ASN.1 Represenation for

GSDB Schema


ASN.1 Representation for Primitive Value Class boolean

boolean ::= INTEGER
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ASN.1 Representation for Primitive Value Class table_id

table-id ::= REAL
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ASN.1 Representation for Controlled Value Class Action_status_rule

Action-status-rule ::= ENUMERATED {
        success (0) ,
        pending (1) ,
        failure (2) ,
        processing (3) ,
        manual (4) }
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ASN.1 Representation for Controlled Value Class Action_tablename_rule

Action-tablename-rule ::= ENUMERATED {
        ImportFile (0) ,
        SequenceStatus (1) ,
        FeatureStatus (2) }
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ASN.1 Representation for Controlled Value Class Comment_link_rule

Comment-link-rule ::= ENUMERATED {
        Sequence (0) ,
        Feature (1) ,
        Component (2) ,
        Source (3) ,
        Reference (4) ,
        ModifiedBase (5) }
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ASN.1 Representation for Controlled Value Class DBLink_link_rule

DBLink-link-rule ::= ENUMERATED {
        GeneInst (0) ,
        ProductInst (1) ,
        Gene (2) ,
        Product (3) ,
        Feature (4) ,
        Reference (5) ,
        Sequence (6) ,
        Source (7) ,
        Component (8) }
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ASN.1 Representation for Controlled Value Class DeletedAccession_type_rule

DeletedAccession-type-rule ::= ENUMERATED {
        Feature (0) ,
        Sequence (1) }
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ASN.1 Representation for Controlled Value Class ReferenceLink_link_rule

ReferenceLink-link-rule ::= ENUMERATED {
        Feature (0) ,
        Source (1) ,
        Sequence (2) ,
        Component (3) }
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ASN.1 Representation for Controlled Value Class aa_rule

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) }
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ASN.1 Representation for Controlled Value Class analysis_link_rule

analysis-link-rule ::= ENUMERATED {
        Feature (0) ,
        Component (1) }
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ASN.1 Representation for Controlled Value Class anticodon_length_rule

anticodon-length-rule ::= ENUMERATED {
        2 (0) ,
        3 (1) ,
        4 (2) }
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ASN.1 Representation for Controlled Value Class codon_start_rule

codon-start-rule ::= ENUMERATED {
        1 (0) ,
        2 (1) ,
        3 (2) }
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ASN.1 Representation for Controlled Value Class collection_link_rule

collection-link-rule ::= ENUMERATED {
        Sequence (0) ,
        EPub (1) ,
        Component (2) ,
        Feature (3) ,
        Collection (4) }
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ASN.1 Representation for Controlled Value Class comp_type_rule

comp-type-rule ::= ENUMERATED {
        assembly (0) ,
        variation (1) ,
        product (2) }
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ASN.1 Representation for Controlled Value Class diff_name_rule

diff-name-rule ::= ENUMERATED {
        transition (0) ,
        transversion (1) ,
        indel (2) ,
        mutation (3) ,
        allele (4) }
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ASN.1 Representation for Controlled Value Class diff_type_rule

diff-type-rule ::= ENUMERATED {
        conflict (0) ,
        variation (1) }
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ASN.1 Representation for Controlled Value Class direction_rule

direction-rule ::= ENUMERATED {
        left (0) ,
        right (1) ,
        both (2) }
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ASN.1 Representation for Controlled Value Class genome_rule

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) }
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ASN.1 Representation for Controlled Value Class import_file_type_rule

import-file-type-rule ::= ENUMERATED {
        GBFF (0) ,
        EMBLFF (1) ,
        DDBJFF (2) ,
        GSDBFF (3) ,
        GIO (4) }
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ASN.1 Representation for Controlled Value Class intron_class_rule

intron-class-rule ::= ENUMERATED {
        I (0) ,
        II (1) ,
        III (2) ,
        other (3) }
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ASN.1 Representation for Controlled Value Class loc_operator_rule

loc-operator-rule ::= ENUMERATED {
        join (0) ,
        order (1) ,
        replace (2) }
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ASN.1 Representation for Controlled Value Class mod_base_rule

