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img_core_v400

URI: https://w3id.org/jgi/img_core_v400

Name: img_core_v400

Classes

Class Description
AccessionTypes
ActinoAbcGenes
ActinoCassette
ActinoCassetteGenes
AltTranscript
Asv5Taxons
BcType
BcgTaxons
BiocycClass
BiocycClassParents
BiocycClassSynonyms
BiocycClassTypes
BiocycComp
BiocycCompExtLinks
BiocycCompSynonyms
BiocycCompTypes
BiocycEnzrxn
BiocycEnzrxnExtLinks
BiocycEnzrxnProsthGroups
BiocycEnzrxnSynonyms
BiocycPathway
BiocycPathwayComments
BiocycPathwayExtLinks
BiocycPathwayInSpecies
BiocycPathwayPwyLinks
BiocycPathwaySubPwys
BiocycPathwaySuperPwys
BiocycPathwayTaxonRange
BiocycPathwayTypes
BiocycProtein
BiocycProteinCatalyzes
BiocycProteinExtLinks
BiocycProteinInSpecies
BiocycProteinSynonyms
BiocycProteinTypes
BiocycReaction
BiocycReactionExtLinks
BiocycReactionInPwys
BiocycReactionLeftHand
BiocycReactionRightHand
BiocycReactionSynonyms
BiocycReactionTypes
CathFunfam
Cog
Cog2014
CogFamilies
CogFunction
CogFunctions
CogPathway
CogPathwayCogMembers
CogSpecies
Cogfunc2014
Compound
CompoundAliases
CompoundExtLinks
DbSource
DeleteGenes
DeleteScaffolds
DeleteTaxons
DtAllPhyloTaxonStats
DtCog
DtCogStats
DtHtHits
DtImgGeneProtPepSample
DtImgTerm
DtImgTermPath
DtIntergenic
DtKo
DtKoEcCogPfam
DtKogStats
DtPfam
DtPhyloTaxonStats
DtPhylodistNewTaxons
DtPhylumDistGenes
DtPhylumDistStats
DtScogGenes
DtScogs
DtTaxonKmoduleMcr
DtTaxonNodeLite
DtTfam
DtTfamsToExclude
Enzyme
EnzymeEnzAliases
EnzymeExtLinks
EnzymeProducts
EnzymeSubstrates
EnzymeTransferred
ExcludeFunc
Gene
GeneAliases
GeneBiocycRxns
GeneCathfam
GeneCogGroups
GeneEssentialGenes
GeneExceptions
GeneExtLinks
GeneFeatureTags
GeneFragCoords
GeneGoTerms
GeneImgInterproHits
GeneKoEnzymes
GeneKoEnzymesNew
GeneKoTerms
GeneKogGroups
GeneNotes
GeneParalogs
GenePdbXrefs
GenePfamFamilies
GeneSigPeptides
GeneSmart
GeneSuperfam
GeneTigrfams
GeneXrefFamilies
GenomeProperty
GenomePropertyParents
GoGraphPath
GoTerm
GoTermParents
GoTermSynonyms
ImageRoi
ImageRoiCompounds
ImageRoiEnzymes
ImageRoiKoTerms
ImageRoiReactions
ImgBuild
ImgContentHistory
ImgFuncsInfo
ImgIuigTarballs11202023
ImgOrfType
ImgUmagBinTarballs02062024
ImgnrTaxons062123
Interpro
InterproGoTerms
IsoPlasmids
KeggGene
KeggGeneKoTerms
KeggGeneNcbiGeneIds
KeggGeneUniprotIds
KeggModule
KeggModuleCompounds
KeggModuleKoTerms
KeggModuleReactions
KeggPathway
KeggPathwayModules
KeggPathwayRelatedPathways
KmImageRoi
KmImageRoiKoTerms
Ko2cog
Ko2ec
Ko2go
Ko2module
Ko2pathway
Ko2reaction
Ko2tc
KoTerm
KoTermClasses
KoTermCogs
KoTermEnzymes
KoTermGoIds
KoTermModules
KoTermPathways
KoTermReactions
KoTermTcFamilies
Kog
KogFamilies
KogFunction
KogFunctions
KogPathway
KogPathwayKogMembers
KpActino
KpPseudo
KpTaxons
MapTaxonPairs
MerfsGeneMapping
MvGeneTmhmmStats
NewTaxons
NewTaxonsBatch
OldTaxons
ParalogGroup
ParalogGroupGenes
Pfam2go
PfamClan
PfamClanPfamFamilies
PfamDead
PfamFamily
PfamFamilyCogs
PfamFamilyExtLinks
PfamFamilyGenomeProperties
PositionalCluster
PositionalClusterGenes
PropertyStep
PropertyStepEvidences
Reaction
ReactionCompounds
ReactionEnzymes
ReactionExtLinks
RefseqUniprot
Scaffold
ScaffoldExtLinks
ScaffoldNxFeature
ScaffoldRepeats
ScaffoldStats
Smart
Superfamily
T1
T2
T3
TarballRefreshTaxons
Taxon
TaxonAssemblyStats
TaxonCathfunfamCount
TaxonCogCount
TaxonCrisprDetails
TaxonCrisprSummary
TaxonDw
TaxonEcCount
TaxonExtLinks
TaxonGenePrefix
TaxonGtdbtkLineage
TaxonKoCount
TaxonNodeLite
TaxonPfamCount
TaxonProdVw
TaxonReplacements
TaxonReplacementsView
TaxonScafPrefix
TaxonSmartCount
TaxonSmcStats
TaxonStats
TaxonStatsMerfs
TaxonStatsProdVw
TaxonSupfamCount
TaxonTaxonScaffoldInfo
TaxonTigrCount
TcFamily
TigrRole
Tigrfam
TigrfamEnzymes
TigrfamGenomeProperties
TigrfamRoles
TmpGenes
VwGoldTaxon
VwTaxonSc
Yesnocv

