GSDB Schema
NAMED PRIMITIVE VALUE CLASS boolean: TINYINT
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NAMED PRIMITIVE VALUE CLASS table_id: NUMERIC(6)
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CONTROLLED VALUE CLASS Action_status_rule
{ "success",
"pending",
"failure",
"processing",
"manual" }
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CONTROLLED VALUE CLASS Action_tablename_rule
{ "ImportFile",
"SequenceStatus",
"FeatureStatus" }
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CONTROLLED VALUE CLASS Comment_link_rule
{ "Sequence",
"Feature",
"Component",
"Source",
"Reference",
"ModifiedBase" }
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CONTROLLED VALUE CLASS DBLink_link_rule
{ "GeneInst",
"ProductInst",
"Gene",
"Product",
"Feature",
"Reference",
"Sequence",
"Source",
"Component" }
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CONTROLLED VALUE CLASS DeletedAccession_type_rule
{ "Feature",
"Sequence" }
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CONTROLLED VALUE CLASS ReferenceLink_link_rule
{ "Feature",
"Source",
"Sequence",
"Component" }
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CONTROLLED VALUE CLASS aa_rule
{ "Ala",
"Arg",
"Asn",
"Asp",
"Cys",
"Gln",
"Glu",
"Gly",
"His",
"Ile",
"Leu",
"Lys",
"Met",
"Phe",
"Pro",
"Ser",
"Thr",
"Trp",
"Tyr",
"Val",
"Xxx",
"TERM",
"OTHER" }
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CONTROLLED VALUE CLASS analysis_link_rule
{ "Feature",
"Component" }
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CONTROLLED VALUE CLASS anticodon_length_rule
{ 2,
3,
4 }
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CONTROLLED VALUE CLASS codon_start_rule
{ 1,
2,
3 }
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CONTROLLED VALUE CLASS collection_link_rule
{ "Sequence",
"EPub",
"Component",
"Feature",
"Collection" }
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CONTROLLED VALUE CLASS comp_type_rule
{ "assembly",
"variation",
"product" }
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CONTROLLED VALUE CLASS diff_name_rule
{ "transition",
"transversion",
"indel",
"mutation",
"allele" }
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CONTROLLED VALUE CLASS diff_type_rule
{ "conflict",
"variation" }
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CONTROLLED VALUE CLASS direction_rule
{ "left",
"right",
"both" }
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CONTROLLED VALUE CLASS genome_rule
{ "mitochondrion",
"chloroplast",
"kinetoplast",
"plastid",
"cyanelle",
"plasmid",
"cloning vector",
"synthetic gene",
"other synthetic construct",
"micronuclear",
"macronuclear",
"somatic nuclear",
"germline nuclear" }
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CONTROLLED VALUE CLASS import_file_type_rule
{ "GBFF",
"EMBLFF",
"DDBJFF",
"GSDBFF",
"GIO" }
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CONTROLLED VALUE CLASS intron_class_rule
{ "I",
"II",
"III",
"other" }
