SCHEMA
GSDB

Table of Contents

Primitive Value Classes
Controlled Value Classes
Object Classes
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Primitive Value Classes

boolean
table_id
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Controlled Value Classes

Action_status_rule
Action_tablename_rule
Comment_link_rule
DBLink_link_rule
DeletedAccession_type_rule
ReferenceLink_link_rule
aa_rule
analysis_link_rule
anticodon_length_rule
codon_start_rule
collection_link_rule
comp_type_rule
diff_name_rule
diff_type_rule
direction_rule
genome_rule
import_file_type_rule
intron_class_rule
loc_operator_rule
mod_base_rule
molecule_isolated_rule
molecule_sequenced_rule
pub_status_rule
reference_type_rule
strand_orientation_rule
suffix_rule
transl_type_rule
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Object Classes

Address
Analysis
Anticodon
Collection
Comment
Component
DBLink
DeletedAccession
Feature
BindingSite
Repeat
FeatureTypes
Flatfile
Gene
GeneInst
Institution
ModifiedBase
Person
Product
ProductInst
Reference
Sequence
Source
Taxon
TranslationTables
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PRIMITIVE VALUE CLASS boolean
Data Type:
TINYINT
Alternative Representations
OPM Class Definition
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PRIMITIVE VALUE CLASS table_id
Data Type:
NUMERIC(6)
Alternative Representations
OPM Class Definition
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CONTROLLED VALUE CLASS Action_status_rule
Controlled Values or Ranges:
  • success
  • pending
  • failure
  • processing
  • manual
Alternative Representations
OPM Class Definition
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CONTROLLED VALUE CLASS Action_tablename_rule
Controlled Values or Ranges:
  • ImportFile
  • SequenceStatus
  • FeatureStatus
Alternative Representations
OPM Class Definition
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CONTROLLED VALUE CLASS Comment_link_rule
Controlled Values or Ranges:
  • Sequence
  • Feature
  • Component
  • Source
  • Reference
  • ModifiedBase
Alternative Representations
OPM Class Definition
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CONTROLLED VALUE CLASS DBLink_link_rule
Controlled Values or Ranges:
  • GeneInst
  • ProductInst
  • Gene
  • Product
  • Feature
  • Reference
  • Sequence
  • Source
  • Component
Alternative Representations
OPM Class Definition
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CONTROLLED VALUE CLASS DeletedAccession_type_rule
Controlled Values or Ranges:
  • Feature
  • Sequence
Alternative Representations
OPM Class Definition
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CONTROLLED VALUE CLASS ReferenceLink_link_rule
Controlled Values or Ranges:
  • Feature
  • Source
  • Sequence
  • Component
Alternative Representations
OPM Class Definition
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CONTROLLED VALUE CLASS aa_rule
Controlled Values or Ranges:
  • Ala
  • Arg
  • Asn
  • Asp
  • Cys
  • Gln
  • Glu
  • Gly
  • His
  • Ile
  • Leu
  • Lys
  • Met
  • Phe
  • Pro
  • Ser
  • Thr
  • Trp
  • Tyr
  • Val
  • Xxx
  • TERM
  • OTHER
Alternative Representations
OPM Class Definition
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CONTROLLED VALUE CLASS analysis_link_rule
Controlled Values or Ranges:
  • Feature
  • Component
Alternative Representations
OPM Class Definition
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CONTROLLED VALUE CLASS anticodon_length_rule
Controlled Values or Ranges:
  • 2
  • 3
  • 4
Alternative Representations
OPM Class Definition
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CONTROLLED VALUE CLASS codon_start_rule
Controlled Values or Ranges:
  • 1
  • 2
  • 3
Alternative Representations
OPM Class Definition
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CONTROLLED VALUE CLASS collection_link_rule
Controlled Values or Ranges:
  • Sequence
  • EPub
  • Component
  • Feature
  • Collection
Alternative Representations
OPM Class Definition
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CONTROLLED VALUE CLASS comp_type_rule
