<!-- ============================================
     ::DATATOOL:: Generated from "seqfeat.asn"
     ::DATATOOL:: by application DATATOOL version 2.3.1
     ::DATATOOL:: on 12/01/2011 23:05:19
     ============================================ -->

<!-- ============================================ -->
<!-- This section is mapped from module "NCBI-Variation"
================================================= -->

<!--
*** Variation-ref ***********************************************
*
*  Specification of variation features
*
-->

<!-- Elements used by other modules:
          Variation-ref,
          Variation-inst,
          VariantProperties,
          Population-data,
          Phenotype -->

<!-- Elements referenced from other modules:
          Int-fuzz,
          User-object,
          Object-id,
          Dbtag FROM NCBI-General,
          Seq-literal FROM NCBI-Sequence,
          SubSource FROM NCBI-BioSource,
          Seq-loc FROM NCBI-Seqloc,
          Pub FROM NCBI-Pub -->
<!-- ============================================ -->

<!--
 

 Historically, the dbSNP definitions document data structures used in the
 processing and annotation of variations by the dbSNP group.  The intention
 is to provide information to clients that reflect internal information
 produced during the mapping of SNPs
 

-->
<!ELEMENT VariantProperties (
        VariantProperties_version, 
        VariantProperties_resource-link?, 
        VariantProperties_gene-location?, 
        VariantProperties_effect?, 
        VariantProperties_mapping?, 
        VariantProperties_map-weight?, 
        VariantProperties_frequency-based-validation?, 
        VariantProperties_genotype?, 
        VariantProperties_project-data?, 
        VariantProperties_quality-check?, 
        VariantProperties_confidence?, 
        VariantProperties_other-validation?, 
        VariantProperties_allele-origin?, 
        VariantProperties_allele-state?, 
        VariantProperties_allele-frequency?, 
        VariantProperties_is-ancestral-allele?)>

<!ELEMENT VariantProperties_version (%INTEGER;)>
<!--
 NOTE:
 The format for most of these values is as an integer
 Unless otherwise noted, these integers represent a bitwise OR (= simple
 sum) of the possible values, and as such, these values represent the
 specific bit flags that may be set for each of the possible attributes
 here.
-->
<!ELEMENT VariantProperties_resource-link (%INTEGER;)>

<!--
    preserved	-  Clinical, Pubmed, Cited, (0x01)
    provisional	-  Provisional Third Party Annotations (0x02)
    has3D	-  Has 3D strcture SNP3D table (0x04)
    submitterLinkout	-  SNP->SubSNP->Batch link_out (0x08)
    clinical	-  Clinical if LSDB, OMIM, TPA, Diagnostic (0x10)
    genotypeKit	-  Marker exists on high density genotyping kit
         (0x20)
-->
<!ATTLIST VariantProperties_resource-link value (
        preserved |
        provisional |
        has3D |
        submitterLinkout |
        clinical |
        genotypeKit
        ) #IMPLIED >


<!ELEMENT VariantProperties_gene-location (%INTEGER;)>

<!--
    in-gene	-  Sequence intervals covered by a gene ID but not
         having an aligned transcript (0x01)
    near-gene-5	-  Within 2kb of the 5' end of a gene feature
    near-gene-3	-  Within 0.5kb of the 3' end of a gene feature
    intron	-  In Intron (0x08)
    donor	-  In donor splice-site (0x10)
    acceptor	-  In acceptor splice-site (0x20)
    utr-5	-  In 5' UTR (0x40)
    utr-3	-  In 3' UTR (0x80)
    in-start-codon	-  the variant is observed in a start codon
         (0x100)
    in-stop-codon	-  the variant is observed in a stop codon
         (0x200)
    intergenic	-  variant located between genes (0x400)
    conserved-noncoding	-  variant is located in a conserved
         non-coding region (0x800)
-->
<!ATTLIST VariantProperties_gene-location value (
        in-gene |
        near-gene-5 |
        near-gene-3 |
        intron |
        donor |
        acceptor |
        utr-5 |
        utr-3 |
        in-start-codon |
        in-stop-codon |
        intergenic |
        conserved-noncoding
        ) #IMPLIED >


