Class: ScaffoldStats

URI: img_core_v400:ScaffoldStats

classDiagram class ScaffoldStats click ScaffoldStats href "../ScaffoldStats/" ScaffoldStats : count_cds ScaffoldStats : count_cog ScaffoldStats : count_enzymes ScaffoldStats : count_go ScaffoldStats : count_homologs ScaffoldStats : count_interpro ScaffoldStats : count_kegg ScaffoldStats : count_orthologs ScaffoldStats : count_paralogs ScaffoldStats : count_pfam ScaffoldStats : count_rna ScaffoldStats : count_total_gene ScaffoldStats : first_cds ScaffoldStats : first_gene ScaffoldStats : gc_percent ScaffoldStats : mod_date ScaffoldStats : scaffold_oid ScaffoldStats : seq_length ScaffoldStats : taxon ScaffoldStats --> "0..1" Taxon : taxon click Taxon href "../Taxon/" ScaffoldStats : tot_a ScaffoldStats : tot_c ScaffoldStats : tot_g ScaffoldStats : tot_gatc ScaffoldStats : tot_n ScaffoldStats : tot_t ScaffoldStats : tot_x

Slots

Name	Cardinality and Range	Description	Inheritance
scaffold_oid	0..1 Integer		direct
seq_length	0..1 Integer		direct
tot_gatc	0..1 Integer		direct
tot_g	0..1 Integer		direct
tot_a	0..1 Integer		direct
tot_t	0..1 Integer		direct
tot_c	0..1 Integer		direct
tot_n	0..1 Integer		direct
tot_x	0..1 Integer		direct
count_cog	0..1 Integer		direct
count_kegg	0..1 Integer		direct
count_enzymes	0..1 Integer		direct
count_go	0..1 Integer		direct
count_homologs	0..1 Integer		direct
count_orthologs	0..1 Integer		direct
count_paralogs	0..1 Integer		direct
count_interpro	0..1 Integer		direct
count_pfam	0..1 Integer		direct
count_cds	0..1 Integer		direct
count_rna	0..1 Integer		direct
count_total_gene	0..1 Integer		direct
first_gene	0..1 Integer		direct
first_cds	0..1 Integer		direct
gc_percent	0..1 Float		direct
taxon	0..1 Taxon	Foreign key to taxon	direct
mod_date	0..1 Datetime		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:ScaffoldStats
native	img_core_v400:ScaffoldStats