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CONTROLLED VALUE CLASS loc_operator_rule
{ "join",
"order",
"replace" }
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CONTROLLED VALUE CLASS mod_base_rule
{ "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" }
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CONTROLLED VALUE CLASS molecule_isolated_rule
{ "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" }
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CONTROLLED VALUE CLASS molecule_sequenced_rule
{ "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" }
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CONTROLLED VALUE CLASS pub_status_rule
{ "published",
"in press",
"submitted",
"in preparation",
"unpublished" }
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CONTROLLED VALUE CLASS reference_type_rule
{ "journal",
"book",
"thesis",
"proceedings",
"other",
"manuscript",
"letter",
"patent",
"database publication",
"GSDB publication" }
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CONTROLLED VALUE CLASS strand_orientation_rule
{ "forward",
"reverse",
"unknown" }
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CONTROLLED VALUE CLASS suffix_rule
{ "I",
"II",
"III",
"IV",
"Jr.",
"Sr." }
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CONTROLLED VALUE CLASS transl_type_rule
{ "gsdb conceptual",
"user conceptual",
"experimental" }
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OBJECT CLASS Address ATTRIBUTE institution: [0,1] Institution ATTRIBUTE department: [0,1] VARCHAR(255) ATTRIBUTE address: [0,1] VARCHAR(255) ATTRIBUTE mailstop: [0,1] VARCHAR(255) ATTRIBUTE room: [0,1] VARCHAR(255) ATTRIBUTE city: [0,1] VARCHAR(255) ATTRIBUTE state: [0,1] VARCHAR(255) ATTRIBUTE country: [0,1] VARCHAR(255) ATTRIBUTE zip: [0,1] VARCHAR(255) ATTRIBUTE phone_ext_dept: [0,1] VARCHAR(10)
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OBJECT CLASS Analysis ATTRIBUTE name: [1,1] VARCHAR(30) ATTRIBUTE object: [1,1] Feature or Component ATTRIBUTE version: [0,1] FLOAT(8) ATTRIBUTE match: [0,1] FLOAT(8) ATTRIBUTE score: [0,1] FLOAT(8) ATTRIBUTE date_run: [0,1] DATETIME ATTRIBUTE parameters: [0,1] VARCHAR(255) ATTRIBUTE db_searched: [0,1] VARCHAR(30)
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OBJECT CLASS Anticodon ATTRIBUTE feature: [1,1] Feature ATTRIBUTE start: [0,1] INTEGER ATTRIBUTE aa: [1,1] aa_rule ATTRIBUTE length: [1,1] anticodon_length_rule
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OBJECT CLASS BindingSite
isa Feature
ATTRIBUTE bound_moiety: [0,1] VARCHAR(100)
ATTRIBUTE name: [0,1] VARCHAR(100)
ATTRIBUTE binds_to: [0,1] VARCHAR(100)
ATTRIBUTE binds_where: [0,1] VARCHAR(100)
ATTRIBUTE binds_when: [0,1] VARCHAR(100)
ATTRIBUTE preconditions: [0,1] VARCHAR(255)
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OBJECT CLASS Collection ATTRIBUTE description: [0,1] VARCHAR(255) ATTRIBUTE name: [1,1] VARCHAR(100) ATTRIBUTE date_created: [1,1] DATETIME ATTRIBUTE last_updated: [1,1] DATETIME ATTRIBUTE links: set-of [0,] Sequence or Component or Feature or Collection
