Class: NcbiAssembly

URI: gold:NcbiAssembly

classDiagram class NcbiAssembly click NcbiAssembly href "../NcbiAssembly/" NcbiAssembly : annotation_date NcbiAssembly : annotation_name NcbiAssembly : annotation_provider NcbiAssembly : asm_name NcbiAssembly : asm_not_live_date NcbiAssembly : asm_submitter NcbiAssembly : assembly_accession NcbiAssembly : assembly_accession_no_version NcbiAssembly : assembly_level NcbiAssembly : assembly_method NcbiAssembly : assembly_type NcbiAssembly : bioproject NcbiAssembly : biosample NcbiAssembly : contig_count NcbiAssembly : excluded_from_refseq NcbiAssembly : expected_final_version NcbiAssembly : ftp_path NcbiAssembly : gbrs_paired_asm NcbiAssembly : gc_percent NcbiAssembly : genbank_json NcbiAssembly : genome_coverage NcbiAssembly : genome_rep NcbiAssembly : genome_size NcbiAssembly : genome_size_ungapped NcbiAssembly : group_ NcbiAssembly : infraspecific_name NcbiAssembly : isolate NcbiAssembly : ncbi_assembly_id NcbiAssembly : non_coding_gene_count NcbiAssembly : organism_name NcbiAssembly : paired_asm_comp NcbiAssembly : protein_coding_gene_count NcbiAssembly : pubmed_id NcbiAssembly : refseq_assembly_accession NcbiAssembly : refseq_category NcbiAssembly : relation_to_type_material NcbiAssembly : release_type NcbiAssembly : replicon_count NcbiAssembly : scaffold_count NcbiAssembly : seq_rel_date NcbiAssembly : sequencing_technology NcbiAssembly : species_taxid NcbiAssembly : taxid NcbiAssembly : total_gene_count NcbiAssembly : version_status NcbiAssembly : wgs_master

Slots

Name	Cardinality and Range	Inheritance
ncbi_assembly_id	0..1 Float	direct
assembly_accession	0..1 String	direct
assembly_accession_no_version	0..1 String	direct
bioproject	0..1 String	direct
biosample	0..1 String	direct
wgs_master	0..1 String	direct
refseq_category	0..1 String	direct
taxid	0..1 Float	direct
species_taxid	0..1 Float	direct
organism_name	0..1 String	direct
infraspecific_name	0..1 String	direct
isolate	0..1 String	direct
version_status	0..1 String	direct
assembly_level	0..1 String	direct
release_type	0..1 String	direct
genome_rep	0..1 String	direct
seq_rel_date	0..1 Datetime	direct
asm_name	0..1 String	direct
asm_submitter	0..1 String	direct
gbrs_paired_asm	0..1 String	direct
paired_asm_comp	0..1 String	direct
ftp_path	0..1 String	direct
excluded_from_refseq	0..1 String	direct
relation_to_type_material	0..1 String	direct
asm_not_live_date	0..1 Datetime	direct
assembly_type	0..1 String	direct
group_	0..1 String	direct
genome_size	0..1 Float	direct
genome_size_ungapped	0..1 Float	direct
gc_percent	0..1 Float	direct
replicon_count	0..1 Float	direct
scaffold_count	0..1 Float	direct
contig_count	0..1 Float	direct
annotation_provider	0..1 String	direct
annotation_name	0..1 String	direct
annotation_date	0..1 Datetime	direct
total_gene_count	0..1 Float	direct
protein_coding_gene_count	0..1 Float	direct
non_coding_gene_count	0..1 Float	direct
pubmed_id	0..1 String	direct
assembly_method	0..1 String	direct
expected_final_version	0..1 String	direct
genome_coverage	0..1 String	direct
sequencing_technology	0..1 String	direct
refseq_assembly_accession	0..1 String	direct
genbank_json	0..1 String	direct

