src/objects/gbseq/gbseq.asn

--$Revision: 61002 $
--*********************************************************
--
-- ASN.1 and XML for the components of a GenBank format sequence
-- J.Ostell 2002
-- Updated 25 May 2010
--
--*********************************************************

NCBI-GBSeq DEFINITIONS ::=
BEGIN

--********
--  GBSeq represents the elements in a GenBank style report
--    of a sequence with some small additions to structure and support
--    for protein (GenPept) versions of GenBank format as seen in
--    Entrez. While this represents the simplification, reduction of
--    detail, and flattening to a single sequence perspective of GenBank
--    format (compared with the full ASN.1 or XML from which GenBank and
--    this format is derived at NCBI), it is presented in ASN.1 or XML for
--    automated parsing and processing. It is hoped that this compromise
--    will be useful for those bulk processing at the GenBank format level
--    of detail today. Since it is a compromise, a number of pragmatic
--    decisions have been made.
--
--  In pursuit of simplicity and familiarity a number of
--    fields do not have full substructure defined here where there is
--    already a standard GenBank format string. For example:
--
--   Date  DD-Mon-YYYY
--   Authors   LastName, Intials (with periods)
--   Journal   JounalName Volume (issue), page-range (year)
--   FeatureLocations as per GenBank feature table, but FeatureIntervals
--    may also be provided as a convenience
--   FeatureQualifiers  as per GenBank feature table
--   Primary has a string that represents a table to construct
--    a third party (TPA) sequence.
--   other-seqids can have strings with the "vertical bar format" sequence
--    identifiers used in BLAST for example, when they are non-genbank types.
--    Currently in GenBank format you only see GI, but there are others, like
--    patents, submitter clone names, etc which will appear here, as they
--    always have in the ASN.1 format, and full XML format.
--   source-db is a formatted text block for peptides in GenPept format that
--    carries information from the source protein database.
--
--  There are also a number of elements that could have been
--   more exactly specified, but in the interest of simplicity
--   have been simply left as options. For example..
--
--  accession and accession.version will always appear in a GenBank record
--   they are optional because this format can also be used for non-GenBank
--   sequences, and in that case will have only "other-seqids".
--
--  sequences will normally all have "sequence" filled in. But contig records
--    will have a "join" statement in the "contig" slot, and no "sequence".
--    We also may consider a retrieval option with no sequence of any kind
--     and no feature table to quickly check minimal values.
--
--  a reference may have an author list, or be from a consortium, or both.
--
--  some fields, such as taxonomy, do appear as separate elements in GenBank
--    format but without a specific linetype (in GenBank format this comes
--    under ORGANISM). Another example is the separation of primary accession
--    from the list of secondary accessions. In GenBank format primary
--    accession is just the first one on the list that includes all secondaries
--    after it.
--
--  create-date deserves special comment. The date you see on the right hand
--    side of the LOCUS line in GenBank format is actually the last date the
--    the record was modified (or the update-date). The date the record was
--    first submitted to GenBank appears in the first submission citation in
--    the reference section. Internally in the databases and ASN.1 NCBI keeps
--    the first date the record was released into the sequence database at
--    NCBI as create-date. For records from EMBL, which supports create-date,
--    it is the date provided by EMBL. For DDBJ records, which do not supply
--    a create-date (same as GenBank format) the create-date is the first date
--    NCBI saw the record from DDBJ. For older GenBank records, before NCBI
--    took responsibility for GenBank, it is just the first date NCBI saw the
--    record. Create-date can be very useful, so we expose it here, but users
--    must understand it is only an approximation and comes from many sources,
--    and with many exceptions and caveats. It does NOT tell you the first
--    date the public might have seen this record and thus is NOT an accurate
--    measure for legal issues of precedence.
--
--********