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OBJECT CLASS Comment ATTRIBUTE long_comment: [0,1] TEXT ATTRIBUTE short_comment: [0,1] VARCHAR(255) ATTRIBUTE object: [1,1] Source or Feature or Component or Sequence or Reference or ModifiedBase
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OBJECT CLASS Component
ATTRIBUTE baseseq_id: [1,1] Sequence
ATTRIBUTE compseq_id: [1,1] Sequence
ATTRIBUTE type: [1,1] comp_type_rule
ATTRIBUTE created: [1,1] DATETIME
ATTRIBUTE last_released: [0,1] DATETIME
ATTRIBUTE comments
DERIVATION: ! object [ Comment ]
ATTRIBUTE locations (loc_baseseq_start, loc_baseseq_end, loc_compseq_start,
loc_compseq_end, strand_orientation):
set-of [0,] ([1,1] INTEGER, [1,1] INTEGER, [1,1] INTEGER, [1,1]
INTEGER, [1,1] strand_orientation_rule)
ATTRIBUTE differences (diff_type, name, diff_baseseq_start, diff_baseseq_end,
diff_compseq_start, diff_compseq_end, base_seq,
comp_seq):
set-of [0,] ([1,1] diff_type_rule, [0,1] diff_name_rule, [1,1]
INTEGER, [1,1] INTEGER, [1,1] INTEGER, [1,1]
INTEGER, [0,1] VARCHAR(255), [0,1]
VARCHAR(255))
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OBJECT CLASS DBLink ATTRIBUTE object: [1,1] GeneInst or ProductInst or Gene or Product or Feature or Reference or Sequence or Source or Component ATTRIBUTE extdb: [0,1] VARCHAR(100) ATTRIBUTE extid: [0,1] VARCHAR(100) ATTRIBUTE url: [0,1] VARCHAR(255)
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OBJECT CLASS DeletedAccession ATTRIBUTE type: [1,1] DeletedAccession_type_rule ATTRIBUTE gsdb_accession: [0,1] VARCHAR(100) ATTRIBUTE ic_accession: [0,1] CHAR(10) ATTRIBUTE delete_date: [1,1] DATETIME ATTRIBUTE deleted_by: [1,1] VARCHAR(30) ATTRIBUTE owned_by: [1,1] VARCHAR(30) ATTRIBUTE reason: [0,1] VARCHAR(255) ATTRIBUTE superceding_id: [0,1] VARCHAR(30) ATTRIBUTE flatfile: [0,1] TEXT
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OBJECT CLASS Feature
ATTRIBUTE sequence: [1,1] Sequence
ATTRIBUTE feature_accession: [0,1] VARCHAR(100)
ATTRIBUTE type: [1,1] VARCHAR(100)
ATTRIBUTE standard_type: [1,1] BOOLEAN
ATTRIBUTE codon_start: [0,1] codon_start_rule
ATTRIBUTE exp_determined: [1,1] BOOLEAN
ATTRIBUTE function: [0,1] VARCHAR(255)
ATTRIBUTE map_location: [0,1] VARCHAR(40)
ATTRIBUTE number: [0,1] VARCHAR(100)
ATTRIBUTE pseudo: [1,1] BOOLEAN
ATTRIBUTE standard_name: [0,1] VARCHAR(100)
ATTRIBUTE direction: [0,1] direction_rule
ATTRIBUTE PCR_conditions: [0,1] TEXT
ATTRIBUTE is_5_complete: [1,1] BOOLEAN
ATTRIBUTE is_3_complete: [1,1] BOOLEAN
ATTRIBUTE fits_consensus: [1,1] BOOLEAN
ATTRIBUTE fits_consensus5: [1,1] BOOLEAN
ATTRIBUTE fits_consensus3: [1,1] BOOLEAN
ATTRIBUTE created: [1,1] DATETIME
ATTRIBUTE first_released: [0,1] DATETIME
ATTRIBUTE last_released: [0,1] DATETIME
ATTRIBUTE loc_operator: [0,1] loc_operator_rule
ATTRIBUTE is_rna_preedited: [1,1] BOOLEAN
ATTRIBUTE self_splice_intron_class: [0,1] intron_class_rule
ATTRIBUTE comments
DERIVATION: ! object [ Comment ]
