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<!-- ============================================
::DATATOOL:: Generated from "docsum.asn"
::DATATOOL:: by application DATATOOL version 1.9.0
::DATATOOL:: on 04/10/2008 16:04:22
============================================ -->
<!-- ============================================ -->
<!-- This section is mapped from module "NSE"
================================================= -->
<!-- Elements used by other modules:
ExchangeSet,
Rs,
Ss,
MapLoc,
FxnSet,
Assembly,
Assay,
BaseURL,
PrimarySequence,
RsStruct,
RsLinkout,
Component -->
<!-- ============================================ -->
<!-- Set of dbSNP refSNP docsums -->
<!ELEMENT ExchangeSet (
ExchangeSet_setType?,
ExchangeSet_setDepth?,
ExchangeSet_specVersion?,
ExchangeSet_dbSnpBuild?,
ExchangeSet_generated?,
ExchangeSet_sourceDatabase,
ExchangeSet_rs?,
ExchangeSet_assay?,
ExchangeSet_query?,
ExchangeSet_summary,
ExchangeSet_baseURL)>
<!-- set-type: full dump; from query; single refSNP -->
<!ELEMENT ExchangeSet_setType (#PCDATA)>
<!-- content depth: brief XML (only refSNP properties and summary subSNP element content); full XML (full refSNP, full subSNP content; all flanking sequences) -->
<!ELEMENT ExchangeSet_setDepth (#PCDATA)>
<!-- version number of docsum.asn/docsum.dtd specification -->
<!ELEMENT ExchangeSet_specVersion (#PCDATA)>
<!-- build number of database for this export -->
<!ELEMENT ExchangeSet_dbSnpBuild (%INTEGER;)>
<!-- Generated date -->
<!ELEMENT ExchangeSet_generated (#PCDATA)>
<!ELEMENT ExchangeSet_sourceDatabase (
ExchangeSet_sourceDatabase_taxId,
ExchangeSet_sourceDatabase_organism,
ExchangeSet_sourceDatabase_dbSnpOrgAbbr?,
ExchangeSet_sourceDatabase_gpipeOrgAbbr?)>
<!-- NCBI taxonomy ID for variation -->
<!ELEMENT ExchangeSet_sourceDatabase_taxId (%INTEGER;)>
<!-- common name for species used as part of database name. -->
<!ELEMENT ExchangeSet_sourceDatabase_organism (#PCDATA)>
<!-- organism abbreviation used in dbSNP. -->
<!ELEMENT ExchangeSet_sourceDatabase_dbSnpOrgAbbr (#PCDATA)>
<!-- organism abbreviation used within NCBI genome pipeline data dumps. -->
<!ELEMENT ExchangeSet_sourceDatabase_gpipeOrgAbbr (#PCDATA)>
<!ELEMENT ExchangeSet_rs (Rs*)>
<!ELEMENT ExchangeSet_assay (Assay)>
<!ELEMENT ExchangeSet_query (
ExchangeSet_query_date?,
ExchangeSet_query_string?)>
<!-- yyyy-mm-dd -->
<!ELEMENT ExchangeSet_query_date (#PCDATA)>
<!-- Query terms or search constraints -->
<!ELEMENT ExchangeSet_query_string (#PCDATA)>
<!ELEMENT ExchangeSet_summary (
ExchangeSet_summary_numRsIds?,
ExchangeSet_summary_totalSeqLength?,
ExchangeSet_summary_numContigHits?,
ExchangeSet_summary_numGeneHits?,
ExchangeSet_summary_numGiHits?,
ExchangeSet_summary_num3dStructs?,
ExchangeSet_summary_numAlleleFreqs?,
ExchangeSet_summary_numStsHits?,
ExchangeSet_summary_numUnigeneCids?)>
<!-- Total number of refsnp-ids in this exchange set -->
