gbseq.asn

ncbi源码

--$Revision: 1000.1 $
--*********************************************************
--
-- ASN.1 and XML for the components of a GenBank format sequence
-- J.Ostell 2002
--
--*********************************************************

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.
--
--********

GBSeq ::= SEQUENCE {
	locus VisibleString ,
	length INTEGER ,
	strandedness INTEGER {
		not-set (0) ,
		single-stranded (1) ,
		double-stranded (2) ,
		mixed-stranded (3) } DEFAULT not-set ,
	moltype INTEGER {
		nucleic-acid (0) ,
		dna (1) ,
		rna (2) ,
		trna (3) ,
		rrna (4) ,
		mrna (5) ,
		urna (6) ,
		snrna (7) ,
		snorna (8) ,
		peptide (9) } DEFAULT nucleic-acid ,
	topology INTEGER {
		linear (1) ,
		circular (2) } DEFAULT linear ,
	division VisibleString ,
	update-date VisibleString ,
	create-date VisibleString ,
	update-release VisibleString OPTIONAL ,
	create-release VisibleString OPTIONAL ,
	definition VisibleString ,
	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,
	keywords SEQUENCE OF GBKeyword OPTIONAL ,
	segment VisibleString OPTIONAL ,
	source VisibleString ,
	organism VisibleString ,
	taxonomy VisibleString ,
	references SEQUENCE OF GBReference ,
	comment VisibleString OPTIONAL ,
	primary VisibleString OPTIONAL ,
	source-db VisibleString OPTIONAL ,
	database-reference VisibleString OPTIONAL ,
	feature-table SEQUENCE OF GBFeature OPTIONAL ,
	sequence VisibleString OPTIONAL ,  -- Optional for other dump forms
	contig VisibleString OPTIONAL }

	GBSecondary-accn ::= VisibleString

	GBSeqid ::= VisibleString

	GBKeyword ::= VisibleString

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

	GBAuthor ::= VisibleString

	GBFeature ::= SEQUENCE {
		key VisibleString ,
		location VisibleString ,
		intervals SEQUENCE OF GBInterval OPTIONAL ,
		quals SEQUENCE OF GBQualifier OPTIONAL }

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

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

	GBSet ::= SEQUENCE OF GBSeq
		
END