Class: EggnogMapperAnnotations

EggNOG-mapper v2 functional annotations for genes. Provides: - COG functional categories - GO term annotations - KEGG pathway/ortholog mappings - EC enzyme numbers - PFAM domain annotations

COVERAGE: 93,558,330 annotated genes (~9% of total)

COG CATEGORY DISTRIBUTION (most common): - S (function unknown): Most common - J (translation): ~8% - K (transcription): ~6% - C (energy): ~5% - E (amino acid metabolism): ~5%

URI: https://w3id.org/kbase/kbase_ke_pangenome/EggnogMapperAnnotations

classDiagram class EggnogMapperAnnotations click EggnogMapperAnnotations href "../EggnogMapperAnnotations/" EggnogMapperAnnotations : COG_category EggnogMapperAnnotations : Description EggnogMapperAnnotations : EC EggnogMapperAnnotations : eggNOG_OGs EggnogMapperAnnotations : evalue EggnogMapperAnnotations : GOs EggnogMapperAnnotations : KEGG_ko EggnogMapperAnnotations : KEGG_Pathway EggnogMapperAnnotations : PFAMs EggnogMapperAnnotations : Preferred_name EggnogMapperAnnotations : query_name EggnogMapperAnnotations : score EggnogMapperAnnotations : seed_ortholog

Slots

Name	Cardinality and Range	Description	Inheritance
query_name	1 String	Gene ID - links to Gene	direct
seed_ortholog	0..1 String	Best matching seed ortholog from eggNOG database	direct
evalue	0..1 Float	E-value of seed ortholog match (lower = better match)	direct
score	0..1 Float	Bit score of seed ortholog alignment	direct
eggNOG_OGs	0..1 String	Hierarchical EggNOG ortholog groups from root to most specific	direct
COG_category	0..1 String	COG functional category code(s)	direct
Description	0..1 String	Functional description from seed ortholog	direct
Preferred_name	0..1 String	Gene symbol when available, "-" if none	direct
GOs	0..1 String	GO terms, comma-separated	direct
EC	0..1 String	EC enzyme numbers, comma-separated	direct
KEGG_ko	0..1 String	KEGG Orthology IDs	direct
KEGG_Pathway	0..1 String	KEGG pathway IDs, comma-separated	direct
PFAMs	0..1 String	PFAM domain annotations, comma-separated	direct

Identifier and Mapping Information

Annotations

property	value
source_table	eggnog_mapper_annotations
row_count	93558330

Schema Source

from schema: https://w3id.org/kbase/kbase_ke_pangenome

Mappings

Mapping Type	Mapped Value
self	https://w3id.org/kbase/kbase_ke_pangenome/EggnogMapperAnnotations
native	https://w3id.org/kbase/kbase_ke_pangenome/EggnogMapperAnnotations

LinkML Source

Direct

name: EggnogMapperAnnotations
annotations:
  source_table:
    tag: source_table
    value: eggnog_mapper_annotations
  row_count:
    tag: row_count
    value: '93558330'
description: 'EggNOG-mapper v2 functional annotations for genes. Provides: - COG functional
  categories - GO term annotations - KEGG pathway/ortholog mappings - EC enzyme numbers
  - PFAM domain annotations

  COVERAGE: 93,558,330 annotated genes (~9% of total)

