Schema docsum_2005.xsd

schema location:	ftp://ftp.ncbi.nlm.nih.gov/snp/specs/docsum_2005.xsd
attribute form default:	unqualified
element form default:	qualified
targetNamespace:	http://www.ncbi.nlm.nih.gov/SNP/docsum

Elements

Assay

Assembly

BaseURL

Component

ExchangeSet

FxnSet

MapLoc

PrimarySequence

Rs

RsLinkout

RsStruct

Ss

element Assay

diagram
namespace	http://www.ncbi.nlm.nih.gov/SNP/docsum
properties	content  complex
children	Method Taxonomy Strains Comment Citation
used by	element  ExchangeSet
attributes	Name   Type   Use   Default   Fixed   Annotation handle   xsd:string          batch   xsd:string          batchId   xsd:int          batchType   derived by: xsd:string          molType   derived by: xsd:string          sampleSize   xsd:int          population   xsd:string          linkoutUrl   xsd:string

element Assay/Method

diagram
namespace	http://www.ncbi.nlm.nih.gov/SNP/docsum
properties	isRef  0 content  complex
children	Exception
attributes	Name   Type   Use   Default   Fixed   Annotation name   xsd:string          documentation Submitters method identifier Id   xsd:string          documentation dbSNP method identifier

element Assay/Method/Exception

diagram
namespace	http://www.ncbi.nlm.nih.gov/SNP/docsum
type	xsd:string
properties	isRef  0 content  simple
annotation	documentation description of deviation from/addition to given method

element Assay/Taxonomy

diagram
namespace	http://www.ncbi.nlm.nih.gov/SNP/docsum
properties	isRef  0 content  complex
attributes	Name   Type   Use   Default   Fixed   Annotation id   xsd:int required         documentation NCBI taxonomy ID for variation organism   xsd:string

element Assay/Strains

diagram
namespace	http://www.ncbi.nlm.nih.gov/SNP/docsum
type	xsd:string
properties	isRef  0 minOcc  0 maxOcc  unbounded content  simple

element Assay/Comment

diagram
namespace	http://www.ncbi.nlm.nih.gov/SNP/docsum
type	xsd:string
properties	isRef  0 minOcc  0 maxOcc  1 content  simple

element Assay/Citation

diagram
namespace	http://www.ncbi.nlm.nih.gov/SNP/docsum
type	xsd:string
properties	isRef  0 minOcc  0 maxOcc  unbounded content  simple

element Assembly

diagram
namespace	http://www.ncbi.nlm.nih.gov/SNP/docsum
properties	content  complex
children	Component SnpStat
used by	element  Rs
attributes	Name   Type   Use   Default   Fixed   Annotation dbSnpBuild   xsd:int required         documentation dbSNP build number defining the rsid set aligned to this assembly genomeBuild   xsd:string required         documentation assembly build number with possible 'subbuild' version numbers to reflect updates in gene annotation (human e.g. 34_3, 35_1, 36_1) groupLabel   xsd:string optional         documentation High-level classification of the assembly to distinguish reference projects from alternate solutions. GroupLabel field from organism/build-specific ContigInfo tables. "reference" is occasionally used as the preferred assembly; standards will converge as additional organism genome projects are finished. Note that some organism assembly names include extended characters like '~' and '/' that may be incompatible with OS filename conventions. assemblySource   xsd:string optional         documentation Name of the group(s) or organization(s) that generated the assembly current   xsd:boolean          documentation Marks the current genomic assembly reference   xsd:boolean
annotation	documentation A collection of genome sequence records (curated gene regions (NG's), contigs (NWNT's)  and chromosomes (NC/AC's) produced by a genome sequence project. Structure is populated from ContigInfo tables.

element Assembly/SnpStat

diagram
namespace	http://www.ncbi.nlm.nih.gov/SNP/docsum
properties	isRef  0 content  complex
attributes	Name   Type   Use   Default   Fixed   Annotation mapWeight   derived by: xsd:string required         documentation summary measure of placement precision in the assembly chromCount   xsd:int optional         documentation number of distinct chromosomes in the mapset placedContigCount   xsd:int optional         documentation number of distinct contigs [ gi | accession[.version] ] in the mapset unplacedContigCount   xsd:int optional         documentation number of sequence postions to a contig with unknown chromosomal assignment seqlocCount   xsd:int optional         documentation total number of sequence positions in the mapset hapCount   xsd:int optional         documentation Number of hits to alternative genomic haplotypes (e.g. HLA DR region, KIR, or pseudo-autosomal regions like PAR) within the assembly mapset. Note that positions on haplotypes defined in other assemblies (a different assembly_group_label value) will not be counted in this value.