Controlled Values or Ranges:
  • assembly
  • variation
  • product
Alternative Representations
OPM Class Definition
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CONTROLLED VALUE CLASS diff_name_rule
Controlled Values or Ranges:
  • transition
  • transversion
  • indel
  • mutation
  • allele
Alternative Representations
OPM Class Definition
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CONTROLLED VALUE CLASS diff_type_rule
Controlled Values or Ranges:
  • conflict
  • variation
Alternative Representations
OPM Class Definition
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CONTROLLED VALUE CLASS direction_rule
Controlled Values or Ranges:
  • left
  • right
  • both
Alternative Representations
OPM Class Definition
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CONTROLLED VALUE CLASS genome_rule
Controlled Values or Ranges:
  • mitochondrion
  • chloroplast
  • kinetoplast
  • plastid
  • cyanelle
  • plasmid
  • cloning vector
  • synthetic gene
  • other synthetic construct
  • micronuclear
  • macronuclear
  • somatic nuclear
  • germline nuclear
Alternative Representations
OPM Class Definition
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CONTROLLED VALUE CLASS import_file_type_rule
Controlled Values or Ranges:
  • GBFF
  • EMBLFF
  • DDBJFF
  • GSDBFF
  • GIO
Alternative Representations
OPM Class Definition
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CONTROLLED VALUE CLASS intron_class_rule
Controlled Values or Ranges:
  • I
  • II
  • III
  • other
Alternative Representations
OPM Class Definition
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CONTROLLED VALUE CLASS loc_operator_rule
Controlled Values or Ranges:
  • join
  • order
  • replace
Alternative Representations
OPM Class Definition
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CONTROLLED VALUE CLASS mod_base_rule
Controlled Values or Ranges:
  • ac4c
  • chm5u
  • cm
  • cmnm5s2u
  • cmnm5u
  • d
  • fm
  • galq
  • gm
  • i
  • i6a
  • m1a
  • m1f
  • m1g
  • m1i
  • m22g
  • m2a
  • m2g
  • m3c
  • m5c
  • m6a
  • m7g
  • mam5s2u
  • mam5u
  • manq
  • mcm5s2u
  • mcm5u
  • mo5u
  • ms2i6a
  • ms2t6a
  • mt6a
  • mv
  • o5u
  • osyw
  • p
  • q
  • s2c
  • s2t
  • s2u
  • s4u
  • t
  • t6a
  • tm
  • um
  • x
  • yw
  • OTHER
Alternative Representations
OPM Class Definition
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CONTROLLED VALUE CLASS molecule_isolated_rule
Controlled Values or Ranges:
  • ds-DNA
  • ss-mRNA
  • ss-RNA
  • ss-rRNA
  • ds-RNA
  • ms-DNA
  • ms-RNA
  • ss-DNA
  • ss-cRNA
  • ss-gRNA
  • ss-tRNA
  • ss-uRNA
  • ss-xRNA
  • DNA
  • cRNA
  • gRNA
  • mRNA
  • xRNA
  • RNA
  • tRNA
  • uRNA
  • rRNA
Alternative Representations
OPM Class Definition
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CONTROLLED VALUE CLASS molecule_sequenced_rule
Controlled Values or Ranges:
  • DNA
  • ds-DNA
  • ss-DNA
  • RNA
  • cDNA
  • cDNA to genomic RNA
  • cDNA to mRNA
  • cDNA to other RNA
  • cDNA to rRNA
  • mRNA
  • rRNA
  • scRNA
  • snRNA
  • tRNA
Alternative Representations
OPM Class Definition
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CONTROLLED VALUE CLASS pub_status_rule
Controlled Values or Ranges:
  • published
  • in press
  • submitted
  • in preparation
  • unpublished
Alternative Representations
OPM Class Definition
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CONTROLLED VALUE CLASS reference_type_rule
Controlled Values or Ranges:
  • journal
  • book
  • thesis
  • proceedings
  • other
  • manuscript
  • letter
  • patent
  • database publication
  • GSDB publication
Alternative Representations
OPM Class Definition
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CONTROLLED VALUE CLASS strand_orientation_rule
Controlled Values or Ranges:
  • forward
  • reverse
  • unknown
Alternative Representations
OPM Class Definition
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CONTROLLED VALUE CLASS suffix_rule
Controlled Values or Ranges:
  • I
  • II
  • III
  • IV
  • Jr.
  • Sr.