GBSet ::= SEQUENCE OF GBSeq
        
GBSeq ::= SEQUENCE {
    locus VisibleString OPTIONAL ,
    length INTEGER ,
    strandedness VisibleString OPTIONAL ,
    moltype VisibleString ,
    topology VisibleString OPTIONAL ,
    division VisibleString OPTIONAL ,
    update-date VisibleString OPTIONAL ,
    create-date VisibleString OPTIONAL ,
    update-release VisibleString OPTIONAL ,
    create-release VisibleString OPTIONAL ,
    definition VisibleString OPTIONAL ,
    primary-accession VisibleString OPTIONAL ,
    entry-version VisibleString OPTIONAL ,
    accession-version VisibleString OPTIONAL ,
    other-seqids SEQUENCE OF GBSeqid OPTIONAL ,
    secondary-accessions SEQUENCE OF GBSecondary-accn OPTIONAL,
    project VisibleString OPTIONAL ,
    keywords SEQUENCE OF GBKeyword OPTIONAL ,
    segment VisibleString OPTIONAL ,
    source VisibleString OPTIONAL ,
    organism VisibleString OPTIONAL ,
    taxonomy VisibleString OPTIONAL ,
    references SEQUENCE OF GBReference OPTIONAL ,
    comment VisibleString OPTIONAL ,
    comment-set SEQUENCE OF GBComment OPTIONAL ,
    struc-comments SEQUENCE OF GBStrucComment OPTIONAL ,
    primary VisibleString OPTIONAL ,
    source-db VisibleString OPTIONAL ,
    database-reference VisibleString OPTIONAL ,
    feature-table SEQUENCE OF GBFeature OPTIONAL ,
    feature-set SEQUENCE OF GBFeatureSet OPTIONAL ,
    sequence VisibleString OPTIONAL ,  -- Optional for contig, wgs, etc.
    contig VisibleString OPTIONAL ,
    alt-seq SEQUENCE OF GBAltSeqData OPTIONAL ,
    xrefs SEQUENCE OF GBXref OPTIONAL
}

GBSeqid ::= VisibleString

GBSecondary-accn ::= VisibleString

GBKeyword ::= VisibleString

GBReference ::= SEQUENCE {
    reference VisibleString ,
    position VisibleString OPTIONAL ,
    authors SEQUENCE OF GBAuthor OPTIONAL ,
    consortium VisibleString OPTIONAL ,
    title VisibleString OPTIONAL ,
    journal VisibleString ,
    xref SEQUENCE OF GBXref OPTIONAL ,
    pubmed INTEGER OPTIONAL ,
    remark VisibleString OPTIONAL
}

GBAuthor ::= VisibleString

GBXref ::= SEQUENCE {
    dbname VisibleString ,
    id VisibleString
}

GBComment ::= SEQUENCE {
    type VisibleString OPTIONAL ,
    paragraphs SEQUENCE OF GBCommentParagraph
}

GBCommentParagraph ::= VisibleString

GBStrucComment ::= SEQUENCE {
    name VisibleString OPTIONAL ,
    items SEQUENCE OF GBStrucCommentItem
}

GBStrucCommentItem ::= SEQUENCE {
    tag VisibleString OPTIONAL ,
    value VisibleString OPTIONAL ,
    url VisibleString OPTIONAL
}

GBFeatureSet ::= SEQUENCE {
    annot-source VisibleString OPTIONAL ,
    features SEQUENCE OF GBFeature
}

GBFeature ::= SEQUENCE {
    key VisibleString ,
    location VisibleString ,
    intervals SEQUENCE OF GBInterval OPTIONAL ,
    operator VisibleString OPTIONAL ,
    partial5 BOOLEAN OPTIONAL ,
    partial3 BOOLEAN OPTIONAL ,
    quals SEQUENCE OF GBQualifier OPTIONAL ,
    xrefs SEQUENCE OF GBXref OPTIONAL
}

GBInterval ::= SEQUENCE {
    from INTEGER OPTIONAL ,
    to INTEGER OPTIONAL ,
    point INTEGER OPTIONAL ,
    iscomp BOOLEAN OPTIONAL ,
    interbp BOOLEAN OPTIONAL ,
    accession VisibleString
}

GBQualifier ::= SEQUENCE {
    name VisibleString ,
    value VisibleString OPTIONAL
}

GBAltSeqData ::= SEQUENCE {
    name VisibleString ,  -- e.g., contig, wgs, scaffold, cage, genome
    items SEQUENCE OF GBAltSeqItem OPTIONAL
}

GBAltSeqItem ::= SEQUENCE {
    interval GBInterval OPTIONAL ,
    isgap BOOLEAN OPTIONAL ,
    gap-length INTEGER OPTIONAL ,
    gap-type VisibleString OPTIONAL ,
    gap-linkage VisibleString OPTIONAL ,
    gap-comment VisibleString OPTIONAL ,
    first-accn VisibleString OPTIONAL ,
    last-accn VisibleString OPTIONAL ,
    value VisibleString OPTIONAL
}

END