element BaseURL

diagram
namespace	http://www.ncbi.nlm.nih.gov/SNP/docsum
type	extension of xsd:string
properties	content  complex
used by	element  ExchangeSet
attributes	Name   Type   Use   Default   Fixed   Annotation urlId   xsd:int          documentation Resource identifier from dbSNP_main.baseURL. resourceName   xsd:string          documentation Name of linked resource resourceId   xsd:string          documentation identifier expected by resource for URL
annotation	documentation URL value from dbSNP_main.BaseURL links table. attributes provide context information and URL id that is referenced within individual refSNP objects.

element Component

diagram
namespace	http://www.ncbi.nlm.nih.gov/SNP/docsum
properties	content  complex
children	MapLoc
used by	element  Assembly
attributes	Name   Type   Use   Default   Fixed   Annotation componentType   derived by: xsd:string          documentation type of component: chromosome, contig, gene_region, etc. ctgId   xsd:int          documentation dbSNP contig_id used to join on contig hit / mapset data to these assembly properties accession   xsd:string          documentation Accession[.version] for the sequence component name   xsd:string          documentation contig name defined as either a submitter local id, element of a whole genome assembly set, or internal NCBI local id chromosome   xsd:string          documentation Organism appropriate chromosome tag, 'Un' reserved for default case of unplaced components start   xsd:int          documentation component starting position on the chromosome (base 0 inclusive) end   xsd:int          documentation component ending position on the chromosome (base 0 inclusive) orientation   derived by: xsd:string          documentation orientation of this component to chromosome, forward (fwd) = 0, reverse (rev) = 1, unknown = NULL in ContigInfo.orient. gi   xsd:string          documentation NCBI gi for component sequence (equivalent to accession.version) for nucleotide sequence. groupTerm   xsd:string          documentation Identifier label for the genome assembly that defines the contigs in this mapset and their placement within the organism genome. contigLabel   xsd:string          documentation Display label for component

element ExchangeSet

diagram
namespace	http://www.ncbi.nlm.nih.gov/SNP/docsum
properties	content  complex
children	SourceDatabase Rs Assay Query Summary BaseURL
attributes	Name   Type   Use   Default   Fixed   Annotation setType   xsd:string          documentation set-type: full dump; from query; single refSNP setDepth   xsd:string optional         documentation content depth: brief XML (only refSNP properties and summary subSNP element content); full XML (full refSNP, full subSNP content; all flanking sequences) specVersion   xsd:string          documentation version number of docsum.asn/docsum.dtd specification dbSnpBuild   xsd:int          documentation build number of database for this export generated   xsd:string          documentation Generated date
annotation	documentation Set of dbSNP refSNP docsums

element ExchangeSet/SourceDatabase

diagram
namespace	http://www.ncbi.nlm.nih.gov/SNP/docsum
properties	isRef  0 content  complex
attributes	Name   Type   Use   Default   Fixed   Annotation taxId   xsd:int required         documentation NCBI taxonomy ID for variation organism   xsd:string required         documentation common name for species used as part of database name. dbSnpOrgAbbr   xsd:string          documentation organism abbreviation used in dbSNP. gpipeOrgAbbr   xsd:string          documentation organism abbreviation used within NCBI genome pipeline data dumps.

