliphile, Pathogen, Symbiont, Biofilm, etc. (159 terms) - Metabolism: Denitrifying, Nitrogen fixation, Methanogen, Sulfate reducer, etc. (157 terms) - Energy source: Autotroph, Heterotroph, Phototroph, Chemolithotroph, etc. (31 terms) - Oxygen requirement: Aerobe, Anaerobe, Facultative, Microaerophilic (7 terms) - Cell shape: Rod-shaped, Coccus-shaped, Spiral-shaped, Filament-shaped, etc. (18 terms) - Motility: Motile, Nonmotile (2 terms) - Sporulation: Sporulating, Nonsporulating (2 terms)

EXAMPLE TRAITS (from GOLD cvphenotype): | ID | Term | Usage Count | |----|----------------------|-------------| | 122| Pathogen | 3,132 | | 104| Non-Pathogen | 576 | | 35 | Catalase negative | 520 | | 36 | Catalase positive | 414 | | 116| Opportunistic Pathogen| 279 | | 4 | Acidophile | 143 | | 134| Probiotic | 106 | | 138| Radiation resistant | 49 | | 88 | Magnetotactic | (rare) | | 27 | Bioluminescent | (rare) |

URI: https://w3id.org/kbase/nmdc_core/TraitUnified

classDiagram class TraitUnified click TraitUnified href "../TraitUnified/" TraitUnified : definition TraitUnified : synonyms TraitUnified : trait_category TraitUnified : trait_id TraitUnified : trait_name

Slots

Name Cardinality and Range Description Inheritance
trait_id 1
String		 Unified trait identifier direct
trait_name 0..1
String		 Human-readable trait name direct
trait_category 0..1
String		 Category of trait (phenotype, metabolism, energy_source, oxygen_req, cell_sha... direct
definition 0..1
String		 Formal definition of the trait direct
synonyms 0..1
String		 Semicolon-separated alternative names direct

Identifier and Mapping Information

Annotations

property value
source_table trait_unified
status planned

Schema Source

  • from schema: https://w3id.org/kbase/nmdc_core

Mappings

Mapping Type Mapped Value
self https://w3id.org/kbase/nmdc_core/TraitUnified
native https://w3id.org/kbase/nmdc_core/TraitUnified

LinkML Source

Direct

name: TraitUnified
annotations:
  source_table:
    tag: source_table
    value: trait_unified
  status:
    tag: status
    value: planned
description: 'Unified trait annotations across samples from multiple sources. Provides
  consistent trait vocabulary across studies.

  STATUS: PLANNED - Not yet implemented in NMDC database.

  INTENDED SOURCES: - GOLD organism_phenotype (7,113 curated organism-phenotype mappings)
  - IMG phenotype_rule_taxons (2M+ predicted trait-taxon mappings) - Literature-derived
  trait annotations

  INTENDED TRAIT CATEGORIES (from available sources): - Phenotype: Acidophile, Alkaliphile,
  Pathogen, Symbiont, Biofilm, etc. (159 terms) - Metabolism: Denitrifying, Nitrogen
  fixation, Methanogen, Sulfate reducer, etc. (157 terms) - Energy source: Autotroph,
  Heterotroph, Phototroph, Chemolithotroph, etc. (31 terms) - Oxygen requirement:
  Aerobe, Anaerobe, Facultative, Microaerophilic (7 terms) - Cell shape: Rod-shaped,
  Coccus-shaped, Spiral-shaped, Filament-shaped, etc. (18 terms) - Motility: Motile,
  Nonmotile (2 terms) - Sporulation: Sporulating, Nonsporulating (2 terms)

  EXAMPLE TRAITS (from GOLD cvphenotype): | ID | Term                  | Usage Count
  | |----|----------------------|-------------| | 122| Pathogen             | 3,132       |
  | 104| Non-Pathogen         | 576         | | 35 | Catalase negative    | 520         |
  | 36 | Catalase positive    | 414         | | 116| Opportunistic Pathogen| 279        |
  | 4  | Acidophile           | 143         | | 134| Probiotic            | 106         |
  | 138| Radiation resistant  | 49          | | 88 | Magnetotactic        | (rare)      |
  | 27 | Bioluminescent       | (rare)      |'
from_schema: https://w3id.org/kbase/nmdc_core
attributes:
  trait_id:
    name: trait_id
    description: Unified trait identifier
    examples:
    - value: TRAIT:0000122
      description: Pathogen trait
    - value: TRAIT:0000004
      description: Acidophile trait
    from_schema: https://w3id.org/kbase/nmdc_core
    rank: 1000
    identifier: true
    domain_of:
    - TraitUnified
    - TraitTaxonomyMapping
    range: string
    required: true
  trait_name:
    name: trait_name
    description: Human-readable trait name
    examples:
    - value: Pathogen
    - value: Acidophile
    - value: Nitrogen fixation
    - value: Aerobe
    from_schema: https://w3id.org/kbase/nmdc_core
    rank: 1000
    domain_of:
    - TraitUnified
    range: string
  trait_category:
    name: trait_category
    description: Category of trait (phenotype, metabolism, energy_source, oxygen_req,
      cell_shape, motility, sporulation)
    examples:
    - value: phenotype
    - value: metabolism
    - value: energy_source
    - value: oxygen_req
    from_schema: https://w3id.org/kbase/nmdc_core
    rank: 1000
    domain_of:
    - TraitUnified
    range: string
  definition:
    name: definition
    description: Formal definition of the trait
    from_schema: https://w3id.org/kbase/nmdc_core
    domain_of:
    - GoTerms
    - KeggKoTerms
    - TraitUnified
    range: string
  synonyms:
    name: synonyms
    description: Semicolon-separated alternative names
    from_schema: https://w3id.org/kbase/nmdc_core
    domain_of:
    - GoTerms
    - EcTerms
    - TraitUnified
    range: string

