geno.asn

ncbi源码

--
-- ===========================================================================
-- PRODUCTION $Log: geno.asn,v $
-- PRODUCTION Revision 1000.0  2003/10/29 21:10:30  gouriano
-- PRODUCTION PRODUCTION: IMPORTED [ORIGINAL] Dev-tree R1.3
-- PRODUCTION
-- ===========================================================================
--

-- $Id: geno.asn,v 1000.0 2003/10/29 21:10:30 gouriano Exp $
-- $Log: geno.asn,v $
-- Revision 1000.0  2003/10/29 21:10:30  gouriano
-- PRODUCTION: IMPORTED [ORIGINAL] Dev-tree R1.3
--
-- Revision 1.3  2002/12/03 15:28:32  kholodov
-- Backup
--
-- Revision 1.2  2002/08/16 16:48:16  kholodov
-- Fixed syntax errors, made enums 1 based
--
-- Revision 1.1  2002/08/16 16:31:23  kholodov
-- First commit
--


GENO DEFINITIONS ::=
BEGIN

EXPORTS GENO-PopSum, GENO-Ped, GENO-Ind, GENO-SnpSum, 
	    GENO-IndBySnp, GENO-IndBySnpList, GENO-IndGeno,  
        GENO-SnpByIndList, GENO-SnpByInd, GENO-SnpGeno;

GENO-PopSum ::= SEQUENCE {
	pop-id INTEGER,						-- internal pop_id	Subpop table
	pop-class INTEGER,					-- population geographic class
	handle VisibleString,				-- institution identifier
	loc-pop-id VisibleString,			-- external population identifier
	ped-list SET OF GENO-Ped OPTIONAL, 	-- set of pedigrees in this population 
	ind-list SET OF GENO-Ind OPTIONAL, 	-- set of individuals in this population
	snp-list SET OF GENO-SnpSum 	 	-- summary of the genotype information for this population 	
}

GENO-Ped ::= SEQUENCE {
	ped-id INTEGER OPTIONAL,			-- pedigree number all peds within population
	ind-id INTEGER ,					-- individual id 
	ma INTEGER ,			        	-- mothers id
	pa INTEGER ,			        	-- fathers id	
	ped-curator VisibleString,			-- pedigree  curator
	curator-ped-id VisibleString,		-- curator ped id
	curator-ped-ind-id VisibleString,   -- curator pedigree_individual id	
	sex INTEGER 						-- individuals sex
}

GENO-Ind ::= SEQUENCE {
	pop-id INTEGER,						-- internal pop_id	Subpop and SubInd table
	pop-class VisibleString,			        -- population geographic class
	loc-pop-id VisibleString,           -- external pop_id  Population table
	handle VisibleString,			    -- institution identifier
	ped-id INTEGER OPTIONAL,		    -- pedigree number
	sub-ind-id INTEGER ,			        -- individual id
	loc-ind-id VisibleString,		    -- external individual id	
	source-name VisibleString OPTIONAL,	-- source (i.e., coriell, ceph) IndividualSourceCode.name
	source-id VisibleString OPTIONAL		    -- source id IndividualBySource.source_ind_id
}

GENO-SnpSum ::= SEQUENCE {
	rs INTEGER,							-- referrence snp SubInd table
	ss INTEGER,							-- submitted snp
	chrom INTEGER,						-- chromosome
	position  INTEGER,					-- chromosome position
	data-type ENUMERATED{
		pop (1),						-- constrain geno-freq by a specific population	
		all (2)							-- geno-freq over all populations.  
			},
    	geno-freq SET OF REAL,			-- genotypes and frequencies for this SNP limited to population
    	allele-freq SET OF REAL,		-- allele Frequencies for this SNP limited to population
    	est-het REAL,                  		-- estimated heterozygousity
    	obs-het REAL, 						-- observed heterozygousity
	samplesize INTEGER,		 					-- chromosomes genotyped for this snp 
	hw-prob REAL OPTIONAL,				-- Hardy Weinberg probabliity	Calculated
	hw-chi2 REAL OPTIONAL,				-- Hardy Weinberg chi square    Calculated
	hw-df   INTEGER						-- Hardy Weinberg degrees of freedom Calculated	 
	
}


GENO-IndBySnpList ::= SEQUENCE { 	     -- makes the Ind By SNP report
	snp-list SET OF GENO-IndBySnp
}

GENO-IndBySnp ::= SEQUENCE {
	snp-header GENO-SnpSum,				-- header info for Individuals by SNP report all populations
	individuals SET OF GENO-IndGeno		-- genotypes by individual
}


GENO-IndGeno ::= SEQUENCE {
	pop-class INTEGER,					-- population geographic class
	handle VisibleString,				-- institution identifie
	pop-id INTEGER,						-- internal pop_id
	ped-id INTEGER OPTIONAL,			-- internal pedigree number
	ind-id INTEGER ,					-- individual id
	loc-pop-id VisibleString,         	-- external pop_id -----Population table
	loc-ind-id VisibleString,			-- external individual id	
	sample-id VisibleString OPTIONAL,	-- source (i.e., coriell, ceph)
	sample-src-id INTEGER OPTIONAL,		-- source id
	allele1 VisibleString OPTIONAL,		-- first allele in genotype
	allele2 VisibleString OPTIONAL,		-- second allele in genotype
	flag INTEGER{
		none (1),						-- No known errors	
		incompatible (2),				-- genotype incompatible
		inconsistent(3),				-- genotype inconsistent
		orient (4)		 				-- Orientation of allele not specified
	}		
}

GENO-SnpByIndList ::= SEQUENCE {
	genotypes  SET OF GENO-SnpByInd     --Snps by Ind report
}

GENO-SnpByInd ::= SEQUENCE {
	individual GENO-Ind,		       --population individual info
	genotypes  SET OF GENO-SnpGeno     --genotypes
}

GENO-SnpGeno ::= SEQUENCE {
	rs INTEGER,				-- referrence snp
	ss INTEGER,				-- submitted snp
	chrom VisibleString OPTIONAL,			-- chromosome
	position  INTEGER OPTIONAL,		-- chromosome position
	allele1 VisibleString OPTIONAL,		-- first allele in genotype
	allele2 VisibleString OPTIONAL,		-- second allele in genotype
	flag INTEGER {
		none (1),			-- No known errors	
		inc (2),			-- genotype inconsitency
		orient (3),			-- orientation flag
		incompat (4)			-- genotype incompatible with parent				
	} DEFAULT 1		

}		
END