src/objects/seqblock/seqblock.asn

--$Revision: 32084 $
--*********************************************************************
--
-- 1990 - J.Ostell
-- Version 3.0 - June 1994
--
--*********************************************************************
--*********************************************************************
--
--  EMBL specific data
--  This block of specifications was developed by Reiner Fuchs of EMBL
--  Updated by J.Ostell, 1994
--
--*********************************************************************

EMBL-General DEFINITIONS ::=
BEGIN

EXPORTS EMBL-dbname, EMBL-xref, EMBL-block;

IMPORTS Date, Object-id FROM NCBI-General;

EMBL-dbname ::= CHOICE {
    code ENUMERATED {
        embl(0),
        genbank(1),
        ddbj(2),
        geninfo(3),
        medline(4),
        swissprot(5),
        pir(6),
        pdb(7),
        epd(8),
        ecd(9),
        tfd(10),
        flybase(11),
        prosite(12),
        enzyme(13),
        mim(14),
        ecoseq(15),
        hiv(16) ,
        other (255) } ,
    name    VisibleString }

EMBL-xref ::= SEQUENCE {
    dbname EMBL-dbname,
    id SEQUENCE OF Object-id }

EMBL-block ::= SEQUENCE {
    class ENUMERATED {
        not-set(0),
        standard(1),
        unannotated(2),
        other(255) } DEFAULT standard,
    div ENUMERATED {
        fun(0),
        inv(1),
        mam(2),
        org(3),
        phg(4),
        pln(5),
        pri(6),
        pro(7),
        rod(8),
        syn(9),
        una(10),
        vrl(11),
        vrt(12),
        pat(13),
        est(14),
        sts(15),
        other (255) } OPTIONAL,
    creation-date Date,
    update-date Date,
    extra-acc SEQUENCE OF VisibleString OPTIONAL,
    keywords SEQUENCE OF VisibleString OPTIONAL,
    xref SEQUENCE OF EMBL-xref OPTIONAL }

END

--*********************************************************************
--
--  SWISSPROT specific data
--  This block of specifications was developed by Mark Cavanaugh of
--      NCBI working with Amos Bairoch of SWISSPROT
--
--*********************************************************************

SP-General DEFINITIONS ::=
BEGIN

EXPORTS SP-block;

IMPORTS Date, Dbtag FROM NCBI-General
        Seq-id FROM NCBI-Seqloc;

SP-block ::= SEQUENCE {         -- SWISSPROT specific descriptions
    class ENUMERATED {
        not-set (0) ,
        standard (1) ,      -- conforms to all SWISSPROT checks
        prelim (2) ,        -- only seq and biblio checked
        other (255) } ,
    extra-acc SET OF VisibleString OPTIONAL ,  -- old SWISSPROT ids
    imeth BOOLEAN DEFAULT FALSE ,  -- seq known to start with Met
    plasnm SET OF VisibleString OPTIONAL,  -- plasmid names carrying gene
    seqref SET OF Seq-id OPTIONAL,         -- xref to other sequences
    dbref SET OF Dbtag OPTIONAL ,          -- xref to non-sequence dbases
    keywords SET OF VisibleString OPTIONAL , -- keywords
    created Date OPTIONAL ,         -- creation date
    sequpd Date OPTIONAL ,          -- sequence update
    annotupd Date OPTIONAL }        -- annotation update

END

--*********************************************************************
--
--  PIR specific data
--  This block of specifications was developed by Jim Ostell of
--      NCBI
--
--*********************************************************************

PIR-General DEFINITIONS ::=
BEGIN

EXPORTS PIR-block;

IMPORTS Seq-id FROM NCBI-Seqloc;

PIR-block ::= SEQUENCE {          -- PIR specific descriptions
    had-punct BOOLEAN OPTIONAL ,      -- had punctuation in sequence ?
    host VisibleString OPTIONAL ,
    source VisibleString OPTIONAL ,     -- source line
    summary VisibleString OPTIONAL ,
    genetic VisibleString OPTIONAL ,
    includes VisibleString OPTIONAL ,
    placement VisibleString OPTIONAL ,
    superfamily VisibleString OPTIONAL ,
    keywords SEQUENCE OF VisibleString OPTIONAL ,
    cross-reference VisibleString OPTIONAL ,
    date VisibleString OPTIONAL ,
    seq-raw VisibleString OPTIONAL ,  -- seq with punctuation
    seqref SET OF Seq-id OPTIONAL }         -- xref to other sequences

END

--*********************************************************************
--
--  GenBank specific data
--  This block of specifications was developed by Jim Ostell of
--      NCBI
--
--*********************************************************************

GenBank-General DEFINITIONS ::=
BEGIN

EXPORTS GB-block;

IMPORTS Date FROM NCBI-General;

GB-block ::= SEQUENCE {          -- GenBank specific descriptions
    extra-accessions SEQUENCE OF VisibleString OPTIONAL ,
    source VisibleString OPTIONAL ,     -- source line
    keywords SEQUENCE OF VisibleString OPTIONAL ,
    origin VisibleString OPTIONAL,
    date VisibleString OPTIONAL ,       -- OBSOLETE old form Entry Date
    entry-date Date OPTIONAL ,          -- replaces date
    div VisibleString OPTIONAL ,        -- GenBank division
    taxonomy VisibleString OPTIONAL }   -- continuation line of organism

END

--**********************************************************************
-- PRF specific definition
--    PRF is a protein sequence database crated and maintained by
--    Protein Research Foundation, Minoo-city, Osaka, Japan.
--
--    Written by A.Ogiwara, Inst.Chem.Res. (Dr.Kanehisa's Lab),
--            Kyoto Univ., Japan
--
--**********************************************************************

PRF-General DEFINITIONS ::=
BEGIN

EXPORTS PRF-block;

PRF-block ::= SEQUENCE {
      extra-src       PRF-ExtraSrc OPTIONAL,
      keywords        SEQUENCE OF VisibleString OPTIONAL
}

PRF-ExtraSrc ::= SEQUENCE {
      host    VisibleString OPTIONAL,
      part    VisibleString OPTIONAL,
      state   VisibleString OPTIONAL,
      strain  VisibleString OPTIONAL,
      taxon   VisibleString OPTIONAL
}

END

--*********************************************************************
--
--  PDB specific data
--  This block of specifications was developed by Jim Ostell and
--      Steve Bryant of NCBI
--
--*********************************************************************

PDB-General DEFINITIONS ::=
BEGIN

EXPORTS PDB-block;

IMPORTS Date FROM NCBI-General;

PDB-block ::= SEQUENCE {          -- PDB specific descriptions
    deposition Date ,         -- deposition date  month,year
    class VisibleString ,
    compound SEQUENCE OF VisibleString ,
    source SEQUENCE OF VisibleString ,
    exp-method VisibleString OPTIONAL ,  -- present if NOT X-ray diffraction
    replace PDB-replace OPTIONAL } -- replacement history

PDB-replace ::= SEQUENCE {
    date Date ,
    ids SEQUENCE OF VisibleString }   -- entry ids replace by this one

END