GSDB Schema
boolean ::= INTEGERBack to Class Definition
table-id ::= REALBack to Class Definition
Action-status-rule ::= ENUMERATED { success (0) , pending (1) , failure (2) , processing (3) , manual (4) }Back to Class Definition
Action-tablename-rule ::= ENUMERATED { ImportFile (0) , SequenceStatus (1) , FeatureStatus (2) }Back to Class Definition
Comment-link-rule ::= ENUMERATED { Sequence (0) , Feature (1) , Component (2) , Source (3) , Reference (4) , ModifiedBase (5) }Back to Class Definition
DBLink-link-rule ::= ENUMERATED { GeneInst (0) , ProductInst (1) , Gene (2) , Product (3) , Feature (4) , Reference (5) , Sequence (6) , Source (7) , Component (8) }Back to Class Definition
DeletedAccession-type-rule ::= ENUMERATED { Feature (0) , Sequence (1) }Back to Class Definition
ReferenceLink-link-rule ::= ENUMERATED { Feature (0) , Source (1) , Sequence (2) , Component (3) }Back to Class Definition
aa-rule ::= ENUMERATED { Ala (0) , Arg (1) , Asn (2) , Asp (3) , Cys (4) , Gln (5) , Glu (6) , Gly (7) , His (8) , Ile (9) , Leu (10) , Lys (11) , Met (12) , Phe (13) , Pro (14) , Ser (15) , Thr (16) , Trp (17) , Tyr (18) , Val (19) , Xxx (20) , TERM (21) , OTHER (22) }Back to Class Definition
analysis-link-rule ::= ENUMERATED { Feature (0) , Component (1) }Back to Class Definition
anticodon-length-rule ::= ENUMERATED { 2 (0) , 3 (1) , 4 (2) }Back to Class Definition
codon-start-rule ::= ENUMERATED { 1 (0) , 2 (1) , 3 (2) }Back to Class Definition
collection-link-rule ::= ENUMERATED { Sequence (0) , EPub (1) , Component (2) , Feature (3) , Collection (4) }Back to Class Definition
comp-type-rule ::= ENUMERATED { assembly (0) , variation (1) , product (2) }Back to Class Definition
diff-name-rule ::= ENUMERATED { transition (0) , transversion (1) , indel (2) , mutation (3) , allele (4) }Back to Class Definition
diff-type-rule ::= ENUMERATED { conflict (0) , variation (1) }Back to Class Definition
direction-rule ::= ENUMERATED { left (0) , right (1) , both (2) }Back to Class Definition
genome-rule ::= ENUMERATED { mitochondrion (0) , chloroplast (1) , kinetoplast (2) , plastid (3) , cyanelle (4) , plasmid (5) , cloning-vector (6) , synthetic-gene (7) , other-synthetic-construct (8) , micronuclear (9) , macronuclear (10) , somatic-nuclear (11) , germline-nuclear (12) }Back to Class Definition
import-file-type-rule ::= ENUMERATED { GBFF (0) , EMBLFF (1) , DDBJFF (2) , GSDBFF (3) , GIO (4) }Back to Class Definition
intron-class-rule ::= ENUMERATED { I (0) , II (1) , III (2) , other (3) }Back to Class Definition
loc-operator-rule ::= ENUMERATED { join (0) , order (1) , replace (2) }Back to Class Definition
mod-base-rule ::= ENUMERATED { ac4c (0) , chm5u (1) , cm (2) , cmnm5s2u (3) , cmnm5u (4) , d (5) , fm (6) , galq (7) , gm (8) , i (9) , i6a (10) , m1a (11) , m1f (12) , m1g (13) , m1i (14) , m22g (15) , m2a (16) , m2g (17) , m3c (18) , m5c (19) , m6a (20) , m7g (21) , mam5s2u (22) , mam5u (23) , manq (24) , mcm5s2u (25) , mcm5u (26) , mo5u (27) , ms2i6a (28) , ms2t6a (29) , mt6a (30) , mv (31) , o5u (32) , osyw (33) , p (34) , q (35) , s2c (36) , s2t (37) , s2u (38) , s4u (39) , t (40) , t6a (41) , tm (42) , um (43) , x (44) , yw (45) , OTHER (46) }Back to Class Definition
molecule-isolated-rule ::= ENUMERATED { ds-DNA (0) , ss-mRNA (1) , ss-RNA (2) , ss-rRNA (3) , ds-RNA (4) , ms-DNA (5) , ms-RNA (6) , ss-DNA (7) , ss-cRNA (8) , ss-gRNA (9) , ss-tRNA (10) , ss-uRNA (11) , ss-xRNA (12) , DNA (13) , cRNA (14) , gRNA (15) , mRNA (16) , xRNA (17) , RNA (18) , tRNA (19) , uRNA (20) , rRNA (21) }Back to Class Definition
molecule-sequenced-rule ::= ENUMERATED { DNA (0) , ds-DNA (1) , ss-DNA (2) , RNA (3) , cDNA (4) , cDNA-to-genomic-RNA (5) , cDNA-to-mRNA (6) , cDNA-to-other-RNA (7) , cDNA-to-rRNA (8) , mRNA (9) , rRNA (10) , scRNA (11) , snRNA (12) , tRNA (13) }Back to Class Definition