<!ELEMENT VariantProperties_effect (%INTEGER;)>

<!--
    no-change	-  known to cause no functional changes
         since 0 does not combine with any other bit
         value, 'no-change' specifically implies that
         there are no consequences
    synonymous	-  one allele in the set does not change the encoded
         amino acid (0x1)
    nonsense	-  one allele in the set changes to STOP codon
         (TER).  (0x2)
    missense	-  one allele in the set changes protein peptide
         (0x4)
    frameshift	-  one allele in the set changes all downstream
         amino acids (0x8)
    up-regulator	-  the variant causes increased transcription
         (0x10)
    down-regulator	-  the variant causes decreased transcription
         (0x20)
    stop-gain	-  reference codon is not stop codon, but the snp
         variant allele changes the codon to a
         terminating codon.
    stop-loss	-  reverse of STOP-GAIN: reference codon is a
         stop codon, but a snp variant allele changes
         the codon to a non-terminating codon.
-->
<!ATTLIST VariantProperties_effect value (
        no-change |
        synonymous |
        nonsense |
        missense |
        frameshift |
        up-regulator |
        down-regulator |
        methylation |
        stop-gain |
        stop-loss
        ) #IMPLIED >


<!ELEMENT VariantProperties_mapping (%INTEGER;)>

<!--
    has-other-snp	-  Another SNP has the same mapped positions
         on reference assembly (0x01)
    has-assembly-conflict	-  Weight 1 or 2 SNPs that map to different
         chromosomes on different assemblies (0x02)
    is-assembly-specific	-  Only maps to 1 assembly (0x04)
-->
<!ATTLIST VariantProperties_mapping value (
        has-other-snp |
        has-assembly-conflict |
        is-assembly-specific
        ) #IMPLIED >

<!--
 map-weight captures specificity of placement
 NOTE: This is *NOT* a bitfield
-->
<!ELEMENT VariantProperties_map-weight (%INTEGER;)>
<!ATTLIST VariantProperties_map-weight value (
        is-uniquely-placed |
        placed-twice-on-same-chrom |
        placed-twice-on-diff-chrom |
        many-placements
        ) #IMPLIED >


<!ELEMENT VariantProperties_frequency-based-validation (%INTEGER;)>

<!--
    is-mutation	-  low frequency variation that is cited in
         journal or other reputable sources (0x01)
    above-5pct-all	-  >5% minor allele freq in each and all
         populations (0x02)
    above-5pct-1plus	-  >5% minor allele freq in 1+ populations (0x04)
    validated	-  Bit is set if the variant has a minor allele
         observed in two or more separate chromosomes
    above-1pct-all	-  >1% minor allele freq in each and all
         populations (0x10)
    above-1pct-1plus	-  >1% minor allele freq in 1+ populations (0x20)
-->
<!ATTLIST VariantProperties_frequency-based-validation value (
        is-mutation |
        above-5pct-all |
        above-5pct-1plus |
        validated |
        above-1pct-all |
        above-1pct-1plus
        ) #IMPLIED >


<!ELEMENT VariantProperties_genotype (%INTEGER;)>

<!--
    in-haplotype-set	-  Exists in a haplotype tagging set (0x01)
    has-genotypes	-  SNP has individual genotype (0x02)
-->
<!ATTLIST VariantProperties_genotype value (
        in-haplotype-set |
        has-genotypes
        ) #IMPLIED >


<!--
 project IDs are IDs from BioProjects
 in order to report information about project relationships, we
 require projects to be registered
 This field in many ways duplicates dbxrefs; however, the
 intention of this field is to more adequately reflect
 ownership and data source

 11/9/2010: DO NOT USE
 This field was changed in the spec in a breaking way; using it will
 break clients.  We are officially suppressing / abandoning this field.
 Clients who need to use this should instead place the data in
 Seq-feat.dbxref, using the db name 'BioProject'
-->
<!ELEMENT VariantProperties_project-data (VariantProperties_project-data_E*)>


