docsum.asn

ncbi源码

	prot-gi INTEGER,                    -- GI of the protein with variation (SNP3D.master_gi)
    	prot-loc INTEGER,                   -- position of the residue for the protein GI (SNP3D.aa_position)
    	prot-res VisibleString,             -- residue specified for protein at prot-loc location (SNP3D.contig_res)
    	rs-res VisibleString,               -- alternative residue specified by variation sequence (SNP3D.var_res)
	struct-gi INTEGER,                  -- GI of the structure neighbor (SNP3D.neighbor_gi)
	struct-loc INTEGER,                 -- position of the residue for the structure GI (SNP3D.neighbor_pos)
	struct-res VisibleString            -- residue specified for protein at struct-loc location (SNP3D.neighbor_res)
}
	
   
NSE-rsUnigene ::= SEQUENCE {
	cluster-id INTEGER,		   -- unigene_cid from UnigeneSnp
	gi-set SET OF INTEGER		   -- list of gi's per unigene cluster
} 



NSE-ss-popinfo ::= SEQUENCE {
 	type VisibleString, 			-- batch type (HET, ALLE)		SubPop.type
	handle VisibleString,               -- submitter抯 handle
	batch-id INTEGER,
	pop-name VisibleString,			-- submitter population ID		SubPop.loc_pop_id
	pop-id INTEGER,				-- dbSNP population ID			SubPop.pop_id
	pop-class VisibleString OPTIONAL,  --dbSNP population class
	samplesize INTEGER OPTIONAL,		-- sample size				SubPop.samplesize                    
 	sub-het REAL OPTIONAL,			-- submitted heterozygosity		SubPop.sub_heterozygosity
	est-het REAL OPTIONAL,			-- estimated heterogygosity		SubPop.est_heterozygosity
 	est-het-se-sq REAL OPTIONAL,		-- est het std. error
	sub-het-se-sq REAL OPTIONAL,		-- submitted het std. error
	allele-info SET OF NSE-alleleinfo OPTIONAL  -- allele frequency data, genotype frequency data 
                                                     -- available in Genotype Report
}



NSE-alleleinfo ::= SEQUENCE {
	snp-allele  VisibleString OPTIONAL,	-- allele if ACTG			                       
	other-allele VisibleString OPTIONAL,	-- all other cases	
 	freq REAL OPTIONAL,			-- frequency as percentage		
	count REAL OPTIONAL			-- frequency as count
}


NSE-Date ::= CHOICE {
    str VisibleString ,        			-- for those unparsed dates
    std NSE-Date-std }             		-- use this if you can

NSE-Date-std ::= SEQUENCE {        		-- NOTE: this is NOT a unix tm struct
    year INTEGER ,             			-- full year (including 1900)
    month INTEGER OPTIONAL ,   			-- month (1-12)
    day INTEGER OPTIONAL ,     			-- day of month (1-31)
    season VisibleString OPTIONAL }  		-- for "spring", "may-june", etc