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) }
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ASN.1 Representation for Controlled Value Class molecule_isolated_rule

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) }
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ASN.1 Representation for Controlled Value Class molecule_sequenced_rule

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) }
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ASN.1 Representation for Controlled Value Class pub_status_rule

pub-status-rule ::= ENUMERATED {
        published (0) ,
        in-press (1) ,
        submitted (2) ,
        in-preparation (3) ,
        unpublished (4) }
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ASN.1 Representation for Controlled Value Class reference_type_rule

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) }
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ASN.1 Representation for Controlled Value Class strand_orientation_rule

strand-orientation-rule ::= ENUMERATED {
        forward (0) ,
        reverse (1) ,
        unknown (2) }
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ASN.1 Representation for Controlled Value Class suffix_rule

suffix-rule ::= ENUMERATED {
        I (0) ,
        II (1) ,
        III (2) ,
        IV (3) ,
        Jr. (4) ,
        Sr. (5) }
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ASN.1 Representation for Controlled Value Class transl_type_rule

transl-type-rule ::= ENUMERATED {
        gsdb-conceptual (0) ,
        user-conceptual (1) ,
        experimental (2) }
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ASN.1 Representation for Object Class Address

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 }
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ASN.1 Representation for Object Class Analysis

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 }
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ASN.1 Representation for Object Class Anticodon

Anticodon ::= SEQUENCE {
    feature Feature ,
    start INTEGER OPTIONAL ,
    aa aa-rule ,
    length anticodon-length-rule }
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ASN.1 Representation for Object Class BindingSite

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 }
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ASN.1 Representation for Object Class Collection

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 }
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ASN.1 Representation for Object Class Comment

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 } }
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ASN.1 Representation for Object Class Component

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 }
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ASN.1 Representation for Object Class DBLink

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 }
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ASN.1 Representation for Object Class DeletedAccession

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 }
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ASN.1 Representation for Object Class Feature

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 }
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ASN.1 Representation for Object Class FeatureTypes

FeatureTypes ::= SEQUENCE {
    name VisibleString }
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ASN.1 Representation for Object Class Flatfile

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 }
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ASN.1 Representation for Object Class Gene

Gene ::= SEQUENCE {
    authoritative-name VisibleString ,
    taxon-id Taxon }
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ASN.1 Representation for Object Class GeneInst

GeneInst ::= SEQUENCE {
    feature Feature ,
    gene Gene OPTIONAL ,
    authoritative-name VisibleString OPTIONAL ,
    name VisibleString }
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ASN.1 Representation for Object Class Institution

Institution ::= SEQUENCE {
    name VisibleString ,
    phone-num VisibleString OPTIONAL ,
    fax-num VisibleString OPTIONAL ,
    email VisibleString OPTIONAL }
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ASN.1 Representation for Object Class ModifiedBase

ModifiedBase ::= SEQUENCE {
    sequence Sequence ,
    mod-base mod-base-rule ,
    bp INTEGER }
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ASN.1 Representation for Object Class Person

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 }
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ASN.1 Representation for Object Class Product

Product ::= SEQUENCE {
    authoritative-name VisibleString }
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ASN.1 Representation for Object Class ProductInst

ProductInst ::= SEQUENCE {
    feature Feature ,
    product Product OPTIONAL ,
    authoritative-name VisibleString OPTIONAL ,
    name VisibleString }
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ASN.1 Representation for Object Class Reference

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 }
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ASN.1 Representation for Object Class Repeat

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 }
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ASN.1 Representation for Object Class Sequence

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 }
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ASN.1 Representation for Object Class Source

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 }
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ASN.1 Representation for Object Class Taxon

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 }
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ASN.1 Representation for Object Class TranslationTables

TranslationTables ::= SEQUENCE {
    start-translation VisibleString ,
    stop-translation VisibleString ,
    internal-translation VisibleString ,
    name VisibleString }
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