Alternative Representations
OPM Class Definition
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CONTROLLED VALUE CLASS transl_type_rule
Controlled Values or Ranges:
  • gsdb conceptual
  • user conceptual
  • experimental
Alternative Representations
OPM Class Definition
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OBJECT CLASS Address
Attributes:
institution
  • Constraints: single-valued, can be null
  • Domain: Institution
department
  • Constraints: single-valued, can be null
  • Domain: VARCHAR(255)
address
  • Constraints: single-valued, can be null
  • Domain: VARCHAR(255)
mailstop
  • Constraints: single-valued, can be null
  • Domain: VARCHAR(255)
room
  • Constraints: single-valued, can be null
  • Domain: VARCHAR(255)
city
  • Constraints: single-valued, can be null
  • Domain: VARCHAR(255)
state
  • Constraints: single-valued, can be null
  • Domain: VARCHAR(255)
country
  • Constraints: single-valued, can be null
  • Domain: VARCHAR(255)
zip
  • Constraints: single-valued, can be null
  • Domain: VARCHAR(255)
phone_ext_dept
  • Constraints: single-valued, can be null
  • Domain: VARCHAR(10)
Alternative Representations
OPM Class Definition
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OBJECT CLASS Analysis
Attributes:
name
  • Constraints: single-valued, not null
  • Domain: VARCHAR(30)
object
version
  • Constraints: single-valued, can be null
  • Domain: FLOAT(8)
match
  • Constraints: single-valued, can be null
  • Domain: FLOAT(8)
score
  • Constraints: single-valued, can be null
  • Domain: FLOAT(8)
date_run
  • Constraints: single-valued, can be null
  • Domain: DATETIME
parameters
  • Constraints: single-valued, can be null
  • Domain: VARCHAR(255)
db_searched
  • Constraints: single-valued, can be null
  • Domain: VARCHAR(30)
Alternative Representations
OPM Class Definition
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OBJECT CLASS Anticodon
Attributes:
feature
  • Constraints: single-valued, not null
  • Domain: Feature
start
  • Constraints: single-valued, can be null
  • Domain: INTEGER
aa
  • Constraints: single-valued, not null
  • Domain: aa_rule
length
Alternative Representations
OPM Class Definition
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OBJECT CLASS BindingSite
Superclasses:
Feature
Attributes:
bound_moiety
  • Constraints: single-valued, can be null
  • Domain: VARCHAR(100)
name
  • Constraints: single-valued, can be null
  • Domain: VARCHAR(100)
binds_to
  • Constraints: single-valued, can be null
  • Domain: VARCHAR(100)
binds_where
  • Constraints: single-valued, can be null
  • Domain: VARCHAR(100)
binds_when
  • Constraints: single-valued, can be null
  • Domain: VARCHAR(100)
preconditions
  • Constraints: single-valued, can be null
  • Domain: VARCHAR(255)
Alternative Representations
OPM Class Definition
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OBJECT CLASS Collection
Attributes:
description
  • Constraints: single-valued, can be null
  • Domain: VARCHAR(255)
name
  • Constraints: single-valued, not null
  • Domain: VARCHAR(100)
date_created
  • Constraints: single-valued, not null
  • Domain: DATETIME
last_updated
  • Constraints: single-valued, not null
  • Domain: DATETIME
links
Alternative Representations
OPM Class Definition
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OBJECT CLASS Comment
Attributes:
long_comment
  • Constraints: single-valued, can be null
  • Domain: TEXT
short_comment
  • Constraints: single-valued, can be null
  • Domain: VARCHAR(255)
object
Alternative Representations
OPM Class Definition
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OBJECT CLASS Component
Attributes:
baseseq_id
  • Constraints: single-valued, not null
  • Domain: Sequence
compseq_id
  • Constraints: single-valued, not null
  • Domain: Sequence
type
created
  • Constraints: single-valued, not null
  • Domain: DATETIME
last_released
  • Constraints: single-valued, can be null
  • Domain: DATETIME
comments
  • Derivation: inverse of object [ Comment ]
locations (loc_baseseq_start, loc_baseseq_end, loc_compseq_start, loc_compseq_end, strand_orientation)
  • Constraints: set-valued, Min # of values: 0
  • Component Attributes:
    loc_baseseq_start
    • Domain: INTEGER
    • Constraints: not null
    loc_baseseq_end
    • Domain: INTEGER
    • Constraints: not null