Slots

Slot Description
aa_checksum
aa_residue
aa_seq_length
abbr_name
accession
accession_id
add_date
aliases
align_length
alt_transcript_oid
altitude
amino_acid_metabolism
amino_acid_metabolism_pc
analysis_product_name
analysis_project_id
analysis_project_type
ani_species
archaea
assertion_error
assign_basis
average_scp
avg_cov_assembled_seq
avg_gene_length
bacteria
balance_state
base_url
bc_code
bc_desc
bgc_count
bin_count
biocyc_enzrxn
biocyc_enzyme Foreign key to biocyc_protein
biocyc_gene
biocyc_rxn
biotic_rel
bit_score
build_date
build_number
build_oid
carbohydrate_metabolism
carbohydrate_metabolism_pc
cas_number
category
cds_frag_coord
cds_genes
cds_genes_pc
cell_cycle
cell_cycle_pc
cell_motility
cell_motility_pc
cell_shape
cell_wall_biogenesis
cell_wall_biogenesis_pc
change_status
checkm_completeness
checkm_contamination
checksum
chlorophyll_concentration
chromatin_structure
chromatin_structure_pc
chromosome
clade
class
cluster_name
cnt
code
coenzyme_transport
coenzyme_transport_pc
cog
cog_clusters
cog_id
cog_members Foreign key to cog
cog_name
cog_pathway_name
cog_pathway_oid
cog_species_name
cogs Foreign key to cog
combined_sample_flag
comments
common_name
compartment
compound_name
compounds Foreign key to compound
contig_id
contig_id_map
contig_id_orig
coord_string
copy_number
count_cds
count_cog
count_enzymes
count_go
count_homologs
count_interpro
count_kegg
count_orthologs
count_paralogs
count_pfam
count_rna
count_total_gene
coverage
credits
crispr_count
crispr_no
culture_type
custom_url
cytoskeleton
cytoskeleton_pc
data_type
datatype
date_last_updated
db_code
db_name
db_source Foreign key to db_source
dead_pfam_id
defense_mechanisms
defense_mechanisms_pc
definition
depth
description
display_name
distance
dna_md5checksum
dna_seq_length
domain
domaindb
domaindesc
domainid
ec
ec_number
ecosystem
ecosystem_category
ecosystem_subtype
ecosystem_type
ecotype
end_coord
end_coord_w
energy_production
energy_production_pc
env_sample
enz_aliases
enzrxn Foreign key to biocyc_enzrxn
enzyme_name
enzymes
essentiality Foreign key to yesnocv
est_avg_genome_size
est_copy
est_copy_30
est_copy_60
est_copy_90
est_num_of_genomes
euk_bin_count
euk_semibin_count
eukaryota
evalue
exception
exp_oid
expanded_name
ext_accession
ext_id
extracellular_structures
extracellular_structures_pc
f1
f2
f3
families
family
feature_type
first_cds
first_gene
flag_cv
formula
frag_order
func
func_cat
func_id
func_role
func_status
function Foreign key to cog_function
function_code
function_group
function_id
function_unknown
function_unknown_pc
functions
funding_agency
gb_tag
gc_content
gc_percent
gene
gene_count
gene_count_30
gene_count_60
gene_count_90
gene_display_name
gene_oid
gene_seq_length
gene_symbol
general_function_only
general_function_only_pc
genes
genes_hor_transfer
genes_hor_transfer_pc
genes_in_bcgs
genes_in_bcgs_pc
genes_in_biosynthetic
genes_in_biosynthetic_pc
genes_in_cathfunfam
genes_in_cathfunfam_pc
genes_in_cog
genes_in_cog_pc
genes_in_enzymes
genes_in_enzymes_pc
genes_in_kegg
genes_in_kegg_pc
genes_in_ko
genes_in_ko_pc
genes_in_kog
genes_in_kog_pc
genes_in_metacyc
genes_in_metacyc_pc
genes_in_myimg
genes_in_myimg_pc
genes_in_paralogs
genes_in_paralogs_pc
genes_in_pfam
genes_in_pfam_pc
genes_in_smart
genes_in_smart_pc
genes_in_sp
genes_in_sp_pc
genes_in_supfam
genes_in_supfam_pc
genes_in_tigrfam
genes_in_tigrfam_pc
genes_not_in_kegg
genes_not_in_kegg_pc
genes_not_in_ko
genes_not_in_ko_pc
genes_not_in_metacyc
genes_not_in_metacyc_pc
genes_not_in_sp