ATTRIBUTE translations (is_t_ta_stop, protein_translation, transl_type):
set-of [0,] ([1,1] BOOLEAN, [1,1] TEXT, [1,1]
transl_type_rule)
ATTRIBUTE transl_excepts (left_bp, right_bp, aa):
set-of [0,] ([1,1] INTEGER, [1,1] INTEGER, [1,1] aa_rule)
ATTRIBUTE genes
DERIVATION: ! feature [ GeneInst ] gene [ Gene ]
ATTRIBUTE locations (loc_sequence, left_start, left_end, right_start,
right_end, complement, exclusive, literal_sequence,
loc_order, x_oid):
set-of [0,] ([1,1] Sequence, [0,1] INTEGER, [0,1] INTEGER, [0,1]
INTEGER, [0,1] INTEGER, [1,1] BOOLEAN, [1,1]
BOOLEAN, [0,1] VARCHAR(255), [1,1] INTEGER, [1,1]
table_id)
ATTRIBUTE products
DERIVATION: ! feature [ ProductInst ] product [ Product ]
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OBJECT CLASS FeatureTypes ATTRIBUTE name: [1,1] VARCHAR(30)
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OBJECT CLASS Flatfile ATTRIBUTE sequence: [1,1] Sequence ATTRIBUTE sequence_accession: [1,1] VARCHAR(100) ATTRIBUTE ff_version: [1,1] VARCHAR(20) ATTRIBUTE name: [0,1] CHAR(10) ATTRIBUTE ic_accession: [0,1] VARCHAR(20) ATTRIBUTE flatfile: [1,1] TEXT ATTRIBUTE first_distributed: [0,1] DATETIME ATTRIBUTE last_distributed: [0,1] DATETIME ATTRIBUTE new_flatfile: [1,1] BOOLEAN
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OBJECT CLASS Gene
ATTRIBUTE authoritative_name: [1,1] VARCHAR(80)
ATTRIBUTE taxon_id: [1,1] Taxon
ATTRIBUTE instances
DERIVATION: ! gene [ GeneInst ]
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OBJECT CLASS GeneInst ATTRIBUTE feature: [1,1] Feature ATTRIBUTE gene: [0,1] Gene ATTRIBUTE authoritative_name: [0,1] VARCHAR(200) ATTRIBUTE name: [1,1] VARCHAR(200)
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OBJECT CLASS Institution ATTRIBUTE name: [1,1] VARCHAR(255) ATTRIBUTE phone_num: [0,1] VARCHAR(30) ATTRIBUTE fax_num: [0,1] VARCHAR(30) ATTRIBUTE email: [0,1] VARCHAR(255)
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OBJECT CLASS ModifiedBase ATTRIBUTE sequence: [1,1] Sequence ATTRIBUTE mod_base: [1,1] mod_base_rule ATTRIBUTE bp: [1,1] INTEGER
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OBJECT CLASS Person ATTRIBUTE address_id: [0,1] Address ATTRIBUTE last_name: [1,1] VARCHAR(30) ATTRIBUTE first_name: [0,1] VARCHAR(30) ATTRIBUTE initial: [0,1] VARCHAR(10) ATTRIBUTE suffix: [0,1] VARCHAR(10) ATTRIBUTE email: [1,1] VARCHAR(255) ATTRIBUTE work_phone: [0,1] VARCHAR(30) ATTRIBUTE phone_ext: [0,1] VARCHAR(10) ATTRIBUTE fax_number: [0,1] VARCHAR(30) ATTRIBUTE is_email_valid: [1,1] BOOLEAN ATTRIBUTE account_created_person_id: [0,1] Person ATTRIBUTE dblogin: [0,1] VARCHAR(30) ATTRIBUTE account_created: [0,1] DATETIME ATTRIBUTE hardware: [0,1] VARCHAR(255)
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OBJECT CLASS Product
ATTRIBUTE authoritative_name: [1,1] VARCHAR(200)
ATTRIBUTE instances
DERIVATION: ! product [ ProductInst ]