    loc_compseq_start
    • Domain: INTEGER
    • Constraints: not null
    loc_compseq_end
    • Domain: INTEGER
    • Constraints: not null
    strand_orientation
differences (diff_type, name, diff_baseseq_start, diff_baseseq_end, diff_compseq_start, diff_compseq_end, base_seq, comp_seq)
  • Constraints: set-valued, Min # of values: 0
  • Component Attributes:
    diff_type
    name
    diff_baseseq_start
    • Domain: INTEGER
    • Constraints: not null
    diff_baseseq_end
    • Domain: INTEGER
    • Constraints: not null
    diff_compseq_start
    • Domain: INTEGER
    • Constraints: not null
    diff_compseq_end
    • Domain: INTEGER
    • Constraints: not null
    base_seq
    • Domain: VARCHAR(255)
    • Constraints: can be null
    comp_seq
    • Domain: VARCHAR(255)
    • Constraints: can be null
Alternative Representations
OPM Class Definition
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OBJECT CLASS DBLink
Attributes:
object
extdb
  • Constraints: single-valued, can be null
  • Domain: VARCHAR(100)
extid
  • Constraints: single-valued, can be null
  • Domain: VARCHAR(100)
url
  • Constraints: single-valued, can be null
  • Domain: VARCHAR(255)
Link to:
  • Class Gene (in schema HGD) (description: External reference to GDB Gene from GSDB. May be \ associated with GSDB Gene, GeneInstance, Product or \ ProductInstance)
Alternative Representations
OPM Class Definition
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OBJECT CLASS DeletedAccession
Attributes:
type
gsdb_accession
  • Constraints: single-valued, can be null
  • Domain: VARCHAR(100)
ic_accession
  • Constraints: single-valued, can be null
  • Domain: CHAR(10)
delete_date
  • Constraints: single-valued, not null
  • Domain: DATETIME
deleted_by
  • Constraints: single-valued, not null
  • Domain: VARCHAR(30)
owned_by
  • Constraints: single-valued, not null
  • Domain: VARCHAR(30)
reason
  • Constraints: single-valued, can be null
  • Domain: VARCHAR(255)
superceding_id
  • Constraints: single-valued, can be null
  • Domain: VARCHAR(30)
flatfile
  • Constraints: single-valued, can be null
  • Domain: TEXT
Alternative Representations
OPM Class Definition
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OBJECT CLASS Feature
Subclasses:
BindingSite Repeat
Attributes:
sequence
  • Constraints: single-valued, not null
  • Domain: Sequence
feature_accession
  • Constraints: single-valued, can be null
  • Domain: VARCHAR(100)
type
  • Constraints: single-valued, not null
  • Domain: VARCHAR(100)
standard_type
  • Constraints: single-valued, not null
  • Domain: BOOLEAN
codon_start
exp_determined
  • Constraints: single-valued, not null
  • Domain: BOOLEAN
function
  • Constraints: single-valued, can be null
  • Domain: VARCHAR(255)
map_location
  • Constraints: single-valued, can be null
  • Domain: VARCHAR(40)
number
  • Constraints: single-valued, can be null
  • Domain: VARCHAR(100)
pseudo
  • Constraints: single-valued, not null
  • Domain: BOOLEAN
standard_name
  • Constraints: single-valued, can be null
  • Domain: VARCHAR(100)
direction
PCR_conditions
  • Constraints: single-valued, can be null
  • Domain: TEXT
is_5_complete
  • Constraints: single-valued, not null
  • Domain: BOOLEAN
is_3_complete
  • Constraints: single-valued, not null
  • Domain: BOOLEAN
fits_consensus
  • Constraints: single-valued, not null
  • Domain: BOOLEAN
fits_consensus5
  • Constraints: single-valued, not null
  • Domain: BOOLEAN
fits_consensus3
  • Constraints: single-valued, not null
  • Domain: BOOLEAN
created
  • Constraints: single-valued, not null
  • Domain: DATETIME
first_released
  • Constraints: single-valued, can be null
  • Domain: DATETIME
last_released
  • Constraints: single-valued, can be null
  • Domain: DATETIME
loc_operator
is_rna_preedited
  • Constraints: single-valued, not null
  • Domain: BOOLEAN
self_splice_intron_class
comments
  • Derivation: inverse of object [ Comment ]
translations (is_t_ta_stop, protein_translation, transl_type)
  • Constraints: set-valued, Min # of values: 0
  • Component Attributes:
    is_t_ta_stop
    • Domain: BOOLEAN
    • Constraints: not null
    protein_translation
    • Domain: TEXT
    • Constraints: not null
    transl_type
transl_excepts (left_bp, right_bp, aa)
  • Constraints: set-valued, Min # of values: 0
  • Component Attributes:
    left_bp
