SchemaSpy Analysis of cxgn.public - Columns

 Generated by
SchemaSpy
Generated by SchemaSpy on Wed May 20 01:40 EDT 2009
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Primary key columns
Columns with indexes
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Related columns Constraint names Comments Legend
cxgn.public contains 691 columns:
Column Table Type Size Nulls Auto Default Children Parents Comments
abbreviation organism varchar 255  √  null
abstract pubabstract text 2147483647  √  null
abstract_tsvector pubabstract tsvector 2147483647  √  null
accession dbxref varchar 255 The local part of the identifier. Guaranteed by the db authority to be unique for that db
accession_id forward_amplicon_sequence_information text 2147483647  √  null
action bug text 2147483647  √  null
affected_page bug text 2147483647  √  null
agi ara_annotation varchar 16
ara_domain.agi Implied Constraint
ara_gfp_ms.agi Implied Constraint
ara_intron.agi Implied Constraint
ara_properties.agi Implied Constraint
ara_scop.agi Implied Constraint
ara_sequence.agi Implied Constraint
ara_signalp.agi Implied Constraint
ara_targetp.agi Implied Constraint
agi ara_domain varchar 16  √  null
ara_annotation.agi Implied Constraint
agi ara_gfp_ms varchar 16  √  null
ara_annotation.agi Implied Constraint
agi ara_intron varchar 16  √  null
ara_annotation.agi Implied Constraint
agi ara_properties varchar 16
ara_annotation.agi Implied Constraint
agi ara_scop varchar 16  √  null
ara_annotation.agi Implied Constraint
agi ara_sequence varchar 16
ara_annotation.agi Implied Constraint
agi ara_signalp varchar 16
ara_annotation.agi Implied Constraint
agi ara_targetp varchar 16
ara_annotation.agi Implied Constraint
algorithm analysis varchar 255  √  null
aliases ara_annotation text 2147483647  √  null
alignment_seq family_member text 2147483647  √  null
alt_id ara_go_term varchar 12  √  null
analysis_id analysis serial 10  √  nextval('analysis_analysis_id_seq'::regclass)
analysisfeature.analysis_id analysisfeature_analysis_id_fkey
analysisprop.analysis_id analysisprop_analysis_id_fkey
analysis_id analysisfeature int4 10
analysis.analysis_id analysisfeature_analysis_id_fkey
analysis_id analysisprop int4 10
analysis.analysis_id analysisprop_analysis_id_fkey
analysisfeature_id analysisfeature serial 10  √  nextval('analysisfeature_analysisfeature_id_seq'::regclass)
analysisprop_id analysisprop serial 10  √  nextval('analysisprop_analysisprop_id_seq'::regclass)
app_name ara_domain varchar 32  √  null
assay_id phenotype int4 10  √  null
cvterm.cvterm_id phenotype_assay_id_fkey
assigned_to pub_curator int4 10  √  null
attr_id phenotype int4 10  √  null
cvterm.cvterm_id phenotype_attr_id_fkey
attribute gff3atts varchar 2147483647  √  null
attribute gffatts varchar 2147483647  √  null
author ara_interactome_all varchar 32  √  null
bac_locus ara_family varchar 128  √  null
band_position fpc_band int4 10  √  null
blastwatch_queries_id blastwatch_queries serial 10  √  nextval('blastwatch_queries_blastwatch_queries_id_seq'::regclass)
blastwatch_results.blastwatch_queries_id blastwatch_results_blastwatch_queries_id_fkey
blastwatch_queries_id blastwatch_results int4 10
blastwatch_queries.blastwatch_queries_id blastwatch_results_blastwatch_queries_id_fkey
blastwatch_results_id blastwatch_results serial 10  √  nextval('blastwatch_results_blastwatch_results_id_seq'::regclass)
bug_id bug serial 10  √  nextval('bug_bug_id_seq'::regclass)
build_date family_build timestamp 29,6  √  null
build_nr family_build int8 19  √  null
c_score ara_targetp float4 8,8  √  null
cdna ara_sequence text 2147483647  √  null
cds ara_sequence text 2147483647  √  null
cds_id family_member int8 19  √  null
cds_id signalp int8 19  √  null
cds_id unigene_signalp int8 19  √  null
children ara_go_term text 2147483647  √  null
chromosome ara_map bpchar 1  √  null
clone_feature_id clone_feature serial 10  √  nextval('clone_feature_clone_feature_id_seq'::regclass)
clone_id clone_feature int8 19  √  null
clone_id clone_in_silico_digestion int4 10  √  null
clone_id fpc_contig_clone int8 19
clone_id fpc_fingerprint int4 10
clone_in_silico_digestion_bands_id clone_in_silico_digestion_bands serial 10  √  nextval('clone_in_silico_digestion_ban_clone_in_silico_digestion_ban_seq'::regclass)
clone_in_silico_digestion_id clone_in_silico_digestion serial 10  √  nextval('clone_in_silico_digestion_clone_in_silico_digestion_id_seq'::regclass)
clone_in_silico_digestion_bands.clone_in_silico_digestion_id clone_in_silico_digestion_ban_clone_in_silico_digestion_id_fkey
clone_in_silico_digestion_id clone_in_silico_digestion_bands int4 10  √  null
clone_in_silico_digestion.clone_in_silico_digestion_id clone_in_silico_digestion_ban_clone_in_silico_digestion_id_fkey
code ara_evidef varchar 10  √  null
comment fpc_build text 2147483647  √  null
comment organism text 2147483647  √  null
common_name organism varchar 255  √  null
confirm_email ara_users bool 1  √  null
create_date bug timestamptz 35,6  √  null
create_date image timestamptz 35,6  √  null
create_date image_locus timestamptz 35,6  √  now()
create_date tag timestamptz 35,6  √  now()
create_date tag_experiment timestamptz 35,6  √  now()
create_date tag_image timestamptz 35,6  √  now()
created_by bug int8 19  √  null
criteria ara_family text 2147483647  √  null
curated_by pub_curator int4 10  √  null
cv_id cv serial 10  √  nextval('cv_cv_id_seq'::regclass)
cvterm.cv_id cvterm_cv_id_fkey
cvtermpath.cv_id cvtermpath_cv_id_fkey
cv_id cvterm int4 10
cv.cv_id cvterm_cv_id_fkey
The cv/ontology/namespace to which
this cvterm belongs
cv_id cvtermpath int4 10
cv.cv_id cvtermpath_cv_id_fkey
Closures will mostly be within
one cv. If the closure of a relationship traverses a cv, then this
refers to the cv of the object_id cvterm
cvalue_id phenotype int4 10  √  null
cvterm.cvterm_id phenotype_cvalue_id_fkey
cvterm_dbxref_id cvterm_dbxref serial 10  √  nextval('cvterm_dbxref_cvterm_dbxref_id_seq'::regclass)
cvterm_id cvterm serial 10  √  nextval('cvterm_cvterm_id_seq'::regclass)
analysisprop.type_id analysisprop_type_id_fkey
cvterm_dbxref.cvterm_id cvterm_dbxref_cvterm_id_fkey
cvterm_pub_ranking.cvterm_id cvterm_pub_ranking_cvterm_id_fkey
cvterm_relationship.object_id cvterm_relationship_object_id_fkey
cvterm_relationship.subject_id cvterm_relationship_subject_id_fkey
cvterm_relationship.type_id cvterm_relationship_type_id_fkey
cvtermpath.object_id cvtermpath_object_id_fkey
cvtermpath.subject_id cvtermpath_subject_id_fkey
cvtermpath.type_id cvtermpath_type_id_fkey
cvtermprop.cvterm_id cvtermprop_cvterm_id_fkey
cvtermprop.type_id cvtermprop_type_id_fkey
cvtermsynonym.cvterm_id cvtermsynonym_cvterm_id_fkey
cvtermsynonym.type_id cvtermsynonym_type_id_fkey
dbxrefprop.type_id dbxrefprop_type_id_fkey
feature.type_id feature_type_id_fkey
feature_cvterm.cvterm_id feature_cvterm_cvterm_id_fkey
feature_cvtermprop.type_id feature_cvtermprop_type_id_fkey
feature_relationship.type_id feature_relationship_type_id_fkey
feature_relationshipprop.type_id feature_relationshipprop_type_id_fkey
featureprop.type_id featureprop_type_id_fkey
organism_relationship.type_id organism_relationship_type_id_fkey
organismpath.type_id organismpath_type_id_fkey
organismprop.type_id organismprop_type_id_fkey
phenotype.assay_id phenotype_assay_id_fkey
phenotype.attr_id phenotype_attr_id_fkey
phenotype.cvalue_id phenotype_cvalue_id_fkey
phenotype.observable_id phenotype_observable_id_fkey
phenotype_cvterm.cvterm_id phenotype_cvterm_cvterm_id_fkey
pub.type_id pub_type_id_fkey
pub_relationship.type_id pub_relationship_type_id_fkey
pubprop.type_id pubprop_type_id_fkey
synonym.type_id synonym_type_id_fkey
cvterm_id cvterm_dbxref int4 10
cvterm.cvterm_id cvterm_dbxref_cvterm_id_fkey
cvterm_id cvterm_pub_ranking int4 10  √  null
cvterm.cvterm_id cvterm_pub_ranking_cvterm_id_fkey
cvterm_id cvtermprop int4 10