<!ELEMENT ExchangeSet_summary_numRsIds (%INTEGER;)>
<!-- Total length of exemplar flanking sequences -->
<!ELEMENT ExchangeSet_summary_totalSeqLength (%INTEGER;)>
<!-- Total number of contig locations from SNPContigLoc -->
<!ELEMENT ExchangeSet_summary_numContigHits (%INTEGER;)>
<!-- Total number of locus ids from SNPContigLocusId -->
<!ELEMENT ExchangeSet_summary_numGeneHits (%INTEGER;)>
<!-- Total number of gi hits from MapLink -->
<!ELEMENT ExchangeSet_summary_numGiHits (%INTEGER;)>
<!-- Total number of 3D structures from SNP3D -->
<!ELEMENT ExchangeSet_summary_num3dStructs (%INTEGER;)>
<!-- Total number of allele frequences from SubPopAllele -->
<!ELEMENT ExchangeSet_summary_numAlleleFreqs (%INTEGER;)>
<!-- Total number of STS hits from SnpInSts -->
<!ELEMENT ExchangeSet_summary_numStsHits (%INTEGER;)>
<!-- Total number of unigene cluster ids from UnigeneSnp -->
<!ELEMENT ExchangeSet_summary_numUnigeneCids (%INTEGER;)>
<!ELEMENT ExchangeSet_baseURL (BaseURL*)>
<!-- 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 (
Rs_rsId,
Rs_snpClass,
Rs_snpType,
Rs_molType,
Rs_validProbMin?,
Rs_validProbMax?,
Rs_genotype?,
Rs_het?,
Rs_validation,
Rs_create,
Rs_update?,
Rs_sequence,
Rs_ss,
Rs_assembly?,
Rs_primarySequence?,
Rs_rsStruct?,
Rs_rsLinkout?,
Rs_mergeHistory?)>
<!-- refSNP (rs) number -->
<!ELEMENT Rs_rsId (%INTEGER;)>
<!ELEMENT Rs_snpClass %ENUM;>
<!ATTLIST Rs_snpClass value (
snp |
in-del |
heterozygous |
microsatellite |
named-locus |
no-variation |
mixed |
multinucleotide-polymorphism
) #REQUIRED >
<!ELEMENT Rs_snpType %ENUM;>
<!ATTLIST Rs_snpType value (
notwithdrawn |
artifact |
gene-duplication |
duplicate-submission |
notspecified |
ambiguous-location |
low-map-quality
) #REQUIRED >
<!ELEMENT Rs_molType %ENUM;>
<!ATTLIST Rs_molType value (
genomic |
cDNA |
mito |
chloro |
unknown
) #REQUIRED >
<!-- minimum reported success rate of all submissions in cluster -->
<!ELEMENT Rs_validProbMin (%INTEGER;)>
<!-- maximum reported success rate of all submissions in cluster -->
<!ELEMENT Rs_validProbMax (%INTEGER;)>
<!-- at least one genotype reported for this refSNP -->
<!ELEMENT Rs_genotype EMPTY>
<!ATTLIST Rs_genotype value ( true | false ) #REQUIRED >
<!ELEMENT Rs_het (
Rs_het_type,
Rs_het_value,
Rs_het_stdError?)>
<!-- Est=Estimated average het from allele frequencies, Obs=Observed from genotype data -->
<!ELEMENT Rs_het_type %ENUM;>
<!ATTLIST Rs_het_type value (
est |
obs
) #REQUIRED >
<!-- Heterozygosity -->
<!ELEMENT Rs_het_value (%REAL;)>
<!-- Standard error of Het estimate -->
<!ELEMENT Rs_het_stdError (%REAL;)>
<!ELEMENT Rs_validation (
Rs_validation_byCluster?,
Rs_validation_byFrequency?,
Rs_validation_byOtherPop?,
Rs_validation_by2Hit2Allele?,
Rs_validation_byHapMap?,
Rs_validation_otherPopBatchId?,
Rs_validation_twoHit2AlleleBatchId?)>
<!-- at least one subsnp in cluster has frequency data submitted -->
