Class: GeneCogGroups

URI: img_core_v400:GeneCogGroups

classDiagram class GeneCogGroups click GeneCogGroups href "../GeneCogGroups/" GeneCogGroups : align_length GeneCogGroups : bit_score GeneCogGroups : cog GeneCogGroups : evalue GeneCogGroups : gene_oid GeneCogGroups : percent_identity GeneCogGroups : query_end GeneCogGroups : query_start GeneCogGroups : rank_order GeneCogGroups : scaffold GeneCogGroups : subj_end GeneCogGroups : subj_start GeneCogGroups : taxon GeneCogGroups --> "0..1" Taxon : taxon click Taxon href "../Taxon/"

Slots

Name	Cardinality and Range	Description	Inheritance
gene_oid	0..1 Integer		direct
cog	0..1 String		direct
percent_identity	0..1 Float		direct
query_start	0..1 Integer		direct
query_end	0..1 Integer		direct
subj_start	0..1 Integer		direct
subj_end	0..1 Integer		direct
evalue	0..1 Float		direct
bit_score	0..1 Float		direct
align_length	0..1 Integer		direct
rank_order	0..1 Integer		direct
taxon	0..1 Taxon	Foreign key to taxon	direct
scaffold	0..1 Integer		direct

Identifier and Mapping Information

Schema Source

from schema: https://w3id.org/jgi/img_core_v400

Mappings

Mapping Type	Mapped Value
self	img_core_v400:GeneCogGroups
native	img_core_v400:GeneCogGroups

LinkML Source

Direct

name: gene_cog_groups
from_schema: https://w3id.org/jgi/img_core_v400
attributes:
  gene_oid:
    name: gene_oid
    from_schema: https://w3id.org/jgi/img_core_v400
    domain_of:
    - actino_abc_genes
    - delete_genes
    - dt_ht_hits
    - dt_img_gene_prot_pep_sample
    - dt_phylum_dist_genes
    - dt_scog_genes
    - gene
    - gene_aliases
    - gene_biocyc_rxns
    - gene_cathfam
    - gene_cog_groups
    - gene_essential_genes
    - gene_exceptions
    - gene_ext_links
    - gene_feature_tags
    - gene_frag_coords
    - gene_go_terms
    - gene_img_interpro_hits
    - gene_ko_enzymes
    - gene_ko_enzymes_new
    - gene_ko_terms
    - gene_kog_groups
    - gene_notes
    - gene_paralogs
    - gene_pdb_xrefs
    - gene_pfam_families
    - gene_sig_peptides
    - gene_smart
    - gene_superfam
    - gene_tigrfams
    - gene_xref_families
    - kp_pseudo
    - merfs_gene_mapping
    - mv_gene_tmhmm_stats
    - tmp_genes
    range: integer
    required: false
  cog:
    name: cog
    from_schema: https://w3id.org/jgi/img_core_v400
    domain_of:
    - cog2014
    - dt_ko_ec_cog_pfam
    - gene_cog_groups
    - pfam_family_cogs
    range: string
    required: false
  percent_identity:
    name: percent_identity
    from_schema: https://w3id.org/jgi/img_core_v400
    domain_of:
    - dt_phylum_dist_genes
    - gene_cathfam
    - gene_cog_groups
    - gene_ko_terms
    - gene_kog_groups
    - gene_paralogs
    - gene_pfam_families
    - gene_smart
    - gene_superfam
    - gene_tigrfams
    range: float
    required: false
  query_start:
    name: query_start
    from_schema: https://w3id.org/jgi/img_core_v400
    domain_of:
    - gene_cathfam
    - gene_cog_groups
    - gene_ko_terms
    - gene_kog_groups
    - gene_paralogs
    - gene_pfam_families
    - gene_smart
    - gene_superfam
    range: integer
    required: false
  query_end:
    name: query_end
    from_schema: https://w3id.org/jgi/img_core_v400
    domain_of:
    - gene_cathfam
    - gene_cog_groups
    - gene_ko_terms
    - gene_kog_groups
    - gene_paralogs
    - gene_pfam_families
    - gene_smart
    - gene_superfam
    range: integer
    required: false
  subj_start:
    name: subj_start
    from_schema: https://w3id.org/jgi/img_core_v400
    rank: 1000
    domain_of:
    - gene_cog_groups
    - gene_ko_terms
    - gene_kog_groups
    - gene_paralogs
    - gene_pfam_families
    range: integer
    required: false
  subj_end:
    name: subj_end
    from_schema: https://w3id.org/jgi/img_core_v400
    rank: 1000
    domain_of:
    - gene_cog_groups
    - gene_ko_terms
    - gene_kog_groups
    - gene_paralogs
    - gene_pfam_families
    range: integer
    required: false
  evalue:
    name: evalue
    from_schema: https://w3id.org/jgi/img_core_v400
    domain_of:
    - gene_cathfam
    - gene_cog_groups
    - gene_ko_terms
    - gene_kog_groups
    - gene_paralogs
    - gene_pfam_families
    - gene_smart
    - gene_superfam
    - gene_tigrfams
    range: float
    required: false
  bit_score:
    name: bit_score
    from_schema: https://w3id.org/jgi/img_core_v400
    domain_of:
    - dt_phylum_dist_genes
    - gene_cathfam
    - gene_cog_groups
    - gene_ko_terms
    - gene_kog_groups
    - gene_paralogs
    - gene_pfam_families
    - gene_smart
    - gene_superfam
    - gene_tigrfams
    range: float
    required: false
  align_length:
    name: align_length
    from_schema: https://w3id.org/jgi/img_core_v400
    domain_of:
    - gene_cathfam
    - gene_cog_groups
    - gene_ko_terms
    - gene_kog_groups
    - gene_pfam_families
    - gene_smart
    - gene_superfam
    range: integer
    required: false
  rank_order:
    name: rank_order
    from_schema: https://w3id.org/jgi/img_core_v400
    rank: 1000
    domain_of:
    - gene_cog_groups
    - gene_kog_groups
    range: integer
    required: false
  taxon:
    name: taxon
    description: Foreign key to taxon
    from_schema: https://w3id.org/jgi/img_core_v400
    domain_of:
    - cog_species
    - dt_img_gene_prot_pep_sample
    - dt_taxon_node_lite
    - gene
    - gene_biocyc_rxns
    - gene_cathfam
    - gene_cog_groups
    - gene_img_interpro_hits
    - gene_ko_enzymes
    - gene_ko_enzymes_new
    - gene_ko_terms
    - gene_kog_groups
    - gene_pfam_families
    - gene_smart
    - gene_superfam
    - gene_tigrfams
    - gene_xref_families
    - kp_pseudo
    - merfs_gene_mapping
    - paralog_group
    - scaffold
    - scaffold_stats
    - taxon_node_lite
    range: taxon
    required: false
  scaffold:
    name: scaffold
    from_schema: https://w3id.org/jgi/img_core_v400
    domain_of:
    - gene
    - gene_biocyc_rxns
    - gene_cathfam
    - gene_cog_groups
    - gene_img_interpro_hits
    - gene_ko_enzymes
    - gene_ko_enzymes_new
    - gene_ko_terms
    - gene_kog_groups
    - gene_pfam_families
    - gene_smart
    - gene_superfam
    - gene_tigrfams
    - gene_xref_families
    - iso_plasmids
    - kp_pseudo
    range: integer
    required: false