cvterm.cvterm_id cvtermprop_cvterm_id_fkey
cvterm_id cvtermsynonym int4 10
cvterm.cvterm_id cvtermsynonym_cvterm_id_fkey
cvterm_id feature_cvterm int4 10
cvterm.cvterm_id feature_cvterm_cvterm_id_fkey
cvterm_id phenotype_cvterm int4 10
cvterm.cvterm_id phenotype_cvterm_cvterm_id_fkey
cvterm_relationship_id cvterm_relationship serial 10  √  nextval('cvterm_relationship_cvterm_relationship_id_seq'::regclass)
cvtermpath_id cvtermpath serial 10  √  nextval('cvtermpath_cvtermpath_id_seq'::regclass)
cvtermprop_id cvtermprop serial 10  √  nextval('cvtermprop_cvtermprop_id_seq'::regclass)
cvtermsynonym_id cvtermsynonym serial 10  √  nextval('cvtermsynonym_cvtermsynonym_id_seq'::regclass)
cxgn_production_visible forward_amplicon_sequence_information bool 1  √  null
cxgn_production_visible forward_amplicon_sequence_markers bool 1  √  null
database ara_interactome_all varchar 32  √  null
database blastwatch_queries varchar 50
database_name family_member varchar 20  √  null
date fpc_build date 13
date_curated pub_curator timestamptz 35,6  √  null
date_stored pub_curator timestamptz 35,6  √  now()
db_id db serial 10  √  nextval('db_db_id_seq'::regclass)
dbxref.db_id dbxref_db_id_fkey
db_id dbxref int4 10
db.db_id dbxref_db_id_fkey
dbxref_id cvterm int4 10
dbxref.dbxref_id cvterm_dbxref_id_fkey
Primary identifier dbxref - The
unique global OBO identifier for this cvterm.  Note that a cvterm may
have multiple secondary dbxrefs - see also table: cvterm_dbxref
dbxref_id cvterm_dbxref int4 10
dbxref.dbxref_id cvterm_dbxref_dbxref_id_fkey
dbxref_id dbxref serial 10  √  nextval('dbxref_dbxref_id_seq'::regclass)
cvterm.dbxref_id cvterm_dbxref_id_fkey
cvterm_dbxref.dbxref_id cvterm_dbxref_dbxref_id_fkey
dbxrefprop.dbxref_id dbxrefprop_dbxref_id_fkey
feature.dbxref_id feature_dbxref_id_fkey
feature_cvterm_dbxref.dbxref_id feature_cvterm_dbxref_dbxref_id_fkey
feature_dbxref.dbxref_id feature_dbxref_dbxref_id_fkey
organism_dbxref.dbxref_id organism_dbxref_dbxref_id_fkey
pub_dbxref.dbxref_id pub_dbxref_dbxref_id_fkey
unigene_dbxref.dbxref_id unigene_dbxref_dbxref_id_fkey
dbxref_id dbxrefprop int4 10
dbxref.dbxref_id dbxrefprop_dbxref_id_fkey
dbxref_id feature int4 10  √  null
dbxref.dbxref_id feature_dbxref_id_fkey
An optional primary public stable
identifier for this feature. Secondary identifiers and external
dbxrefs go in table:feature_dbxref
dbxref_id feature_cvterm_dbxref int4 10
dbxref.dbxref_id feature_cvterm_dbxref_dbxref_id_fkey
dbxref_id feature_dbxref int4 10
dbxref.dbxref_id feature_dbxref_dbxref_id_fkey
dbxref_id organism_dbxref int4 10
dbxref.dbxref_id organism_dbxref_dbxref_id_fkey
dbxref_id pub_dbxref int4 10
dbxref.dbxref_id pub_dbxref_dbxref_id_fkey
dbxref_id unigene_dbxref int8 19
dbxref.dbxref_id unigene_dbxref_dbxref_id_fkey
dbxrefprop_id dbxrefprop serial 10  √  nextval('dbxrefprop_dbxrefprop_id_seq'::regclass)
definition ara_go_term text 2147483647  √  null
definition cv text 2147483647  √  null A text description of the criteria for
membership of this ontology
definition cvterm text 2147483647  √  null A human-readable text
definition
definition glossary text 2147483647
deleted cxgn_bac_pipeline_genbank_log bool 1 false
deleted cxgn_bac_pipeline_loading_log bool 1 false
deleted cxgn_bac_pipeline_processing_log bool 1 false
deleted cxgn_indexedlog_test_feel_free_to_delete_me bool 1 false
deleted itag_loading_log bool 1 false
description analysis text 2147483647  √  null
description ara_evidef text 2147483647  √  null
description ara_scop text 2147483647  √  null
description bug text 2147483647  √  null
description db varchar 255  √  null
description dbxref text 2147483647  √  null
description image text 2147483647  √  null
description project varchar 255
description tag text 2147483647  √  null
direction ara_map bpchar 1  √  null
dom_desc ara_domain varchar 32  √  null
dom_end ara_domain int4 10  √  null
dom_id ara_domain varchar 12  √  null
dom_start ara_domain int4 10  √  null
e_value ara_domain varchar 16  √  null
e_value ara_scop varchar 32  √  null
editor pubauthor bool 1  √  false indicates whether the author is an editor for linked publication. Note: this is a boolean field but does not follow the normal chado convention for naming booleans
email ara_users varchar 32  √  null
ending forward_amplicon_sequence_information text 2147483647  √  null
ending forward_amplicon_sequence_markers text 2147483647  √  null
endpos ara_map int4 10  √  null
enzyme_id clone_in_silico_digestion int4 10  √  null
enzyme_id enzyme_restriction_sites int4 10  √  null
enzyme_id fpc_fingerprint int4 10
enzyme_restriction_sites_id enzyme_restriction_sites serial 10  √  nextval('enzyme_restriction_sites_enzyme_restriction_sites_id_seq'::regclass)
evalue blastwatch_queries float8 17,17
evalue blastwatch_results float8 17,17
evidence ara_myristoylation varchar 8  √  null
experiment_id image_experiment int8 19  √  null
experiment_id tag_experiment int8 19  √  null
expert_annotation ara_family text 2147483647  √  null
expression resource_file text 2147483647
family_annotation family text 2147483647  √  null
family_build_id family int8 19  √  null
family_build_id family_build int8 19  √  null
family_id family int8 19  √  null
family_id family_member int8 19  √  null
family_member_id family_member int8 19  √  null
family_nr family int4 10  √  null
feature_cvterm_dbxref_id feature_cvterm_dbxref serial 10  √  nextval('feature_cvterm_dbxref_feature_cvterm_dbxref_id_seq'::regclass)
feature_cvterm_id feature_cvterm serial 10  √  nextval('feature_cvterm_feature_cvterm_id_seq'::regclass)
feature_cvterm_dbxref.feature_cvterm_id feature_cvterm_dbxref_feature_cvterm_id_fkey
feature_cvterm_pub.feature_cvterm_id feature_cvterm_pub_feature_cvterm_id_fkey
feature_cvtermprop.feature_cvterm_id feature_cvtermprop_feature_cvterm_id_fkey
feature_cvterm_id feature_cvterm_dbxref int4 10
feature_cvterm.feature_cvterm_id feature_cvterm_dbxref_feature_cvterm_id_fkey
feature_cvterm_id feature_cvterm_pub int4 10
feature_cvterm.feature_cvterm_id feature_cvterm_pub_feature_cvterm_id_fkey
feature_cvterm_id feature_cvtermprop int4 10
feature_cvterm.feature_cvterm_id feature_cvtermprop_feature_cvterm_id_fkey
feature_cvterm_pub_id feature_cvterm_pub serial 10  √  nextval('feature_cvterm_pub_feature_cvterm_pub_id_seq'::regclass)
feature_cvtermprop_id feature_cvtermprop serial 10  √  nextval('feature_cvtermprop_feature_cvtermprop_id_seq'::regclass)
feature_dbxref_id feature_dbxref serial 10  √  nextval('feature_dbxref_feature_dbxref_id_seq'::regclass)
feature_id analysisfeature int4 10
feature.feature_id analysisfeature_feature_id_fkey
feature_id clone_feature int8 19  √  null
feature.feature_id clone_feature_feature_id_fkey
feature_id feature serial 10  √  nextval('feature_feature_id_seq'::regclass)
analysisfeature.feature_id analysisfeature_feature_id_fkey
clone_feature.feature_id clone_feature_feature_id_fkey
feature_cvterm.feature_id feature_cvterm_feature_id_fkey
feature_dbxref.feature_id feature_dbxref_feature_id_fkey
feature_pub.feature_id feature_pub_feature_id_fkey
feature_relationship.object_id feature_relationship_object_id_fkey
feature_relationship.subject_id feature_relationship_subject_id_fkey
feature_synonym.feature_id feature_synonym_feature_id_fkey
featureloc.feature_id featureloc_feature_id_fkey
featureloc.srcfeature_id featureloc_srcfeature_id_fkey
featureprop.feature_id featureprop_feature_id_fkey
feature_id feature_cvterm int4 10
feature.feature_id feature_cvterm_feature_id_fkey
feature_id feature_dbxref int4 10
feature.feature_id feature_dbxref_feature_id_fkey
feature_id feature_pub int4 10
feature.feature_id feature_pub_feature_id_fkey
feature_id feature_synonym int4 10
feature.feature_id feature_synonym_feature_id_fkey
feature_id featureloc int4 10
feature.feature_id featureloc_feature_id_fkey
The feature that is being located. Any feature can have zero or more featurelocs