element ExchangeSet/Query

diagram
namespace	http://www.ncbi.nlm.nih.gov/SNP/docsum
properties	isRef  0 minOcc  0 maxOcc  1 content  complex
attributes	Name   Type   Use   Default   Fixed   Annotation date   xsd:string          documentation yyyy-mm-dd string   xsd:string          documentation Query terms or search constraints

element ExchangeSet/Summary

diagram
namespace	http://www.ncbi.nlm.nih.gov/SNP/docsum
properties	isRef  0 content  complex
attributes	Name   Type   Use   Default   Fixed   Annotation numRsIds   xsd:integer optional         documentation Total number of refsnp-ids in this exchange set totalSeqLength   xsd:integer optional         documentation Total length of exemplar flanking sequences numContigHits   xsd:integer optional         documentation Total number of contig locations from SNPContigLoc numGeneHits   xsd:integer optional         documentation Total number of locus ids from SNPContigLocusId numGiHits   xsd:integer optional         documentation Total number of gi hits from MapLink num3dStructs   xsd:integer optional         documentation Total number of 3D structures from SNP3D numAlleleFreqs   xsd:integer optional         documentation Total number of allele frequences from SubPopAllele numStsHits   xsd:integer optional         documentation Total number of STS hits from SnpInSts numUnigeneCids   xsd:integer optional         documentation Total number of unigene cluster ids from UnigeneSnp

element FxnSet

diagram
namespace	http://www.ncbi.nlm.nih.gov/SNP/docsum
properties	content  complex
used by	element  MapLoc
attributes	Name   Type   Use   Default   Fixed   Annotation geneId   xsd:int          documentation gene-id of gene as aligned to contig symbol   xsd:string          documentation symbol (official if present in Entrez Gene) of gene mrnaAcc   xsd:string          documentation mRNA accession if variation in transcript mrnaVer   xsd:int          documentation mRNA sequence version if variation is in transcripot protAcc   xsd:string          documentation protein accession if variation in protein protVer   xsd:int          documentation protein version if variation is in protein fxnClass   derived by: xsd:string          readingFrame   xsd:int          allele   xsd:string          documentation variation allele: * suffix indicates allele of contig at this location residue   xsd:string          documentation translated amino acid residue for allele aaPosition   xsd:int          documentation position of the variant residue in peptide sequence
annotation	documentation functional relationship of SNP (and possibly alleles) to genes at contig location as defined in organism-specific bxxx_SNPContigLocusId_xxx tables.

element MapLoc

diagram
namespace	http://www.ncbi.nlm.nih.gov/SNP/docsum
properties	content  complex
children	FxnSet
used by	elements  Component PrimarySequence
attributes	Name   Type   Use   Default   Fixed   Annotation asnFrom   xsd:integer required         documentation beginning of variation as feature on contig asnTo   xsd:integer required         documentation end position of variation as feature on contig locType   derived by: xsd:string required         documentation defines the seq-loc symbol if asn_from != asn_to alnQuality   xsd:double optional         documentation alignment qualiity orient   derived by: xsd:string optional         documentation orientation of refSNP sequence to contig sequence physMapInt   xsd:int          documentation chromosome position as integer for sorting leftFlankNeighborPos   xsd:int          documentation nearest aligned position in 5' flanking sequence of snp rightFlankNeighborPos   xsd:int          documentation nearest aligned position in 3' flanking sequence of snp leftContigNeighborPos   xsd:int          documentation nearest aligned position in 5' contig alignment of snp rightContigNeighborPos   xsd:int          documentation nearest aligned position in 3' contig alignment of snp numberOfMismatches   xsd:int          documentation number of Mismatched positions in this alignment numberOfDeletions   xsd:int          documentation number of deletions in this alignment numberOfInsertions   xsd:int          documentation number of insetions in this alignment
annotation	documentation Position of a single hit of a variation on a contig

element PrimarySequence

diagram
namespace	http://www.ncbi.nlm.nih.gov/SNP/docsum
properties	content  complex
children	MapLoc
used by	element  Rs
attributes	Name   Type   Use   Default   Fixed   Annotation dbSnpBuild   xsd:int required         gi   xsd:int required         source   derived by: xsd:string          accession   xsd:string

element Rs

diagram
namespace	http://www.ncbi.nlm.nih.gov/SNP/docsum
properties	content  complex
children	Het Validation Create Update Sequence Ss Assembly PrimarySequence RsStruct RsLinkout MergeHistory
used by	element  ExchangeSet
attributes	Name   Type   Use   Default   Fixed   Annotation rsId   xsd:int required         documentation refSNP (rs) number snpClass   derived by: xsd:string required         snpType   derived by: xsd:string required         molType   derived by: xsd:string required         validProbMin   xsd:integer optional         documentation minimum reported success rate of all submissions in cluster validProbMax   xsd:integer optional         documentation maximum reported success rate of all submissions in cluster genotype   xsd:boolean optional         documentation at least one genotype reported for this refSNP
annotation	documentation defines the docsum structure for refSNP clusters, where a refSNP cluster (rs) is a grouping of individual dbSNP submissions that all refer to the same variation. The refsnp provides a single unified record for annotation of NCBI resources such as reference genome sequence.