<!ELEMENT Rs_validation_byCluster EMPTY>
<!ATTLIST Rs_validation_byCluster value ( true | false ) #REQUIRED >
<!-- cluster has 2+ submissions, with 1+ submissions assayed with a non-computational method -->
<!ELEMENT Rs_validation_byFrequency EMPTY>
<!ATTLIST Rs_validation_byFrequency value ( true | false ) #REQUIRED >
<!ELEMENT Rs_validation_byOtherPop EMPTY>
<!ATTLIST Rs_validation_byOtherPop value ( true | false ) #REQUIRED >
<!-- cluster has 2+ submissions, with 1+ submissions assayed with a non-computational method -->
<!ELEMENT Rs_validation_by2Hit2Allele EMPTY>
<!ATTLIST Rs_validation_by2Hit2Allele value ( true | false ) #REQUIRED >
<!-- TBD -->
<!ELEMENT Rs_validation_byHapMap EMPTY>
<!ATTLIST Rs_validation_byHapMap value ( true | false ) #REQUIRED >
<!-- dbSNP batch-id's for other pop snp validation data. -->
<!ELEMENT Rs_validation_otherPopBatchId (Rs_validation_otherPopBatchId_E*)>
<!ELEMENT Rs_validation_otherPopBatchId_E (%INTEGER;)>
<!-- dbSNP batch-id's for double-hit snp validation data. Use batch-id to get methods, etc. -->
<!ELEMENT Rs_validation_twoHit2AlleleBatchId (Rs_validation_twoHit2AlleleBatchId_E*)>
<!ELEMENT Rs_validation_twoHit2AlleleBatchId_E (%INTEGER;)>
<!-- date the refsnp cluster was instantiated -->
<!ELEMENT Rs_create (
Rs_create_build?,
Rs_create_date?)>
<!-- build number when the cluster was created -->
<!ELEMENT Rs_create_build (%INTEGER;)>
<!-- yyyy-mm-dd -->
<!ELEMENT Rs_create_date (#PCDATA)>
<!-- most recent date the cluster was updated (member added or deleted) -->
<!ELEMENT Rs_update (
Rs_update_build?,
Rs_update_date?)>
<!-- build number when the cluster was updated -->
<!ELEMENT Rs_update_build (%INTEGER;)>
<!-- yyyy-mm-dd -->
<!ELEMENT Rs_update_date (#PCDATA)>
<!ELEMENT Rs_sequence (
Rs_sequence_exemplarSs,
Rs_sequence_seq5?,
Rs_sequence_observed,
Rs_sequence_seq3?)>
<!-- dbSNP ss# selected as source of refSNP flanking sequence, ss# part of ss-list below -->
<!ELEMENT Rs_sequence_exemplarSs (%INTEGER;)>
<!-- 5' sequence that flanks the variation -->
<!ELEMENT Rs_sequence_seq5 (#PCDATA)>
<!-- list of all nucleotide alleles observed in ss-list members, correcting for reverse complementation of memebers reported in reverse orientation -->
<!ELEMENT Rs_sequence_observed (#PCDATA)>
<!-- 3' sequence that flanks the variation -->
<!ELEMENT Rs_sequence_seq3 (#PCDATA)>
<!ELEMENT Rs_ss (Ss*)>
<!ELEMENT Rs_assembly (Assembly*)>
<!ELEMENT Rs_primarySequence (PrimarySequence*)>
<!ELEMENT Rs_rsStruct (RsStruct*)>
<!ELEMENT Rs_rsLinkout (RsLinkout*)>
<!ELEMENT Rs_mergeHistory (Rs_mergeHistory_E*)>
<!ELEMENT Rs_mergeHistory_E (
Rs_mergeHistory_E_rsId,
Rs_mergeHistory_E_buildId?,
Rs_mergeHistory_E_orientFlip?)>
<!-- previously issued rs id whose member assays have now been merged -->
<!ELEMENT Rs_mergeHistory_E_rsId (%INTEGER;)>
<!-- build id when rs id was merged into parent rs -->
<!ELEMENT Rs_mergeHistory_E_buildId (%INTEGER;)>