    • Domain: INTEGER
    • Constraints: not null
    right_bp
    • Domain: INTEGER
    • Constraints: not null
    aa
    • Domain: aa_rule
    • Constraints: not null
genes
locations (loc_sequence, left_start, left_end, right_start, right_end, complement, exclusive, literal_sequence, loc_order, x_oid)
  • Constraints: set-valued, Min # of values: 0
  • Component Attributes:
    loc_sequence
    • Domain: Sequence
    • Constraints: not null
    left_start
    • Domain: INTEGER
    • Constraints: can be null
    left_end
    • Domain: INTEGER
    • Constraints: can be null
    right_start
    • Domain: INTEGER
    • Constraints: can be null
    right_end
    • Domain: INTEGER
    • Constraints: can be null
    complement
    • Domain: BOOLEAN
    • Constraints: not null
    exclusive
    • Domain: BOOLEAN
    • Constraints: not null
    literal_sequence
    • Domain: VARCHAR(255)
    • Constraints: can be null
    loc_order
    • Domain: INTEGER
    • Constraints: not null
    x_oid
    • Domain: table_id
    • Constraints: not null
products
Alternative Representations
OPM Class Definition
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OBJECT CLASS FeatureTypes
Attributes:
name
  • Constraints: single-valued, not null
  • Domain: VARCHAR(30)
Alternative Representations
OPM Class Definition
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OBJECT CLASS Flatfile
Attributes:
sequence
  • Constraints: single-valued, not null
  • Domain: Sequence
sequence_accession
  • Constraints: single-valued, not null
  • Domain: VARCHAR(100)
ff_version
  • Constraints: single-valued, not null
  • Domain: VARCHAR(20)
name
  • Constraints: single-valued, can be null
  • Domain: CHAR(10)
ic_accession
  • Constraints: single-valued, can be null
  • Domain: VARCHAR(20)
flatfile
  • Constraints: single-valued, not null
  • Domain: TEXT
first_distributed
  • Constraints: single-valued, can be null
  • Domain: DATETIME
last_distributed
  • Constraints: single-valued, can be null
  • Domain: DATETIME
new_flatfile
  • Constraints: single-valued, not null
  • Domain: BOOLEAN
Alternative Representations
OPM Class Definition
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OBJECT CLASS Gene
Attributes:
authoritative_name
  • Constraints: single-valued, not null
  • Domain: VARCHAR(80)
taxon_id
  • Constraints: single-valued, not null
  • Domain: Taxon
instances
  • Derivation: inverse of gene [ GeneInst ]
Similar Classes:
  • Class Gene (in schema HGD) (comment: GDB gene)
Alternative Representations
OPM Class Definition
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OBJECT CLASS GeneInst
Attributes:
feature
  • Constraints: single-valued, not null
  • Domain: Feature
gene
  • Constraints: single-valued, can be null
  • Domain: Gene
authoritative_name
  • Constraints: single-valued, can be null
  • Domain: VARCHAR(200)
name
  • Constraints: single-valued, not null
  • Domain: VARCHAR(200)
Similar Classes:
  • Class Gene (in schema HGD) (comment: GDB gene)
Alternative Representations
OPM Class Definition
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OBJECT CLASS Institution
Attributes:
name
  • Constraints: single-valued, not null
  • Domain: VARCHAR(255)
phone_num
  • Constraints: single-valued, can be null
  • Domain: VARCHAR(30)
fax_num
  • Constraints: single-valued, can be null
  • Domain: VARCHAR(30)
email
  • Constraints: single-valued, can be null
  • Domain: VARCHAR(255)
Alternative Representations
OPM Class Definition
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OBJECT CLASS ModifiedBase
Attributes:
sequence
  • Constraints: single-valued, not null
  • Domain: Sequence
mod_base
bp
  • Constraints: single-valued, not null
  • Domain: INTEGER
Alternative Representations
OPM Class Definition
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OBJECT CLASS Person
Attributes:
address_id
  • Constraints: single-valued, can be null
  • Domain: Address
last_name
  • Constraints: single-valued, not null
  • Domain: VARCHAR(30)
first_name
  • Constraints: single-valued, can be null
  • Domain: VARCHAR(30)
initial
  • Constraints: single-valued, can be null
  • Domain: VARCHAR(10)
suffix
  • Constraints: single-valued, can be null
  • Domain: VARCHAR(10)
email
  • Constraints: single-valued, not null
  • Domain: VARCHAR(255)
work_phone