  COG CATEGORY DISTRIBUTION (most common): - S (function unknown): Most common - J
  (translation): ~8% - K (transcription): ~6% - C (energy): ~5% - E (amino acid metabolism):
  ~5%'
from_schema: https://w3id.org/kbase/kbase_ke_pangenome
attributes:
  query_name:
    name: query_name
    description: Gene ID - links to Gene.gene_id
    comments:
    - 'Foreign key: Gene.gene_id'
    examples:
    - value: DBFF01000060.1_2
    - value: CALVBM010000003.1_96
    from_schema: https://w3id.org/kbase/kbase_ke_pangenome
    rank: 1000
    identifier: true
    domain_of:
    - EggnogMapperAnnotations
    range: string
    required: true
  seed_ortholog:
    name: seed_ortholog
    description: 'Best matching seed ortholog from eggNOG database. Format: taxon_id.locus_tag'
    examples:
    - value: 42256.RradSPS_0079
    - value: 1548153.LR59_00700
    from_schema: https://w3id.org/kbase/kbase_ke_pangenome
    rank: 1000
    domain_of:
    - EggnogMapperAnnotations
    range: string
  evalue:
    name: evalue
    description: E-value of seed ortholog match (lower = better match)
    examples:
    - value: '3.06e-109'
    - value: '0.0'
      description: Exact match
    - value: 1e-50
    from_schema: https://w3id.org/kbase/kbase_ke_pangenome
    rank: 1000
    domain_of:
    - EggnogMapperAnnotations
    range: float
    minimum_value: 0.0
  score:
    name: score
    description: Bit score of seed ortholog alignment
    examples:
    - value: '339.0'
    - value: '876.0'
    from_schema: https://w3id.org/kbase/kbase_ke_pangenome
    rank: 1000
    domain_of:
    - EggnogMapperAnnotations
    - GapmindPathways
    range: float
  eggNOG_OGs:
    name: eggNOG_OGs
    description: 'Hierarchical EggNOG ortholog groups from root to most specific.
      Format: COG@level|taxon pairs, comma-separated.'
    examples:
    - value: COG0154@1|root,COG0154@2|Bacteria,2GKPZ@201174|Actinobacteria,4CPJR@84995|Rubrobacteria
    - value: COG0439@1|root,COG0439@2|Bacteria,1MU4H@1224|Proteobacteria
    from_schema: https://w3id.org/kbase/kbase_ke_pangenome
    rank: 1000
    domain_of:
    - EggnogMapperAnnotations
    range: string
  COG_category:
    name: COG_category
    description: COG functional category code(s). Single letter or combinations. See
      CogFunctionalCategory enum for meanings.
    examples:
    - value: J
      description: Translation/ribosome
    - value: I
      description: Lipid metabolism
    - value: CG
      description: Energy + Carbohydrate
    - value: S
      description: Function unknown
    from_schema: https://w3id.org/kbase/kbase_ke_pangenome
    rank: 1000
    domain_of:
    - EggnogMapperAnnotations
    range: string
  Description:
    name: Description
    description: Functional description from seed ortholog
    examples:
    - value: Belongs to the amidase family
    - value: Biotin carboxylase
    - value: DNA-directed RNA polymerase subunit beta
    from_schema: https://w3id.org/kbase/kbase_ke_pangenome
    rank: 1000
    domain_of:
    - EggnogMapperAnnotations
    range: string
  Preferred_name:
    name: Preferred_name
    description: Gene symbol when available, "-" if none
    examples:
    - value: pycA
    - value: rpoB
    - value: '-'
    from_schema: https://w3id.org/kbase/kbase_ke_pangenome
    rank: 1000
    domain_of:
    - EggnogMapperAnnotations
    range: string
  GOs:
    name: GOs
    description: GO terms, comma-separated. "-" if none.
    examples:
    - value: GO:0003824,GO:0016021
    - value: GO:0005524,GO:0004329,GO:0006633
    - value: '-'
    from_schema: https://w3id.org/kbase/kbase_ke_pangenome
    rank: 1000
    domain_of:
    - EggnogMapperAnnotations
    range: string
  EC:
    name: EC
    description: EC enzyme numbers, comma-separated
    examples:
    - value: 3.5.1.4
    - value: 6.3.4.14,6.4.1.1,6.4.1.2
    - value: 2.7.7.6
    from_schema: https://w3id.org/kbase/kbase_ke_pangenome
    rank: 1000
    domain_of:
    - EggnogMapperAnnotations
    range: string
  KEGG_ko:
    name: KEGG_ko
    description: KEGG Orthology IDs
    examples:
    - value: ko:K01426
    - value: ko:K01959,ko:K01961
    from_schema: https://w3id.org/kbase/kbase_ke_pangenome
    rank: 1000
    domain_of:
    - EggnogMapperAnnotations
    range: string
  KEGG_Pathway:
    name: KEGG_Pathway
    description: KEGG pathway IDs, comma-separated
    examples:
    - value: ko00330,ko00360,map00330,map00360
    - value: ko00020,ko00061,ko00620,ko00640
    from_schema: https://w3id.org/kbase/kbase_ke_pangenome
    rank: 1000
    domain_of:
    - EggnogMapperAnnotations
    range: string
  PFAMs:
    name: PFAMs
    description: PFAM domain annotations, comma-separated
    examples:
    - value: Amidase
    - value: Biotin_carb_C,Biotin_carb_N,CPSase_L_D2
    - value: RNA_pol_Rpb2_1,RNA_pol_Rpb2_2
    from_schema: https://w3id.org/kbase/kbase_ke_pangenome
    rank: 1000
    domain_of:
    - EggnogMapperAnnotations
    range: string