<!-- TRUE if strand of rs id is reverse to parent object's current strand -->
<!ELEMENT Rs_mergeHistory_E_orientFlip EMPTY>
<!ATTLIST Rs_mergeHistory_E_orientFlip value ( true | false ) #REQUIRED >
<!-- data for an individual submission to dbSNP -->
<!ELEMENT Ss (
Ss_ssId,
Ss_handle,
Ss_batchId,
Ss_locSnpId?,
Ss_subSnpClass?,
Ss_orient?,
Ss_strand?,
Ss_molType?,
Ss_buildId?,
Ss_methodClass?,
Ss_validated?,
Ss_linkoutUrl?,
Ss_sequence)>
<!-- dbSNP accession number for submission -->
<!ELEMENT Ss_ssId (%INTEGER;)>
<!-- Tag for the submitting laboratory -->
<!ELEMENT Ss_handle (#PCDATA)>
<!-- dbSNP number for batch submission -->
<!ELEMENT Ss_batchId (%INTEGER;)>
<!-- submission (ss#) submitter ID -->
<!ELEMENT Ss_locSnpId (#PCDATA)>
<!-- SubSNP classification by type of variation -->
<!ELEMENT Ss_subSnpClass %ENUM;>
<!ATTLIST Ss_subSnpClass value (
snp |
in-del |
heterozygous |
microsatellite |
named-locus |
no-variation |
mixed |
multinucleotide-polymorphism
) #REQUIRED >
<!-- orientation of refsnp cluster members to refsnp cluster sequence -->
<!ELEMENT Ss_orient %ENUM;>
<!--
forward - ss flanking sequence is in same orientation as seq-ss-exemplar
reverse - lanking sequence and alleles are reverse complement of refSNP as defined by ss exemplar
-->
<!ATTLIST Ss_orient value (
forward |
reverse
) #REQUIRED >
<!-- strand is defined as TOP/BOTTOM by nature of flanking nucleotide sequence -->
<!ELEMENT Ss_strand %ENUM;>
<!ATTLIST Ss_strand value (
top |
bottom
) #REQUIRED >
<!-- moltype from Batch table -->
<!ELEMENT Ss_molType %ENUM;>
<!ATTLIST Ss_molType value (
genomic |
cDNA |
mito |
chloro |
unknown
) #REQUIRED >
<!-- dbSNP build number when ss# was added to a refSNP (rs#) cluster -->
<!ELEMENT Ss_buildId (%INTEGER;)>
<!-- class of method used to assay for the variation -->
<!ELEMENT Ss_methodClass %ENUM;>
<!--
dHPLC - Denaturing High Pressure Liquid Chromatography used to detect SNP
hybridize - a hybridization method (e.g. chip) was used to assay for variation
computed - variation was mined from sequence alignment with software
sequence - samples were sequenced and resulting alignment used to define variation
-->
<!ATTLIST Ss_methodClass value (
dHPLC |
hybridize |
computed |
sSCP |
other |
unknown |
rFLP |
sequence
) #REQUIRED >
<!ELEMENT Ss_validated %ENUM;>
<!--
by-submitter - subsnp has been experimentally validated by submitter
by-frequency - subsnp has frequency data submitted
by-cluster - has 2+ submissions, with 1+ submission assayed with a non-computational method
-->
<!ATTLIST Ss_validated value (
by-submitter |
by-frequency |
by-cluster
) #REQUIRED >
<!-- append loc-snp-id to this base URL to construct a pointer to submitter data. -->
<!ELEMENT Ss_linkoutUrl (#PCDATA)>
<!ELEMENT Ss_sequence (
Ss_sequence_seq5?,
Ss_sequence_observed,
Ss_sequence_seq3?)>
<!-- 5' sequence that flanks the variation -->