feature_id featureprop int4 10
feature.feature_id featureprop_feature_id_fkey
feature_id gff3atts int4 10  √  null
feature_id gff3view int4 10  √  null
feature_id gffatts int4 10  √  null
feature_id tmp_gff_load_cache int4 10  √  null
feature_pub_id feature_pub serial 10  √  nextval('feature_pub_feature_pub_id_seq'::regclass)
feature_relationship_id feature_relationship serial 10  √  nextval('feature_relationship_feature_relationship_id_seq'::regclass)
feature_relationship_pub.feature_relationship_id feature_relationship_pub_feature_relationship_id_fkey
feature_relationshipprop.feature_relationship_id feature_relationshipprop_feature_relationship_id_fkey
feature_relationship_id feature_relationship_pub int4 10
feature_relationship.feature_relationship_id feature_relationship_pub_feature_relationship_id_fkey
feature_relationship_id feature_relationshipprop int4 10
feature_relationship.feature_relationship_id feature_relationshipprop_feature_relationship_id_fkey
feature_relationship_pub_id feature_relationship_pub serial 10  √  nextval('feature_relationship_pub_feature_relationship_pub_id_seq'::regclass)
feature_relationshipprop_id feature_relationshipprop serial 10  √  nextval('feature_relationshipprop_feature_relationshipprop_id_seq'::regclass)
feature_relationshipprop_pub.feature_relationshipprop_id feature_relationshipprop_pub_feature_relationshipprop_id_fkey
feature_relationshipprop_id feature_relationshipprop_pub int4 10
feature_relationshipprop.feature_relationshipprop_id feature_relationshipprop_pub_feature_relationshipprop_id_fkey
feature_relationshipprop_pub_id feature_relationshipprop_pub serial 10  √  nextval('feature_relationshipprop_pub_feature_relationshipprop_pub_i_seq'::regclass)
feature_synonym_id feature_synonym serial 10  √  nextval('feature_synonym_feature_synonym_id_seq'::regclass)
featureloc_id featureloc serial 10  √  nextval('featureloc_featureloc_id_seq'::regclass)
featureloc_pub.featureloc_id featureloc_pub_featureloc_id_fkey
featureloc_id featureloc_pub int4 10
featureloc.featureloc_id featureloc_pub_featureloc_id_fkey
featureloc_pub_id featureloc_pub serial 10  √  nextval('featureloc_pub_featureloc_pub_id_seq'::regclass)
featureprop_id featureprop serial 10  √  nextval('featureprop_featureprop_id_seq'::regclass)
featureprop_pub.featureprop_id featureprop_pub_featureprop_id_fkey
featureprop_id featureprop_pub int4 10
featureprop.featureprop_id featureprop_pub_featureprop_id_fkey
featureprop_pub_id featureprop_pub serial 10  √  nextval('featureprop_pub_featureprop_pub_id_seq'::regclass)
fend gff3view int4 10  √  null
file_base fpc_build text 2147483647 file basename relative to the base path for keeping fpc data.  the actual filenames are file_base.cor and file_base.fpc
file_ext image varchar 20  √  null
fish_result_id image_fish_result int8 19  √  null
fmax featureloc int4 10  √  null The rightmost/maximal boundary in the linear range represented by the featureloc. Sometimes (eg in bioperl) this is called -end- although this is confusing because it does not necessarily represent the 3-prime coordinate. IMPORTANT: This is space-based (INTERBASE) coordinates, counting from zero. No conversion is required to go from fmax to the rightmost coordinate in a base-oriented system that counts from 1 (eg GFF, bioperl)
fmin featureloc int4 10  √  null The leftmost/minimal boundary in the linear range represented by the featureloc. Sometimes (eg in bioperl) this is called -start- although this is confusing because it does not necessarily represent the 5-prime coordinate. IMPORTANT: This is space-based (INTERBASE) coordinates, counting from zero. To convert this to the leftmost position in a base-oriented system (eg GFF, bioperl), add 1 to fmin
forward_amplicon_sequence_information_id forward_amplicon_sequence_information serial 10  √  nextval('forward_amplicon_sequence_inf_forward_amplicon_sequence_inf_seq'::regclass)
forward_amplicon_sequence_markers_id forward_amplicon_sequence_markers serial 10  √  nextval('forward_amplicon_sequence_mar_forward_amplicon_sequence_mar_seq'::regclass)
fpc_band_id fpc_band serial 10  √  nextval('fpc_band_fpc_band_id_seq'::regclass)
fpc_build_fpc_fingerprint_id fpc_build_fpc_fingerprint bigserial 19  √  nextval('fpc_build_fpc_fingerprint_fpc_build_fpc_fingerprint_id_seq'::regclass)
fpc_build_id fpc_build serial 10  √  nextval('fpc_build_fpc_build_id_seq'::regclass)
fpc_build_fpc_fingerprint.fpc_build_id fpc_build_fpc_fingerprint_fpc_build_id_fkey
fpc_contig.fpc_build_id fpc_contig_fpc_build_id_fkey
fpc_build_id fpc_build_fpc_fingerprint int4 10  √  null
fpc_build.fpc_build_id fpc_build_fpc_fingerprint_fpc_build_id_fkey
fpc_build_id fpc_contig int4 10
fpc_build.fpc_build_id fpc_contig_fpc_build_id_fkey
fpc_contig_clone_id fpc_contig_clone bigserial 19  √  nextval('fpc_contig_clone_fpc_contig_clone_id_seq'::regclass)
fpc_contig_id fpc_contig bigserial 19  √  nextval('fpc_contig_fpc_contig_id_seq'::regclass)
fpc_contig_clone.fpc_contig_id fpc_contig_clone_fpc_contig_id_fkey
fpc_contig_id fpc_contig_clone int8 19
fpc_contig.fpc_contig_id fpc_contig_clone_fpc_contig_id_fkey
fpc_fingerprint_id fpc_band int4 10
fpc_fingerprint.fpc_fingerprint_id fpc_band_fpc_fingerprint_id_fkey
fpc_fingerprint_id fpc_build_fpc_fingerprint int8 19  √  null
fpc_fingerprint.fpc_fingerprint_id fpc_build_fpc_fingerprint_fpc_fingerprint_id_fkey
fpc_fingerprint_id fpc_fingerprint serial 10  √  nextval('fpc_fingerprint_fpc_fingerprint_id_seq'::regclass)
fpc_band.fpc_fingerprint_id fpc_band_fpc_fingerprint_id_fkey
fpc_build_fpc_fingerprint.fpc_fingerprint_id fpc_build_fpc_fingerprint_fpc_fingerprint_id_fkey
fpc_series_id fpc_build int4 10
fpc_series.fpc_series_id fpc_build_fpc_series_id_fkey
fpc_series_id fpc_series serial 10  √  nextval('fpc_series_fpc_series_id_seq'::regclass)
fpc_build.fpc_series_id fpc_build_fpc_series_id_fkey
fragment_size clone_in_silico_digestion_bands int4 10  √  null
fragment_size fpc_band int4 10  √  null
fstart gff3view int4 10  √  null
fulltext ara_annotation tsvector 2147483647  √  null
function ara_annotation text 2147483647  √  null
function_evidence ara_annotation text 2147483647  √  null
gb_locus ara_family varchar 128  √  null
gb_mrna_id ara_annotation varchar 16  √  null
gb_prot_id ara_annotation varchar 16  √  null
gbi ara_family varchar 64  √  null
gel_name fpc_fingerprint varchar 30  √  null
genbank_gi ara_annotation int8 19  √  null
genbank_taxon_id organism int4 10
gene_alias ara_family varchar 128  √  null
gene_family ara_family varchar 128  √  null
gene_name ara_family varchar 128  √  null
genecount ara_prefix_info int4 10  √  null
genomepos ara_properties varchar 64  √  null
genomic ara_sequence text 2147483647  √  null
genus organism varchar 255
gfp_all ara_gfp_ms text 2147483647  √  null
givennames pubauthor varchar 100  √  null first name, initials
glossary_id glossary serial 10  √  nextval('glossary_glossary_id_seq'::regclass)
go_id ara_go_term varchar 12
group_id family_build int8 19  √  null
headline cvterm_pub_ranking text 2147483647  √  null
headline locus_pub_ranking text 2147483647  √  null
hmm_cd ara_signalp bpchar 1  √  null
hmm_cd signalp bpchar 1  √  null
hmm_cd unigene_signalp bpchar 1  √  null
hmm_cmax ara_signalp float4 8,8  √  null
hmm_cmax signalp float4 8,8  √  null
hmm_cmax unigene_signalp float4 8,8  √  null
hmm_cpos ara_signalp int4 10  √  null
hmm_cpos signalp int2 5  √  null
hmm_cpos unigene_signalp int2 5  √  null
hmm_d ara_signalp bpchar 1  √  null
hmm_d signalp bpchar 1  √  null
hmm_d unigene_signalp bpchar 1  √  null
hmm_sprob ara_signalp float4 8,8  √  null
hmm_sprob signalp float4 8,8  √  null
hmm_sprob unigene_signalp float4 8,8  √  null
hmm_type ara_signalp bpchar 1  √  null
hmm_type signalp bpchar 1  √  null
hmm_type unigene_signalp bpchar 1  √  null
host cxgn_bac_pipeline_genbank_log varchar 40
host cxgn_bac_pipeline_loading_log varchar 40
