SCHEMA
GSDB
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Primitive Value Classes
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Controlled Value Classes
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Object Classes
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boolean
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table_id
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Action_status_rule
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Action_tablename_rule
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Comment_link_rule
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DBLink_link_rule
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DeletedAccession_type_rule
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ReferenceLink_link_rule
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aa_rule
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analysis_link_rule
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anticodon_length_rule
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codon_start_rule
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collection_link_rule
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comp_type_rule
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diff_name_rule
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diff_type_rule
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direction_rule
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genome_rule
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import_file_type_rule
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intron_class_rule
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loc_operator_rule
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mod_base_rule
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molecule_isolated_rule
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molecule_sequenced_rule
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pub_status_rule
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reference_type_rule
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strand_orientation_rule
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suffix_rule
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transl_type_rule
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Address
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Analysis
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Anticodon
-
Collection
-
Comment
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Component
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DBLink
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DeletedAccession
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Feature
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BindingSite
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Repeat
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FeatureTypes
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Flatfile
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Gene
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GeneInst
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Institution
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ModifiedBase
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Person
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Product
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ProductInst
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Reference
-
Sequence
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Source
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Taxon
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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:
- 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:
- Alternative Representations
- OPM Class Definition
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CONTROLLED VALUE CLASS anticodon_length_rule
- Controlled Values or Ranges:
- Alternative Representations
- OPM Class Definition
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CONTROLLED VALUE CLASS codon_start_rule
- Controlled Values or Ranges:
- 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:
- Alternative Representations
- OPM Class Definition
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CONTROLLED VALUE CLASS direction_rule
- Controlled Values or Ranges:
- 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:
- Alternative Representations
- OPM Class Definition
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CONTROLLED VALUE CLASS loc_operator_rule
- Controlled Values or Ranges:
- 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:
- Alternative Representations
- OPM Class Definition
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CONTROLLED VALUE CLASS suffix_rule
- Controlled Values or Ranges:
- 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
- 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
- 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
- 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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