<!ELEMENT VariantProperties_project-data_E (%INTEGER;)>

<!ELEMENT VariantProperties_quality-check (%INTEGER;)>

<!--
    contig-allele-missing	-  Reference sequence allele at the mapped
         position is not present in the SNP
         allele list, adjusted for orientation
         (0x01)
    withdrawn-by-submitter	-  One member SS is withdrawn by submitter
         (0x02)
    non-overlapping-alleles	-  RS set has 2+ alleles from different
         submissions and these sets share no
         alleles in common (0x04)
    strain-specific	-  Straing specific fixed difference (0x08)
    genotype-conflict	-  Has Genotype Conflict (0x10)
-->
<!ATTLIST VariantProperties_quality-check value (
        contig-allele-missing |
        withdrawn-by-submitter |
        non-overlapping-alleles |
        strain-specific |
        genotype-conflict
        ) #IMPLIED >


<!ELEMENT VariantProperties_confidence (%INTEGER;)>
<!ATTLIST VariantProperties_confidence value (
        unknown |
        likely-artifact |
        other
        ) #IMPLIED >


<!--
 has this variant been validated?
 While a boolean flag offers no subtle distinctions of validation
 methods, occasionally it is only known as a single boolean value
 NOTE: this flag is redundant and should be omitted if more comprehensive
 validation information is present
-->
<!ELEMENT VariantProperties_other-validation EMPTY>
<!ATTLIST VariantProperties_other-validation value ( true | false ) #REQUIRED >

<!--
 origin of this allele, if known
 note that these are powers-of-two, and represent bits; thus, we can
 represent more than one state simultaneously through a bitwise OR
-->
<!ELEMENT VariantProperties_allele-origin (%INTEGER;)>

<!--
    other	-  stopper - 2^31
-->
<!ATTLIST VariantProperties_allele-origin value (
        unknown |
        germline |
        somatic |
        inherited |
        paternal |
        maternal |
        de-novo |
        biparental |
        uniparental |
        not-tested |
        tested-inconclusive |
        not-reported |
        other
        ) #IMPLIED >

<!--
 observed allele state, if known
 NOTE: THIS IS NOT A BITFIELD!
-->
<!ELEMENT VariantProperties_allele-state (%INTEGER;)>
<!ATTLIST VariantProperties_allele-state value (
        unknown |
        homozygous |
        heterozygous |
        hemizygous |
        nullizygous |
        other
        ) #IMPLIED >


<!--
 NOTE:
 'allele-frequency' here refers to the minor allele frequency of the
 default population
-->
<!ELEMENT VariantProperties_allele-frequency (%REAL;)>

<!-- is this variant the ancestral allele? -->
<!ELEMENT VariantProperties_is-ancestral-allele EMPTY>
<!ATTLIST VariantProperties_is-ancestral-allele value ( true | false ) #REQUIRED >


<!ELEMENT Phenotype (
        Phenotype_source?, 
        Phenotype_term?, 
        Phenotype_xref?, 
        Phenotype_clinical-significance?)>

<!ELEMENT Phenotype_source (#PCDATA)>

<!ELEMENT Phenotype_term (#PCDATA)>

<!ELEMENT Phenotype_xref (Dbtag*)>
<!-- does this variant have known clinical significance? -->
<!ELEMENT Phenotype_clinical-significance (%INTEGER;)>
<!ATTLIST Phenotype_clinical-significance value (
        unknown |
        untested |
        non-pathogenic |
        probable-non-pathogenic |
        probable-pathogenic |
        pathogenic |
        drug-response |
        histocompatibility |
        other
        ) #IMPLIED >


<!ELEMENT Population-data (
        Population-data_population, 
        Population-data_genotype-frequency?, 
        Population-data_chromosomes-tested?, 
        Population-data_sample-ids?, 
        Population-data_allele-frequency?, 
        Population-data_flags?)>

<!-- assayed population (e.g. HAPMAP-CEU) -->
<!ELEMENT Population-data_population (#PCDATA)>