<!ELEMENT Ss_sequence_seq5 (#PCDATA)>
<!-- list of all nucleotide alleles observed in ss-list members, correcting for reverse complementation of memebers reported in reverse orientation -->
<!ELEMENT Ss_sequence_observed (#PCDATA)>
<!-- 3' sequence that flanks the variation -->
<!ELEMENT Ss_sequence_seq3 (#PCDATA)>
<!-- Position of a single hit of a variation on a contig -->
<!ELEMENT MapLoc (
MapLoc_asnFrom,
MapLoc_asnTo,
MapLoc_locType,
MapLoc_alnQuality?,
MapLoc_orient?,
MapLoc_physMapInt?,
MapLoc_leftFlankNeighborPos?,
MapLoc_rightFlankNeighborPos?,
MapLoc_leftContigNeighborPos?,
MapLoc_rightContigNeighborPos?,
MapLoc_numberOfMismatches?,
MapLoc_numberOfDeletions?,
MapLoc_numberOfInsertions?,
MapLoc_fxnSet?)>
<!-- beginning of variation as feature on contig -->
<!ELEMENT MapLoc_asnFrom (%INTEGER;)>
<!-- end position of variation as feature on contig -->
<!ELEMENT MapLoc_asnTo (%INTEGER;)>
<!-- defines the seq-loc symbol if asn_from != asn_to -->
<!ELEMENT MapLoc_locType %ENUM;>
<!--
insertion - insertion on contig
exact - asn-from = asn-to write as 'asn-from'
deletion - deletion on contig
-->
<!ATTLIST MapLoc_locType value (
insertion |
exact |
deletion |
range-ins |
range-exact |
range-del
) #REQUIRED >
<!-- alignment qualiity -->
<!ELEMENT MapLoc_alnQuality (%REAL;)>
<!-- orientation of refSNP sequence to contig sequence -->
<!ELEMENT MapLoc_orient %ENUM;>
<!ATTLIST MapLoc_orient value (
forward |
reverse
) #REQUIRED >
<!-- chromosome position as integer for sorting -->
<!ELEMENT MapLoc_physMapInt (%INTEGER;)>
<!-- nearest aligned position in 5' flanking sequence of snp -->
<!ELEMENT MapLoc_leftFlankNeighborPos (%INTEGER;)>
<!-- nearest aligned position in 3' flanking sequence of snp -->
<!ELEMENT MapLoc_rightFlankNeighborPos (%INTEGER;)>
<!-- nearest aligned position in 5' contig alignment of snp -->
<!ELEMENT MapLoc_leftContigNeighborPos (%INTEGER;)>
<!-- nearest aligned position in 3' contig alignment of snp -->
<!ELEMENT MapLoc_rightContigNeighborPos (%INTEGER;)>
<!-- number of Mismatched positions in this alignment -->
<!ELEMENT MapLoc_numberOfMismatches (%INTEGER;)>
<!-- number of deletions in this alignment -->
<!ELEMENT MapLoc_numberOfDeletions (%INTEGER;)>
<!-- number of insetions in this alignment -->
<!ELEMENT MapLoc_numberOfInsertions (%INTEGER;)>
<!ELEMENT MapLoc_fxnSet (FxnSet*)>
<!-- functional relationship of SNP (and possibly alleles) to genes at contig location as defined in organism-specific bxxx_SNPContigLocusId_xxx tables. -->
<!ELEMENT FxnSet (
FxnSet_geneId?,
FxnSet_symbol?,
FxnSet_mrnaAcc?,
FxnSet_mrnaVer?,
FxnSet_protAcc?,
FxnSet_protVer?,
FxnSet_fxnClass?,
FxnSet_readingFrame?,
FxnSet_allele?,
FxnSet_residue?,
FxnSet_aaPosition?)>
<!-- gene-id of gene as aligned to contig -->
<!ELEMENT FxnSet_geneId (%INTEGER;)>
<!-- symbol (official if present in Entrez Gene) of gene -->
<!ELEMENT FxnSet_symbol (#PCDATA)>