  • Constraints: single-valued, can be null
  • Domain: VARCHAR(30)
phone_ext
  • Constraints: single-valued, can be null
  • Domain: VARCHAR(10)
fax_number
  • Constraints: single-valued, can be null
  • Domain: VARCHAR(30)
is_email_valid
  • Constraints: single-valued, not null
  • Domain: BOOLEAN
account_created_person_id
  • Constraints: single-valued, can be null
  • Domain: Person
dblogin
  • Constraints: single-valued, can be null
  • Domain: VARCHAR(30)
account_created
  • Constraints: single-valued, can be null
  • Domain: DATETIME
hardware
  • Constraints: single-valued, can be null
  • Domain: VARCHAR(255)
Alternative Representations
OPM Class Definition
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OBJECT CLASS Product
Attributes:
authoritative_name
  • Constraints: single-valued, not null
  • Domain: VARCHAR(200)
instances
Alternative Representations
OPM Class Definition
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OBJECT CLASS ProductInst
Attributes:
feature
  • Constraints: single-valued, not null
  • Domain: Feature
product
  • Constraints: single-valued, can be null
  • Domain: Product
authoritative_name
  • Constraints: single-valued, can be null
  • Domain: VARCHAR(200)
name
  • Constraints: single-valued, not null
  • Domain: VARCHAR(200)
Alternative Representations
OPM Class Definition
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OBJECT CLASS Reference
Attributes:
publication
  • Constraints: single-valued, can be null
  • Domain: VARCHAR(100)
volume
  • Constraints: single-valued, can be null
  • Domain: VARCHAR(20)
issue
  • Constraints: single-valued, can be null
  • Domain: VARCHAR(10)
start_page
  • Constraints: single-valued, can be null
  • Domain: VARCHAR(10)
end_page
  • Constraints: single-valued, can be null
  • Domain: VARCHAR(10)
year
  • Constraints: single-valued, can be null
  • Domain: SMALLINT
pub_status
reference_type
title
  • Constraints: single-valued, can be null
  • Domain: VARCHAR(255)
publisher
  • Constraints: single-valued, can be null
  • Domain: VARCHAR(100)
university
  • Constraints: single-valued, can be null
  • Domain: VARCHAR(100)
address
  • Constraints: single-valued, can be null
  • Domain: VARCHAR(255)
authors_string
  • Constraints: single-valued, can be null
  • Domain: TEXT
dates
  • Constraints: single-valued, can be null
  • Domain: VARCHAR(100)
patent_number
  • Constraints: single-valued, can be null
  • Domain: VARCHAR(200)
old_gsdbid
  • Constraints: single-valued, can be null
  • Domain: CHAR(10)
comments
  • Derivation: inverse of object [ Comment ]
authors (author_order, author_last_name, author_first_name, author_initials, author_suffix)
  • Constraints: set-valued, Min # of values: 0
  • Component Attributes:
    author_order
    • Domain: SMALLINT
    • Constraints: not null
    author_last_name
    • Domain: VARCHAR(40)
    • Constraints: not null
    author_first_name
    • Domain: VARCHAR(20)
    • Constraints: can be null
    author_initials
    • Domain: VARCHAR(10)
    • Constraints: can be null
    author_suffix
editor (editor_order, editor_last_name, editor_first_name, editor_initials, editor_suffix)
  • Constraints: set-valued, Min # of values: 0
  • Component Attributes:
    editor_order
    • Domain: SMALLINT
    • Constraints: not null
    editor_last_name
    • Domain: VARCHAR(40)
    • Constraints: not null
    editor_first_name
    • Domain: VARCHAR(20)
    • Constraints: can be null
    editor_initials
    • Domain: VARCHAR(10)
    • Constraints: can be null
    editor_suffix
links (tableid, loc_start, loc_end, ref_order)
  • Constraints: set-valued, Min # of values: 0
  • Component Attributes:
    tableid
    loc_start
    • Domain: INTEGER
    • Constraints: can be null
    loc_end
    • Domain: INTEGER
    • Constraints: can be null
    ref_order
    • Domain: SMALLINT
    • Constraints: not null
Link to:
  • Class Medline_entry (in schema NCBI) (description: Reference.medline_xref link to Medline_entry.uid)
Alternative Representations
OPM Class Definition
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OBJECT CLASS Repeat
Superclasses:
Feature
Attributes:
name
  • Constraints: single-valued, not null
  • Domain: VARCHAR(100)
is_tandem
  • Constraints: single-valued, not null
  • Domain: BOOLEAN
is_flanking
  • Constraints: single-valued, not null