host cxgn_bac_pipeline_processing_log varchar 40
host cxgn_indexedlog_test_feel_free_to_delete_me varchar 40
host itag_loading_log varchar 40
hotlist ara_users text 2147483647  √  null
i_value family_build float8 17,17  √  null
id ara_users serial 10  √  nextval('ara_users_id_seq'::regclass)
id cxgn_bac_pipeline_genbank_log serial 10  √  nextval('cxgn_bac_pipeline_genbank_log_id_seq'::regclass)
id cxgn_bac_pipeline_loading_log serial 10  √  nextval('cxgn_bac_pipeline_loading_log_id_seq'::regclass)
id cxgn_bac_pipeline_processing_log serial 10  √  nextval('cxgn_bac_pipeline_processing_log_id_seq'::regclass)
id cxgn_indexedlog_test_feel_free_to_delete_me serial 10  √  nextval('cxgn_indexedlog_test_feel_free_to_delete_me_id_seq'::regclass)
id itag_loading_log serial 10  √  nextval('itag_loading_log_id_seq'::regclass)
identity analysisfeature float8 17,17  √  null
image_experiment_id image_experiment serial 10  √  nextval('image_experiment_image_experiment_id_seq'::regclass)
image_fish_result_id image_fish_result serial 10  √  nextval('image_fish_result_image_fish_result_id_seq'::regclass)
image_id image serial 10  √  nextval('image_image_id_seq'::regclass)
image_experiment.image_id image_experiment_image_id_fkey
image_fish_result.image_id image_fish_result_image_id_fkey
image_individual.image_id image_individual_image_id_fkey
image_locus.image_id image_locus_image_id_fkey
tag_image.image_id tag_image_image_id_fkey
image_id image_experiment int8 19  √  null
image.image_id image_experiment_image_id_fkey
image_id image_fish_result int8 19  √  null
image.image_id image_fish_result_image_id_fkey
image_id image_individual int8 19  √  null
image.image_id image_individual_image_id_fkey
image_id image_locus int8 19  √  null
image.image_id image_locus_image_id_fkey
image_id tag_image int8 19  √  null
image.image_id tag_image_image_id_fkey
image_individual_id image_individual serial 10  √  nextval('image_individual_image_individual_id_seq'::regclass)
image_locus_id image_locus serial 10  √  nextval('image_locus_image_locus_id_seq'::regclass)
indexed materialized_view text 2147483647  √  null
individual_id image_individual int8 19  √  null
individual_id phenotype int4 10
interactioncount ara_properties int4 10  √  null
interpro_dom ara_domain text 2147483647  √  null
interpro_id ara_domain varchar 12  √  null
intron_num ara_intron int2 5  √  null
introncount ara_properties int2 5  √  null
is_a ara_go_term text 2147483647  √  null
is_analysis feature bool 1 false Boolean indicating whether this
feature is annotated or the result of an automated analysis. Analysis
results also use the companalysis module. Note that the dividing line
between analysis/annotation may be fuzzy, this should be determined on
a per-project basis in a consistent manner. One requirement is that
there should only be one non-analysis version of each wild-type gene
feature in a genome, whereas the same gene feature can be predicted
multiple times in different analyses
is_current feature_dbxref bool 1 true the is_current boolean indicates whether the linked dbxref is the  current -official- dbxref for the linked feature
is_current feature_synonym bool 1 true the is_current boolean indicates whether the linked synonym is the  current -official- symbol for the linked feature
is_current pub_dbxref bool 1 true
is_fmax_partial featureloc bool 1 false This is typically
false, but may be true if the value for column:fmax is inaccurate or
the rightmost part of the range is unknown/unbounded
is_fmin_partial featureloc bool 1 false This is typically
false, but may be true if the value for column:fmin is inaccurate or
the leftmost part of the range is unknown/unbounded
is_for_definition cvterm_dbxref int4 10 0 A
cvterm.definition should be supported by one or more references. If
this column is true, the dbxref is not for a term in an external db -
it is a dbxref for provenance information for the definition
is_internal feature_synonym bool 1 false typically a synonym exists so that somebody querying the db with an obsolete name can find the object theyre looking for (under its current name.  If the synonym has been used publicly & deliberately (eg in a paper), it my also be listed in reports as a synonym.   If the synonym was not used deliberately (eg, there was a typo which went public), then the is_internal boolean may be set to -true- so that it is known that the 
synonym is -internal- and should be queryable but should not be listed in reports as a valid synonym
is_not feature_cvterm bool 1 false if this is set to true, then this annotation is interpreted as a NEGATIVE annotation - ie the feature does NOT have the specified function, process, component, part, etc. See GO docs for more details
is_obsolete cvterm int4 10 0 Boolean 0=false,1=true; see
GO documentation for details of obsoletion.  note that two terms with
different primary dbxrefs may exist if one is obsolete
is_obsolete feature bool 1 false Boolean indicating whether this
feature has been obsoleted. Some chado instances may choose to simply
remove the feature altogether, others may choose to keep an obsolete
row in the table
is_obsolete pub bool 1  √  false
is_relationshiptype cvterm int4 10 0 Boolean
0=false,1=true relations or relationship types (also known as Typedefs
in OBO format, or as properties or slots) form a cv/ontology in
themselves. We use this flag to indicate whether this cvterm is an
actual term/class/universal or a relation. Relations may be drawn from
the OBO Relations ontology, but are not exclusively drawn from there
is_updateable tableinfo int4 10 1
is_view tableinfo int4 10 0
isoelectric ara_properties float4 8,8  √  null
issue pub varchar 255  √  null
last_update materialized_view timestamp 29,6  √  null
lbound ara_intron int4 10  √  null
lbound ara_scop int4 10  √  null
lists ara_users text 2147483647  √  null
localization ara_annotation text 2147483647  √  null
localization_evidence ara_annotation text 2147483647  √  null
location ara_targetp bpchar 1  √  null
locgroup featureloc int4 10 0 This is used to manifest redundant,
derivable extra locations for a feature. The default locgroup=0 is
used for the DIRECT location of a feature. !! MOST CHADO USERS MAY
NEVER USE featurelocs WITH logroup>0 !! Transitively derived locations
are indicated with locgroup>0. For example, the position of an exon on
a BAC and in global chromosome coordinates. This column is used to
differentiate these groupings of locations. the default locgroup 0
is used for the main/primary location, from which the others can be
derived via coordinate transformations. another example of redundant
locations is storing ORF coordinates relative to both transcript and
genome. redundant locations open the possibility of the database
getting into inconsistent states; this schema gives us the flexibility
of both warehouse instantiations with redundant locations (easier for
querying) and management instantiations with no redundant
locations. An example of using both locgroup and rank: imagine a
feature indicating a conserved region between the chromosomes of two
different species. we may want to keep redundant locations on both
contigs and chromosomes. we would thus have 4 locations for the single
conserved region feature - two distinct locgroups (contig level and
chromosome level) and two distinct ranks (for the two species)
locus ara_annotation varchar 16  √  null
locus ara_domain varchar 16  √  null
locus ara_family varchar 128  √  null
locus ara_gfp_ms varchar 16  √  null
locus ara_interactome_all varchar 16  √  null
locus ara_interactome_unique varchar 16  √  null
locus ara_intron varchar 16  √  null
locus ara_map varchar 16  √  null
locus ara_myristoylation varchar 12  √  null
locus ara_properties varchar 16  √  null
locus ara_scop varchar 16  √  null
locus ara_sequence varchar 16  √  null
