all.asn

ncbi源码

    subtype INTEGER {
        chromosome (1) ,
        map (2) ,
        clone (3) ,
        subclone (4) ,
        haplotype (5) ,
        genotype (6) ,
        sex (7) ,
        cell-line (8) ,
        cell-type (9) ,
        tissue-type (10) ,
        clone-lib (11) ,
        dev-stage (12) ,
        frequency (13) ,
        germline (14) ,
        rearranged (15) ,
        lab-host (16) ,
        pop-variant (17) ,
        tissue-lib (18) ,
        plasmid-name (19) ,
        transposon-name (20) ,
        insertion-seq-name (21) ,
        plastid-name (22) ,
	country (23) ,
	segment (24) ,
	endogenous-virus-name (25) ,
        other (255) } ,
    name VisibleString ,
    attrib VisibleString OPTIONAL }    -- attribution/source of this name
        
END

--**********************************************************************
--
--  NCBI Protein
--  by James Ostell, 1990
--  version 0.8
--
--**********************************************************************

NCBI-Protein DEFINITIONS ::=
BEGIN

EXPORTS Prot-ref;

IMPORTS Dbtag FROM NCBI-General;

--*** Prot-ref ***********************************************
--*
--*  Reference to a protein name
--*

Prot-ref ::= SEQUENCE {
    name SET OF VisibleString OPTIONAL ,      -- protein name
    desc VisibleString OPTIONAL ,      -- description (instead of name)
    ec SET OF VisibleString OPTIONAL , -- E.C. number(s)
    activity SET OF VisibleString OPTIONAL ,  -- activities
    db SET OF Dbtag OPTIONAL ,         -- ids in other dbases
    processed ENUMERATED {             -- processing status
       not-set (0) ,
       preprotein (1) ,
       mature (2) ,
	   signal-peptide (3) ,
	   transit-peptide (4) } DEFAULT not-set }



END 
--********************************************************************
--
--  Transcription Initiation Site Feature Data Block
--  James Ostell, 1991
--  Philip Bucher, David Ghosh
--  version 1.1
--
--  
--
--********************************************************************

NCBI-TxInit DEFINITIONS ::=
BEGIN

EXPORTS Txinit;

IMPORTS Gene-ref FROM NCBI-Gene
        Prot-ref FROM NCBI-Protein
        Org-ref FROM NCBI-Organism;

Txinit ::= SEQUENCE {
    name VisibleString ,    -- descriptive name of initiation site
    syn SEQUENCE OF VisibleString OPTIONAL ,   -- synonyms
    gene SEQUENCE OF Gene-ref OPTIONAL ,  -- gene(s) transcribed
    protein SEQUENCE OF Prot-ref OPTIONAL ,   -- protein(s) produced
    rna SEQUENCE OF VisibleString OPTIONAL ,  -- rna(s) produced
    expression VisibleString OPTIONAL ,  -- tissue/time of expression
    txsystem ENUMERATED {       -- transcription apparatus used at this site
        unknown (0) ,
        pol1 (1) ,      -- eukaryotic Pol I
        pol2 (2) ,      -- eukaryotic Pol II
        pol3 (3) ,      -- eukaryotic Pol III
        bacterial (4) ,
        viral (5) ,
        rna (6) ,       -- RNA replicase
        organelle (7) ,
        other (255) } ,
    txdescr VisibleString OPTIONAL ,   -- modifiers on txsystem
    txorg Org-ref OPTIONAL ,  -- organism supplying transcription apparatus
    mapping-precise BOOLEAN DEFAULT FALSE ,  -- mapping precise or approx
    location-accurate BOOLEAN DEFAULT FALSE , -- does Seq-loc reflect mapping
    inittype ENUMERATED {
        unknown (0) ,
        single (1) ,
        multiple (2) ,
        region (3) } OPTIONAL ,
    evidence SET OF Tx-evidence OPTIONAL }

Tx-evidence ::= SEQUENCE {
    exp-code ENUMERATED {
        unknown (0) ,    
        rna-seq (1) ,   -- direct RNA sequencing
        rna-size (2) ,  -- RNA length measurement
        np-map (3) ,    -- nuclease protection mapping with homologous sequence ladder
        np-size (4) ,   -- nuclease protected fragment length measurement
        pe-seq (5) ,    -- dideoxy RNA sequencing 
        cDNA-seq (6) ,  -- full-length cDNA sequencing
        pe-map (7) ,    -- primer extension mapping with homologous sequence ladder    
        pe-size (8) ,   -- primer extension product length measurement
        pseudo-seq (9) , -- full-length processed pseudogene sequencing
        rev-pe-map (10) ,   -- see NOTE (1) below
        other (255) } ,
    expression-system ENUMERATED {
        unknown (0) ,
        physiological (1) ,
        in-vitro (2) ,
        oocyte (3) ,
        transfection (4) ,
        transgenic (5) ,
        other (255) } DEFAULT physiological ,
    low-prec-data BOOLEAN DEFAULT FALSE ,
    from-homolog BOOLEAN DEFAULT FALSE }     -- experiment actually done on
                                             --  close homolog

