seqfeat.asn

ncbi源码

--*** Org-ref ***********************************************
--*
--*  Reference to an organism
--*     defines only the organism.. lower levels of detail for biological
--*     molecules are provided by the Source object
--*

Org-ref ::= SEQUENCE {
    taxname VisibleString OPTIONAL ,   -- preferred formal name
    common VisibleString OPTIONAL ,    -- common name
    mod SET OF VisibleString OPTIONAL , -- unstructured modifiers
    db SET OF Dbtag OPTIONAL ,         -- ids in taxonomic or culture dbases
    syn SET OF VisibleString OPTIONAL ,  -- synonyms for taxname or common
    orgname OrgName OPTIONAL }
    

OrgName ::= SEQUENCE {
    name CHOICE {
        binomial BinomialOrgName ,         -- genus/species type name
        virus VisibleString ,              -- virus names are different
        hybrid MultiOrgName ,              -- hybrid between organisms
        namedhybrid BinomialOrgName ,      -- some hybrids have genus x species name
        partial PartialOrgName } OPTIONAL , -- when genus not known
    attrib VisibleString OPTIONAL ,        -- attribution of name
    mod SEQUENCE OF OrgMod OPTIONAL ,
    lineage VisibleString OPTIONAL ,       -- lineage with semicolon separators
    gcode INTEGER OPTIONAL ,               -- genetic code (see CdRegion)
    mgcode INTEGER OPTIONAL ,              -- mitochondrial genetic code
    div VisibleString OPTIONAL }           -- GenBank division code
    

OrgMod ::= SEQUENCE {
    subtype INTEGER {
        strain (2) ,
        substrain (3) ,
        type (4) ,
        subtype (5) ,
        variety (6) ,
        serotype (7) ,
        serogroup (8) ,
        serovar (9) ,
        cultivar (10) ,
        pathovar (11) ,
        chemovar (12) ,
        biovar (13) ,
        biotype (14) ,
        group (15) ,
        subgroup (16) ,
        isolate (17) ,
        common (18) ,
        acronym (19) ,
        dosage (20) ,		-- chromosome dosage of hybrid
        nat-host (21) ,		-- natural host of this specimen
        sub-species (22) ,
        specimen-voucher (23) ,
        authority (24) ,
        forma (25) ,
        forma-specialis (26) ,
        ecotype (27) ,
        synonym (28) ,
        anamorph (29) ,
        teleomorph (30) ,
        breed (31) ,
        gb-acronym (32) ,       -- used by taxonomy database
        gb-anamorph (33) ,      -- used by taxonomy database
        gb-synonym (34) ,       -- used by taxonomy database
        old-lineage (253) ,
        old-name (254) ,
        other (255) } ,         -- ASN5: old-name (254) will be added to next spec
    subname VisibleString ,
    attrib VisibleString OPTIONAL }  -- attribution/source of name

BinomialOrgName ::= SEQUENCE {
    genus VisibleString ,               -- required
    species VisibleString OPTIONAL ,    -- species required if subspecies used
    subspecies VisibleString OPTIONAL }

MultiOrgName ::= SEQUENCE OF OrgName   -- the first will be used to assign division

PartialOrgName ::= SEQUENCE OF TaxElement  -- when we don't know the genus

TaxElement ::= SEQUENCE {
    fixed-level INTEGER {
       other (0) ,                     -- level must be set in string
       family (1) ,
       order (2) ,
       class (3) } ,
    level VisibleString OPTIONAL ,
    name VisibleString }

END


--**********************************************************************
--
--  NCBI BioSource
--  by James Ostell, 1994
--  version 3.0
--
--**********************************************************************

NCBI-BioSource DEFINITIONS ::=
BEGIN

EXPORTS BioSource;

IMPORTS Org-ref FROM NCBI-Organism;

--********************************************************************
--
-- BioSource gives the source of the biological material
--   for sequences
--
--********************************************************************

BioSource ::= SEQUENCE {
    genome INTEGER {		 -- biological context
        unknown (0) ,
        genomic (1) ,
        chloroplast (2) ,
        chromoplast (3) ,
        kinetoplast (4) ,
        mitochondrion (5) ,
        plastid (6) ,
        macronuclear (7) ,
        extrachrom (8) ,
        plasmid (9) ,
        transposon (10) ,
        insertion-seq (11) ,
        cyanelle (12) ,
        proviral (13) ,
        virion (14) ,
        nucleomorph (15) ,
        apicoplast (16) ,
        leucoplast (17) ,
        proplastid (18) ,
        endogenous-virus (19)
      } DEFAULT unknown ,
                                       -- 4 more genome values coming
                                       -- nucleomorph (15)
                                       -- apicoplast (16)
                                       -- leucoplast (17)
                                       -- proplastid (18)
    origin INTEGER {
      unknown (0) ,
      natural (1) ,                    -- normal biological entity
      natmut (2) ,                     -- naturally occurring mutant
      mut (3) ,                        -- artificially mutagenized
      artificial (4) ,                 -- artificially engineered
      synthetic (5) ,                  -- purely synthetic
      other (255) } DEFAULT unknown , 
    org Org-ref ,
    subtype SEQUENCE OF SubSource OPTIONAL ,
    is-focus NULL OPTIONAL }   -- to distinguish biological focus

SubSource ::= SEQUENCE {
    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) ,
        transgenic (26) ,
        environmental-sample (27) ,
        isolation-source (28) ,
        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