locus ara_signalp varchar 16  √  null
locus ara_targetp varchar 16  √  null
locus_id image_locus int8 19  √  null
locus_id locus_pub_ranking int4 10  √  null
locus_id locus_pub_ranking_validate int4 10  √  null
locus_interact ara_interactome_all varchar 16  √  null
locus_interact ara_interactome_unique varchar 16  √  null
longdescription ara_evidef text 2147483647  √  null
m_score ara_targetp float4 8,8  √  null
marker_id marker_names int4 10  √  null
marker_name forward_amplicon_sequence_markers text 2147483647  √  null
match_type cvterm_pub_ranking text 2147483647  √  null
match_type locus_pub_ranking text 2147483647  √  null
materialized_view_id materialized_view serial 10  √  nextval('materialized_view_materialized_view_id_seq'::regclass)
matrix blastwatch_queries varchar 10
md5checksum feature bpchar 32  √  null The 32-character checksum of the sequence,
calculated using the MD5 algorithm. This is practically guaranteed to
be unique for any feature. This column thus acts as a unique
identifier on the mathematical sequence
member_count family int4 10  √  null
message cxgn_bac_pipeline_genbank_log text 2147483647  √  null
message cxgn_bac_pipeline_loading_log text 2147483647  √  null
message cxgn_bac_pipeline_processing_log text 2147483647  √  null
message cxgn_indexedlog_test_feel_free_to_delete_me text 2147483647  √  null
message itag_loading_log text 2147483647  √  null
miniref pub varchar 255  √  null
modification_date tableinfo date 13 now()
modified_date bug timestamptz 35,6  √  null
modified_date image timestamptz 35,6  √  null
modified_date image_locus timestamptz 35,6  √  null
modified_date tag timestamptz 35,6  √  null
modified_date tag_experiment timestamptz 35,6  √  null
modified_date tag_image timestamptz 35,6  √  null
ms_all ara_gfp_ms text 2147483647  √  null
mv_schema materialized_view varchar 64  √  null
mv_specs materialized_view text 2147483647  √  null
mv_table materialized_view varchar 128  √  null
name analysis varchar 255  √  null
name ara_go_term text 2147483647  √  null
name cv varchar 255 The name of the ontology. This
corresponds to the obo-format -namespace-. cv names uniquely identify
the cv. In obo file format, the cv.name is known as the namespace
name cvterm varchar 1024 A concise human-readable name or
label for the cvterm. uniquely identifies a cvterm within a cv
name db varchar 255
name feature varchar 255  √  null The optional human-readable common name for
a feature, for display purposes
name fpc_contig varchar 20
name fpc_series varchar 50  √  null
name gff3view varchar 255  √  null
name image varchar 100  √  null
name marker_names text 2147483647  √  null
name materialized_view varchar 64  √  null
name project varchar 255
name resource_file varchar 40
name synonym varchar 255 The synonym itself. Should be human-readable machine-searchable ascii text
name tableinfo varchar 30
name tag varchar 100  √  null
namespace ara_go_term varchar 32  √  null
new_results blastwatch_queries bool 1 false
nn_cd ara_signalp bpchar 1  √  null
nn_cd signalp bpchar 1  √  null
nn_cd unigene_signalp bpchar 1  √  null
nn_cmax ara_signalp float4 8,8  √  null
nn_cmax signalp float4 8,8  √  null
nn_cmax unigene_signalp float4 8,8  √  null
nn_cpos ara_signalp int4 10  √  null
nn_cpos signalp int2 5  √  null
nn_cpos unigene_signalp int2 5  √  null
nn_d ara_signalp bpchar 1  √  null
nn_d signalp bpchar 1  √  null
nn_d unigene_signalp bpchar 1  √  null
nn_score ara_signalp float4 8,8  √  null
nn_score signalp float4 8,8  √  null
nn_score unigene_signalp float4 8,8  √  null
nn_sd ara_signalp bpchar 1  √  null
nn_sd signalp bpchar 1  √  null
nn_sd unigene_signalp bpchar 1  √  null
nn_smax ara_signalp float4 8,8  √  null
nn_smax signalp float4 8,8  √  null
nn_smax unigene_signalp float4 8,8  √  null
nn_smean ara_signalp float4 8,8  √  null
nn_smean signalp float4 8,8  √  null
nn_smean unigene_signalp float4 8,8  √  null
nn_smeand ara_signalp bpchar 1  √  null
nn_smeand signalp bpchar 1  √  null
nn_smeand unigene_signalp bpchar 1  √  null
nn_spos ara_signalp int4 10  √  null
nn_spos signalp int2 5  √  null
nn_spos unigene_signalp int2 5  √  null
nn_yd ara_signalp bpchar 1  √  null
nn_yd signalp bpchar 1  √  null
nn_yd unigene_signalp bpchar 1  √  null
nn_ymax ara_signalp float4 8,8  √  null
nn_ymax signalp float4 8,8  √  null
nn_ymax unigene_signalp float4 8,8  √  null
nn_ypos ara_signalp int4 10  √  null
nn_ypos signalp int2 5  √  null
nn_ypos unigene_signalp int2 5  √  null
normscore analysisfeature float8 17,17  √  null
num_child ara_go_term int4 10  √  null
num_desc ara_go_term int4 10  √  null
num_results blastwatch_queries int4 10 0
o_score ara_targetp float4 8,8  √  null
object_id cvterm_relationship int4 10
cvterm.cvterm_id cvterm_relationship_object_id_fkey
the object of the
subj-predicate-obj sentence. The cvterm_relationship refers to the
object. In a graph, this typically corresponds to the parent node
object_id cvtermpath int4 10
cvterm.cvterm_id cvtermpath_object_id_fkey
object_id feature_relationship int4 10
feature.feature_id feature_relationship_object_id_fkey
the object of the subj-predicate-obj sentence. This is typically the container feature
object_id organism_relationship int4 10
organism.organism_id organism_relationship_object_id_fkey
object_id organismpath int4 10
organism.organism_id organismpath_object_id_fkey
object_id pub_relationship int4 10
pub.pub_id pub_relationship_object_id_fkey
observable_id phenotype int4 10  √  null
cvterm.cvterm_id phenotype_observable_id_fkey
obsolete bug bool 1  √  null
obsolete image bool 1  √  false
obsolete image_individual bool 1  √  false
obsolete image_locus bool 1  √  false
obsolete organism int4 10  √  null
obsolete tag bool 1  √  false
obsolete tag_experiment bool 1  √  false
obsolete tag_image bool 1  √  false
org_id ara_family varchar 128  √  null
organism_dbxref_id organism_dbxref serial 10  √  nextval('organism_dbxref_organism_dbxref_id_seq'::regclass)
organism_group_id family_member int8 19  √  null
organism_id feature int4 10
organism.organism_id feature_organism_id_fkey
The organism to which this feature
belongs. This column is mandatory
organism_id gff3view int4 10  √  null
organism_id organism serial 10  √  nextval('organism_organism_id_seq'::regclass)
feature.organism_id feature_organism_id_fkey
organism.sgn_organism_id organism_sgn_organism_id_fkey
organism_dbxref.organism_id organism_dbxref_organism_id_fkey
organism_relationship.object_id organism_relationship_object_id_fkey
organism_relationship.subject_id organism_relationship_subject_id_fkey
organismpath.object_id organismpath_object_id_fkey
organismpath.subject_id organismpath_subject_id_fkey
organismprop.organism_id organismprop_organism_id_fkey
organism_id organism_dbxref int4 10
organism.organism_id organism_dbxref_organism_id_fkey
organism_id organismprop int4 10
organism.organism_id organismprop_organism_id_fkey
organism_id tmp_gff_load_cache int4 10  √  null
organism_name forward_amplicon_sequence_information text 2147483647  √  null
organism_relationship_id organism_relationship serial 10  √  nextval('organism_relationship_organism_relationship_id_seq'::regclass)
organismpath_id organismpath serial 10  √  nextval('organismpath_organismpath_id_seq'::regclass)
organismprop_id organismprop serial 10  √  nextval('organismprop_organismprop_id_seq'::regclass)
original_filename image varchar 100  √  null
pages pub varchar 255  √  null page number range[s], eg, 457--459, viii + 664pp, lv--lvii
password ara_users varchar 32  √  null
path ara_go_term text 2147483647  √  null
pathdistance cvtermpath int4 10  √  null The number of steps
required to get from the subject cvterm to the object cvterm, counting
from zero (reflexive relationship)
pathdistance organismpath int4 10  √  null
people_id ara_family varchar 128  √  null
phase featureloc int4 10  √  null phase of translation wrt srcfeature_id.