<!ELEMENT Population-data_genotype-frequency (%REAL;)>

<!ELEMENT Population-data_chromosomes-tested (%INTEGER;)>

<!ELEMENT Population-data_sample-ids (Object-id*)>

<!ELEMENT Population-data_allele-frequency (%REAL;)>
<!--
 This field is an explicit bit-field
 Valid values should be a bitwise combination (= simple sum)
 of any of the values below
-->
<!ELEMENT Population-data_flags (%INTEGER;)>
<!ATTLIST Population-data_flags value (
        is-default-population |
        is-minor-allele |
        is-rare-allele
        ) #IMPLIED >


<!ELEMENT Ext-loc (
        Ext-loc_id, 
        Ext-loc_location)>

<!ELEMENT Ext-loc_id (Object-id)>

<!ELEMENT Ext-loc_location (Seq-loc)>


<!ELEMENT Variation-ref (
        Variation-ref_id?, 
        Variation-ref_parent-id?, 
        Variation-ref_sample-id?, 
        Variation-ref_other-ids?, 
        Variation-ref_name?, 
        Variation-ref_synonyms?, 
        Variation-ref_description?, 
        Variation-ref_phenotype?, 
        Variation-ref_method?, 
        Variation-ref_population-data?, 
        Variation-ref_variant-prop?, 
        Variation-ref_validated?, 
        Variation-ref_clinical-test?, 
        Variation-ref_allele-origin?, 
        Variation-ref_allele-state?, 
        Variation-ref_allele-frequency?, 
        Variation-ref_is-ancestral-allele?, 
        Variation-ref_pub?, 
        Variation-ref_data, 
        Variation-ref_consequence?, 
        Variation-ref_location?, 
        Variation-ref_ext-locs?, 
        Variation-ref_ext?, 
        Variation-ref_somatic-origin?)>

<!--
 ids (i.e., SNP rsid / ssid, dbVar nsv/nssv)
 expected values include 'dbSNP|rs12334', 'dbSNP|ss12345', 'dbVar|nsv1'

 we relate three kinds of IDs here:
  - our current object's id
  - the id of this object's parent, if it exists
  - the sample ID that this item originates from
-->
<!ELEMENT Variation-ref_id (Dbtag)>

<!ELEMENT Variation-ref_parent-id (Dbtag)>

<!ELEMENT Variation-ref_sample-id (Object-id)>

<!ELEMENT Variation-ref_other-ids (Dbtag*)>

<!--
 names and synonyms
 some variants have well-known canonical names and possible accepted
 synonyms
-->
<!ELEMENT Variation-ref_name (#PCDATA)>

<!ELEMENT Variation-ref_synonyms (Variation-ref_synonyms_E*)>


<!ELEMENT Variation-ref_synonyms_E (#PCDATA)>

<!-- tag for comment and descriptions -->
<!ELEMENT Variation-ref_description (#PCDATA)>

<!-- phenotype -->
<!ELEMENT Variation-ref_phenotype (Phenotype*)>
<!-- sequencing / acuisition method -->
<!ELEMENT Variation-ref_method (Variation-ref_method_E*)>


<!ELEMENT Variation-ref_method_E (%INTEGER;)>
<!ATTLIST Variation-ref_method_E value (
        unknown |
        bac-acgh |
        computational |
        curated |
        digital-array |
        expression-array |
        fish |
        flanking-sequence |
        maph |
        mcd-analysis |
        mlpa |
        oea-assembly |
        oligo-acgh |
        paired-end |
        pcr |
        qpcr |
        read-depth |
        roma |
        rt-pcr |
        sage |
        sequence-alignment |
        sequencing |
        snp-array |
        snp-genoytyping |
        southern |
        western |
        optical-mapping |
        other
        ) #IMPLIED >


<!--
 Note about SNP representation and pretinent fields: allele-frequency,
 population, quality-codes:
 The case of multiple alleles for a SNP would be described by
 parent-feature of type Variation-set.diff-alleles, where the child
 features of type Variation-inst, all at the same location, would
 describe individual alleles.
 population data
 DEPRECATED - do not use
-->
<!ELEMENT Variation-ref_population-data (Population-data*)>

<!-- variant properties bit fields -->
<!ELEMENT Variation-ref_variant-prop (VariantProperties)>

<!--
 has this variant been validated?
 DEPRECATED: new field = VariantProperties.other-validation
-->
<!ELEMENT Variation-ref_validated EMPTY>
<!ATTLIST Variation-ref_validated value ( true | false ) #REQUIRED >