element Rs/Het

diagram
namespace	http://www.ncbi.nlm.nih.gov/SNP/docsum
properties	isRef  0 minOcc  0 maxOcc  1 content  complex
attributes	Name   Type   Use   Default   Fixed   Annotation type   derived by: xsd:string required         documentation Est=Estimated average het from allele frequencies, Obs=Observed from genotype data value   xsd:float required         documentation Heterozygosity stdError   xsd:float          documentation Standard error of Het estimate

element Rs/Validation

diagram
namespace	http://www.ncbi.nlm.nih.gov/SNP/docsum
properties	isRef  0 content  complex
children	otherPopBatchId twoHit2AlleleBatchId
attributes	Name   Type   Use   Default   Fixed   Annotation byCluster   xsd:boolean          documentation at least one subsnp in cluster has frequency data submitted byFrequency   xsd:boolean          documentation cluster has 2+ submissions, with 1+ submissions assayed with a non-computational method byOtherPop   xsd:boolean          by2Hit2Allele   xsd:boolean          documentation cluster has 2+ submissions, with 1+ submissions assayed with a non-computational method byHapMap   xsd:boolean          documentation TBD

element Rs/Validation/otherPopBatchId

diagram
namespace	http://www.ncbi.nlm.nih.gov/SNP/docsum
type	xsd:int
properties	isRef  0 minOcc  0 maxOcc  unbounded content  simple
annotation	documentation dbSNP batch-id's for other pop snp validation data.

element Rs/Validation/twoHit2AlleleBatchId

diagram
namespace	http://www.ncbi.nlm.nih.gov/SNP/docsum
type	xsd:int
properties	isRef  0 minOcc  0 maxOcc  unbounded content  simple
annotation	documentation dbSNP batch-id's for double-hit snp validation data. Use batch-id to get methods, etc.

element Rs/Create

diagram
namespace	http://www.ncbi.nlm.nih.gov/SNP/docsum
properties	isRef  0 content  complex
attributes	Name   Type   Use   Default   Fixed   Annotation build   xsd:int          documentation build number when the cluster was created date   xsd:string          documentation yyyy-mm-dd
annotation	documentation date the refsnp cluster was instantiated

element Rs/Update

diagram
namespace	http://www.ncbi.nlm.nih.gov/SNP/docsum
properties	isRef  0 minOcc  0 maxOcc  1 content  complex
attributes	Name   Type   Use   Default   Fixed   Annotation build   xsd:int          documentation build number when the cluster was updated date   xsd:string          documentation yyyy-mm-dd
annotation	documentation most recent date the cluster was updated (member added or deleted)

element Rs/Sequence

diagram
namespace	http://www.ncbi.nlm.nih.gov/SNP/docsum
properties	isRef  0 content  complex
children	Seq5 Observed Seq3
attributes	Name   Type   Use   Default   Fixed   Annotation exemplarSs   xsd:int required         documentation dbSNP ss# selected as source of refSNP flanking sequence, ss# part of ss-list below

element Rs/Sequence/Seq5

diagram
namespace	http://www.ncbi.nlm.nih.gov/SNP/docsum
type	xsd:string
properties	isRef  0 minOcc  0 maxOcc  1 content  simple
annotation	documentation 5' sequence that flanks the variation

element Rs/Sequence/Observed

diagram
namespace	http://www.ncbi.nlm.nih.gov/SNP/docsum
type	xsd:string
properties	isRef  0 content  simple
annotation	documentation list of all nucleotide alleles observed in ss-list members, correcting for reverse complementation of memebers reported in reverse orientation