    -- NOTE (1) length measurement of a reverse direction primer-extension
    --          product (blocked  by  RNA  5'end)  by  comparison with
    --          homologous sequence ladder (J. Mol. Biol. 199, 587)

    
END

--$Revision: 1000.1 $
--**********************************************************************
--
--  NCBI Sequence Analysis Results (other than alignments)
--  by James Ostell, 1990
--
--**********************************************************************

NCBI-Seqres DEFINITIONS ::=
BEGIN

EXPORTS Seq-graph;

IMPORTS Seq-loc FROM NCBI-Seqloc;

--*** Sequence Graph ********************************
--*
--*   for values mapped by residue or range to sequence
--*

Seq-graph ::= SEQUENCE {
    title VisibleString OPTIONAL ,
    comment VisibleString OPTIONAL ,
    loc Seq-loc ,                       -- region this applies to
    title-x VisibleString OPTIONAL ,    -- title for x-axis
    title-y VisibleString OPTIONAL ,
    comp INTEGER OPTIONAL ,             -- compression (residues/value)
    a REAL OPTIONAL ,                   -- for scaling values
    b REAL OPTIONAL ,                   -- display = (a x value) + b
    numval INTEGER ,                    -- number of values in graph
    graph CHOICE {
        real Real-graph ,
        int Int-graph ,
        byte Byte-graph } }

Real-graph ::= SEQUENCE {
    max REAL ,                          -- top of graph
    min REAL ,                          -- bottom of graph
    axis REAL ,                         -- value to draw axis on
    values SEQUENCE OF REAL }

Int-graph ::= SEQUENCE {
    max INTEGER ,
    min INTEGER ,
    axis INTEGER ,
    values SEQUENCE OF INTEGER } 

Byte-graph ::= SEQUENCE {              -- integer from 0-255
    max INTEGER ,
    min INTEGER ,
    axis INTEGER ,
    values OCTET STRING }

END

--$Revision: 1000.1 $
--**********************************************************************
--
--  NCBI Sequence Collections
--  by James Ostell, 1990
--
--  Version 3.0 - 1994
--
--**********************************************************************

NCBI-Seqset DEFINITIONS ::=
BEGIN

EXPORTS Bioseq-set, Seq-entry;

IMPORTS Bioseq, Seq-annot, Seq-descr FROM NCBI-Sequence
        Object-id, Dbtag, Date FROM NCBI-General;

--*** Sequence Collections ********************************
--*

Bioseq-set ::= SEQUENCE {      -- just a collection
    id Object-id OPTIONAL ,
    coll Dbtag OPTIONAL ,          -- to identify a collection
    level INTEGER OPTIONAL ,       -- nesting level
    class ENUMERATED {
        not-set (0) ,
        nuc-prot (1) ,              -- nuc acid and coded proteins
        segset (2) ,                -- segmented sequence + parts
        conset (3) ,                -- constructed sequence + parts
        parts (4) ,                 -- parts for 2 or 3
        gibb (5) ,                  -- geninfo backbone
        gi (6) ,                    -- geninfo
        genbank (7) ,               -- converted genbank
        pir (8) ,                   -- converted pir
        pub-set (9) ,               -- all the seqs from a single publication
        equiv (10) ,                -- a set of equivalent maps or seqs
        swissprot (11) ,            -- converted SWISSPROT
        pdb-entry (12) ,            -- a complete PDB entry
        mut-set (13) ,              -- set of mutations
        pop-set (14) ,              -- population study
        phy-set (15) ,              -- phylogenetic study
	eco-set (16) ,              -- ecological sample study
        gen-prod-set (17) ,         -- genomic products, chrom+mRNa+protein  
        other (255) } DEFAULT not-set ,
    release VisibleString OPTIONAL ,
    date Date OPTIONAL ,
    descr Seq-descr OPTIONAL ,
    seq-set SEQUENCE OF Seq-entry ,
    annot SET OF Seq-annot OPTIONAL }

