all.asn

ncbi源码

        in-press (2) ,                      -- accepted, not published
        other (255)  } OPTIONAL ,
    part-supi VisibleString OPTIONAL ,      -- part/sup on issue
    retract CitRetract OPTIONAL ,           -- retraction info
    pubstatus PubStatus OPTIONAL ,          -- current status of this publication
    history PubStatusDateSet OPTIONAL }     -- dates for this record

CitRetract ::= SEQUENCE {
    type ENUMERATED {                    -- retraction of an entry
        retracted (1) ,               -- this citation retracted
        notice (2) ,                  -- this citation is a retraction notice
        in-error (3) ,                -- an erratum was published about this
        erratum (4) } ,               -- this is a published erratum
    exp VisibleString OPTIONAL }      -- citation and/or explanation

Meeting ::= SEQUENCE {
    number VisibleString ,
    date Date ,
    place Affil OPTIONAL }

            
END


--$Revision: 1000.1 $
--**********************************************************************
--
--  MEDLINE data definitions
--  James Ostell, 1990
--
--  enhanced in 1996 to support PubMed records as well by simply adding
--    the PubMedId and making MedlineId optional
--
--**********************************************************************

NCBI-Medline DEFINITIONS ::=
BEGIN

EXPORTS Medline-entry, Medline-si;

IMPORTS Cit-art, PubMedId FROM NCBI-Biblio
        Date FROM NCBI-General;

                                -- a MEDLINE or PubMed entry
Medline-entry ::= SEQUENCE {
    uid INTEGER OPTIONAL ,      -- MEDLINE UID, sometimes not yet available if from PubMed
    em Date ,                   -- Entry Month
    cit Cit-art ,               -- article citation
    abstract VisibleString OPTIONAL ,
    mesh SET OF Medline-mesh OPTIONAL ,
    substance SET OF Medline-rn OPTIONAL ,
    xref SET OF Medline-si OPTIONAL ,
    idnum SET OF VisibleString OPTIONAL ,  -- ID Number (grants, contracts)
    gene SET OF VisibleString OPTIONAL ,
    pmid PubMedId OPTIONAL ,               -- MEDLINE records may include the PubMedId
    pub-type SET OF VisibleString OPTIONAL, -- may show publication types (review, etc)
    mlfield SET OF Medline-field OPTIONAL ,  -- additional Medline field types
    status INTEGER {
	publisher (1) ,      -- record as supplied by publisher
        premedline (2) ,     -- premedline record
        medline (3) } DEFAULT medline }  -- regular medline record

Medline-mesh ::= SEQUENCE {
    mp BOOLEAN DEFAULT FALSE ,       -- TRUE if main point (*)
    term VisibleString ,                   -- the MeSH term
    qual SET OF Medline-qual OPTIONAL }    -- qualifiers

Medline-qual ::= SEQUENCE {
    mp BOOLEAN DEFAULT FALSE ,       -- TRUE if main point
    subh VisibleString }             -- the subheading

Medline-rn ::= SEQUENCE {       -- medline substance records
    type ENUMERATED {           -- type of record
        nameonly (0) ,
        cas (1) ,               -- CAS number
        ec (2) } ,              -- EC number
    cit VisibleString OPTIONAL ,  -- CAS or EC number if present
    name VisibleString }          -- name (always present)

Medline-si ::= SEQUENCE {       -- medline cross reference records
    type ENUMERATED {           -- type of xref
        ddbj (1) ,              -- DNA Data Bank of Japan
        carbbank (2) ,          -- Carbohydrate Structure Database
        embl (3) ,              -- EMBL Data Library
        hdb (4) ,               -- Hybridoma Data Bank
        genbank (5) ,           -- GenBank
        hgml (6) ,              -- Human Gene Map Library
        mim (7) ,               -- Mendelian Inheritance in Man
        msd (8) ,               -- Microbial Strains Database
        pdb (9) ,               -- Protein Data Bank (Brookhaven)
        pir (10) ,              -- Protein Identification Resource
        prfseqdb (11) ,         -- Protein Research Foundation (Japan)
        psd (12) ,              -- Protein Sequence Database (Japan)
        swissprot (13) ,        -- SwissProt
        gdb (14) } ,            -- Genome Data Base
    cit VisibleString OPTIONAL }    -- the citation/accession number

Medline-field ::= SEQUENCE {
    type INTEGER {              -- Keyed type
	other (0) ,             -- look in line code
	comment (1) ,           -- comment line
        erratum (2) } ,         -- retracted, corrected, etc
    str VisibleString ,         -- the text
    ids SEQUENCE OF DocRef OPTIONAL }  -- pointers relevant to this text