Usages

used by	used in	type	used
NcbiGenbank	ncbi_assembly_id	range	NcbiAssembly

Identifier and Mapping Information

Schema Source

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

Mappings

Mapping Type	Mapped Value
self	gold:NcbiAssembly
native	gold:NcbiAssembly

LinkML Source

Direct

name: ncbi_assembly
from_schema: https://w3id.org/jgi/gold
attributes:
  ncbi_assembly_id:
    name: ncbi_assembly_id
    from_schema: https://w3id.org/jgi/gold
    rank: 1000
    domain_of:
    - ncbi_assembly
    - ncbi_genbank
    range: float
    required: false
  assembly_accession:
    name: assembly_accession
    from_schema: https://w3id.org/jgi/gold
    rank: 1000
    domain_of:
    - ncbi_assembly
    - project
    range: string
    required: false
  assembly_accession_no_version:
    name: assembly_accession_no_version
    from_schema: https://w3id.org/jgi/gold
    rank: 1000
    domain_of:
    - ncbi_assembly
    range: string
    required: false
  bioproject:
    name: bioproject
    from_schema: https://w3id.org/jgi/gold
    rank: 1000
    domain_of:
    - ncbi_assembly
    range: string
    required: false
  biosample:
    name: biosample
    from_schema: https://w3id.org/jgi/gold
    rank: 1000
    domain_of:
    - ncbi_assembly
    range: string
    required: false
  wgs_master:
    name: wgs_master
    from_schema: https://w3id.org/jgi/gold
    rank: 1000
    domain_of:
    - ncbi_assembly
    range: string
    required: false
  refseq_category:
    name: refseq_category
    from_schema: https://w3id.org/jgi/gold
    rank: 1000
    domain_of:
    - ncbi_assembly
    range: string
    required: false
  taxid:
    name: taxid
    from_schema: https://w3id.org/jgi/gold
    rank: 1000
    domain_of:
    - ncbi_assembly
    range: float
    required: false
  species_taxid:
    name: species_taxid
    from_schema: https://w3id.org/jgi/gold
    rank: 1000
    domain_of:
    - ncbi_assembly
    range: float
    required: false
  organism_name:
    name: organism_name
    from_schema: https://w3id.org/jgi/gold
    domain_of:
    - assembly
    - ncbi_assembly
    - organism_v2
    range: string
    required: false
  infraspecific_name:
    name: infraspecific_name
    from_schema: https://w3id.org/jgi/gold
    rank: 1000
    domain_of:
    - ncbi_assembly
    range: string
    required: false
  isolate:
    name: isolate
    from_schema: https://w3id.org/jgi/gold
    rank: 1000
    domain_of:
    - ncbi_assembly
    range: string
    required: false
  version_status:
    name: version_status
    from_schema: https://w3id.org/jgi/gold
    rank: 1000
    domain_of:
    - ncbi_assembly
    range: string
    required: false
  assembly_level:
    name: assembly_level
    from_schema: https://w3id.org/jgi/gold
    rank: 1000
    domain_of:
    - ncbi_assembly
    range: string
    required: false
  release_type:
    name: release_type
    from_schema: https://w3id.org/jgi/gold
    rank: 1000
    domain_of:
    - ncbi_assembly
    range: string
    required: false
  genome_rep:
    name: genome_rep
    from_schema: https://w3id.org/jgi/gold
    rank: 1000
    domain_of:
    - ncbi_assembly
    range: string
    required: false
  seq_rel_date:
    name: seq_rel_date
    from_schema: https://w3id.org/jgi/gold
    rank: 1000
    domain_of:
    - ncbi_assembly
    range: datetime
    required: false
  asm_name:
    name: asm_name
    from_schema: https://w3id.org/jgi/gold
    rank: 1000
    domain_of:
    - ncbi_assembly
    range: string
    required: false
  asm_submitter:
    name: asm_submitter
    from_schema: https://w3id.org/jgi/gold
    rank: 1000
    domain_of:
    - ncbi_assembly
    range: string
    required: false
  gbrs_paired_asm:
    name: gbrs_paired_asm
    from_schema: https://w3id.org/jgi/gold
    rank: 1000
    domain_of:
    - ncbi_assembly
    range: string
    required: false
  paired_asm_comp:
    name: paired_asm_comp
    from_schema: https://w3id.org/jgi/gold
    rank: 1000
    domain_of:
    - ncbi_assembly
    range: string
    required: false
  ftp_path:
    name: ftp_path
    from_schema: https://w3id.org/jgi/gold
    rank: 1000
    domain_of:
    - ncbi_assembly
    range: string
    required: false
  excluded_from_refseq:
    name: excluded_from_refseq
