gbseq.asn
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- --$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