pub-status-rule ::= ENUMERATED { published (0) , in-press (1) , submitted (2) , in-preparation (3) , unpublished (4) }Back to Class Definition
reference-type-rule ::= ENUMERATED { journal (0) , book (1) , thesis (2) , proceedings (3) , other (4) , manuscript (5) , letter (6) , patent (7) , database-publication (8) , GSDB-publication (9) }Back to Class Definition
strand-orientation-rule ::= ENUMERATED { forward (0) , reverse (1) , unknown (2) }Back to Class Definition
suffix-rule ::= ENUMERATED { I (0) , II (1) , III (2) , IV (3) , Jr. (4) , Sr. (5) }Back to Class Definition
transl-type-rule ::= ENUMERATED { gsdb-conceptual (0) , user-conceptual (1) , experimental (2) }Back to Class Definition
Address ::= SEQUENCE { institution Institution OPTIONAL , department VisibleString OPTIONAL , address VisibleString OPTIONAL , mailstop VisibleString OPTIONAL , room VisibleString OPTIONAL , city VisibleString OPTIONAL , state VisibleString OPTIONAL , country VisibleString OPTIONAL , zip VisibleString OPTIONAL , phone-ext-dept VisibleString OPTIONAL }Back to Class Definition
Analysis ::= SEQUENCE { name VisibleString , object CHOICE { choice-1 Feature , choice-2 Component } , version REAL OPTIONAL , match REAL OPTIONAL , score REAL OPTIONAL , date-run VisibleString OPTIONAL , parameters VisibleString OPTIONAL , db-searched VisibleString OPTIONAL }Back to Class Definition
Anticodon ::= SEQUENCE { feature Feature , start INTEGER OPTIONAL , aa aa-rule , length anticodon-length-rule }Back to Class Definition
BindingSite ::= SEQUENCE { isa-Feature Feature , bound-moiety VisibleString OPTIONAL , name VisibleString OPTIONAL , binds-to VisibleString OPTIONAL , binds-where VisibleString OPTIONAL , binds-when VisibleString OPTIONAL , preconditions VisibleString OPTIONAL }Back to Class Definition
Collection ::= SEQUENCE { description VisibleString OPTIONAL , name VisibleString , date-created VisibleString , last-updated VisibleString , links SET OF CHOICE { choice-1 Sequence , choice-2 Component , choice-3 Feature , choice-4 Collection } OPTIONAL }Back to Class Definition
Comment ::= SEQUENCE { long-comment VisibleString OPTIONAL , short-comment VisibleString OPTIONAL , object CHOICE { choice-1 Source , choice-2 Feature , choice-3 Component , choice-4 Sequence , choice-5 Reference , choice-6 ModifiedBase } }Back to Class Definition
Component ::= SEQUENCE { baseseq-id Sequence , compseq-id Sequence , type comp-type-rule , created VisibleString , last-released VisibleString OPTIONAL , locations SET OF SEQUENCE { loc-baseseq-start INTEGER , loc-baseseq-end INTEGER , loc-compseq-start INTEGER , loc-compseq-end INTEGER , strand-orientation strand-orientation-rule } OPTIONAL , differences SET OF SEQUENCE { diff-type diff-type-rule , name diff-name-rule OPTIONAL , diff-baseseq-start INTEGER , diff-baseseq-end INTEGER , diff-compseq-start INTEGER , diff-compseq-end INTEGER , base-seq VARCHAR(255) OPTIONAL , comp-seq VARCHAR(255) OPTIONAL } OPTIONAL }Back to Class Definition
DBLink ::= SEQUENCE { object CHOICE { choice-1 GeneInst , choice-2 ProductInst , choice-3 Gene , choice-4 Product , choice-5 Feature , choice-6 Reference , choice-7 Sequence , choice-8 Source , choice-9 Component } , extdb VisibleString OPTIONAL , extid VisibleString OPTIONAL , url VisibleString OPTIONAL }Back to Class Definition
DeletedAccession ::= SEQUENCE { type DeletedAccession-type-rule , gsdb-accession VisibleString OPTIONAL , ic-accession VisibleString OPTIONAL , delete-date VisibleString , deleted-by VisibleString , owned-by VisibleString , reason VisibleString OPTIONAL , superceding-id VisibleString OPTIONAL , flatfile VisibleString OPTIONAL }Back to Class Definition