  • Domain: BOOLEAN
is_inverted
  • Constraints: single-valued, not null
  • Domain: BOOLEAN
is_terminal
  • Constraints: single-valued, not null
  • Domain: BOOLEAN
is_direct
  • Constraints: single-valued, not null
  • Domain: BOOLEAN
is_dispersed
  • Constraints: single-valued, not null
  • Domain: BOOLEAN
family
  • Constraints: single-valued, can be null
  • Domain: VARCHAR(100)
sub_family
  • Constraints: single-valued, can be null
  • Domain: VARCHAR(100)
Alternative Representations
OPM Class Definition
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OBJECT CLASS Sequence
Attributes:
sequence
  • Constraints: single-valued, can be null
  • Domain: TEXT
length
  • Constraints: single-valued, can be null
  • Domain: INTEGER
counts (a_count, c_count, g_count, t_count, other_count)
  • Constraints: single-valued, can be null
  • Component Attributes:
    a_count
    • Domain: INTEGER
    • Constraints: can be null
    c_count
    • Domain: INTEGER
    • Constraints: can be null
    g_count
    • Domain: INTEGER
    • Constraints: can be null
    t_count
    • Domain: INTEGER
    • Constraints: can be null
    other_count
    • Domain: INTEGER
    • Constraints: can be null
ic_accession
  • Constraints: single-valued, can be null
  • Domain: VARCHAR(20)
sequence_accession
  • Constraints: single-valued, can be null
  • Domain: VARCHAR(100)
is_discontiguous
  • Constraints: single-valued, not null
  • Domain: BOOLEAN
is_experimental
  • Constraints: single-valued, not null
  • Domain: BOOLEAN
is_transpliced
  • Constraints: single-valued, not null
  • Domain: BOOLEAN
transl_table_id
  • Constraints: single-valued, can be null
  • Domain: INTEGER
flatfile_date
  • Constraints: single-valued, can be null
  • Domain: DATETIME
description
  • Constraints: single-valued, can be null
  • Domain: VARCHAR(255)
name
  • Constraints: single-valued, can be null
  • Domain: CHAR(10)
is_complete_genome
  • Constraints: single-valued, not null
  • Domain: BOOLEAN
is_clone_end
  • Constraints: single-valued, not null
  • Domain: BOOLEAN
origin
  • Constraints: single-valued, can be null
  • Domain: VARCHAR(80)
created
  • Constraints: single-valued, not null
  • Domain: DATETIME
first_released
  • Constraints: single-valued, can be null
  • Domain: DATETIME
last_released
  • Constraints: single-valued, can be null
  • Domain: DATETIME
release
  • Constraints: single-valued, not null
  • Domain: BOOLEAN
text_last_modified
  • Constraints: single-valued, not null
  • Domain: DATETIME
hold_until
  • Constraints: single-valued, can be null
  • Domain: DATETIME
confidences (loc_start, loc_end, confidence, multiple_read, double_stranded)
  • Constraints: set-valued, Min # of values: 0
  • Component Attributes:
    loc_start
    • Domain: INTEGER
    • Constraints: not null
    loc_end
    • Domain: INTEGER
    • Constraints: not null
    confidence
    • Domain: FLOAT(8)
    • Constraints: not null
    multiple_read
    • Domain: BOOLEAN
    • Constraints: not null
    double_stranded
    • Domain: BOOLEAN
    • Constraints: not null
keywords
  • Constraints: set-valued, Min # of values: 0
  • Domain: VARCHAR(200)
modified_bases
secondary_ic_accession
  • Constraints: set-valued, Min # of values: 0
  • Domain: VARCHAR(20)
sequence_pieces (sp_id, seq_order, distance_from_left, uncertainty, strand_orientation, type)
  • Constraints: set-valued, Min # of values: 0
  • Component Attributes:
    sp_id
    • Domain: Sequence
    • Constraints: not null
    seq_order
    • Domain: INTEGER
    • Constraints: can be null
    distance_from_left
    • Domain: FLOAT(8)
    • Constraints: can be null
    uncertainty
    • Domain: FLOAT(8)
    • Constraints: can be null
    strand_orientation
    type
    • Domain: VARCHAR(20)
    • Constraints: can be null
comments
  • Derivation: inverse of object [ Comment ]
sources
  • Derivation: inverse of sequence [ Source ]
Link to:
  • Class NucleicAcidSequenceLink (in schema HGD) (description: External reference to GSDB nucleic acid sequence from GDB - reverse link)
  • Class Seq_entry (in schema NCBI) (description: Shared sequence data, linked by accession numbers)
Alternative Representations
OPM Class Definition
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OBJECT CLASS Source
Attributes:
sequence
  • Constraints: single-valued, not null