Induced

name: gene_cog_groups
from_schema: https://w3id.org/jgi/img_core_v400
attributes:
  gene_oid:
    name: gene_oid
    from_schema: https://w3id.org/jgi/img_core_v400
    alias: gene_oid
    owner: gene_cog_groups
    domain_of:
    - actino_abc_genes
    - delete_genes
    - dt_ht_hits
    - dt_img_gene_prot_pep_sample
    - dt_phylum_dist_genes
    - dt_scog_genes
    - gene
    - gene_aliases
    - gene_biocyc_rxns
    - gene_cathfam
    - gene_cog_groups
    - gene_essential_genes
    - gene_exceptions
    - gene_ext_links
    - gene_feature_tags
    - gene_frag_coords
    - gene_go_terms
    - gene_img_interpro_hits
    - gene_ko_enzymes
    - gene_ko_enzymes_new
    - gene_ko_terms
    - gene_kog_groups
    - gene_notes
    - gene_paralogs
    - gene_pdb_xrefs
    - gene_pfam_families
    - gene_sig_peptides
    - gene_smart
    - gene_superfam
    - gene_tigrfams
    - gene_xref_families
    - kp_pseudo
    - merfs_gene_mapping
    - mv_gene_tmhmm_stats
    - tmp_genes
    range: integer
    required: false
  cog:
    name: cog
    from_schema: https://w3id.org/jgi/img_core_v400
    alias: cog
    owner: gene_cog_groups
    domain_of:
    - cog2014
    - dt_ko_ec_cog_pfam
    - gene_cog_groups
    - pfam_family_cogs
    range: string
    required: false
  percent_identity:
    name: percent_identity
    from_schema: https://w3id.org/jgi/img_core_v400
    alias: percent_identity
    owner: gene_cog_groups
    domain_of:
    - dt_phylum_dist_genes
    - gene_cathfam
    - gene_cog_groups
    - gene_ko_terms
    - gene_kog_groups
    - gene_paralogs
    - gene_pfam_families
    - gene_smart
    - gene_superfam
    - gene_tigrfams
    range: float
    required: false
  query_start:
    name: query_start
    from_schema: https://w3id.org/jgi/img_core_v400
    alias: query_start
    owner: gene_cog_groups
    domain_of:
    - gene_cathfam
    - gene_cog_groups
    - gene_ko_terms
    - gene_kog_groups
    - gene_paralogs
    - gene_pfam_families
    - gene_smart
    - gene_superfam
    range: integer
    required: false
  query_end:
    name: query_end
    from_schema: https://w3id.org/jgi/img_core_v400
    alias: query_end
    owner: gene_cog_groups
    domain_of:
    - gene_cathfam
    - gene_cog_groups
    - gene_ko_terms
    - gene_kog_groups
    - gene_paralogs
    - gene_pfam_families
    - gene_smart
    - gene_superfam
    range: integer
    required: false
  subj_start:
    name: subj_start
    from_schema: https://w3id.org/jgi/img_core_v400
    rank: 1000
    alias: subj_start
    owner: gene_cog_groups
    domain_of:
    - gene_cog_groups
    - gene_ko_terms
    - gene_kog_groups
    - gene_paralogs
    - gene_pfam_families
    range: integer
    required: false
  subj_end:
    name: subj_end
    from_schema: https://w3id.org/jgi/img_core_v400
    rank: 1000
    alias: subj_end
    owner: gene_cog_groups
    domain_of:
    - gene_cog_groups
    - gene_ko_terms
    - gene_kog_groups
    - gene_paralogs
    - gene_pfam_families
    range: integer
    required: false
  evalue:
    name: evalue
    from_schema: https://w3id.org/jgi/img_core_v400
    alias: evalue
    owner: gene_cog_groups
    domain_of:
    - gene_cathfam
    - gene_cog_groups
    - gene_ko_terms
    - gene_kog_groups
    - gene_paralogs
    - gene_pfam_families
    - gene_smart
    - gene_superfam
    - gene_tigrfams
    range: float
    required: false
  bit_score:
    name: bit_score
    from_schema: https://w3id.org/jgi/img_core_v400
    alias: bit_score
    owner: gene_cog_groups
    domain_of:
    - dt_phylum_dist_genes
    - gene_cathfam
    - gene_cog_groups
    - gene_ko_terms
    - gene_kog_groups
    - gene_paralogs
    - gene_pfam_families
    - gene_smart
    - gene_superfam
    - gene_tigrfams
    range: float
    required: false
  align_length:
    name: align_length
    from_schema: https://w3id.org/jgi/img_core_v400
    alias: align_length
    owner: gene_cog_groups
    domain_of:
    - gene_cathfam
    - gene_cog_groups
    - gene_ko_terms
    - gene_kog_groups
    - gene_pfam_families
    - gene_smart
    - gene_superfam
    range: integer
    required: false
  rank_order:
    name: rank_order
    from_schema: https://w3id.org/jgi/img_core_v400
    rank: 1000
    alias: rank_order
    owner: gene_cog_groups
    domain_of:
    - gene_cog_groups
    - gene_kog_groups
    range: integer
    required: false
  taxon:
    name: taxon
    description: Foreign key to taxon
    from_schema: https://w3id.org/jgi/img_core_v400
    alias: taxon
    owner: gene_cog_groups
    domain_of:
    - cog_species
    - dt_img_gene_prot_pep_sample
    - dt_taxon_node_lite
    - gene
    - gene_biocyc_rxns
    - gene_cathfam
    - gene_cog_groups
    - gene_img_interpro_hits
    - gene_ko_enzymes
    - gene_ko_enzymes_new
    - gene_ko_terms
    - gene_kog_groups
    - gene_pfam_families
    - gene_smart
    - gene_superfam
    - gene_tigrfams
    - gene_xref_families
    - kp_pseudo
    - merfs_gene_mapping
    - paralog_group
    - scaffold
    - scaffold_stats
    - taxon_node_lite
    range: taxon
    required: false
  scaffold:
    name: scaffold
    from_schema: https://w3id.org/jgi/img_core_v400
    alias: scaffold
    owner: gene_cog_groups
    domain_of:
    - gene
    - gene_biocyc_rxns
    - gene_cathfam
    - gene_cog_groups
    - gene_img_interpro_hits
    - gene_ko_enzymes
    - gene_ko_enzymes_new
    - gene_ko_terms
    - gene_kog_groups
    - gene_pfam_families
    - gene_smart
    - gene_superfam
    - gene_tigrfams
    - gene_xref_families
    - iso_plasmids
    - kp_pseudo
    range: integer
    required: false