genes_not_in_sp_pc
genes_obsolete
genes_obsolete_pc
genes_revised
genes_revised_pc
genes_signalp
genes_signalp_pc
genes_transmembrane
genes_transmembrane_pc
genes_w_func_pred
genes_w_func_pred_pc
genome_completion
genome_property Foreign key to genome_property
genome_type
genus
geo_location
gfragment
go_category
go_evidence
go_id
go_ids Foreign key to go_term
go_info
go_term
go_terms
go_type
gold_id
gram_stain
graph_path_id
group_name
group_oid
gtdbtk_class
gtdbtk_domain
gtdbtk_family
gtdbtk_genus
gtdbtk_lineage
gtdbtk_order
gtdbtk_phylum
gtdbtk_species
has_coverage
has_per_sample_coverage
height
high_quality_flag
homolog
homolog_taxon
host_gender
host_name
host_ncbi_taxid
host_ncbi_taxon_id
id
id_prefix
image_file
image_id
img_class
img_domain
img_family
img_ko_flag
img_order
img_phylum
img_product_source
img_status
img_version
in_file Foreign key to yesnocv
in_pwys Foreign key to biocyc_pathway
in_species
inch_i_key
inchi
inchi_key
intracellular_trafficking
intracellular_trafficking_pc
ion_transport
ion_transport_pc
iprdesc
iprid
ir_class
ir_order
is_big_euk Foreign key to yesnocv
is_obsolete Foreign key to yesnocv
is_official_ec Foreign key to yesnocv
is_orphan Foreign key to yesnocv
is_pangenome Foreign key to yesnocv
is_partial_w
is_pseudogene
is_public Foreign key to yesnocv
is_replaced Foreign key to yesnocv
is_required
is_root Foreign key to yesnocv
is_scp_marker
is_spontaneous Foreign key to yesnocv
isolates
isology_type
its_ap_id
jgi_genomes
jgi_project_id
jgi_rnd_flag
jgi_species_code
kegg_gene
kegg_gene_id
kegg_id
kegg_module
ko_id
ko_name
ko_pathway_id
ko_term Foreign key to ko_term
ko_terms
kog
kog_clusters
kog_id
kog_members Foreign key to kog
kog_name
kog_pathway_name
kog_pathway_oid
last_update
last_updated_date
latitude
length
lipid_metabolism
lipid_metabolism_pc
locus_tag
locus_type
longhurst_code
longhurst_description
longitude
ls_ga_domain
ls_ga_model
ls_nc_domain
ls_nc_model
ls_tc_domain
ls_tc_model
main_role
map_term
max_value
mcr
median_scp
merfs_gene_id
metagenomes
method
min_value
mobilome
mobilome_pc
mod_date
mode_scp
modified_by
module_id
module_name
module_type
modules Foreign key to kegg_module
mol_topology
mol_type
mol_weight
mol_wt
motility
n_copies
n_scaffolds
name
ncbi_class
ncbi_family
ncbi_gene_id
ncbi_genus
ncbi_kingdom
ncbi_order
ncbi_phylum
ncbi_species
ncbi_species_code
ncbi_taxon_id
net_rxn_eqn
new_pfam_id
new_taxon_oid
nitrate_concentration
no_bases
node_oid
notes
nuclear_structure
nuclear_structure_pc
nucleotide_metabolism
nucleotide_metabolism_pc
num_atoms
num_filtered_reads
num_mapped_reads
obsolete_flag
old_taxon_name
old_taxon_oid
orf_type
other_rna_genes
other_rna_genes_pc
oxygen_concentration
oxygen_req
paralog
paralog_groups
parent
parent_class
parents Foreign key to biocyc_class
partial_gene
pathway Foreign key to kegg_pathway
pathway_name
pathway_oid
pep_seq_length
pep_spectral_cnt
peptide_oid
peptide_seq
perc_ident_bin
percent_identity
pfam
pfam_clusters
pfam_families
pfam_family
pfam_id
ph
phylo_level
phylo_val
phylodist_date
phylodist_method
phylum
plasmid_id
plasmids
pos
posttrans_modification
posttrans_modification_pc
pp_subset
predicted_plasmid_contigs
predicted_viral_contigs
pressure
previous_name
product_name
products Foreign key to compound
prop_accession
property Foreign key to genome_property
property_step Foreign key to property_step
proport_isolation
proport_ocean
proport_station
proport_woa_dissolved_oxygen
proport_woa_nitrate
proport_woa_phosphate
proport_woa_salinity