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OBJECT CLASS ProductInst ATTRIBUTE feature: [1,1] Feature ATTRIBUTE product: [0,1] Product ATTRIBUTE authoritative_name: [0,1] VARCHAR(200) ATTRIBUTE name: [1,1] VARCHAR(200)
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OBJECT CLASS Reference
ATTRIBUTE publication: [0,1] VARCHAR(100)
ATTRIBUTE volume: [0,1] VARCHAR(20)
ATTRIBUTE issue: [0,1] VARCHAR(10)
ATTRIBUTE start_page: [0,1] VARCHAR(10)
ATTRIBUTE end_page: [0,1] VARCHAR(10)
ATTRIBUTE year: [0,1] SMALLINT
ATTRIBUTE pub_status: [0,1] pub_status_rule
ATTRIBUTE reference_type: [1,1] reference_type_rule
ATTRIBUTE title: [0,1] VARCHAR(255)
ATTRIBUTE publisher: [0,1] VARCHAR(100)
ATTRIBUTE university: [0,1] VARCHAR(100)
ATTRIBUTE address: [0,1] VARCHAR(255)
ATTRIBUTE authors_string: [0,1] TEXT
ATTRIBUTE dates: [0,1] VARCHAR(100)
ATTRIBUTE patent_number: [0,1] VARCHAR(200)
ATTRIBUTE old_gsdbid: [0,1] CHAR(10)
ATTRIBUTE comments
DERIVATION: ! object [ Comment ]
ATTRIBUTE authors (author_order, author_last_name, author_first_name,
author_initials, author_suffix):
set-of [0,] ([1,1] SMALLINT, [1,1] VARCHAR(40), [0,1]
VARCHAR(20), [0,1] VARCHAR(10), [0,1]
suffix_rule)
ATTRIBUTE editor (editor_order, editor_last_name, editor_first_name,
editor_initials, editor_suffix):
set-of [0,] ([1,1] SMALLINT, [1,1] VARCHAR(40), [0,1]
VARCHAR(20), [0,1] VARCHAR(10), [0,1]
suffix_rule)
ATTRIBUTE links (tableid, loc_start, loc_end, ref_order):
set-of [0,] ([1,1] Feature or Source or Sequence or
Component, [0,1] INTEGER, [0,1] INTEGER, [1,1]
SMALLINT)
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OBJECT CLASS Repeat
isa Feature
ATTRIBUTE name: [1,1] VARCHAR(100)
ATTRIBUTE is_tandem: [1,1] BOOLEAN
ATTRIBUTE is_flanking: [1,1] BOOLEAN
ATTRIBUTE is_inverted: [1,1] BOOLEAN
ATTRIBUTE is_terminal: [1,1] BOOLEAN
ATTRIBUTE is_direct: [1,1] BOOLEAN
ATTRIBUTE is_dispersed: [1,1] BOOLEAN
ATTRIBUTE family: [0,1] VARCHAR(100)
ATTRIBUTE sub_family: [0,1] VARCHAR(100)
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OBJECT CLASS Sequence
ATTRIBUTE sequence: [0,1] TEXT
ATTRIBUTE length: [0,1] INTEGER
ATTRIBUTE counts (a_count, c_count, g_count, t_count, other_count):
[0,1] ([0,1] INTEGER, [0,1] INTEGER, [0,1] INTEGER, [0,1]
INTEGER, [0,1] INTEGER)
ATTRIBUTE ic_accession: [0,1] VARCHAR(20)
ATTRIBUTE sequence_accession: [0,1] VARCHAR(100)
ATTRIBUTE is_discontiguous: [1,1] BOOLEAN
ATTRIBUTE is_experimental: [1,1] BOOLEAN
ATTRIBUTE is_transpliced: [1,1] BOOLEAN
ATTRIBUTE transl_table_id: [0,1] INTEGER
ATTRIBUTE flatfile_date: [0,1] DATETIME
ATTRIBUTE description: [0,1] VARCHAR(255)
ATTRIBUTE name: [0,1] CHAR(10)
ATTRIBUTE is_complete_genome: [1,1] BOOLEAN
ATTRIBUTE is_clone_end: [1,1] BOOLEAN
ATTRIBUTE origin: [0,1] VARCHAR(80)
ATTRIBUTE created: [1,1] DATETIME
ATTRIBUTE first_released: [0,1] DATETIME
ATTRIBUTE last_released: [0,1] DATETIME
ATTRIBUTE release: [1,1] BOOLEAN
ATTRIBUTE text_last_modified: [1,1] DATETIME
ATTRIBUTE hold_until: [0,1] DATETIME
ATTRIBUTE confidences (loc_start, loc_end, confidence, multiple_read,
double_stranded):