Feature ::= SEQUENCE { sequence Sequence , feature-accession VisibleString OPTIONAL , type VisibleString , standard-type BOOLEAN , codon-start codon-start-rule OPTIONAL , exp-determined BOOLEAN , function VisibleString OPTIONAL , map-location VisibleString OPTIONAL , number VisibleString OPTIONAL , pseudo BOOLEAN , standard-name VisibleString OPTIONAL , direction direction-rule OPTIONAL , PCR-conditions VisibleString OPTIONAL , is-5-complete BOOLEAN , is-3-complete BOOLEAN , fits-consensus BOOLEAN , fits-consensus5 BOOLEAN , fits-consensus3 BOOLEAN , created VisibleString , first-released VisibleString OPTIONAL , last-released VisibleString OPTIONAL , loc-operator loc-operator-rule OPTIONAL , is-rna-preedited BOOLEAN , self-splice-intron-class intron-class-rule OPTIONAL , translations SET OF SEQUENCE { is-t-ta-stop BOOLEAN , protein-translation TEXT , transl-type transl-type-rule } OPTIONAL , transl-excepts SET OF SEQUENCE { left-bp INTEGER , right-bp INTEGER , aa aa-rule } OPTIONAL , locations SET OF SEQUENCE { loc-sequence Sequence , left-start INTEGER OPTIONAL , left-end INTEGER OPTIONAL , right-start INTEGER OPTIONAL , right-end INTEGER OPTIONAL , complement BOOLEAN , exclusive BOOLEAN , literal-sequence VARCHAR(255) OPTIONAL , loc-order INTEGER , x-oid table-id } OPTIONAL }Back to Class Definition
FeatureTypes ::= SEQUENCE { name VisibleString }Back to Class Definition
Flatfile ::= SEQUENCE { sequence Sequence , sequence-accession VisibleString , ff-version VisibleString , name VisibleString OPTIONAL , ic-accession VisibleString OPTIONAL , flatfile VisibleString , first-distributed VisibleString OPTIONAL , last-distributed VisibleString OPTIONAL , new-flatfile BOOLEAN }Back to Class Definition
Gene ::= SEQUENCE { authoritative-name VisibleString , taxon-id Taxon }Back to Class Definition
GeneInst ::= SEQUENCE { feature Feature , gene Gene OPTIONAL , authoritative-name VisibleString OPTIONAL , name VisibleString }Back to Class Definition
Institution ::= SEQUENCE { name VisibleString , phone-num VisibleString OPTIONAL , fax-num VisibleString OPTIONAL , email VisibleString OPTIONAL }Back to Class Definition
ModifiedBase ::= SEQUENCE { sequence Sequence , mod-base mod-base-rule , bp INTEGER }Back to Class Definition
Person ::= SEQUENCE { address-id Address OPTIONAL , last-name VisibleString , first-name VisibleString OPTIONAL , initial VisibleString OPTIONAL , suffix VisibleString OPTIONAL , email VisibleString , work-phone VisibleString OPTIONAL , phone-ext VisibleString OPTIONAL , fax-number VisibleString OPTIONAL , is-email-valid BOOLEAN , account-created-person-id Person OPTIONAL , dblogin VisibleString OPTIONAL , account-created VisibleString OPTIONAL , hardware VisibleString OPTIONAL }Back to Class Definition
Product ::= SEQUENCE { authoritative-name VisibleString }Back to Class Definition
ProductInst ::= SEQUENCE { feature Feature , product Product OPTIONAL , authoritative-name VisibleString OPTIONAL , name VisibleString }Back to Class Definition
Reference ::= SEQUENCE { publication VisibleString OPTIONAL , volume VisibleString OPTIONAL , issue VisibleString OPTIONAL , start-page VisibleString OPTIONAL , end-page VisibleString OPTIONAL , year INTEGER OPTIONAL , pub-status pub-status-rule OPTIONAL , reference-type reference-type-rule , title VisibleString OPTIONAL , publisher VisibleString OPTIONAL , university VisibleString OPTIONAL , address VisibleString OPTIONAL , authors-string VisibleString OPTIONAL , dates VisibleString OPTIONAL , patent-number VisibleString OPTIONAL , old-gsdbid VisibleString OPTIONAL , authors SET OF SEQUENCE { author-order SMALLINT , author-last-name VARCHAR(40) , author-first-name VARCHAR(20) OPTIONAL , author-initials VARCHAR(10) OPTIONAL , author-suffix suffix-rule OPTIONAL } OPTIONAL , editor SET OF SEQUENCE { editor-order SMALLINT , editor-last-name VARCHAR(40) , editor-first-name VARCHAR(20) OPTIONAL , editor-initials VARCHAR(10) OPTIONAL , editor-suffix suffix-rule OPTIONAL } OPTIONAL , links SET OF SEQUENCE { tableid CHOICE { choice-1 Feature , choice-2 Source , choice-3 Sequence , choice-4 Component } , loc-start INTEGER OPTIONAL , loc-end INTEGER OPTIONAL , ref-order SMALLINT } OPTIONAL }Back to Class Definition