<!-- mRNA accession if variation in transcript -->
<!ELEMENT FxnSet_mrnaAcc (#PCDATA)>
<!-- mRNA sequence version if variation is in transcripot -->
<!ELEMENT FxnSet_mrnaVer (%INTEGER;)>
<!-- protein accession if variation in protein -->
<!ELEMENT FxnSet_protAcc (#PCDATA)>
<!-- protein version if variation is in protein -->
<!ELEMENT FxnSet_protVer (%INTEGER;)>
<!ELEMENT FxnSet_fxnClass %ENUM;>
<!--
locus-region - variation in region of gene, but not in transcript
-->
<!ATTLIST FxnSet_fxnClass value (
locus-region |
coding-unknown |
coding-synonymous |
coding-nonsynonymous |
mrna-utr |
intron |
splice-site |
reference |
coding-exception
) #REQUIRED >
<!ELEMENT FxnSet_readingFrame (%INTEGER;)>
<!-- variation allele: * suffix indicates allele of contig at this location -->
<!ELEMENT FxnSet_allele (#PCDATA)>
<!-- translated amino acid residue for allele -->
<!ELEMENT FxnSet_residue (#PCDATA)>
<!-- position of the variant residue in peptide sequence -->
<!ELEMENT FxnSet_aaPosition (%INTEGER;)>
<!-- 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 (
Assembly_dbSnpBuild,
Assembly_genomeBuild,
Assembly_groupLabel?,
Assembly_assemblySource?,
Assembly_current?,
Assembly_reference?,
Assembly_component?,
Assembly_snpStat)>
<!-- dbSNP build number defining the rsid set aligned to this assembly -->
<!ELEMENT Assembly_dbSnpBuild (%INTEGER;)>
<!-- assembly build number with possible 'subbuild' version numbers to reflect updates in gene annotation (human e.g. 34_3, 35_1, 36_1) -->
<!ELEMENT Assembly_genomeBuild (#PCDATA)>
<!-- 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. -->
<!ELEMENT Assembly_groupLabel (#PCDATA)>
<!-- Name of the group(s) or organization(s) that generated the assembly -->
<!ELEMENT Assembly_assemblySource (#PCDATA)>
<!-- Marks the current genomic assembly -->
<!ELEMENT Assembly_current EMPTY>
<!ATTLIST Assembly_current value ( true | false ) #REQUIRED >
<!ELEMENT Assembly_reference EMPTY>
<!ATTLIST Assembly_reference value ( true | false ) #REQUIRED >
<!ELEMENT Assembly_component (Component*)>
<!ELEMENT Assembly_snpStat (
Assembly_snpStat_mapWeight,
Assembly_snpStat_chromCount?,
Assembly_snpStat_placedContigCount?,
Assembly_snpStat_unplacedContigCount?,
Assembly_snpStat_seqlocCount?,
Assembly_snpStat_hapCount?)>
<!-- summary measure of placement precision in the assembly -->
<!ELEMENT Assembly_snpStat_mapWeight %ENUM;>
<!ATTLIST Assembly_snpStat_mapWeight value (
unmapped |
unique-in-contig |
two-hits-in-contig |
less-10-hits |
multiple-hits
) #REQUIRED >
<!-- number of distinct chromosomes in the mapset -->
<!ELEMENT Assembly_snpStat_chromCount (%INTEGER;)>
<!-- number of distinct contigs [ gi | accession[.version] ] in the mapset -->
<!ELEMENT Assembly_snpStat_placedContigCount (%INTEGER;)>
<!-- number of sequence postions to a contig with unknown chromosomal assignment -->
<!ELEMENT Assembly_snpStat_unplacedContigCount (%INTEGER;)>