Values are 0,1,2. It may not be possible to manifest this column for
some features such as exons, because the phase is dependant on the
spliceform (the same exon can appear in multiple spliceforms). This column is mostly useful for predicted exons and CDSs
phase gff3view int4 10  √  null
phenotype_cvterm_id phenotype_cvterm serial 10 nextval('phenotype_cvterm_phenotype_cvterm_id_seq'::regclass)
phenotype_id phenotype serial 10  √  nextval('phenotype_phenotype_id_seq'::regclass)
phenotype_cvterm.phenotype_id phenotype_cvterm_phenotype_id_fkey
phenotype_id phenotype_cvterm int4 10
phenotype.phenotype_id phenotype_cvterm_phenotype_id_fkey
pid cxgn_bac_pipeline_genbank_log int4 10
pid cxgn_bac_pipeline_loading_log int4 10
pid cxgn_bac_pipeline_processing_log int4 10
pid cxgn_indexedlog_test_feel_free_to_delete_me int4 10
pid itag_loading_log int4 10
plant_number forward_amplicon_sequence_information int4 10  √  null
plausible fpc_contig_clone bool 1 true
pmid ara_family varchar 128  √  null
pmid ara_interactome_all varchar 64  √  null
pmid ara_pmidlink int8 19  √  null
prefix ara_prefix_info varchar 12  √  null
primary_key_column tableinfo varchar 30  √  null
process ara_annotation text 2147483647  √  null
process_evidence ara_annotation text 2147483647  √  null
progname cxgn_bac_pipeline_genbank_log varchar 80
progname cxgn_bac_pipeline_loading_log varchar 80
progname cxgn_bac_pipeline_processing_log varchar 80
progname cxgn_indexedlog_test_feel_free_to_delete_me varchar 80  √  null
progname itag_loading_log varchar 80
program analysis varchar 255
program blastwatch_queries varchar 10
programversion analysis varchar 255
project_id project serial 10  √  nextval('project_project_id_seq'::regclass)
prot_length ara_domain int4 10  √  null
protein ara_sequence text 2147483647  √  null
pub_curator_id pub_curator serial 10  √  nextval('pub_curator_pub_curator_id_seq'::regclass)
pub_dbxref_id pub_dbxref serial 10  √  nextval('pub_dbxref_pub_dbxref_id_seq'::regclass)
pub_id cvterm_pub_ranking int4 10  √  null
pub.pub_id cvterm_pub_ranking_pub_id_fkey
pub_id feature_cvterm int4 10
pub.pub_id feature_cvterm_pub_id_fkey
Provenance for the annotation. Each annotation should have a single primary publication (which may be of the appropriate type for computational analyses) where more details can be found. Additional provenance dbxrefs can be attached using feature_cvterm_dbxref
pub_id feature_cvterm_pub int4 10
pub.pub_id feature_cvterm_pub_pub_id_fkey
pub_id feature_pub int4 10
pub.pub_id feature_pub_pub_id_fkey
pub_id feature_relationship_pub int4 10
pub.pub_id feature_relationship_pub_pub_id_fkey
pub_id feature_relationshipprop_pub int4 10
pub.pub_id feature_relationshipprop_pub_pub_id_fkey
pub_id feature_synonym int4 10
pub.pub_id feature_synonym_pub_id_fkey
the pub_id link is for relating the usage of a given synonym to the publication in which it was used
pub_id featureloc_pub int4 10
pub.pub_id featureloc_pub_pub_id_fkey
pub_id featureprop_pub int4 10
pub.pub_id featureprop_pub_pub_id_fkey
pub_id locus_pub_ranking int4 10  √  null
pub.pub_id locus_pub_ranking_pub_id_fkey
pub_id locus_pub_ranking_validate int4 10  √  null
pub.pub_id locus_pub_ranking_validate_pub_id_fkey
pub_id pub serial 10  √  nextval('pub_pub_id_seq'::regclass)
cvterm_pub_ranking.pub_id cvterm_pub_ranking_pub_id_fkey
feature_cvterm.pub_id feature_cvterm_pub_id_fkey
feature_cvterm_pub.pub_id feature_cvterm_pub_pub_id_fkey
feature_pub.pub_id feature_pub_pub_id_fkey
feature_relationship_pub.pub_id feature_relationship_pub_pub_id_fkey
feature_relationshipprop_pub.pub_id feature_relationshipprop_pub_pub_id_fkey
feature_synonym.pub_id feature_synonym_pub_id_fkey
featureloc_pub.pub_id featureloc_pub_pub_id_fkey
featureprop_pub.pub_id featureprop_pub_pub_id_fkey
locus_pub_ranking.pub_id locus_pub_ranking_pub_id_fkey
locus_pub_ranking_validate.pub_id locus_pub_ranking_validate_pub_id_fkey
pub_curator.pub_id pub_curator_pub_id_fkey
pub_dbxref.pub_id pub_dbxref_pub_id_fkey
pub_relationship.object_id pub_relationship_object_id_fkey
pub_relationship.subject_id pub_relationship_subject_id_fkey
pubabstract.pub_id pubabstract_pub_id_fkey
pubauthor.pub_id pubauthor_pub_id_fkey
pubprop.pub_id pubprop_pub_id_fkey
pub_id pub_curator int4 10  √  null
pub.pub_id pub_curator_pub_id_fkey
pub_id pub_dbxref int4 10
pub.pub_id pub_dbxref_pub_id_fkey
pub_id pubabstract int4 10  √  null
pub.pub_id pubabstract_pub_id_fkey
pub_id pubauthor int4 10
pub.pub_id pubauthor_pub_id_fkey
pub_id pubprop int4 10
pub.pub_id pubprop_pub_id_fkey
pub_relationship_id pub_relationship serial 10  √  nextval('pub_relationship_pub_relationship_id_seq'::regclass)
pubabstract_id pubabstract serial 10  √  nextval('pubabstract_pubabstract_id_seq'::regclass)
pubauthor_id pubauthor serial 10  √  nextval('pubauthor_pubauthor_id_seq'::regclass)
publisher pub varchar 255  √  null
pubplace pub varchar 255  √  null
pubprop_id pubprop serial 10  √  nextval('pubprop_pubprop_id_seq'::regclass)
pyear pub varchar 255  √  null
query materialized_view text 2147483647  √  null
query_id blastwatch_results varchar 50
rank cvterm_pub_ranking float4 8,8  √  null
rank cvtermprop int4 10 0 Property-Value ordering. Any
cvterm can have multiple values for any particular property type -
these are ordered in a list using rank, counting from zero. For
properties that are single-valued rather than multi-valued, the
default 0 value should be used
rank dbxrefprop int4 10 0
rank feature_cvtermprop int4 10 0 Property-Value
ordering. Any feature_cvterm can have multiple values for any particular
property type - these are ordered in a list using rank, counting from
zero. For properties that are single-valued rather than multi-valued,
the default 0 value should be used
rank feature_relationship int4 10 0 The ordering of subject features with respect to the object feature may be important (for example, exon ordering on a transcript - not always derivable if you take trans spliced genes into consideration). rank is used to order these; starts from zero
rank feature_relationshipprop int4 10 0 Property-Value
ordering. Any feature_relationship can have multiple values for any particular
property type - these are ordered in a list using rank, counting from
zero. For properties that are single-valued rather than multi-valued,
the default 0 value should be used
rank featureloc int4 10 0 Used when a feature has >1
location, otherwise the default rank 0 is used. Some features (eg
blast hits and HSPs) have two locations - one on the query and one on
the subject. Rank is used to differentiate these. Rank=0 is always
used for the query, Rank=1 for the subject. For multiple alignments,
assignment of rank is arbitrary. Rank is also used for
sequence_variant features, such as SNPs. Rank=0 indicates the wildtype
(or baseline) feature, Rank=1 indicates the mutant (or compared) feature
rank featureprop int4 10 0 Property-Value ordering. Any
feature can have multiple values for any particular property type -
these are ordered in a list using rank, counting from zero. For
properties that are single-valued rather than multi-valued, the
default 0 value should be used
rank locus_pub_ranking float4 8,8  √  null
rank organismprop int4 10 0
rank phenotype_cvterm int4 10 0