Repeat ::= SEQUENCE { isa-Feature Feature , name VisibleString , is-tandem BOOLEAN , is-flanking BOOLEAN , is-inverted BOOLEAN , is-terminal BOOLEAN , is-direct BOOLEAN , is-dispersed BOOLEAN , family VisibleString OPTIONAL , sub-family VisibleString OPTIONAL }Back to Class Definition
Sequence ::= SEQUENCE { sequence VisibleString OPTIONAL , length INTEGER OPTIONAL , counts SEQUENCE { a-count INTEGER OPTIONAL , c-count INTEGER OPTIONAL , g-count INTEGER OPTIONAL , t-count INTEGER OPTIONAL , other-count INTEGER OPTIONAL } OPTIONAL , ic-accession VisibleString OPTIONAL , sequence-accession VisibleString OPTIONAL , is-discontiguous BOOLEAN , is-experimental BOOLEAN , is-transpliced BOOLEAN , transl-table-id INTEGER OPTIONAL , flatfile-date VisibleString OPTIONAL , description VisibleString OPTIONAL , name VisibleString OPTIONAL , is-complete-genome BOOLEAN , is-clone-end BOOLEAN , origin VisibleString OPTIONAL , created VisibleString , first-released VisibleString OPTIONAL , last-released VisibleString OPTIONAL , release BOOLEAN , text-last-modified VisibleString , hold-until VisibleString OPTIONAL , confidences SET OF SEQUENCE { loc-start INTEGER , loc-end INTEGER , confidence FLOAT(8) , multiple-read BOOLEAN , double-stranded BOOLEAN } OPTIONAL , keywords SET OF VisibleString OPTIONAL , secondary-ic-accession SET OF VisibleString OPTIONAL , sequence-pieces SET OF SEQUENCE { sp-id Sequence , seq-order INTEGER OPTIONAL , distance-from-left FLOAT(8) OPTIONAL , uncertainty FLOAT(8) OPTIONAL , strand-orientation strand-orientation-rule OPTIONAL , type VARCHAR(20) OPTIONAL } OPTIONAL }Back to Class Definition
Source ::= SEQUENCE { sequence Sequence , loc-start INTEGER OPTIONAL , loc-end INTEGER OPTIONAL , taxon-id Taxon , genome genome-rule OPTIONAL , taxonomy VisibleString OPTIONAL , is-linear BOOLEAN , molecule-sequenced molecule-sequenced-rule OPTIONAL , molecule-isolated molecule-isolated-rule OPTIONAL , division-code VisibleString OPTIONAL , tissue-lib VisibleString OPTIONAL , tissue-type VisibleString OPTIONAL , cell-line VisibleString OPTIONAL , cell-type VisibleString OPTIONAL , chromosome VisibleString OPTIONAL , clone VisibleString OPTIONAL , clone-lib VisibleString OPTIONAL , dev-stage VisibleString OPTIONAL , haplotype VisibleString OPTIONAL , is-transposon BOOLEAN , isolate VisibleString OPTIONAL , lab-host VisibleString OPTIONAL , natural-host VisibleString OPTIONAL , cultivar VisibleString OPTIONAL , pop-variant VisibleString OPTIONAL , is-proviral BOOLEAN , sex VisibleString OPTIONAL , strain VisibleString OPTIONAL , sub-clone VisibleString OPTIONAL , sub-strain VisibleString OPTIONAL , variety VisibleString OPTIONAL , sub-species VisibleString OPTIONAL , is-rearranged BOOLEAN , vector VisibleString OPTIONAL , culture-collection VisibleString OPTIONAL }Back to Class Definition
Taxon ::= SEQUENCE { authority VisibleString OPTIONAL , scientific-name VisibleString , common-name VisibleString OPTIONAL , domain VisibleString OPTIONAL , kingdom VisibleString OPTIONAL , phylum VisibleString OPTIONAL , division VisibleString OPTIONAL , class VisibleString OPTIONAL , tax-order VisibleString OPTIONAL , family VisibleString OPTIONAL , genus VisibleString OPTIONAL , species VisibleString OPTIONAL , tax-abbrev VisibleString OPTIONAL , old-gsdbid VisibleString OPTIONAL }Back to Class Definition
TranslationTables ::= SEQUENCE { start-translation VisibleString , stop-translation VisibleString , internal-translation VisibleString , name VisibleString }Back to Class Definition