LinkML Source

Direct

name: scaffold_stats
from_schema: https://w3id.org/jgi/img_core_v400
attributes:
  scaffold_oid:
    name: scaffold_oid
    from_schema: https://w3id.org/jgi/img_core_v400
    domain_of:
    - delete_scaffolds
    - dt_intergenic
    - scaffold
    - scaffold_ext_links
    - scaffold_nx_feature
    - scaffold_repeats
    - scaffold_stats
    range: integer
    required: false
  seq_length:
    name: seq_length
    from_schema: https://w3id.org/jgi/img_core_v400
    domain_of:
    - cog
    - kog
    - pfam_family
    - scaffold_nx_feature
    - scaffold_stats
    range: integer
    required: false
  tot_gatc:
    name: tot_gatc
    from_schema: https://w3id.org/jgi/img_core_v400
    rank: 1000
    domain_of:
    - scaffold_stats
    range: integer
    required: false
  tot_g:
    name: tot_g
    from_schema: https://w3id.org/jgi/img_core_v400
    rank: 1000
    domain_of:
    - scaffold_stats
    range: integer
    required: false
  tot_a:
    name: tot_a
    from_schema: https://w3id.org/jgi/img_core_v400
    rank: 1000
    domain_of:
    - scaffold_stats
    range: integer
    required: false
  tot_t:
    name: tot_t
    from_schema: https://w3id.org/jgi/img_core_v400
    rank: 1000
    domain_of:
    - scaffold_stats
    range: integer
    required: false
  tot_c:
    name: tot_c
    from_schema: https://w3id.org/jgi/img_core_v400
    rank: 1000
    domain_of:
    - scaffold_stats
    range: integer
    required: false
  tot_n:
    name: tot_n
    from_schema: https://w3id.org/jgi/img_core_v400
    rank: 1000
    domain_of:
    - scaffold_stats
    range: integer
    required: false
  tot_x:
    name: tot_x
    from_schema: https://w3id.org/jgi/img_core_v400
    rank: 1000
    domain_of:
    - scaffold_stats
    range: integer
    required: false
  count_cog:
    name: count_cog
    from_schema: https://w3id.org/jgi/img_core_v400
    rank: 1000
    domain_of:
    - scaffold_stats
    range: integer
    required: false
  count_kegg:
    name: count_kegg
    from_schema: https://w3id.org/jgi/img_core_v400
    rank: 1000
    domain_of:
    - scaffold_stats
    range: integer
    required: false
  count_enzymes:
    name: count_enzymes
    from_schema: https://w3id.org/jgi/img_core_v400
    rank: 1000
    domain_of:
    - scaffold_stats
    range: integer
    required: false
  count_go:
    name: count_go
    from_schema: https://w3id.org/jgi/img_core_v400
    rank: 1000
    domain_of:
    - scaffold_stats
    - taxon_stats
    range: integer
    required: false
  count_homologs:
    name: count_homologs
    from_schema: https://w3id.org/jgi/img_core_v400
    rank: 1000
    domain_of:
    - scaffold_stats
    range: integer
    required: false
  count_orthologs:
    name: count_orthologs
    from_schema: https://w3id.org/jgi/img_core_v400
    rank: 1000
    domain_of:
    - scaffold_stats
    range: integer
    required: false
  count_paralogs:
    name: count_paralogs
    from_schema: https://w3id.org/jgi/img_core_v400
    rank: 1000
    domain_of:
    - scaffold_stats
    range: integer
    required: false
  count_interpro:
    name: count_interpro
    from_schema: https://w3id.org/jgi/img_core_v400
    rank: 1000
    domain_of:
    - scaffold_stats
    range: integer
    required: false
  count_pfam:
    name: count_pfam
    from_schema: https://w3id.org/jgi/img_core_v400
    rank: 1000
    domain_of:
    - scaffold_stats
    range: integer
    required: false
  count_cds:
    name: count_cds
    from_schema: https://w3id.org/jgi/img_core_v400
    rank: 1000
    domain_of:
    - scaffold_stats
    range: integer
    required: false
  count_rna:
    name: count_rna
    from_schema: https://w3id.org/jgi/img_core_v400
    rank: 1000
    domain_of:
    - scaffold_stats
    range: integer
    required: false
  count_total_gene:
    name: count_total_gene
    from_schema: https://w3id.org/jgi/img_core_v400
    rank: 1000
    domain_of:
    - scaffold_stats
    range: integer
    required: false
  first_gene:
    name: first_gene
    from_schema: https://w3id.org/jgi/img_core_v400
    rank: 1000
    domain_of:
    - scaffold_stats
    range: integer
    required: false
  first_cds:
    name: first_cds
    from_schema: https://w3id.org/jgi/img_core_v400
    rank: 1000
    domain_of:
    - scaffold_stats
    range: integer
    required: false
  gc_percent:
    name: gc_percent
    from_schema: https://w3id.org/jgi/img_core_v400
    domain_of:
    - gene
    - scaffold_stats
    - taxon_stats
    - taxon_stats_merfs
    - taxon_stats_prod_vw
    range: float
    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
  mod_date:
    name: mod_date
    from_schema: https://w3id.org/jgi/img_core_v400
    domain_of:
    - gene
    - img_orf_type
    - scaffold_stats
    - taxon
    - taxon_prod_vw
    - taxon_stats
    - taxon_stats_merfs
    - taxon_stats_prod_vw
    range: datetime
    required: false

