NCBI C Toolkit Cross Reference

   --$Revision: 6.7 $
   --*********************************************************
   --
   -- ASN.1 and XML for the components of a GenBank format sequence
   -- J.Ostell 2002
   -- Updated 15 January 2009
   --
   --*********************************************************
   
  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 ,
      length INTEGER ,
      strandedness VisibleString OPTIONAL ,
      moltype VisibleString ,
      topology VisibleString OPTIONAL ,
      division VisibleString ,
      update-date VisibleString ,
      create-date VisibleString OPTIONAL ,
      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,
     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 ,
     tagset GBTagset 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
 
 GBAuthor ::= VisibleString
 
 GBReference ::= SEQUENCE {
     reference VisibleString ,
     position VisibleString OPTIONAL ,
     authors SEQUENCE OF GBAuthor OPTIONAL ,
     consortium VisibleString OPTIONAL ,
     title VisibleString OPTIONAL ,
     journal VisibleString ,
     xref SET OF GBXref OPTIONAL ,
     pubmed INTEGER OPTIONAL ,
     remark VisibleString OPTIONAL
 }
 
 GBXref ::= SEQUENCE {
     dbname VisibleString ,
     id VisibleString
 }
 
 GBTagset ::= SEQUENCE {
     authority VisibleString OPTIONAL ,
     version VisibleString OPTIONAL ,
     url VisibleString OPTIONAL ,
     tags GBTags OPTIONAL
 }
 
 GBTags ::= SEQUENCE OF GBTag
 
 GBTag ::= SEQUENCE {
     name VisibleString OPTIONAL ,
     value VisibleString OPTIONAL ,
     unit VisibleString OPTIONAL
 }
 
 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
 }
 
 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
 }
 
 GBTagsetRules ::= SEQUENCE {
     authority VisibleString OPTIONAL ,
     version VisibleString OPTIONAL ,
     mandatorytags GBTagNames OPTIONAL ,
     optionaltags GBTagNames OPTIONAL ,
     uniquetags GBTagNames OPTIONAL ,
     extensible BOOLEAN OPTIONAL
 }
 
 GBTagNames ::= SEQUENCE OF VisibleString
 
 GBTagsetRuleSet ::= SEQUENCE OF GBTagsetRules
 
 END