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add current DTD for clinvar esummary (#4619)
* added current DTD for clinvar esummary * added to contrib * fixed contrib
This commit is contained in:
Rudolf Koopmann
GitHub
314
Bio/Entrez/DTDs/esummary_clinvar.dtd
Normal file
314
Bio/Entrez/DTDs/esummary_clinvar.dtd
Normal file
@ -0,0 +1,314 @@
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<!-- DocSum DTD for clinvar database -->
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<!--~~ !dtd
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~~json
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<json type='esummary' version='0.3'>
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<config lcnames='true'/>
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</json>
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~~-->
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<!ENTITY % T_string "(#PCDATA)">
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<!-- Members definition of Structure type: T_variation_xref -->
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<!ELEMENT db_source %T_string;>
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<!ELEMENT db_id %T_string;>
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<!-- Definition of Structure type: T_variation_xref -->
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<!--~~ <variation_xref>
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~~json <object/>
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~~-->
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<!ENTITY % T_variation_xref "(
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db_source?,
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db_id?
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)
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">
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<!-- Definition of List type: T_VariationXRefList -->
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<!ELEMENT variation_xref %T_variation_xref;>
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<!ENTITY % T_VariationXRefList "(variation_xref)*">
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<!-- Definition of List type: T_AliasesType -->
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<!ELEMENT string %T_string;>
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<!ENTITY % T_AliasesType "(string)*">
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<!-- Members definition of Structure type: T_assembly_set -->
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<!ELEMENT status %T_string;>
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<!ELEMENT assembly_name %T_string;>
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<!ELEMENT chr %T_string;>
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<!ELEMENT band %T_string;>
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<!ELEMENT start %T_string;>
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<!ELEMENT stop %T_string;>
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<!ELEMENT inner_start %T_string;>
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<!ELEMENT inner_stop %T_string;>
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<!ELEMENT outer_start %T_string;>
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<!ELEMENT outer_stop %T_string;>
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<!ELEMENT display_start %T_string;>
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<!ELEMENT display_stop %T_string;>
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<!ELEMENT assembly_acc_ver %T_string;>
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<!ELEMENT annotation_release %T_string;>
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<!ELEMENT alt %T_string;>
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<!ELEMENT ref %T_string;>
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<!-- Definition of Structure type: T_assembly_set -->
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<!--~~ <assembly_set>
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~~json <object/>
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~~-->
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<!ENTITY % T_assembly_set "(
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status?,
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assembly_name?,
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chr?,
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band?,
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start?,
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stop?,
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inner_start?,
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inner_stop?,
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outer_start?,
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outer_stop?,
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display_start?,
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display_stop?,
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assembly_acc_ver?,
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annotation_release?,
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alt?,
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ref?
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)
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">
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<!-- Definition of List type: T_VariationLocType -->
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<!ELEMENT assembly_set %T_assembly_set;>
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<!ENTITY % T_VariationLocType "(assembly_set)*">
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<!-- Members definition of Structure type: T_allele_freq -->
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<!ELEMENT source %T_string;>
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<!ELEMENT value %T_string;>
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<!ELEMENT minor_allele %T_string;>
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<!-- Definition of Structure type: T_allele_freq -->
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<!--~~ <allele_freq>
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~~json <object/>
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~~-->
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<!ENTITY % T_allele_freq "(
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source?,
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value?,
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minor_allele?
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)
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">
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<!-- Definition of List type: T_AlleleFreqSetType -->
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<!ELEMENT allele_freq %T_allele_freq;>
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<!ENTITY % T_AlleleFreqSetType "(allele_freq)*">
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<!-- Members definition of Structure type: T_variation -->
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<!ELEMENT measure_id %T_string;>
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<!ELEMENT variation_xrefs %T_VariationXRefList;>
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<!ELEMENT variation_name %T_string;>
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<!ELEMENT cdna_change %T_string;>
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<!ELEMENT aliases %T_AliasesType;>
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<!ELEMENT variation_loc %T_VariationLocType;>
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<!ELEMENT allele_freq_set %T_AlleleFreqSetType;>
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<!ELEMENT variant_type %T_string;>
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<!ELEMENT canonical_spdi %T_string;>
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<!-- Definition of Structure type: T_variation -->
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<!--~~ <variation>
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~~json <object/>
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~~-->
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<!ENTITY % T_variation "(
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measure_id?,
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variation_xrefs?,
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variation_name?,
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cdna_change?,
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aliases?,
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variation_loc?,
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allele_freq_set?,
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variant_type?,
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canonical_spdi?
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)
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">
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<!-- Definition of List type: T_VariationSetType -->
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<!ELEMENT variation %T_variation;>
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<!ENTITY % T_VariationSetType "(variation)*">
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<!-- Definition of List type: T_SCVType -->
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<!-- Already defined ...
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string as %T_string;>
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... Already defined -->
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<!ENTITY % T_SCVType "(string)*">
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<!-- Definition of List type: T_RCVType -->
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<!-- Already defined ...
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string as %T_string;>
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... Already defined -->
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<!ENTITY % T_RCVType "(string)*">
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<!-- Members definition of Structure type: T_SupportingSubmissionsType -->
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<!ELEMENT scv %T_SCVType;>
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<!ELEMENT rcv %T_RCVType;>
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<!-- Definition of Structure type: T_SupportingSubmissionsType -->
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<!--~~ <SupportingSubmissionsType>
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~~json <object/>
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~~-->
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<!ENTITY % T_SupportingSubmissionsType "(
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scv?,
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rcv?
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)
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">
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<!ENTITY % T_date "(#PCDATA)">
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<!-- Members definition of Structure type: T_trait_xref -->
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<!-- Already defined ...