    from_schema: https://w3id.org/jgi/gold
    rank: 1000
    domain_of:
    - ncbi_assembly
    range: string
    required: false
  relation_to_type_material:
    name: relation_to_type_material
    from_schema: https://w3id.org/jgi/gold
    rank: 1000
    domain_of:
    - ncbi_assembly
    range: string
    required: false
  asm_not_live_date:
    name: asm_not_live_date
    from_schema: https://w3id.org/jgi/gold
    rank: 1000
    domain_of:
    - ncbi_assembly
    range: datetime
    required: false
  assembly_type:
    name: assembly_type
    from_schema: https://w3id.org/jgi/gold
    domain_of:
    - assembly
    - ncbi_assembly
    range: string
    required: false
  group_:
    name: group_
    from_schema: https://w3id.org/jgi/gold
    rank: 1000
    domain_of:
    - ncbi_assembly
    range: string
    required: false
  genome_size:
    name: genome_size
    from_schema: https://w3id.org/jgi/gold
    rank: 1000
    domain_of:
    - ncbi_assembly
    range: float
    required: false
  genome_size_ungapped:
    name: genome_size_ungapped
    from_schema: https://w3id.org/jgi/gold
    rank: 1000
    domain_of:
    - ncbi_assembly
    range: float
    required: false
  gc_percent:
    name: gc_percent
    from_schema: https://w3id.org/jgi/gold
    rank: 1000
    domain_of:
    - ncbi_assembly
    - project
    range: float
    required: false
  replicon_count:
    name: replicon_count
    from_schema: https://w3id.org/jgi/gold
    rank: 1000
    domain_of:
    - ncbi_assembly
    range: float
    required: false
  scaffold_count:
    name: scaffold_count
    from_schema: https://w3id.org/jgi/gold
    domain_of:
    - analysis_project
    - ncbi_assembly
    - project
    range: float
    required: false
  contig_count:
    name: contig_count
    from_schema: https://w3id.org/jgi/gold
    domain_of:
    - analysis_project
    - ncbi_assembly
    - project
    range: float
    required: false
  annotation_provider:
    name: annotation_provider
    from_schema: https://w3id.org/jgi/gold
    rank: 1000
    domain_of:
    - ncbi_assembly
    range: string
    required: false
  annotation_name:
    name: annotation_name
    from_schema: https://w3id.org/jgi/gold
    rank: 1000
    domain_of:
    - ncbi_assembly
    range: string
    required: false
  annotation_date:
    name: annotation_date
    from_schema: https://w3id.org/jgi/gold
    rank: 1000
    domain_of:
    - ncbi_assembly
    range: datetime
    required: false
  total_gene_count:
    name: total_gene_count
    from_schema: https://w3id.org/jgi/gold
    rank: 1000
    domain_of:
    - ncbi_assembly
    range: float
    required: false
  protein_coding_gene_count:
    name: protein_coding_gene_count
    from_schema: https://w3id.org/jgi/gold
    rank: 1000
    domain_of:
    - ncbi_assembly
    range: float
    required: false
  non_coding_gene_count:
    name: non_coding_gene_count
    from_schema: https://w3id.org/jgi/gold
    rank: 1000
    domain_of:
    - ncbi_assembly
    range: float
    required: false
  pubmed_id:
    name: pubmed_id
    from_schema: https://w3id.org/jgi/gold
    rank: 1000
    domain_of:
    - ncbi_assembly
    range: string
    required: false
  assembly_method:
    name: assembly_method
    from_schema: https://w3id.org/jgi/gold
    rank: 1000
    domain_of:
    - ncbi_assembly
    range: string
    required: false
  expected_final_version:
    name: expected_final_version
    from_schema: https://w3id.org/jgi/gold
    rank: 1000
    domain_of:
    - ncbi_assembly
    range: string
    required: false
  genome_coverage:
    name: genome_coverage
    from_schema: https://w3id.org/jgi/gold
    rank: 1000
    domain_of:
    - ncbi_assembly
    range: string
    required: false
  sequencing_technology:
    name: sequencing_technology
    from_schema: https://w3id.org/jgi/gold
    rank: 1000
    domain_of:
    - ncbi_assembly
    range: string
    required: false
  refseq_assembly_accession:
    name: refseq_assembly_accession
    from_schema: https://w3id.org/jgi/gold
    rank: 1000
    domain_of:
    - ncbi_assembly
    range: string
    required: false
  genbank_json:
    name: genbank_json
    from_schema: https://w3id.org/jgi/gold
    rank: 1000
    domain_of:
    - ncbi_assembly
    range: string
    required: false