DocRef ::= SEQUENCE {           -- reference to a document
    type INTEGER {
        medline (1) ,
        pubmed (2) ,
        ncbigi (3) } ,
    uid INTEGER }

END

--$Revision: 1000.1 $
--**********************************************************************
--
--  MEDLARS data definitions
--  Grigoriy Starchenko, 1997
--
--**********************************************************************

NCBI-Medlars DEFINITIONS ::=
BEGIN

EXPORTS Medlars-entry, Medlars-record;

IMPORTS PubMedId FROM NCBI-Biblio;

Medlars-entry ::= SEQUENCE {     -- a MEDLARS entry
    pmid PubMedId,               -- All entries in PubMed must have it
    muid INTEGER OPTIONAL,       -- Medline(OCCS) id
    recs SET OF Medlars-record   -- List of Medlars records
}

Medlars-record ::= SEQUENCE {
    code INTEGER,                -- Unit record field type integer form
    abbr VisibleString OPTIONAL, -- Unit record field type abbreviation form
    data VisibleString           -- Unit record data
}

END
--$Revision: 1000.1 $
--********************************************************************
--
--  Publication common set
--  James Ostell, 1990
--
--  This is the base class definitions for Publications of all sorts
--
--  support for PubMedId added in 1996
--********************************************************************

NCBI-Pub DEFINITIONS ::=
BEGIN

EXPORTS Pub, Pub-set, Pub-equiv;

IMPORTS Medline-entry FROM NCBI-Medline
        Cit-art, Cit-jour, Cit-book, Cit-proc, Cit-pat, Id-pat, Cit-gen,
        Cit-let, Cit-sub, PubMedId FROM NCBI-Biblio;

Pub ::= CHOICE {
    gen Cit-gen ,        -- general or generic unparsed
    sub Cit-sub ,        -- submission
    medline Medline-entry ,
    muid INTEGER ,       -- medline uid
    article Cit-art ,
    journal Cit-jour ,
    book Cit-book ,
    proc Cit-proc ,      -- proceedings of a meeting
    patent Cit-pat ,
    pat-id Id-pat ,      -- identify a patent
    man Cit-let ,        -- manuscript, thesis, or letter
    equiv Pub-equiv,     -- to cite a variety of ways
	pmid PubMedId }      -- PubMedId

Pub-equiv ::= SET OF Pub   -- equivalent identifiers for same citation

Pub-set ::= CHOICE {
    pub SET OF Pub ,
    medline SET OF Medline-entry ,
    article SET OF Cit-art ,
    journal SET OF Cit-jour ,
    book SET OF Cit-book ,
    proc SET OF Cit-proc ,      -- proceedings of a meeting
    patent SET OF Cit-pat }

END

--$Revision: 1000.1 $
--**********************************************************************
--
--  PUBMED data definitions
--
--**********************************************************************

NCBI-PubMed DEFINITIONS ::=
BEGIN

EXPORTS Pubmed-entry, Pubmed-url;

IMPORTS PubMedId FROM NCBI-Biblio
        Medline-entry FROM NCBI-Medline;

Pubmed-entry ::= SEQUENCE {        -- a PubMed entry
    -- PUBMED records must include the PubMedId
    pmid PubMedId,

    -- Medline entry information
    medent Medline-entry OPTIONAL,

    -- Publisher name
    publisher VisibleString OPTIONAL,

    -- List of URL to publisher cite
    urls SET OF Pubmed-url OPTIONAL,

    -- Publisher's article identifier
    pubid VisibleString OPTIONAL
}

Pubmed-url ::= SEQUENCE {
    location VisibleString OPTIONAL, -- Location code
    url VisibleString                -- Selected URL for location
}

END
--$Revision: 1000.1 $
--**********************************************************************
--
--  NCBI Sequence location and identifier elements
--  by James Ostell, 1990
--
--  Version 3.0 - 1994
--
--**********************************************************************

NCBI-Seqloc DEFINITIONS ::=
BEGIN

EXPORTS Seq-id, Seq-loc, Seq-interval, Packed-seqint, Seq-point, Packed-seqpnt,
        Na-strand, Giimport-id;

IMPORTS Object-id, Int-fuzz, Dbtag, Date FROM NCBI-General
        Id-pat FROM NCBI-Biblio
        Feat-id FROM NCBI-Seqfeat;