END

-- $Log: docsum.asn,v $
-- Revision 1000.1  2004/06/01 19:31:58  gouriano
-- PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.42
--
-- Revision 1.42  2004/05/27 18:15:35  kholodov
-- Modified: allele info moved to popinfo structure
--
-- Revision 1.41  2004/05/24 18:38:34  kholodov
-- Changed val-hapmap to validated-by-hapmap
--
-- Revision 1.40  2004/05/24 14:07:44  kholodov
-- Added: val-hapmap field
--
-- Revision 1.39  2003/10/15 14:24:33  kholodov
-- Modified: sequences now optional for NSE-rs
--
-- Revision 1.38  2003/09/22 20:14:58  kholodov
-- Added: copyright notice
--
-- Revision 1.37  2003/07/09 19:36:33  kholodov
-- Syntax error fixed
--
-- Revision 1.36  2003/07/09 18:10:39  sherry
-- *** empty log message ***
--
-- Revision 1.35  2002/12/03 20:18:51  kholodov
-- Modified: validation status is represented by 4 boolean values
--
-- Revision 1.34  2002/09/03 20:09:59  kholodov
-- Added moltype for rs and ss, create-build, update-build for rs
--
-- Revision 1.33  2002/06/12 14:02:54  kholodov
-- sts-info and unigene-info added
--
-- Revision 1.32  2002/04/12 13:53:14  kholodov
-- Fixed wrong type name NSE-date to NSE-Date
--
-- Revision 1.31  2002/04/11 20:40:41  sherry
-- added NSE-ss linkout-url, validation status; NSE-rs create-date, update-date; NSE-popinfo pop-class, and new section NSE-rsStruct with 3D structure data
--
-- Revision 1.30  2002/03/15 16:39:58  sherry
-- added subsnp method-class and dbSNP-build-id
--
-- Revision 1.29  2002/01/22 16:27:16  kholodov
-- Fixed syntax bug
--
-- Revision 1.27  2002/01/18 19:20:29  sherry
-- added dense option to hit-quality for SNPs mapped to dense regions like HLA
--
-- Revision 1.26  2001/11/28 21:41:42  sherry
-- correction to golden path (UCSC) contig hits
--
-- Revision 1.25  2001/11/28 20:58:42  sherry
-- added UCSC mapping coordinates, and added amino-acid position to function-set
--
-- Revision 1.24  2001/08/21 14:52:56  sherry
-- added subsnp-class (8) = mnp for multiple nucleotide polymorphisms with alleles of common length > 1 bp
--
-- Revision 1.23  2001/08/20 20:27:57  sherry
-- added source-db (5) for RefSeq-genomic and ncbi-build-id for build number of genome mapping data
--
-- Revision 1.22  2001/08/20 20:19:45  sherry
-- source-db (2) defined for GenBank STS division
--
-- Revision 1.21  2001/08/03 14:29:11  sherry
-- added snp-class 'mnp' for variants with allele length > 1
--
-- Revision 1.20  2001/07/11 13:08:05  sherry
-- typo correction and clarification of fxn-class names to fxn-class-contig and fxn-class-mrna
--
-- Revision 1.19  2001/06/08 14:18:59  sherry
--  added exception value (9) to fxn-set
--
-- Revision 1.18  2001/05/02 15:11:19  kholodov
-- Fixed: NSE-ss::orient: refersed -> reversed.
--
-- Revision 1.17  2001/05/01 14:23:44  sherry
-- added seq-ss-exemplar and NSE-ss.orient to report orientation of cluster members to NSE-rs and its exemplar sequence, NSE-rs.seq-ss-exemplar.
--
-- Revision 1.16  2001/04/30 15:21:21  sherry
-- added reference fxn-class if SNP allele is observed on reference contig sequence
--
-- Revision 1.15  2001/04/09 14:21:31  sherry
-- additional documentation regarding refSNP flanking sequence: lowercase for repetititve regions and segmentation of long flanking sequences
--
-- Revision 1.14  2001/03/23 16:17:44  sherry
-- removed unnecessary samplesize from NSE-Pop.. data in NSE-ss-popinfo
--
-- Revision 1.13  2001/03/23 14:10:22  sherry
-- added samplesize to NSE-Pop
--
-- Revision 1.12  2001/03/22 14:04:54  sherry
-- strain added to NSE-Assay
--
-- Revision 1.11  2001/02/01 17:53:01  sherry
-- added MapLinkArchive to Table Source for sequence-mapset
--
-- Revision 1.10  2001/02/01 14:30:45  sherry
-- added orientation to NSE-SeqLoc
--
-- Revision 1.9  2000/12/19 22:32:11  sherry
-- added orientation/hit quality to contig hits, added source database to genbank hits
--
-- Revision 1.8  2000/12/19 22:19:48  sherry
-- added subsnp frequency data and refsnp function via contig annotation
--
-- Revision 1.7  2000/12/05 19:19:57  kholodov
-- Minor errors fixed
--
-- Revision 1.6  2000/12/05 17:06:35  sherry
-- merged docsum.asn and export.asn in this version for a single data structure that can be populated as a brief-set (to emulate docsum.asn) or as a full-set for data exchange (to emulate exchange.asn)
--
--
-- ###
-- ### Revisions to earlier versions of exchange.asn
-- ###
--
-- Revision exchange.asn 1.10  2000/11/03 15:26:41  sherry
-- added subsnp-id to export.asn and made loc-snp-id optional in both export.asn and docsum.asn
--
-- Revision exchange.asn 1.9  2000/11/02 20:58:14  kholodov
-- fixed incorrect field name
--
-- Revision exchange.asn 1.8  2000/10/18 22:07:11  sherry
-- added XML version number and dbSNP_build number to ExchangeSet
--
-- Revision exchange.asn 1.7  2000/10/13 16:08:20  kholodov
-- added commented CVS log
--
-- ###
-- ### Revisions to earlier versions of docsum.asn
-- ###
--
-- Revision docsum.asn 1.5  2000/11/03 15:26:41  sherry
-- added subsnp-id to export.asn and made loc-snp-id optional in both export.asn and docsum.asn
--
-- Revision docsum.asn 1.4  2000/10/20 19:21:41  sherry
-- added ambiguousloc and lowmapquality to legal withdrawn reasons
--
-- Revision docsum.asn 1.3  2000/08/24 14:47:53  sherry
-- added subsnp-class and mixed snp-class type
--
--08/23/00:	changed source of NCBI-RefSNPDocsum.taxid to new taxid column in SNP table
--		added NCBI-RefSNPDocsum.snp-class type (7) for cases of mixed subsnp-class in single refSNP (none currently in database)
--		added NCBI-subsnp-id.subsnp-class to define allele class for subSNP as well as SNP
--06/20/00:	Added 'duplicatesub' and 'NotSpecified' as WITHDRAWN reason for snp-type
--05/22/00:	Added splice to fxn-class, 
--		added map coordinates in contig component coordinates (RefSNPSeqHit),
--		changed RefSNPMaphit to RefSNPContigHit
--04/18/00:	Added subsnp set membership, flanking sequence
--03/22/00:	Added changes to fxn-class and validated
--03/01/00:	Added het-SE for standard error of mean heterozygosity
--02/09/00:     Added unigene/UID/loc_cnt
--02/08/00:	Added mapping, fixed taxid, mapstring definitions
--02/03/00: 	Added RefSNP Docsum definitions
--		Short version of ASN1 for development of genome annotation code