set-of [0,] ([1,1] INTEGER, [1,1] INTEGER, [1,1] FLOAT(8), [1,1]
BOOLEAN, [1,1] BOOLEAN)
ATTRIBUTE keywords: set-of [0,] VARCHAR(200)
ATTRIBUTE modified_bases
DERIVATION: ! sequence [ ModifiedBase ]
ATTRIBUTE secondary_ic_accession: set-of [0,] VARCHAR(20)
ATTRIBUTE sequence_pieces (sp_id, seq_order, distance_from_left, uncertainty,
strand_orientation, type):
set-of [0,] ([1,1] Sequence, [0,1] INTEGER, [0,1] FLOAT(8), [0,1]
FLOAT(8), [0,1] strand_orientation_rule, [0,1]
VARCHAR(20))
ATTRIBUTE comments
DERIVATION: ! object [ Comment ]
ATTRIBUTE sources
DERIVATION: ! sequence [ Source ]
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OBJECT CLASS Source
ATTRIBUTE sequence: [1,1] Sequence
ATTRIBUTE loc_start: [0,1] INTEGER
ATTRIBUTE loc_end: [0,1] INTEGER
ATTRIBUTE taxon_id: [1,1] Taxon
ATTRIBUTE genome: [0,1] genome_rule
ATTRIBUTE taxonomy: [0,1] VARCHAR(255)
ATTRIBUTE is_linear: [1,1] BOOLEAN
ATTRIBUTE molecule_sequenced: [0,1] molecule_sequenced_rule
ATTRIBUTE molecule_isolated: [0,1] molecule_isolated_rule
ATTRIBUTE division_code: [0,1] CHAR(3)
ATTRIBUTE tissue_lib: [0,1] VARCHAR(200)
ATTRIBUTE tissue_type: [0,1] VARCHAR(200)
ATTRIBUTE cell_line: [0,1] VARCHAR(200)
ATTRIBUTE cell_type: [0,1] VARCHAR(200)
ATTRIBUTE chromosome: [0,1] VARCHAR(20)
ATTRIBUTE clone: [0,1] VARCHAR(200)
ATTRIBUTE clone_lib: [0,1] VARCHAR(200)
ATTRIBUTE dev_stage: [0,1] VARCHAR(200)
ATTRIBUTE haplotype: [0,1] VARCHAR(200)
ATTRIBUTE is_transposon: [1,1] BOOLEAN
ATTRIBUTE isolate: [0,1] VARCHAR(200)
ATTRIBUTE lab_host: [0,1] VARCHAR(200)
ATTRIBUTE natural_host: [0,1] VARCHAR(200)
ATTRIBUTE cultivar: [0,1] VARCHAR(200)
ATTRIBUTE pop_variant: [0,1] VARCHAR(200)
ATTRIBUTE is_proviral: [1,1] BOOLEAN
ATTRIBUTE sex: [0,1] VARCHAR(200)
ATTRIBUTE strain: [0,1] VARCHAR(200)
ATTRIBUTE sub_clone: [0,1] VARCHAR(200)
ATTRIBUTE sub_strain: [0,1] VARCHAR(200)
ATTRIBUTE variety: [0,1] VARCHAR(200)
ATTRIBUTE sub_species: [0,1] VARCHAR(200)
ATTRIBUTE is_rearranged: [1,1] BOOLEAN
ATTRIBUTE vector: [0,1] VARCHAR(30)
ATTRIBUTE culture_collection: [0,1] VARCHAR(30)
ATTRIBUTE comments
DERIVATION: ! object [ Comment ]
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OBJECT CLASS Taxon ATTRIBUTE authority: [0,1] VARCHAR(255) ATTRIBUTE scientific_name: [1,1] VARCHAR(80) ATTRIBUTE common_name: [0,1] VARCHAR(80) ATTRIBUTE domain: [0,1] VARCHAR(80) ATTRIBUTE kingdom: [0,1] VARCHAR(80) ATTRIBUTE phylum: [0,1] VARCHAR(80) ATTRIBUTE division: [0,1] VARCHAR(80) ATTRIBUTE class: [0,1] VARCHAR(80) ATTRIBUTE tax_order: [0,1] VARCHAR(80) ATTRIBUTE family: [0,1] VARCHAR(80) ATTRIBUTE genus: [0,1] VARCHAR(80) ATTRIBUTE species: [0,1] VARCHAR(80) ATTRIBUTE tax_abbrev: [0,1] CHAR(3) ATTRIBUTE old_gsdbid: [0,1] CHAR(10)
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OBJECT CLASS TranslationTables ATTRIBUTE start_translation: [1,1] CHAR(64) ATTRIBUTE stop_translation: [1,1] CHAR(64) ATTRIBUTE internal_translation: [1,1] CHAR(64) ATTRIBUTE name: [1,1] VARCHAR(255)
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