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db_source as %T_string;
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... Already defined -->
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<!-- Already defined ...
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db_id as %T_string;
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... Already defined -->
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<!-- Definition of Structure type: T_trait_xref -->
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<!--~~ <trait_xref>
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~~json <object/>
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~~-->
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<!ENTITY % T_trait_xref "(
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db_source?,
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db_id?
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)
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">
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<!-- Definition of List type: T_TraitXrefsType -->
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<!ELEMENT trait_xref %T_trait_xref;>
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<!ENTITY % T_TraitXrefsType "(trait_xref)*">
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<!-- Members definition of Structure type: T_trait -->
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<!ELEMENT trait_xrefs %T_TraitXrefsType;>
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<!ELEMENT trait_name %T_string;>
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<!-- Definition of Structure type: T_trait -->
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<!--~~ <trait>
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~~json <object/>
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~~-->
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<!ENTITY % T_trait "(
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trait_xrefs?,
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trait_name?
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)
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">
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<!-- Definition of List type: T_TraitSetType -->
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<!ELEMENT trait %T_trait;>
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<!ENTITY % T_TraitSetType "(trait)*">
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<!-- Members definition of Structure type: T_ClassificationType -->
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<!ELEMENT description %T_string;>
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<!ELEMENT last_evaluated %T_date;>
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<!ELEMENT review_status %T_string;>
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<!ELEMENT trait_set %T_TraitSetType;>
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<!-- Definition of Structure type: T_ClassificationType -->
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<!--~~ <ClassificationType>
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~~json <object/>
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~~-->
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<!ENTITY % T_ClassificationType "(
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description?,
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last_evaluated?,
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review_status?,
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trait_set?
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)
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">
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<!-- Members definition of Structure type: T_gene -->
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<!ELEMENT symbol %T_string;>
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<!ELEMENT GeneID %T_string;>
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<!ELEMENT strand %T_string;>
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<!-- Already defined ...
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source as %T_string;
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... Already defined -->
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<!-- Definition of Structure type: T_gene -->
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<!--~~ <gene>
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~~json <object/>
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~~-->
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<!ENTITY % T_gene "(
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symbol?,
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GeneID?,
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strand?,
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source?
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)
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">
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<!-- Definition of List type: T_GenesType -->
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<!ELEMENT gene %T_gene;>
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<!ENTITY % T_GenesType "(gene)*">
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<!-- Definition of List type: T_MolecularConsequenceListType -->
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<!-- Already defined ...
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string as %T_string;>
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... Already defined -->
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<!ENTITY % T_MolecularConsequenceListType "(string)*">
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<!-- Members definition of Structure type: T_DocSum -->
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<!ELEMENT obj_type %T_string;>
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<!ELEMENT accession %T_string;>
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<!ELEMENT accession_version %T_string;>
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<!ELEMENT title %T_string;>
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<!ELEMENT variation_set %T_VariationSetType;>
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<!ELEMENT supporting_submissions %T_SupportingSubmissionsType;>
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<!ELEMENT germline_classification %T_ClassificationType;>
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<!ELEMENT clinical_impact_classification %T_ClassificationType;>
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<!ELEMENT oncogenicity_classification %T_ClassificationType;>
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<!ELEMENT record_status %T_string;>
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<!ELEMENT gene_sort %T_string;>
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<!ELEMENT chr_sort %T_string;>
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<!ELEMENT location_sort %T_string;>
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<!ELEMENT variation_set_name %T_string;>
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<!ELEMENT variation_set_id %T_string;>
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<!ELEMENT genes %T_GenesType;>
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<!ELEMENT molecular_consequence_list %T_MolecularConsequenceListType;>
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<!ELEMENT protein_change %T_string;>
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<!ELEMENT fda_recognized_database %T_string;>
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<!ELEMENT error %T_string;>
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<!-- Definition of Structure type: T_DocSum -->
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<!--~~ <DocumentSummary>
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~~json <object name='@uid'/>
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~~-->
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<!ENTITY % T_DocSum "((
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obj_type?,
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accession?,
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accession_version?,
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title?,
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variation_set?,
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supporting_submissions?,
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germline_classification?,
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clinical_impact_classification?,
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oncogenicity_classification?,
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record_status?,
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gene_sort?,
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chr_sort?,
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location_sort?,
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variation_set_name?,
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variation_set_id?,
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genes?,
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molecular_consequence_list?,
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protein_change?,
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fda_recognized_database?
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)
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">
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<!ELEMENT DocumentSummary %T_DocSum;>
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<!ATTLIST DocumentSummary uid CDATA #IMPLIED>
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<!ELEMENT DbBuild %T_string;>
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<!ELEMENT DocumentSummarySet (DbBuild?, DocumentSummary*)>
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<!ATTLIST DocumentSummarySet status CDATA #REQUIRED>
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<!--~~ <DocumentSummarySet>
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~~json
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<object key="result">
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<array key="uids" select='DocumentSummary/@uid'/>
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<members select='DocumentSummary'/>
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</object>
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~~-->
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<!--~~ <eSummaryResult>
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~~ json <member/>
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~~-->
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<!ELEMENT eSummaryResult (DocumentSummarySet?)>
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@ -284,6 +284,7 @@ please open an issue on GitHub or mention it on the mailing list.
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- Robert Sawicki <https://github.com/Battlesheepu>
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- Rodrigo Dorantes-Gilardi <https://github.com/rodogi>
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- Rona Costello <https://github.com/RonaCostello>
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- Rudolf Koopmann <https://github.com/koopmann>
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- Ryan Stecher <https://github.com/rystecher>
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- Sacha Laurent <https://github.com/Cashalow>
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- Saket Choudhary <https://github.com/saketkc>
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