<!--
 link-outs to GeneTests database
 DEPRECATED - do not use
-->
<!ELEMENT Variation-ref_clinical-test (Dbtag*)>
<!--
 origin of this allele, if known
 note that these are powers-of-two, and represent bits; thus, we can
 represent more than one state simultaneously through a bitwise OR
 DEPRECATED: new field = VariantProperties.allele-origin
-->
<!ELEMENT Variation-ref_allele-origin (%INTEGER;)>

<!--
    other	-  stopper - 2^31
-->
<!ATTLIST Variation-ref_allele-origin value (
        unknown |
        germline |
        somatic |
        inherited |
        paternal |
        maternal |
        de-novo |
        biparental |
        uniparental |
        not-tested |
        tested-inconclusive |
        other
        ) #IMPLIED >

<!--
 observed allele state, if known
 DEPRECATED: new field = VariantProperties.allele-state
-->
<!ELEMENT Variation-ref_allele-state (%INTEGER;)>
<!ATTLIST Variation-ref_allele-state value (
        unknown |
        homozygous |
        heterozygous |
        hemizygous |
        nullizygous |
        other
        ) #IMPLIED >


<!--
 NOTE:
 'allele-frequency' here refers to the minor allele frequency of the
 default population
 DEPRECATED: new field = VariantProperties.allele-frequency
-->
<!ELEMENT Variation-ref_allele-frequency (%REAL;)>

<!--
 is this variant the ancestral allele?
 DEPRECATED: new field = VariantProperties.is-ancestral-allele
-->
<!ELEMENT Variation-ref_is-ancestral-allele EMPTY>
<!ATTLIST Variation-ref_is-ancestral-allele value ( true | false ) #REQUIRED >


<!--
 publication support.
 Note: made this pub instead of pub-equiv, since
 Pub can be pub-equiv and pub-equiv is a set of pubs, but it looks like
 Pub is more often used as top-level container
 DEPRECATED - do not use; use Seq-feat.dbxref instead
-->
<!ELEMENT Variation-ref_pub (Pub)>

<!ELEMENT Variation-ref_data (
        Variation-ref_data_unknown | 
        Variation-ref_data_note | 
        Variation-ref_data_uniparental-disomy | 
        Variation-ref_data_instance | 
        Variation-ref_data_set | 
        Variation-ref_data_complex)>

<!ELEMENT Variation-ref_data_unknown EMPTY>

<!--free-form -->
<!ELEMENT Variation-ref_data_note (#PCDATA)>

<!ELEMENT Variation-ref_data_uniparental-disomy EMPTY>

<!-- actual sequence-edit at feat.location -->
<!ELEMENT Variation-ref_data_instance (Variation-inst)>
<!--
 Set of related Variations.
 Location of the set equals to the union of member locations
-->
<!ELEMENT Variation-ref_data_set (
        Variation-ref_data_set_type, 
        Variation-ref_data_set_variations, 
        Variation-ref_data_set_name?)>

<!ELEMENT Variation-ref_data_set_type (%INTEGER;)>

<!--
    compound	-  complex change at the same location on the
         same molecule
    products	-  different products arising from the same
         variation in a precursor, e.g. r.[13g>a,
         13_88del]
    haplotype	-  changes on the same allele, e.g
         r.[13g>a;15u>c]
    genotype	-  changes on different alleles in the same
         genotype, e.g. g.[476C>T]+[476C>T]
    mosaic	-  different genotypes in the same individual
    individual	-  same organism; allele relationship unknown,
         e.g. g.[476C>T(+)183G>C]
    population	-  population
    alleles	-  set represents a set of observed alleles
    package	-  set represents a package of observations at
         a given location, generally containing
         asserted + reference
-->
<!ATTLIST Variation-ref_data_set_type value (
        unknown |
        compound |
        products |
        haplotype |
        genotype |
        mosaic |
        individual |
        population |
        alleles |
        package |
        other
        ) #IMPLIED >