<!-- total number of sequence positions in the mapset -->
<!ELEMENT Assembly_snpStat_seqlocCount (%INTEGER;)>
<!-- 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 Assembly_snpStat_hapCount (%INTEGER;)>
<!ELEMENT Assay (
Assay_handle?,
Assay_batch?,
Assay_batchId?,
Assay_batchType?,
Assay_molType?,
Assay_sampleSize?,
Assay_population?,
Assay_linkoutUrl?,
Assay_method?,
Assay_taxonomy,
Assay_strains?,
Assay_comment?,
Assay_citation?)>
<!ELEMENT Assay_handle (#PCDATA)>
<!ELEMENT Assay_batch (#PCDATA)>
<!ELEMENT Assay_batchId (%INTEGER;)>
<!ELEMENT Assay_batchType %ENUM;>
<!ATTLIST Assay_batchType value (
snpassay |
validation |
doublehit
) #REQUIRED >
<!ELEMENT Assay_molType %ENUM;>
<!ATTLIST Assay_molType value (
genomic |
cDNA |
mito |
chloro
) #REQUIRED >
<!ELEMENT Assay_sampleSize (%INTEGER;)>
<!ELEMENT Assay_population (#PCDATA)>
<!ELEMENT Assay_linkoutUrl (#PCDATA)>
<!ELEMENT Assay_method (
Assay_method_name?,
Assay_method_id?,
Assay_method_exception)>
<!-- Submitters method identifier -->
<!ELEMENT Assay_method_name (#PCDATA)>
<!-- dbSNP method identifier -->
<!ELEMENT Assay_method_id (#PCDATA)>
<!-- description of deviation from/addition to given method -->
<!ELEMENT Assay_method_exception (#PCDATA)>
<!ELEMENT Assay_taxonomy (
Assay_taxonomy_id,
Assay_taxonomy_organism?)>
<!-- NCBI taxonomy ID for variation -->
<!ELEMENT Assay_taxonomy_id (%INTEGER;)>
<!ELEMENT Assay_taxonomy_organism (#PCDATA)>
<!ELEMENT Assay_strains (Assay_strains_E*)>
<!ELEMENT Assay_strains_E (#PCDATA)>
<!ELEMENT Assay_comment (#PCDATA)>
<!ELEMENT Assay_citation (Assay_citation_E*)>
<!ELEMENT Assay_citation_E (#PCDATA)>
<!-- URL value from dbSNP_main.BaseURL links table. attributes provide context information and URL id that is referenced within individual refSNP objects. -->
<!ELEMENT BaseURL (
BaseURL_urlId?,
BaseURL_resourceName?,
BaseURL_resourceId?,
BaseURL_baseURL)>
<!-- Resource identifier from dbSNP_main.baseURL. -->
<!ELEMENT BaseURL_urlId (%INTEGER;)>
<!-- Name of linked resource -->
<!ELEMENT BaseURL_resourceName (#PCDATA)>
<!-- identifier expected by resource for URL -->
<!ELEMENT BaseURL_resourceId (#PCDATA)>
<!ELEMENT BaseURL_baseURL (#PCDATA)>
<!ELEMENT PrimarySequence (
PrimarySequence_dbSnpBuild,
PrimarySequence_gi,
PrimarySequence_source?,
PrimarySequence_accession?,
PrimarySequence_mapLoc)>
<!ELEMENT PrimarySequence_dbSnpBuild (%INTEGER;)>
<!ELEMENT PrimarySequence_gi (%INTEGER;)>
<!ELEMENT PrimarySequence_source %ENUM;>
<!ATTLIST PrimarySequence_source value (
submitter |
blastmb |
xm
) #REQUIRED >
<!ELEMENT PrimarySequence_accession (#PCDATA)>
<!ELEMENT PrimarySequence_mapLoc (MapLoc*)>
<!-- structure information for SNP -->
<!ELEMENT RsStruct (
RsStruct_protAcc?,
RsStruct_protGi?,
RsStruct_protLoc?,
RsStruct_protResidue?,
RsStruct_rsResidue?,
RsStruct_structGi?,
RsStruct_structLoc?,
RsStruct_structResidue?)>