rank pubauthor int4 10 order of author in author list for this pub - order is important
rank pubprop int4 10  √  null
rawscore analysisfeature float8 17,17  √  null
rbound ara_intron int4 10  √  null
rbound ara_scop int4 10  √  null
rc ara_targetp int4 10  √  null
ref gff3view varchar 255  √  null
refresh_time materialized_view int4 10  √  null
residue_info featureloc text 2147483647  √  null Alternative residues,
when these differ from feature.residues. for instance, a SNP feature
located on a wild and mutant protein would have different alresidues.
for alignment/similarity features, the altresidues is used to
represent the alignment string (CIGAR format). Note on variation
features; even if we dont want to instantiate a mutant
chromosome/contig feature, we can still represent a SNP etc with 2
locations, one (rank 0) on the genome, the other (rank 1) would have
most fields null, except for altresidues
residues feature text 2147483647  √  null A sequence of alphabetic characters
representing biological residues (nucleic acids, amino acids). This
column does not need to be manifested for all features; it is optional
for features such as exons where the residues can be derived from the
featureloc. It is recommended that the value for this column be
manifested for features which may may non-contiguous sublocations (eg
transcripts), since derivation at query time is non-trivial. For
expressed sequence, the DNA sequence should be used rather than the
RNA sequence
resource_file_id resource_file serial 10  √  nextval('resource_file_resource_file_id_seq'::regclass)
restriction_site enzyme_restriction_sites text 2147483647  √  null
run_date ara_domain date 13  √  null
s_score ara_targetp float4 8,8  √  null
scop_id ara_scop int4 10  √  null
score blastwatch_results numeric 131089
score gff3view float8 17,17  √  null
search_key cxgn_bac_pipeline_genbank_log varchar 200  √  null
search_key cxgn_bac_pipeline_loading_log varchar 200  √  null
search_key cxgn_bac_pipeline_processing_log varchar 200  √  null
search_key cxgn_indexedlog_test_feel_free_to_delete_me varchar 80  √  null
search_key itag_loading_log varchar 200  √  null
seqlen feature int4 10  √  null The length of the residue feature. See
column:residues. This column is partially redundant with the residues
column, and also with featureloc. This column is required because the
location may be unknown and the residue sequence may not be
manifested, yet it may be desirable to store and query the length of
the feature. The seqlen should always be manifested where the length
of the sequence is known
seqlen gff3view int4 10  √  null
sequence ara_intron text 2147483647  √  null
sequence blastwatch_queries text 2147483647
sequence_name family_member varchar 50  √  null
series_name pub varchar 255  √  null full name of (journal) series
severity bug varchar 20  √  null
sgn_organism_id organism int4 10  √  null
organism.organism_id organism_sgn_organism_id_fkey
signalp_id signalp serial 10  √  nextval('signalp_signalp_id_seq'::regclass)
significance analysisfeature float8 17,17  √  null
source ara_interactome_all varchar 32  √  null
source gff3view varchar 255  √  null
sourcename analysis varchar 255  √  null
sourceuri analysis text 2147483647  √  null
sourceversion analysis varchar 255  √  null
sp_person_id blastwatch_queries int4 10
sp_person_id bug int8 19  √  null
sp_person_id image int8 19  √  null
sp_person_id image_locus int8 19  √  null
sp_person_id phenotype int4 10  √  null
sp_person_id pub_curator int4 10  √  null
sp_person_id tag int8 19  √  null
sp_person_id tag_experiment int4 10  √  null
sp_person_id tag_image int4 10  √  null
species organism varchar 255 A type of organism is always
uniquely identified by genus+species. When mapping from the NCBI
taxonomy names.dmp file, the unique-name column must be used where it
is present, as the name column is not always unique (eg environmental
samples). If a particular strain or subspecies is to be represented,
this is appended onto the species name. Follows standard NCBI taxonomy
pattern
srcfeature_id featureloc int4 10  √  null
feature.feature_id featureloc_srcfeature_id_fkey
The source feature which this location is relative to. Every location is relative to another feature (however, this column is nullable, because the srcfeature may not be known). All locations are -proper- that is, nothing should be located relative to itself. No cycles are allowed in the featureloc graph
startpos ara_map int4 10  √  null
status bug varchar 20  √  null
status family_build bpchar 1  √  null
status pub_curator varchar 32  √  null
strand featureloc int2 5  √  null The orientation/directionality of the
location. Should be 0,-1 or +1
strand gff3view int2 5  √  null
structure_type ara_scop varchar 16  √  null
subject_end blastwatch_results int4 10
subject_id blastwatch_results varchar 50
subject_id cvterm_relationship int4 10
cvterm.cvterm_id cvterm_relationship_subject_id_fkey
the subject of
the subj-predicate-obj sentence. The cvterm_relationship is about the
subject. In a graph, this typically corresponds to the child node
subject_id cvtermpath int4 10
cvterm.cvterm_id cvtermpath_subject_id_fkey
subject_id feature_relationship int4 10
feature.feature_id feature_relationship_subject_id_fkey
the subject of the subj-predicate-obj sentence. This is typically the subfeature
subject_id organism_relationship int4 10
organism.organism_id organism_relationship_subject_id_fkey
subject_id organismpath int4 10
organism.organism_id organismpath_subject_id_fkey
subject_id pub_relationship int4 10
pub.pub_id pub_relationship_subject_id_fkey
subject_start blastwatch_results int4 10
suffix pubauthor varchar 100  √  null Jr., Sr., etc
super_gene_family ara_family varchar 128  √  null
superceded_by unigene_relations int8 19  √  null
superceding_build_nr unigene_relations int4 10  √  null
superceding_organism unigene_relations text 2147483647  √  null
superclass_table_id tableinfo int4 10  √  null
surname pubauthor varchar 100
symbol ara_annotation varchar 256  √  null
synonym cvtermsynonym varchar 1024
synonym_id feature_synonym int4 10
synonym.synonym_id feature_synonym_synonym_id_fkey
synonym_id synonym serial 10  √  nextval('synonym_synonym_id_seq'::regclass)
feature_synonym.synonym_id feature_synonym_synonym_id_fkey
synonym_sgml synonym varchar 255 The fully specified synonym, with any non-ascii characters encoded in SGML
tableinfo_id tableinfo serial 10  √  nextval('tableinfo_tableinfo_id_seq'::regclass)
tag_experiment_id tag_experiment serial 10  √  nextval('tag_experiment_tag_experiment_id_seq'::regclass)
tag_id tag serial 10  √  nextval('tag_tag_id_seq'::regclass)
tag_experiment.tag_id tag_experiment_tag_id_fkey
tag_image.tag_id tag_image_tag_id_fkey
tag_id tag_experiment int8 19  √  null
tag.tag_id tag_experiment_tag_id_fkey
tag_id tag_image int8 19  √  null
tag.tag_id tag_image_tag_id_fkey
tag_image_id tag_image serial 10  √  nextval('tag_image_tag_image_id_seq'::regclass)
tair_annotation ara_annotation text 2147483647  √  null
term glossary text 2147483647
tigr_annotation ara_family text 2147483647  √  null
timeaccessioned feature timestamp 29,6 ('now'::text)::timestamp(6) with time zone for handling object
accession/modification timestamps (as opposed to db auditing info,
handled elsewhere). The expectation is that these fields would be