<!ELEMENT Variation-ref_data_set_variations (Variation-ref*)>

<!ELEMENT Variation-ref_data_set_name (#PCDATA)>

<!--
 variant is a complex and undescribed change at the location
 This type of variant is known to occur in dbVar submissions
-->
<!ELEMENT Variation-ref_data_complex EMPTY>

<!ELEMENT Variation-ref_consequence (Variation-ref_consequence_E*)>


<!ELEMENT Variation-ref_consequence_E (
        Variation-ref_consequence_E_unknown | 
        Variation-ref_consequence_E_splicing | 
        Variation-ref_consequence_E_note | 
        Variation-ref_consequence_E_variation | 
        Variation-ref_consequence_E_frameshift | 
        Variation-ref_consequence_E_loss-of-heterozygosity)>

<!ELEMENT Variation-ref_consequence_E_unknown EMPTY>

<!--some effect on splicing -->
<!ELEMENT Variation-ref_consequence_E_splicing EMPTY>

<!--freeform -->
<!ELEMENT Variation-ref_consequence_E_note (#PCDATA)>

<!--
 Describe resulting variation in the product, e.g. missense,
 nonsense, silent, neutral, etc in a protein, that arises from
 THIS variation.
-->
<!ELEMENT Variation-ref_consequence_E_variation (Variation-ref)>
<!-- see http://www.hgvs.org/mutnomen/recs-prot.html -->
<!ELEMENT Variation-ref_consequence_E_frameshift (
        Variation-ref_consequence_E_frameshift_phase?, 
        Variation-ref_consequence_E_frameshift_x-length?)>

<!ELEMENT Variation-ref_consequence_E_frameshift_phase (%INTEGER;)>

<!ELEMENT Variation-ref_consequence_E_frameshift_x-length (%INTEGER;)>

<!ELEMENT Variation-ref_consequence_E_loss-of-heterozygosity (
        Variation-ref_consequence_E_loss-of-heterozygosity_reference?, 
        Variation-ref_consequence_E_loss-of-heterozygosity_test?)>

<!--
 In germline comparison, it will be reference genome assembly
 (default) or reference/normal population. In somatic mutation,
 it will be a name of the normal tissue.
-->
<!ELEMENT Variation-ref_consequence_E_loss-of-heterozygosity_reference (#PCDATA)>

<!-- Name of the testing subject type or the testing tissue. -->
<!ELEMENT Variation-ref_consequence_E_loss-of-heterozygosity_test (#PCDATA)>

<!--
 Observed location, if different from the parent set or feature.location.
 DEPRECATED - do not use
-->
<!ELEMENT Variation-ref_location (Seq-loc)>

<!--
 reference other locs, e.g. mapped source
 DEPRECATED - do not use
-->
<!ELEMENT Variation-ref_ext-locs (Ext-loc*)>

<!-- DEPRECATED - do not use; use Seq-feat.exts instead -->
<!ELEMENT Variation-ref_ext (User-object)>

<!ELEMENT Variation-ref_somatic-origin (Variation-ref_somatic-origin_E*)>


<!ELEMENT Variation-ref_somatic-origin_E (
        Variation-ref_somatic-origin_E_source?, 
        Variation-ref_somatic-origin_E_condition?)>

<!-- description of the somatic origin itself -->
<!ELEMENT Variation-ref_somatic-origin_E_source (SubSource)>
<!-- condition related to this origin's type -->
<!ELEMENT Variation-ref_somatic-origin_E_condition (
        Variation-ref_somatic-origin_E_condition_description?, 
        Variation-ref_somatic-origin_E_condition_object-id?)>

<!ELEMENT Variation-ref_somatic-origin_E_condition_description (#PCDATA)>

<!-- reference to BioTerm / other descriptive database -->
<!ELEMENT Variation-ref_somatic-origin_E_condition_object-id (Dbtag*)>


<!ELEMENT Delta-item (
        Delta-item_seq?, 
        Delta-item_multiplier?, 
        Delta-item_multiplier-fuzz?, 
        Delta-item_action?)>

<!ELEMENT Delta-item_seq (
        Delta-item_seq_literal | 
        Delta-item_seq_loc | 
        Delta-item_seq_this)>