Seq-entry ::= CHOICE {
        seq Bioseq ,
        set Bioseq-set } 

END

--$Revision: 1000.1 $
--**********************************************************************
--
--  NCBI Sequence elements
--  by James Ostell, 1990
--  Version 3.0 - June 1994
--
--**********************************************************************

NCBI-Sequence DEFINITIONS ::=
BEGIN

EXPORTS Bioseq, Seq-annot, Pubdesc, Seq-descr, Seqdesc, Numbering, Heterogen,
        Seq-hist, GIBB-mol;

IMPORTS Date, Int-fuzz, Dbtag, Object-id, User-object FROM NCBI-General
        Seq-align FROM NCBI-Seqalign
        Seq-feat FROM NCBI-Seqfeat
        Seq-graph FROM NCBI-Seqres
        Pub-equiv FROM NCBI-Pub
        Org-ref FROM NCBI-Organism
        BioSource FROM NCBI-BioSource
        Seq-id, Seq-loc FROM NCBI-Seqloc
        GB-block FROM GenBank-General
        PIR-block FROM PIR-General
        EMBL-block FROM EMBL-General
        SP-block FROM SP-General
        PRF-block FROM PRF-General
        PDB-block FROM PDB-General;

--*** Sequence ********************************
--*

Bioseq ::= SEQUENCE {
    id SET OF Seq-id ,            -- equivalent identifiers
    descr Seq-descr OPTIONAL , -- descriptors
    inst Seq-inst ,            -- the sequence data
    annot SET OF Seq-annot OPTIONAL }

--*** Descriptors *****************************
--*

Seq-descr ::= SET OF Seqdesc

Seqdesc ::= CHOICE {
    mol-type GIBB-mol ,          -- type of molecule
    modif SET OF GIBB-mod ,             -- modifiers
    method GIBB-method ,         -- sequencing method
    name VisibleString ,         -- a name for this sequence
    title VisibleString ,        -- a title for this sequence
    org Org-ref ,                -- if all from one organism
    comment VisibleString ,      -- a more extensive comment
    num Numbering ,              -- a numbering system
    maploc Dbtag ,               -- map location of this sequence
    pir PIR-block ,              -- PIR specific info
    genbank GB-block ,           -- GenBank specific info
    pub Pubdesc ,                -- a reference to the publication
    region VisibleString ,       -- overall region (globin locus)
    user User-object ,           -- user defined object
    sp SP-block ,                -- SWISSPROT specific info
    dbxref Dbtag ,               -- xref to other databases
    embl EMBL-block ,            -- EMBL specific information
    create-date Date ,           -- date entry first created/released
    update-date Date ,           -- date of last update
    prf PRF-block ,              -- PRF specific information
    pdb PDB-block ,              -- PDB specific information
    het Heterogen ,              -- cofactor, etc associated but not bound
    source BioSource ,           -- source of materials, includes Org-ref
    molinfo MolInfo }            -- info on the molecule and techniques

--******* NOTE:
--*       mol-type, modif, method, and org are consolidated and expanded
--*       in Org-ref, BioSource, and MolInfo in this specification. They
--*       will be removed in later specifications. Do not use them in the
--*       the future. Instead expect the new structures.
--*
--***************************

--********************************************************************
--
-- MolInfo gives information on the
-- classification of the type and quality of the sequence
--
-- WARNING: this will replace GIBB-mol, GIBB-mod, GIBB-method
--
--********************************************************************

MolInfo ::= SEQUENCE {
    biomol INTEGER {
        unknown (0) ,
        genomic (1) ,
        pre-RNA (2) ,              -- precursor RNA of any sort really 
        mRNA (3) ,
        rRNA (4) ,
        tRNA (5) ,
        snRNA (6) ,
        scRNA (7) ,
        peptide (8) ,
        other-genetic (9) ,      -- other genetic material
        genomic-mRNA (10) ,      -- reported a mix of genomic and cdna sequence
	cRNA (11) ,              -- viral RNA genome copy intermediate
        other (255) } DEFAULT unknown ,
    tech INTEGER {
        unknown (0) ,
        standard (1) ,          -- standard sequencing
        est (2) ,               -- Expressed Sequence Tag
        sts (3) ,               -- Sequence Tagged Site
        survey (4) ,            -- one-pass genomic sequence
        genemap (5) ,           -- from genetic mapping techniques
        physmap (6) ,           -- from physical mapping techniques
        derived (7) ,           -- derived from other data, not a primary entity
        concept-trans (8) ,     -- conceptual translation
        seq-pept (9) ,          -- peptide was sequenced
        both (10) ,             -- concept transl. w/ partial pept. seq.
        seq-pept-overlap (11) , -- sequenced peptide, ordered by overlap