proport_woa_silicate
proport_woa_temperature
proposal_name
prosth_groups
protein_oid
protein_seq_accid
pseudo_genes
pseudo_genes_pc
pwy_links
query
query_end
query_start
rank
rank_name
rank_order
reaction Foreign key to biocyc_reaction
reaction_id
reactions Foreign key to reaction
read_depth
reference
refseq_protein_id
rel_type
related_pathway Foreign key to kegg_pathway
related_pathways Foreign key to kegg_pathway
release_date
repeat_seq
replication_repair
replication_repair_pc
rev_gene_oid
rna_genes
rna_genes_pc
rna_processing
rna_processing_pc
roi_id
roi_label
roi_type
role_id
roles Foreign key to tigr_role
rrna16s_genes
rrna16s_genes_pc
rrna18s_genes
rrna18s_genes_pc
rrna23s_genes
rrna23s_genes_pc
rrna28s_genes
rrna28s_genes_pc
rrna5s_genes
rrna5s_genes_pc
rrna_genes
rrna_genes_pc
rxn_definition
rxn_desc
rxn_direction
rxn_equation
rxn_name
salinity
salinity_concentration
sample_collect_temp
sample_desc
sample_gold_id
sample_oid
scaf_prefix
scaffold
scaffold_name
scaffold_oid
scaffolds_2kb
scaffolds_4kb
secondary_metabolites
secondary_metabolites_pc
semibin_count
seq_center
seq_dir
seq_file
seq_length
seq_status
sequencing_gold_id
sfcount
sfends
sfscores
sfsends
sfstarts
shape
signal_transduction
signal_transduction_pc
single_copy
smc_bcgs
smc_id
smiles
source
sp_id
spacer_seq
species
species_code
species_family
specific_ecosystem
sporulation
start_coord
start_coord_w
status
std_dev_scp
step_accession
strain
strand
study_gold_id
sub_id
sub_pwys Foreign key to biocyc_pathway
sub_role
subj_end
subj_start
submission_id
substrate Foreign key to biocyc_comp
substrates Foreign key to compound
super_pwys Foreign key to biocyc_pathway
synonyms
systematic_name
tag
taxon
taxon_count
taxon_display_name
taxon_name
taxon_oid
taxon_range
tc_families
tc_family_name
tc_family_num
tc_id
temp_range
term_1 Foreign key to go_term
term_2 Foreign key to go_term
term_oid
tfam_id
threshold
tigrfam_clusters
title
tool_code
tot_a
tot_c
tot_g
tot_gatc
tot_n
tot_size_filtered_reads
tot_size_mapped_reads
tot_t
tot_x
total_a
total_bases
total_bcgs
total_biosynthetic
total_c
total_cassettes
total_coding_bases
total_cog_gene_count
total_g
total_gatc
total_gc
total_gene_count
total_genes
total_genomes
total_kog_gene_count
total_n
total_t
total_x
transcription
transcription_pc
transl_table
translation
translation_pc
trna_genes
trna_genes_pc
type
types
uncharacterized_genes
uncharacterized_genes_pc
uncultured_type
uniprot_id
unique_id
url
value
version_info
viruses
width
x_coord
xref
y_coord

Enumerations

Enumeration Description

Types

Type Description
Boolean A binary (true or false) value
Curie a compact URI
Date a date (year, month and day) in an idealized calendar
DateOrDatetime Either a date or a datetime
Datetime The combination of a date and time
Decimal A real number with arbitrary precision that conforms to the xsd:decimal speci...
Double A real number that conforms to the xsd:double specification
Float A real number that conforms to the xsd:float specification
Integer An integer
Jsonpath A string encoding a JSON Path
Jsonpointer A string encoding a JSON Pointer
Ncname Prefix part of CURIE
Nodeidentifier A URI, CURIE or BNODE that represents a node in a model
Objectidentifier A URI or CURIE that represents an object in the model
Sparqlpath A string encoding a SPARQL Property Path
String A character string
Time A time object represents a (local) time of day, independent of any particular...
Uri a complete URI
Uriorcurie a URI or a CURIE

Subsets

Subset Description