<!ELEMENT Delta-item_seq_literal (Seq-literal)>

<!ELEMENT Delta-item_seq_loc (Seq-loc)>

<!--same location as variation-ref itself -->
<!ELEMENT Delta-item_seq_this EMPTY>

<!--
 Multiplier allows representing a tandem, e.g.  ATATAT as AT*3
 This allows describing CNV/SSR where delta=self  with a
 multiplier which specifies the count of the repeat unit.
assumed 1 if not specified.
-->
<!ELEMENT Delta-item_multiplier (%INTEGER;)>

<!ELEMENT Delta-item_multiplier-fuzz (Int-fuzz)>

<!ELEMENT Delta-item_action (%INTEGER;)>

<!--
    morph	-  replace len(seq) positions starting with location.start with seq
    offset	-  go downstream by distance specified by multiplier (upstream if < 0),
         in genomic context.
    del-at	-  excise sequence at location
         if multiplier is specified, delete len(location)*multiplier
         positions downstream
    ins-before	-  insert seq before the location.start
-->
<!ATTLIST Delta-item_action value (
        morph |
        offset |
        del-at |
        ins-before
        ) #IMPLIED >


<!-- Variation instance -->
<!ELEMENT Variation-inst (
        Variation-inst_type, 
        Variation-inst_delta, 
        Variation-inst_observation?)>

<!ELEMENT Variation-inst_type (%INTEGER;)>

<!--
    unknown	-  delta=[]
    identity	-  delta=[]
    inv	-  delta=[del, ins.seq=
         RevComp(variation-location)]
    snv	-  delta=[morph of length 1]
         NOTE: this is snV not snP; the latter
         requires frequency-based validation to be
         established in VariantProperties
         the strict definition of SNP is an SNV with
         an established population frequency of at
         least 1% in at least 1 popuplation
    mnp	-  delta=[morph of length >1]
    delins	-  delta=[del, ins]
    del	-  delta=[del]
    ins	-  delta=[ins]
    microsatellite	-  delta=[del, ins.seq= repeat-unit with fuzzy
         multiplier]
         variation-location is the microsat expansion
         on the sequence
    transposon	-  delta=[del, ins.seq= known donor or 'this']
         variation-location is equiv of transposon
         locs.
    cnv	-  delta=[del, ins= 'this' with fuzzy
         multiplier]
    direct-copy	-  delta=[ins.seq= upstream location on the
         same strand]
    rev-direct-copy	-  delta=[ins.seq= downstream location on the
         same strand]
    inverted-copy	-  delta=[ins.seq= upstream location on the
         opposite strand]
    everted-copy	-  delta=[ins.seq= downstream location on the
         opposite strand]
    translocation	-  delta=like delins
    prot-missense	-  delta=[morph of length 1]
    prot-nonsense	-  delta=[del]; variation-location is the tail
         of the protein being truncated
    prot-neutral	-  delta=[morph of length 1]
    prot-silent	-  delta=[morph of length 1, same AA as at
         variation-location]
    prot-other	-  delta=any
    other	-  delta=any
-->
<!ATTLIST Variation-inst_type value (
        unknown |
        identity |
        inv |
        snv |
        mnp |
        delins |
        del |
        ins |
        microsatellite |
        transposon |
        cnv |
        direct-copy |
        rev-direct-copy |
        inverted-copy |
        everted-copy |
        translocation |
        prot-missense |
        prot-nonsense |
        prot-neutral |
        prot-silent |
        prot-other |
        other
        ) #IMPLIED >


<!-- Sequence that replaces the location, in biological order. -->
<!ELEMENT Variation-inst_delta (Delta-item*)>
<!--
 'observation' is used to label items in a Variation-ref package
 This field is explicitly a bit-field, so the bitwise OR (= sum) of any
 of the values may be observed.
-->
<!ELEMENT Variation-inst_observation (%INTEGER;)>

<!--
    asserted	-  inst represents the asserted base at a
         position
    reference	-  inst represents the reference base at the
         position
    variant	-  inst represent the observed variant at a
         given position
-->
<!ATTLIST Variation-inst_observation value (
        asserted |
        reference |
        variant
        ) #IMPLIED >