Induced

name: TraitUnified
annotations:
  source_table:
    tag: source_table
    value: trait_unified
  status:
    tag: status
    value: planned
description: 'Unified trait annotations across samples from multiple sources. Provides
  consistent trait vocabulary across studies.

  STATUS: PLANNED - Not yet implemented in NMDC database.

  INTENDED SOURCES: - GOLD organism_phenotype (7,113 curated organism-phenotype mappings)
  - IMG phenotype_rule_taxons (2M+ predicted trait-taxon mappings) - Literature-derived
  trait annotations

  INTENDED TRAIT CATEGORIES (from available sources): - Phenotype: Acidophile, Alkaliphile,
  Pathogen, Symbiont, Biofilm, etc. (159 terms) - Metabolism: Denitrifying, Nitrogen
  fixation, Methanogen, Sulfate reducer, etc. (157 terms) - Energy source: Autotroph,
  Heterotroph, Phototroph, Chemolithotroph, etc. (31 terms) - Oxygen requirement:
  Aerobe, Anaerobe, Facultative, Microaerophilic (7 terms) - Cell shape: Rod-shaped,
  Coccus-shaped, Spiral-shaped, Filament-shaped, etc. (18 terms) - Motility: Motile,
  Nonmotile (2 terms) - Sporulation: Sporulating, Nonsporulating (2 terms)

  EXAMPLE TRAITS (from GOLD cvphenotype): | ID | Term                  | Usage Count
  | |----|----------------------|-------------| | 122| Pathogen             | 3,132       |
  | 104| Non-Pathogen         | 576         | | 35 | Catalase negative    | 520         |
  | 36 | Catalase positive    | 414         | | 116| Opportunistic Pathogen| 279        |
  | 4  | Acidophile           | 143         | | 134| Probiotic            | 106         |
  | 138| Radiation resistant  | 49          | | 88 | Magnetotactic        | (rare)      |
  | 27 | Bioluminescent       | (rare)      |'
from_schema: https://w3id.org/kbase/nmdc_core
attributes:
  trait_id:
    name: trait_id
    description: Unified trait identifier
    examples:
    - value: TRAIT:0000122
      description: Pathogen trait
    - value: TRAIT:0000004
      description: Acidophile trait
    from_schema: https://w3id.org/kbase/nmdc_core
    rank: 1000
    identifier: true
    alias: trait_id
    owner: TraitUnified
    domain_of:
    - TraitUnified
    - TraitTaxonomyMapping
    range: string
    required: true
  trait_name:
    name: trait_name
    description: Human-readable trait name
    examples:
    - value: Pathogen
    - value: Acidophile
    - value: Nitrogen fixation
    - value: Aerobe
    from_schema: https://w3id.org/kbase/nmdc_core
    rank: 1000
    alias: trait_name
    owner: TraitUnified
    domain_of:
    - TraitUnified
    range: string
  trait_category:
    name: trait_category
    description: Category of trait (phenotype, metabolism, energy_source, oxygen_req,
      cell_shape, motility, sporulation)
    examples:
    - value: phenotype
    - value: metabolism
    - value: energy_source
    - value: oxygen_req
    from_schema: https://w3id.org/kbase/nmdc_core
    rank: 1000
    alias: trait_category
    owner: TraitUnified
    domain_of:
    - TraitUnified
    range: string
  definition:
    name: definition
    description: Formal definition of the trait
    from_schema: https://w3id.org/kbase/nmdc_core
    alias: definition
    owner: TraitUnified
    domain_of:
    - GoTerms
    - KeggKoTerms
    - TraitUnified
    range: string
  synonyms:
    name: synonyms
    description: Semicolon-separated alternative names
    from_schema: https://w3id.org/kbase/nmdc_core
    alias: synonyms
    owner: TraitUnified
    domain_of:
    - GoTerms
    - EcTerms
    - TraitUnified
    range: string