Induced

name: EggnogMapperAnnotations
annotations:
  source_table:
    tag: source_table
    value: eggnog_mapper_annotations
  row_count:
    tag: row_count
    value: '93558330'
description: 'EggNOG-mapper v2 functional annotations for genes. Provides: - COG functional
  categories - GO term annotations - KEGG pathway/ortholog mappings - EC enzyme numbers
  - PFAM domain annotations

  COVERAGE: 93,558,330 annotated genes (~9% of total)

  COG CATEGORY DISTRIBUTION (most common): - S (function unknown): Most common - J
  (translation): ~8% - K (transcription): ~6% - C (energy): ~5% - E (amino acid metabolism):
  ~5%'
from_schema: https://w3id.org/kbase/kbase_ke_pangenome
attributes:
  query_name:
    name: query_name
    description: Gene ID - links to Gene.gene_id
    comments:
    - 'Foreign key: Gene.gene_id'
    examples:
    - value: DBFF01000060.1_2
    - value: CALVBM010000003.1_96
    from_schema: https://w3id.org/kbase/kbase_ke_pangenome
    rank: 1000
    identifier: true
    alias: query_name
    owner: EggnogMapperAnnotations
    domain_of:
    - EggnogMapperAnnotations
    range: string
    required: true
  seed_ortholog:
    name: seed_ortholog
    description: 'Best matching seed ortholog from eggNOG database. Format: taxon_id.locus_tag'
    examples:
    - value: 42256.RradSPS_0079
    - value: 1548153.LR59_00700
    from_schema: https://w3id.org/kbase/kbase_ke_pangenome
    rank: 1000
    alias: seed_ortholog
    owner: EggnogMapperAnnotations
    domain_of:
    - EggnogMapperAnnotations
    range: string
  evalue:
    name: evalue
    description: E-value of seed ortholog match (lower = better match)
    examples:
    - value: '3.06e-109'
    - value: '0.0'
      description: Exact match
    - value: 1e-50
    from_schema: https://w3id.org/kbase/kbase_ke_pangenome
    rank: 1000
    alias: evalue
    owner: EggnogMapperAnnotations
    domain_of:
    - EggnogMapperAnnotations
    range: float
    minimum_value: 0.0
  score:
    name: score
    description: Bit score of seed ortholog alignment
    examples:
    - value: '339.0'
    - value: '876.0'
    from_schema: https://w3id.org/kbase/kbase_ke_pangenome
    rank: 1000
    alias: score
    owner: EggnogMapperAnnotations
    domain_of:
    - EggnogMapperAnnotations
    - GapmindPathways
    range: float
  eggNOG_OGs:
    name: eggNOG_OGs
    description: 'Hierarchical EggNOG ortholog groups from root to most specific.
      Format: COG@level|taxon pairs, comma-separated.'
    examples:
    - value: COG0154@1|root,COG0154@2|Bacteria,2GKPZ@201174|Actinobacteria,4CPJR@84995|Rubrobacteria
    - value: COG0439@1|root,COG0439@2|Bacteria,1MU4H@1224|Proteobacteria
    from_schema: https://w3id.org/kbase/kbase_ke_pangenome
    rank: 1000
    alias: eggNOG_OGs
    owner: EggnogMapperAnnotations
    domain_of:
    - EggnogMapperAnnotations
    range: string
  COG_category:
    name: COG_category
    description: COG functional category code(s). Single letter or combinations. See
      CogFunctionalCategory enum for meanings.
    examples:
    - value: J
      description: Translation/ribosome
    - value: I
      description: Lipid metabolism
    - value: CG
      description: Energy + Carbohydrate
    - value: S
      description: Function unknown
    from_schema: https://w3id.org/kbase/kbase_ke_pangenome
    rank: 1000
    alias: COG_category
    owner: EggnogMapperAnnotations
    domain_of:
    - EggnogMapperAnnotations
    range: string
  Description:
    name: Description
    description: Functional description from seed ortholog
    examples:
    - value: Belongs to the amidase family
    - value: Biotin carboxylase
    - value: DNA-directed RNA polymerase subunit beta
    from_schema: https://w3id.org/kbase/kbase_ke_pangenome
    rank: 1000
    alias: Description
    owner: EggnogMapperAnnotations
    domain_of:
    - EggnogMapperAnnotations
    range: string
  Preferred_name:
    name: Preferred_name
    description: Gene symbol when available, "-" if none
    examples:
    - value: pycA
    - value: rpoB
    - value: '-'
    from_schema: https://w3id.org/kbase/kbase_ke_pangenome
    rank: 1000
    alias: Preferred_name
    owner: EggnogMapperAnnotations
    domain_of:
    - EggnogMapperAnnotations
    range: string
  GOs:
    name: GOs
    description: GO terms, comma-separated. "-" if none.
    examples:
    - value: GO:0003824,GO:0016021
    - value: GO:0005524,GO:0004329,GO:0006633
    - value: '-'
    from_schema: https://w3id.org/kbase/kbase_ke_pangenome
    rank: 1000
    alias: GOs
    owner: EggnogMapperAnnotations
    domain_of:
    - EggnogMapperAnnotations
    range: string
  EC:
    name: EC
    description: EC enzyme numbers, comma-separated
    examples:
    - value: 3.5.1.4
    - value: 6.3.4.14,6.4.1.1,6.4.1.2
    - value: 2.7.7.6
    from_schema: https://w3id.org/kbase/kbase_ke_pangenome
    rank: 1000
    alias: EC
    owner: EggnogMapperAnnotations
    domain_of:
    - EggnogMapperAnnotations
    range: string
  KEGG_ko:
    name: KEGG_ko
    description: KEGG Orthology IDs
    examples:
    - value: ko:K01426
    - value: ko:K01959,ko:K01961
    from_schema: https://w3id.org/kbase/kbase_ke_pangenome
    rank: 1000
    alias: KEGG_ko
    owner: EggnogMapperAnnotations
    domain_of:
    - EggnogMapperAnnotations
    range: string
  KEGG_Pathway:
    name: KEGG_Pathway
    description: KEGG pathway IDs, comma-separated
    examples:
    - value: ko00330,ko00360,map00330,map00360
    - value: ko00020,ko00061,ko00620,ko00640
    from_schema: https://w3id.org/kbase/kbase_ke_pangenome
    rank: 1000
    alias: KEGG_Pathway
    owner: EggnogMapperAnnotations
    domain_of:
    - EggnogMapperAnnotations
    range: string
  PFAMs:
    name: PFAMs
    description: PFAM domain annotations, comma-separated
    examples:
    - value: Amidase
    - value: Biotin_carb_C,Biotin_carb_N,CPSase_L_D2
    - value: RNA_pol_Rpb2_1,RNA_pol_Rpb2_2
    from_schema: https://w3id.org/kbase/kbase_ke_pangenome
    rank: 1000
    alias: PFAMs
    owner: EggnogMapperAnnotations
    domain_of:
    - EggnogMapperAnnotations
    range: string