--*** Sequence identifiers ********************************
--*

Seq-id ::= CHOICE {
    local Object-id ,      -- local use
    gibbsq INTEGER ,         -- Geninfo backbone seqid
    gibbmt INTEGER ,         -- Geninfo backbone moltype
    giim Giimport-id ,       -- Geninfo import id
    genbank Textseq-id ,
    embl Textseq-id ,
    pir Textseq-id ,
    swissprot Textseq-id ,
    patent Patent-seq-id ,
    other Textseq-id ,       -- catch all
    general Dbtag ,          -- for other databases
    gi INTEGER ,             -- GenInfo Integrated Database
    ddbj Textseq-id ,        -- DDBJ
    prf Textseq-id ,         -- PRF SEQDB
    pdb PDB-seq-id }         -- PDB sequence

Patent-seq-id ::= SEQUENCE {
    seqid INTEGER ,         -- number of sequence in patent
    cit Id-pat }           -- patent citation

Textseq-id ::= SEQUENCE {
    name VisibleString OPTIONAL ,
    accession VisibleString OPTIONAL ,
    release VisibleString OPTIONAL ,
    version INTEGER OPTIONAL }

Giimport-id ::= SEQUENCE {
    id INTEGER ,               -- the id to use here
    db VisibleString OPTIONAL ,  -- dbase used in
    release VisibleString OPTIONAL }   -- the release

PDB-seq-id ::= SEQUENCE {
    mol PDB-mol-id ,          -- the molecule name
    chain INTEGER DEFAULT 32 ,-- a single ASCII character, chain id
    rel Date OPTIONAL }   -- release date, month and year

PDB-mol-id ::= VisibleString  -- name of mol, 4 chars
    
--*** Sequence locations **********************************
--*

Seq-loc ::= CHOICE {
    null NULL ,           -- not placed
    empty Seq-id ,        -- to NULL one Seq-id in a collection
    whole Seq-id ,        -- whole sequence
    int Seq-interval ,    -- from to
    packed-int Packed-seqint ,
    pnt Seq-point ,
    packed-pnt Packed-seqpnt ,
    mix Seq-loc-mix ,
    equiv Seq-loc-equiv ,  -- equivalent sets of locations
    bond Seq-bond ,
    feat Feat-id }         -- indirect, through a Seq-feat
    

Seq-interval ::= SEQUENCE {
    from INTEGER ,
    to INTEGER ,
    strand Na-strand OPTIONAL ,
    id Seq-id ,    -- WARNING: this used to be optional
    fuzz-from Int-fuzz OPTIONAL ,
    fuzz-to Int-fuzz OPTIONAL }

Packed-seqint ::= SEQUENCE OF Seq-interval

Seq-point ::= SEQUENCE {
    point INTEGER ,
    strand Na-strand OPTIONAL ,
    id Seq-id ,     -- WARNING: this used to be optional
    fuzz Int-fuzz OPTIONAL }

Packed-seqpnt ::= SEQUENCE {
    strand Na-strand OPTIONAL ,
    id Seq-id ,
    fuzz Int-fuzz OPTIONAL ,
    points SEQUENCE OF INTEGER }

Na-strand ::= ENUMERATED {          -- strand of nucleid acid
    unknown (0) ,
    plus (1) ,
    minus (2) ,               
    both (3) ,                -- in forward orientation
    both-rev (4) ,            -- in reverse orientation
    other (255) }

Seq-bond ::= SEQUENCE {         -- bond between residues
    a Seq-point ,           -- connection to a least one residue
    b Seq-point OPTIONAL }  -- other end may not be available

Seq-loc-mix ::= SEQUENCE OF Seq-loc   -- this will hold anything

Seq-loc-equiv ::= SET OF Seq-loc      -- for a set of equivalent locations

END
    

--$Revision: 1000.1 $
--**********************************************************************
--
--  NCBI Sequence Alignment elements
--  by James Ostell, 1990
--
--**********************************************************************

NCBI-Seqalign DEFINITIONS ::=
BEGIN

EXPORTS Seq-align, Score, Score-set, Seq-align-set;

IMPORTS Seq-id, Seq-loc , Na-strand FROM NCBI-Seqloc
        Object-id FROM NCBI-General;

--*** Sequence Alignment ********************************
--*

Seq-align-set ::= SET OF Seq-align

Seq-align ::= SEQUENCE {
    type ENUMERATED {
        not-set (0) ,
        global (1) ,
        diags (2) ,		-- unbroken, but not ordered, diagonals
        partial (3) ,           -- mapping pieces together
	disc (4) ,              -- discontinuous alignment
        other (255) } ,