Induced

name: ncbi_assembly
from_schema: https://w3id.org/jgi/gold
attributes:
  ncbi_assembly_id:
    name: ncbi_assembly_id
    from_schema: https://w3id.org/jgi/gold
    rank: 1000
    alias: ncbi_assembly_id
    owner: ncbi_assembly
    domain_of:
    - ncbi_assembly
    - ncbi_genbank
    range: float
    required: false
  assembly_accession:
    name: assembly_accession
    from_schema: https://w3id.org/jgi/gold
    rank: 1000
    alias: assembly_accession
    owner: ncbi_assembly
    domain_of:
    - ncbi_assembly
    - project
    range: string
    required: false
  assembly_accession_no_version:
    name: assembly_accession_no_version
    from_schema: https://w3id.org/jgi/gold
    rank: 1000
    alias: assembly_accession_no_version
    owner: ncbi_assembly
    domain_of:
    - ncbi_assembly
    range: string
    required: false
  bioproject:
    name: bioproject
    from_schema: https://w3id.org/jgi/gold
    rank: 1000
    alias: bioproject
    owner: ncbi_assembly
    domain_of:
    - ncbi_assembly
    range: string
    required: false
  biosample:
    name: biosample
    from_schema: https://w3id.org/jgi/gold
    rank: 1000
    alias: biosample
    owner: ncbi_assembly
    domain_of:
    - ncbi_assembly
    range: string
    required: false
  wgs_master:
    name: wgs_master
    from_schema: https://w3id.org/jgi/gold
    rank: 1000
    alias: wgs_master
    owner: ncbi_assembly
    domain_of:
    - ncbi_assembly
    range: string
    required: false
  refseq_category:
    name: refseq_category
    from_schema: https://w3id.org/jgi/gold
    rank: 1000
    alias: refseq_category
    owner: ncbi_assembly
    domain_of:
    - ncbi_assembly
    range: string
    required: false
  taxid:
    name: taxid
    from_schema: https://w3id.org/jgi/gold
    rank: 1000
    alias: taxid
    owner: ncbi_assembly
    domain_of:
    - ncbi_assembly
    range: float
    required: false
  species_taxid:
    name: species_taxid
    from_schema: https://w3id.org/jgi/gold
    rank: 1000
    alias: species_taxid
    owner: ncbi_assembly
    domain_of:
    - ncbi_assembly
    range: float
    required: false
  organism_name:
    name: organism_name
    from_schema: https://w3id.org/jgi/gold
    alias: organism_name
    owner: ncbi_assembly
    domain_of:
    - assembly
    - ncbi_assembly
    - organism_v2
    range: string
    required: false
  infraspecific_name:
    name: infraspecific_name
    from_schema: https://w3id.org/jgi/gold
    rank: 1000
    alias: infraspecific_name
    owner: ncbi_assembly
    domain_of:
    - ncbi_assembly
    range: string
    required: false
  isolate:
    name: isolate
    from_schema: https://w3id.org/jgi/gold
    rank: 1000
    alias: isolate
    owner: ncbi_assembly
    domain_of:
    - ncbi_assembly
    range: string
    required: false
  version_status:
    name: version_status
    from_schema: https://w3id.org/jgi/gold
    rank: 1000
    alias: version_status
    owner: ncbi_assembly
    domain_of:
    - ncbi_assembly
    range: string
    required: false
  assembly_level:
    name: assembly_level
    from_schema: https://w3id.org/jgi/gold
    rank: 1000
    alias: assembly_level
    owner: ncbi_assembly
    domain_of:
    - ncbi_assembly
    range: string
    required: false
  release_type:
    name: release_type
    from_schema: https://w3id.org/jgi/gold
    rank: 1000
    alias: release_type
    owner: ncbi_assembly
    domain_of:
    - ncbi_assembly
    range: string
    required: false
  genome_rep:
    name: genome_rep
    from_schema: https://w3id.org/jgi/gold