Induced

name: scaffold_stats
from_schema: https://w3id.org/jgi/img_core_v400
attributes:
  scaffold_oid:
    name: scaffold_oid
    from_schema: https://w3id.org/jgi/img_core_v400
    alias: scaffold_oid
    owner: scaffold_stats
    domain_of:
    - delete_scaffolds
    - dt_intergenic
    - scaffold
    - scaffold_ext_links
    - scaffold_nx_feature
    - scaffold_repeats
    - scaffold_stats
    range: integer
    required: false
  seq_length:
    name: seq_length
    from_schema: https://w3id.org/jgi/img_core_v400
    alias: seq_length
    owner: scaffold_stats
    domain_of:
    - cog
    - kog
    - pfam_family
    - scaffold_nx_feature
    - scaffold_stats
    range: integer
    required: false
  tot_gatc:
    name: tot_gatc
    from_schema: https://w3id.org/jgi/img_core_v400
    rank: 1000
    alias: tot_gatc
    owner: scaffold_stats
    domain_of:
    - scaffold_stats
    range: integer
    required: false
  tot_g:
    name: tot_g
    from_schema: https://w3id.org/jgi/img_core_v400
    rank: 1000
    alias: tot_g
    owner: scaffold_stats
    domain_of:
    - scaffold_stats
    range: integer
    required: false
  tot_a:
    name: tot_a
    from_schema: https://w3id.org/jgi/img_core_v400
    rank: 1000
    alias: tot_a
    owner: scaffold_stats
    domain_of:
    - scaffold_stats
    range: integer
    required: false
  tot_t:
    name: tot_t
    from_schema: https://w3id.org/jgi/img_core_v400
    rank: 1000
    alias: tot_t
    owner: scaffold_stats
    domain_of:
    - scaffold_stats
    range: integer
    required: false
  tot_c:
    name: tot_c
    from_schema: https://w3id.org/jgi/img_core_v400
    rank: 1000
    alias: tot_c
    owner: scaffold_stats
    domain_of:
    - scaffold_stats
    range: integer
    required: false
  tot_n:
    name: tot_n
    from_schema: https://w3id.org/jgi/img_core_v400
    rank: 1000
    alias: tot_n
    owner: scaffold_stats
    domain_of:
    - scaffold_stats
    range: integer
    required: false
  tot_x:
    name: tot_x
    from_schema: https://w3id.org/jgi/img_core_v400
    rank: 1000
    alias: tot_x
    owner: scaffold_stats
    domain_of:
    - scaffold_stats
    range: integer
    required: false
  count_cog:
    name: count_cog
    from_schema: https://w3id.org/jgi/img_core_v400
    rank: 1000
    alias: count_cog
    owner: scaffold_stats
    domain_of:
    - scaffold_stats
    range: integer
    required: false
  count_kegg:
    name: count_kegg
    from_schema: https://w3id.org/jgi/img_core_v400
    rank: 1000
    alias: count_kegg
    owner: scaffold_stats
    domain_of:
    - scaffold_stats
    range: integer
    required: false
  count_enzymes:
    name: count_enzymes
    from_schema: https://w3id.org/jgi/img_core_v400
    rank: 1000
    alias: count_enzymes
    owner: scaffold_stats
    domain_of:
    - scaffold_stats
    range: integer
    required: false
  count_go:
    name: count_go
    from_schema: https://w3id.org/jgi/img_core_v400
    rank: 1000
    alias: count_go
    owner: scaffold_stats
    domain_of:
    - scaffold_stats
    - taxon_stats
    range: integer
    required: false
  count_homologs:
    name: count_homologs
    from_schema: https://w3id.org/jgi/img_core_v400
    rank: 1000
    alias: count_homologs
    owner: scaffold_stats
    domain_of:
    - scaffold_stats
    range: integer
    required: false
  count_orthologs:
    name: count_orthologs
    from_schema: https://w3id.org/jgi/img_core_v400
    rank: 1000
    alias: count_orthologs
    owner: scaffold_stats
    domain_of:
    - scaffold_stats
    range: integer
    required: false
  count_paralogs:
    name: count_paralogs
    from_schema: https://w3id.org/jgi/img_core_v400
    rank: 1000
    alias: count_paralogs
    owner: scaffold_stats
    domain_of:
    - scaffold_stats
    range: integer
    required: false
  count_interpro:
    name: count_interpro
    from_schema: https://w3id.org/jgi/img_core_v400
    rank: 1000
    alias: count_interpro
    owner: scaffold_stats
    domain_of:
    - scaffold_stats
    range: integer
    required: false
  count_pfam:
    name: count_pfam
    from_schema: https://w3id.org/jgi/img_core_v400
    rank: 1000
    alias: count_pfam
    owner: scaffold_stats
    domain_of:
    - scaffold_stats
    range: integer
    required: false
  count_cds:
    name: count_cds
    from_schema: https://w3id.org/jgi/img_core_v400
    rank: 1000
    alias: count_cds
    owner: scaffold_stats
    domain_of:
    - scaffold_stats
    range: integer
    required: false
  count_rna:
    name: count_rna
    from_schema: https://w3id.org/jgi/img_core_v400
    rank: 1000
    alias: count_rna
    owner: scaffold_stats
    domain_of:
    - scaffold_stats
    range: integer
    required: false
  count_total_gene:
    name: count_total_gene
    from_schema: https://w3id.org/jgi/img_core_v400
    rank: 1000
    alias: count_total_gene
    owner: scaffold_stats
    domain_of:
    - scaffold_stats
    range: integer
    required: false
  first_gene:
    name: first_gene
    from_schema: https://w3id.org/jgi/img_core_v400
    rank: 1000
    alias: first_gene
    owner: scaffold_stats
    domain_of:
    - scaffold_stats
    range: integer
    required: false
  first_cds:
    name: first_cds
    from_schema: https://w3id.org/jgi/img_core_v400
    rank: 1000
    alias: first_cds
    owner: scaffold_stats
    domain_of:
    - scaffold_stats
    range: integer
    required: false
  gc_percent:
    name: gc_percent
    from_schema: https://w3id.org/jgi/img_core_v400
    alias: gc_percent
    owner: scaffold_stats
    domain_of:
    - gene
    - scaffold_stats
    - taxon_stats
    - taxon_stats_merfs
    - taxon_stats_prod_vw
    range: float
    required: false
  taxon:
    name: taxon
    description: Foreign key to taxon
    from_schema: https://w3id.org/jgi/img_core_v400
    alias: taxon
    owner: scaffold_stats
    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
  mod_date:
    name: mod_date
    from_schema: https://w3id.org/jgi/img_core_v400
    alias: mod_date
    owner: scaffold_stats
    domain_of:
    - gene
    - img_orf_type
    - scaffold_stats
    - taxon
    - taxon_prod_vw
    - taxon_stats
    - taxon_stats_merfs
    - taxon_stats_prod_vw
    range: datetime
    required: false