element Rs/Sequence/Seq3

diagram
namespace	http://www.ncbi.nlm.nih.gov/SNP/docsum
type	xsd:string
properties	isRef  0 minOcc  0 maxOcc  1 content  simple
annotation	documentation 3' sequence that flanks the variation

element Rs/MergeHistory

diagram
namespace	http://www.ncbi.nlm.nih.gov/SNP/docsum
properties	isRef  0 minOcc  0 maxOcc  unbounded content  complex
attributes	Name   Type   Use   Default   Fixed   Annotation rsId   xsd:int required         documentation previously issued rs id whose member assays have now been merged buildId   xsd:int          documentation build id when rs id was merged into parent rs orientFlip   xsd:boolean          documentation TRUE if strand of rs id is reverse to parent object's current strand

element RsLinkout

diagram
namespace	http://www.ncbi.nlm.nih.gov/SNP/docsum
properties	content  complex
used by	element  Rs
attributes	Name   Type   Use   Default   Fixed   Annotation resourceId   xsd:string required         documentation BaseURLList.url_id linkValue   xsd:string required         documentation value to append to ResourceURL.base-url for complete link
annotation	documentation link data for another resource

element RsStruct

diagram
namespace	http://www.ncbi.nlm.nih.gov/SNP/docsum
properties	content  complex
used by	element  Rs
attributes	Name   Type   Use   Default   Fixed   Annotation protAcc   xsd:string          documentation accession of the protein with variation protGi   xsd:int          documentation GI of the protein with variation protLoc   xsd:int          documentation position of the residue for the protein GI protResidue   xsd:string          documentation residue specified for protein at prot-loc location rsResidue   xsd:string          documentation alternative residue specified by variation sequence structGi   xsd:int          documentation GI of the structure neighbor structLoc   xsd:int          documentation position of the residue for the structure GI structResidue   xsd:string          documentation residue specified for protein at struct-loc location
annotation	documentation structure information for SNP

element Ss

diagram
namespace	http://www.ncbi.nlm.nih.gov/SNP/docsum
properties	content  complex
children	Sequence
used by	element  Rs
attributes	Name   Type   Use   Default   Fixed   Annotation ssId   xsd:int required         documentation dbSNP accession number for submission handle   xsd:string required         documentation Tag for the submitting laboratory batchId   xsd:int required         documentation dbSNP number for batch submission locSnpId   xsd:string          documentation submission (ss#) submitter ID subSnpClass   derived by: xsd:string          documentation SubSNP classification by type of variation orient   derived by: xsd:string          documentation orientation of refsnp cluster members to refsnp cluster sequence strand   derived by: xsd:string          documentation strand is defined as TOP/BOTTOM by nature of flanking nucleotide sequence molType   derived by: xsd:string          documentation moltype from Batch table buildId   xsd:int          documentation dbSNP build number when ss# was added to a refSNP (rs#) cluster methodClass   derived by: xsd:string          documentation class of method used to assay for the variation validated   derived by: xsd:string          linkoutUrl   xsd:string          documentation append loc-snp-id to this base URL to construct a pointer to submitter data.
annotation	documentation data for an individual submission to dbSNP

element Ss/Sequence

diagram
namespace	http://www.ncbi.nlm.nih.gov/SNP/docsum
properties	isRef  0 content  complex
children	Seq5 Observed Seq3

element Ss/Sequence/Seq5

diagram
namespace	http://www.ncbi.nlm.nih.gov/SNP/docsum
type	xsd:string
properties	isRef  0 minOcc  0 maxOcc  1 content  simple
annotation	documentation 5' sequence that flanks the variation

element Ss/Sequence/Observed

diagram
namespace	http://www.ncbi.nlm.nih.gov/SNP/docsum
type	xsd:string
properties	isRef  0 content  simple
annotation	documentation list of all nucleotide alleles observed in ss-list members, correcting for reverse complementation of memebers reported in reverse orientation

element Ss/Sequence/Seq3

diagram
namespace	http://www.ncbi.nlm.nih.gov/SNP/docsum
type	xsd:string
properties	isRef  0 minOcc  0 maxOcc  1 content  simple
annotation	documentation 3' sequence that flanks the variation

XML Schema documentation generated by XMLSpy Schema Editor http://www.altova.com/xmlspy