    rank: 1000
    alias: genome_rep
    owner: ncbi_assembly
    domain_of:
    - ncbi_assembly
    range: string
    required: false
  seq_rel_date:
    name: seq_rel_date
    from_schema: https://w3id.org/jgi/gold
    rank: 1000
    alias: seq_rel_date
    owner: ncbi_assembly
    domain_of:
    - ncbi_assembly
    range: datetime
    required: false
  asm_name:
    name: asm_name
    from_schema: https://w3id.org/jgi/gold
    rank: 1000
    alias: asm_name
    owner: ncbi_assembly
    domain_of:
    - ncbi_assembly
    range: string
    required: false
  asm_submitter:
    name: asm_submitter
    from_schema: https://w3id.org/jgi/gold
    rank: 1000
    alias: asm_submitter
    owner: ncbi_assembly
    domain_of:
    - ncbi_assembly
    range: string
    required: false
  gbrs_paired_asm:
    name: gbrs_paired_asm
    from_schema: https://w3id.org/jgi/gold
    rank: 1000
    alias: gbrs_paired_asm
    owner: ncbi_assembly
    domain_of:
    - ncbi_assembly
    range: string
    required: false
  paired_asm_comp:
    name: paired_asm_comp
    from_schema: https://w3id.org/jgi/gold
    rank: 1000
    alias: paired_asm_comp
    owner: ncbi_assembly
    domain_of:
    - ncbi_assembly
    range: string
    required: false
  ftp_path:
    name: ftp_path
    from_schema: https://w3id.org/jgi/gold
    rank: 1000
    alias: ftp_path
    owner: ncbi_assembly
    domain_of:
    - ncbi_assembly
    range: string
    required: false
  excluded_from_refseq:
    name: excluded_from_refseq
    from_schema: https://w3id.org/jgi/gold
    rank: 1000
    alias: excluded_from_refseq
    owner: ncbi_assembly
    domain_of:
    - ncbi_assembly
    range: string
    required: false
  relation_to_type_material:
    name: relation_to_type_material
    from_schema: https://w3id.org/jgi/gold
    rank: 1000
    alias: relation_to_type_material
    owner: ncbi_assembly
    domain_of:
    - ncbi_assembly
    range: string
    required: false
  asm_not_live_date:
    name: asm_not_live_date
    from_schema: https://w3id.org/jgi/gold
    rank: 1000
    alias: asm_not_live_date
    owner: ncbi_assembly
    domain_of:
    - ncbi_assembly
    range: datetime
    required: false
  assembly_type:
    name: assembly_type
    from_schema: https://w3id.org/jgi/gold
    alias: assembly_type
    owner: ncbi_assembly
    domain_of:
    - assembly
    - ncbi_assembly
    range: string
    required: false
  group_:
    name: group_
    from_schema: https://w3id.org/jgi/gold
    rank: 1000
    alias: group_
    owner: ncbi_assembly
    domain_of:
    - ncbi_assembly
    range: string
    required: false
  genome_size:
    name: genome_size
    from_schema: https://w3id.org/jgi/gold
    rank: 1000
    alias: genome_size
    owner: ncbi_assembly
    domain_of:
    - ncbi_assembly
    range: float
    required: false
  genome_size_ungapped:
    name: genome_size_ungapped
    from_schema: https://w3id.org/jgi/gold
    rank: 1000
    alias: genome_size_ungapped
    owner: ncbi_assembly
    domain_of:
    - ncbi_assembly
    range: float
    required: false
  gc_percent:
    name: gc_percent
    from_schema: https://w3id.org/jgi/gold
    rank: 1000
    alias: gc_percent
    owner: ncbi_assembly
    domain_of:
    - ncbi_assembly
    - project
    range: float
    required: false
  replicon_count:
    name: replicon_count
    from_schema: https://w3id.org/jgi/gold
    rank: 1000
    alias: replicon_count
    owner: ncbi_assembly
    domain_of:
    - ncbi_assembly
    range: float
    required: false
  scaffold_count:
    name: scaffold_count
    from_schema: https://w3id.org/jgi/gold
    alias: scaffold_count
    owner: ncbi_assembly
    domain_of:
    - analysis_project
    - ncbi_assembly
    - project
    range: float
    required: false
  contig_count:
    name: contig_count
    from_schema: https://w3id.org/jgi/gold
    alias: contig_count
    owner: ncbi_assembly
    domain_of:
    - analysis_project
    - ncbi_assembly
    - project
    range: float
    required: false
  annotation_provider:
    name: annotation_provider
    from_schema: https://w3id.org/jgi/gold
    rank: 1000
    alias: annotation_provider
    owner: ncbi_assembly
    domain_of:
    - ncbi_assembly
    range: string
    required: false
  annotation_name:
    name: annotation_name
    from_schema: https://w3id.org/jgi/gold
    rank: 1000
    alias: annotation_name
    owner: ncbi_assembly
    domain_of:
    - ncbi_assembly
    range: string
    required: false
  annotation_date:
    name: annotation_date
    from_schema: https://w3id.org/jgi/gold
    rank: 1000
    alias: annotation_date
    owner: ncbi_assembly
    domain_of:
    - ncbi_assembly
    range: datetime
    required: false
  total_gene_count:
    name: total_gene_count
    from_schema: https://w3id.org/jgi/gold
    rank: 1000
    alias: total_gene_count
    owner: ncbi_assembly
    domain_of:
    - ncbi_assembly
    range: float
    required: false
  protein_coding_gene_count:
    name: protein_coding_gene_count
    from_schema: https://w3id.org/jgi/gold
    rank: 1000
    alias: protein_coding_gene_count
    owner: ncbi_assembly
    domain_of:
    - ncbi_assembly
    range: float
    required: false
  non_coding_gene_count:
    name: non_coding_gene_count
    from_schema: https://w3id.org/jgi/gold
    rank: 1000
    alias: non_coding_gene_count
    owner: ncbi_assembly
    domain_of:
    - ncbi_assembly
    range: float
    required: false
  pubmed_id:
    name: pubmed_id
    from_schema: https://w3id.org/jgi/gold
    rank: 1000
    alias: pubmed_id
    owner: ncbi_assembly
    domain_of:
    - ncbi_assembly
    range: string
    required: false
  assembly_method:
    name: assembly_method
    from_schema: https://w3id.org/jgi/gold
    rank: 1000
    alias: assembly_method
    owner: ncbi_assembly
    domain_of:
    - ncbi_assembly
    range: string
    required: false
  expected_final_version:
    name: expected_final_version
    from_schema: https://w3id.org/jgi/gold
    rank: 1000
    alias: expected_final_version
    owner: ncbi_assembly
    domain_of:
    - ncbi_assembly
    range: string
    required: false
  genome_coverage:
    name: genome_coverage
    from_schema: https://w3id.org/jgi/gold
    rank: 1000
    alias: genome_coverage
    owner: ncbi_assembly
    domain_of:
    - ncbi_assembly
    range: string
    required: false
  sequencing_technology:
    name: sequencing_technology
    from_schema: https://w3id.org/jgi/gold
    rank: 1000
    alias: sequencing_technology
    owner: ncbi_assembly
    domain_of:
    - ncbi_assembly
    range: string
    required: false
  refseq_assembly_accession:
    name: refseq_assembly_accession
    from_schema: https://w3id.org/jgi/gold
    rank: 1000
    alias: refseq_assembly_accession
    owner: ncbi_assembly
    domain_of:
    - ncbi_assembly
    range: string
    required: false
  genbank_json:
    name: genbank_json
    from_schema: https://w3id.org/jgi/gold
    rank: 1000
    alias: genbank_json
    owner: ncbi_assembly
    domain_of:
    - ncbi_assembly
    range: string
    required: false