available to software interacting with chado
timeexecuted analysis timestamp 29,6 ('now'::text)::timestamp(6) with time zone
timelastmodified feature timestamp 29,6 ('now'::text)::timestamp(6) with time zone for handling object
accession/modification timestamps (as opposed to db auditing info,
handled elsewhere). The expectation is that these fields would be
available to software interacting with chado
timestamp cxgn_bac_pipeline_genbank_log timestamp 29,6 now()
timestamp cxgn_bac_pipeline_loading_log timestamp 29,6 now()
timestamp cxgn_bac_pipeline_processing_log timestamp 29,6 now()
timestamp cxgn_indexedlog_test_feel_free_to_delete_me timestamp 29,6 now()
timestamp itag_loading_log timestamp 29,6 now()
title pub text 2147483647  √  null descriptive general heading
title_tsvector pub tsvector 2147483647  √  null
transmemcount ara_properties int2 5  √  null
transmempos ara_properties text 2147483647  √  null
tree_file_location family varchar 2147483647  √  null
tree_log_file_location family varchar 2147483647  √  null
tree_overlap_length family int4 10  √  null
tree_taxa_number family int4 10  √  null
type ara_interactome_all varchar 32  √  null
type gff3atts text 2147483647  √  null
type gff3view varchar 1024  √  null
type gffatts text 2147483647  √  null
type_id analysisprop int4 10
cvterm.cvterm_id analysisprop_type_id_fkey
type_id cvterm_relationship int4 10
cvterm.cvterm_id cvterm_relationship_type_id_fkey
The nature of the
relationship between subject and object. Note that relations are also
housed in the cvterm table, typically from the OBO relationship
ontology, although other relationship types are allowed
type_id cvtermpath int4 10  √  null
cvterm.cvterm_id cvtermpath_type_id_fkey
The relationship type that
this is a closure over. If null, then this is a closure over ALL
relationship types. If non-null, then this references a relationship
cvterm - note that the closure will apply to both this relationship
AND the OBO_REL:is_a (subclass) relationship
type_id cvtermprop int4 10
cvterm.cvterm_id cvtermprop_type_id_fkey
The name of the property/slot is a cvterm. The meaning of the property is defined in that cvterm
type_id cvtermsynonym int4 10  √  null
cvterm.cvterm_id cvtermsynonym_type_id_fkey
A synonym can be exact,
narrow or borader than
type_id dbxrefprop int4 10
cvterm.cvterm_id dbxrefprop_type_id_fkey
type_id feature int4 10
cvterm.cvterm_id feature_type_id_fkey
A required reference to a table:cvterm
giving the feature type. This will typically be a Sequence Ontology
identifier. This column is thus used to subclass the feature table
type_id feature_cvtermprop int4 10
cvterm.cvterm_id feature_cvtermprop_type_id_fkey
The name of the
property/slot is a cvterm. The meaning of the property is defined in
that cvterm. cvterms may come from the OBO evidence code cv
type_id feature_relationship int4 10
cvterm.cvterm_id feature_relationship_type_id_fkey
relationship type between subject and object. This is a cvterm, typically from the OBO relationship ontology, although other relationship types are allowed. The most common relationship type is OBO_REL:part_of. Valid relationship types are constrained by the Sequence Ontology
type_id feature_relationshipprop int4 10
cvterm.cvterm_id feature_relationshipprop_type_id_fkey
The name of the
property/slot is a cvterm. The meaning of the property is defined in
that cvterm. Currently there is no standard ontology for
feature_relationship property types
type_id featureprop int4 10
cvterm.cvterm_id featureprop_type_id_fkey
The name of the
property/slot is a cvterm. The meaning of the property is defined in
that cvterm. Certain property types will only apply to certain feature
types (e.g. the anticodon property will only apply to tRNA features) ;
the types here come from the sequence feature property ontology
type_id organism_relationship int4 10
cvterm.cvterm_id organism_relationship_type_id_fkey
type_id organismpath int4 10
cvterm.cvterm_id organismpath_type_id_fkey
type_id organismprop int4 10
cvterm.cvterm_id organismprop_type_id_fkey
type_id pub int4 10
cvterm.cvterm_id pub_type_id_fkey
the type of the publication (book, journal, poem, graffiti, etc). Uses pub cv
type_id pub_relationship int4 10
cvterm.cvterm_id pub_relationship_type_id_fkey
type_id pubprop int4 10
cvterm.cvterm_id pubprop_type_id_fkey
type_id synonym int4 10
cvterm.cvterm_id synonym_type_id_fkey
types would be symbol and fullname for now
type_id tmp_gff_load_cache int4 10  √  null
uname cxgn_bac_pipeline_genbank_log varchar 40
uname cxgn_bac_pipeline_loading_log varchar 40
uname cxgn_bac_pipeline_processing_log varchar 40
uname cxgn_indexedlog_test_feel_free_to_delete_me varchar 40
uname itag_loading_log varchar 40
unigene_dbxref_id unigene_dbxref serial 10  √  nextval('unigene_dbxref_unigene_dbxref_id_seq'::regclass)
unigene_id unigene_dbxref int8 19
unigene_signalp.unigene_id Implied Constraint
unigene_id unigene_relations int8 19
unigene_signalp.unigene_id Implied Constraint
unigene_id unigene_signalp int8 19
unigene_dbxref.unigene_id Implied Constraint
unigene_relations.unigene_id Implied Constraint
uniprot_id ara_annotation varchar 128  √  null
uniquename feature text 2147483647 The unique name for a feature; may
not be necessarily be particularly human-readable, although this is
prefered. This name must be unique for this type of feature within
this organism
uniquename phenotype text 2147483647
uniquename pub text 2147483647
uniquename tmp_gff_load_cache varchar 1000  √  null
updated_by bug int8 19  √  null
url ara_family text 2147483647  √  null
url ara_pmidlink text 2147483647  √  null
url db varchar 255  √  null
url_name ara_family text 2147483647  √  null
urlprefix db varchar 255  √  null
username ara_users varchar 32  √  null
utr3 ara_sequence text 2147483647  √  null
utr5 ara_sequence text 2147483647  √  null
validate locus_pub_ranking_validate varchar 18  √  null
value analysisprop text 2147483647  √  null
value cvtermprop text 2147483647 ''::text The value of the property, represented as text. Numeric values are converted to their text representation
value dbxrefprop text 2147483647 ''::text
value feature_cvtermprop text 2147483647  √  null The value of the
property, represented as text. Numeric values are converted to their
text representation. This is less efficient than using native database
types, but is easier to query.
value feature_relationship text 2147483647  √  null Additional notes/comments
value feature_relationshipprop text 2147483647  √  null The value of the
property, represented as text. Numeric values are converted to their
text representation. This is less efficient than using native database
types, but is easier to query.
value featureprop text 2147483647  √  null The value of the property, represented as text. Numeric values are converted to their text representation. This is less efficient than using native database types, but is easier to query.
value organismprop text 2147483647  √  null
value phenotype varchar 2147483647  √  null
value pubprop text 2147483647
version dbxref varchar 255 ''::character varying
view_on_table_id tableinfo int4 10  √  null
volume pub varchar 255  √  null
volumetitle pub text 2147483647  √  null title of part if one of a series
weight ara_properties int4 10  √  null