<!-- accession of the protein with variation -->
<!ELEMENT RsStruct_protAcc (#PCDATA)>
<!-- GI of the protein with variation -->
<!ELEMENT RsStruct_protGi (%INTEGER;)>
<!-- position of the residue for the protein GI -->
<!ELEMENT RsStruct_protLoc (%INTEGER;)>
<!-- residue specified for protein at prot-loc location -->
<!ELEMENT RsStruct_protResidue (#PCDATA)>
<!-- alternative residue specified by variation sequence -->
<!ELEMENT RsStruct_rsResidue (#PCDATA)>
<!-- GI of the structure neighbor -->
<!ELEMENT RsStruct_structGi (%INTEGER;)>
<!-- position of the residue for the structure GI -->
<!ELEMENT RsStruct_structLoc (%INTEGER;)>
<!-- residue specified for protein at struct-loc location -->
<!ELEMENT RsStruct_structResidue (#PCDATA)>
<!-- link data for another resource -->
<!ELEMENT RsLinkout (
RsLinkout_resourceId,
RsLinkout_linkValue)>
<!-- BaseURLList.url_id -->
<!ELEMENT RsLinkout_resourceId (#PCDATA)>
<!-- value to append to ResourceURL.base-url for complete link -->
<!ELEMENT RsLinkout_linkValue (#PCDATA)>
<!ELEMENT Component (
Component_componentType?,
Component_ctgId?,
Component_accession?,
Component_name?,
Component_chromosome?,
Component_start?,
Component_end?,
Component_orientation?,
Component_gi?,
Component_groupTerm?,
Component_contigLabel?,
Component_mapLoc)>
<!-- type of component: chromosome, contig, gene_region, etc. -->
<!ELEMENT Component_componentType %ENUM;>
<!ATTLIST Component_componentType value (
contig |
mrna
) #REQUIRED >
<!-- dbSNP contig_id used to join on contig hit / mapset data to these assembly properties -->
<!ELEMENT Component_ctgId (%INTEGER;)>
<!-- Accession[.version] for the sequence component -->
<!ELEMENT Component_accession (#PCDATA)>
<!-- contig name defined as either a submitter local id, element of a whole genome assembly set, or internal NCBI local id -->
<!ELEMENT Component_name (#PCDATA)>
<!-- Organism appropriate chromosome tag, 'Un' reserved for default case of unplaced components -->
<!ELEMENT Component_chromosome (#PCDATA)>
<!-- component starting position on the chromosome (base 0 inclusive) -->
<!ELEMENT Component_start (%INTEGER;)>
<!-- component ending position on the chromosome (base 0 inclusive) -->
<!ELEMENT Component_end (%INTEGER;)>
<!-- orientation of this component to chromosome, forward (fwd) = 0, reverse (rev) = 1, unknown = NULL in ContigInfo.orient. -->
<!ELEMENT Component_orientation %ENUM;>
<!ATTLIST Component_orientation value (
fwd |
rev |
unknown
) #REQUIRED >
<!-- NCBI gi for component sequence (equivalent to accession.version) for nucleotide sequence. -->
<!ELEMENT Component_gi (#PCDATA)>
<!-- Identifier label for the genome assembly that defines the contigs in this mapset and their placement within the organism genome. -->
<!ELEMENT Component_groupTerm (#PCDATA)>
<!-- Display label for component -->
<!ELEMENT Component_contigLabel (#PCDATA)>
<!ELEMENT Component_mapLoc (MapLoc*)>
|