# Generated by OPM Retrofitting Tool V4.1 # Thu Nov 7 16:31:24 1996 NAMED PRIMITIVE VALUE CLASS boolean: TINYINT NAMED PRIMITIVE VALUE CLASS table_id: NUMERIC(6) CONTROLLED VALUE CLASS Action_status_rule { "success", "pending", "failure", "processing", "manual" } CONTROLLED VALUE CLASS Action_tablename_rule { "ImportFile", "SequenceStatus", "FeatureStatus" } CONTROLLED VALUE CLASS Comment_link_rule { "Sequence", "Feature", "Component", "Source", "Reference", "ModifiedBase" } CONTROLLED VALUE CLASS DBLink_link_rule { "GeneInst", "ProductInst", "Gene", "Product", "Feature", "Reference", "Sequence", "Source", "Component" } CONTROLLED VALUE CLASS DeletedAccession_type_rule { "Feature", "Sequence" } CONTROLLED VALUE CLASS ReferenceLink_link_rule { "Feature", "Source", "Sequence", "Component" } 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" } CONTROLLED VALUE CLASS analysis_link_rule { "Feature", "Component" } CONTROLLED VALUE CLASS anticodon_length_rule { 2, 3, 4 } CONTROLLED VALUE CLASS codon_start_rule { 1, 2, 3 } CONTROLLED VALUE CLASS collection_link_rule { "Sequence", "EPub", "Component", "Feature", "Collection" } CONTROLLED VALUE CLASS comp_type_rule { "assembly", "variation", "product" } CONTROLLED VALUE CLASS diff_name_rule { "transition", "transversion", "indel", "mutation", "allele" } CONTROLLED VALUE CLASS diff_type_rule { "conflict", "variation" } CONTROLLED VALUE CLASS direction_rule { "left", "right", "both" } CONTROLLED VALUE CLASS genome_rule { "mitochondrion", "chloroplast", "kinetoplast", "plastid", "cyanelle", "plasmid", "cloning vector", "synthetic gene", "other synthetic construct", "micronuclear", "macronuclear", "somatic nuclear", "germline nuclear" } CONTROLLED VALUE CLASS import_file_type_rule { "GBFF", "EMBLFF", "DDBJFF", "GSDBFF", "GIO" } CONTROLLED VALUE CLASS intron_class_rule { "I", "II", "III", "other" } CONTROLLED VALUE CLASS loc_operator_rule { "join", "order", "replace" } 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" } 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" } 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" } CONTROLLED VALUE CLASS pub_status_rule { "published", "in press", "submitted", "in preparation", "unpublished" } CONTROLLED VALUE CLASS reference_type_rule { "journal", "book", "thesis", "proceedings", "other", "manuscript", "letter", "patent", "database publication", "GSDB publication" } CONTROLLED VALUE CLASS strand_orientation_rule { "forward", "reverse", "unknown" } CONTROLLED VALUE CLASS suffix_rule { "I", "II", "III", "IV", "Jr.", "Sr." } CONTROLLED VALUE CLASS transl_type_rule { "gsdb conceptual", "user conceptual", "experimental" } 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) 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) 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 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) 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 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 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)) 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) 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 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 ] OBJECT CLASS FeatureTypes ATTRIBUTE name: [1,1] VARCHAR(30) 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 OBJECT CLASS Gene ATTRIBUTE authoritative_name: [1,1] VARCHAR(80) ATTRIBUTE taxon_id: [1,1] Taxon ATTRIBUTE instances DERIVATION: ! gene [ GeneInst ] 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) 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) OBJECT CLASS ModifiedBase ATTRIBUTE sequence: [1,1] Sequence ATTRIBUTE mod_base: [1,1] mod_base_rule ATTRIBUTE bp: [1,1] INTEGER 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) OBJECT CLASS Product ATTRIBUTE authoritative_name: [1,1] VARCHAR(200) ATTRIBUTE instances DERIVATION: ! product [ ProductInst ] 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) 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) 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) 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 ] 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 ] 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) 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)