  • Domain: Sequence
loc_start
  • Constraints: single-valued, can be null
  • Domain: INTEGER
loc_end
  • Constraints: single-valued, can be null
  • Domain: INTEGER
taxon_id
  • Constraints: single-valued, not null
  • Domain: Taxon
genome
  • Constraints: single-valued, can be null
  • Domain: genome_rule
taxonomy
  • Constraints: single-valued, can be null
  • Domain: VARCHAR(255)
is_linear
  • Constraints: single-valued, not null
  • Domain: BOOLEAN
molecule_sequenced
molecule_isolated
division_code
  • Constraints: single-valued, can be null
  • Domain: CHAR(3)
tissue_lib
  • Constraints: single-valued, can be null
  • Domain: VARCHAR(200)
tissue_type
  • Constraints: single-valued, can be null
  • Domain: VARCHAR(200)
cell_line
  • Constraints: single-valued, can be null
  • Domain: VARCHAR(200)
cell_type
  • Constraints: single-valued, can be null
  • Domain: VARCHAR(200)
chromosome
  • Constraints: single-valued, can be null
  • Domain: VARCHAR(20)
clone
  • Constraints: single-valued, can be null
  • Domain: VARCHAR(200)
clone_lib
  • Constraints: single-valued, can be null
  • Domain: VARCHAR(200)
dev_stage
  • Constraints: single-valued, can be null
  • Domain: VARCHAR(200)
haplotype
  • Constraints: single-valued, can be null
  • Domain: VARCHAR(200)
is_transposon
  • Constraints: single-valued, not null
  • Domain: BOOLEAN
isolate
  • Constraints: single-valued, can be null
  • Domain: VARCHAR(200)
lab_host
  • Constraints: single-valued, can be null
  • Domain: VARCHAR(200)
natural_host
  • Constraints: single-valued, can be null
  • Domain: VARCHAR(200)
cultivar
  • Constraints: single-valued, can be null
  • Domain: VARCHAR(200)
pop_variant
  • Constraints: single-valued, can be null
  • Domain: VARCHAR(200)
is_proviral
  • Constraints: single-valued, not null
  • Domain: BOOLEAN
sex
  • Constraints: single-valued, can be null
  • Domain: VARCHAR(200)
strain
  • Constraints: single-valued, can be null
  • Domain: VARCHAR(200)
sub_clone
  • Constraints: single-valued, can be null
  • Domain: VARCHAR(200)
sub_strain
  • Constraints: single-valued, can be null
  • Domain: VARCHAR(200)
variety
  • Constraints: single-valued, can be null
  • Domain: VARCHAR(200)
sub_species
  • Constraints: single-valued, can be null
  • Domain: VARCHAR(200)
is_rearranged
  • Constraints: single-valued, not null
  • Domain: BOOLEAN
vector
  • Constraints: single-valued, can be null
  • Domain: VARCHAR(30)
culture_collection
  • Constraints: single-valued, can be null
  • Domain: VARCHAR(30)
comments
  • Derivation: inverse of object [ Comment ]
Alternative Representations
OPM Class Definition
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OBJECT CLASS Taxon
Attributes:
authority
  • Constraints: single-valued, can be null
  • Domain: VARCHAR(255)
scientific_name
  • Constraints: single-valued, not null
  • Domain: VARCHAR(80)
common_name
  • Constraints: single-valued, can be null
  • Domain: VARCHAR(80)
domain
  • Constraints: single-valued, can be null
  • Domain: VARCHAR(80)
kingdom
  • Constraints: single-valued, can be null
  • Domain: VARCHAR(80)
phylum
  • Constraints: single-valued, can be null
  • Domain: VARCHAR(80)
division
  • Constraints: single-valued, can be null
  • Domain: VARCHAR(80)
class
  • Constraints: single-valued, can be null
  • Domain: VARCHAR(80)
tax_order
  • Constraints: single-valued, can be null
  • Domain: VARCHAR(80)
family
  • Constraints: single-valued, can be null
  • Domain: VARCHAR(80)
genus
  • Constraints: single-valued, can be null
  • Domain: VARCHAR(80)
species
  • Constraints: single-valued, can be null
  • Domain: VARCHAR(80)
tax_abbrev
  • Constraints: single-valued, can be null
  • Domain: CHAR(3)
old_gsdbid
  • Constraints: single-valued, can be null
  • Domain: CHAR(10)
Alternative Representations
OPM Class Definition
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OBJECT CLASS TranslationTables
Attributes:
start_translation
  • Constraints: single-valued, not null
  • Domain: CHAR(64)
stop_translation
  • Constraints: single-valued, not null
  • Domain: CHAR(64)
internal_translation
  • Constraints: single-valued, not null
  • Domain: CHAR(64)
name
  • Constraints: single-valued, not null
  • Domain: VARCHAR(255)
Alternative Representations
OPM Class Definition
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