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<!-- ============================================
::DATATOOL:: Generated from "entrezgene.asn"
::DATATOOL:: by application DATATOOL version 2.4.4
::DATATOOL:: on 02/14/2013 23:04:00
============================================ -->
<!-- ============================================ -->
<!-- This section is mapped from module "NCBI-Entrezgene"
================================================= -->
<!--
$Revision: 389081 $
**********************************************************************
NCBI Entrezgene
by James Ostell, 2001
Generic "Gene" object for Entrez Genes
This object is designed to incorporate a subset of information from
LocusLink and from records in Entrez Genomes to provide indexing,
linkage, and a useful summary report in Entrez for "Genes"
**********************************************************************
-->
<!-- Elements used by other modules:
Entrezgene,
Entrezgene-Set,
Gene-track,
Gene-commentary -->
<!-- Elements referenced from other modules:
Gene-ref FROM NCBI-Gene,
Prot-ref FROM NCBI-Protein,
BioSource FROM NCBI-BioSource,
RNA-ref FROM NCBI-RNA,
Dbtag,
Date FROM NCBI-General,
Seq-loc FROM NCBI-Seqloc,
Pub FROM NCBI-Pub -->
<!-- ============================================ -->
<!--
********************************************
Entrezgene is the "document" indexed in Entrez
and presented in the full display
It also contains the Entrez ID and date information
*******************************************
-->
<!ELEMENT Entrezgene (
Entrezgene_track-info?,
Entrezgene_type,
Entrezgene_source,
Entrezgene_gene,
Entrezgene_prot?,
Entrezgene_rna?,
Entrezgene_summary?,
Entrezgene_location?,
Entrezgene_gene-source?,
Entrezgene_locus?,
Entrezgene_properties?,
Entrezgene_refgene?,
Entrezgene_homology?,
Entrezgene_comments?,
Entrezgene_unique-keys?,
Entrezgene_xtra-index-terms?,
Entrezgene_xtra-properties?,
Entrezgene_xtra-iq?,
Entrezgene_non-unique-keys?)>
<!-- not in submission, but in retrieval -->
<!ELEMENT Entrezgene_track-info (Gene-track)>
<!-- type of Gene -->
<!ELEMENT Entrezgene_type (%INTEGER;)>
<!ATTLIST Entrezgene_type value (
unknown |
tRNA |
rRNA |
snRNA |
scRNA |
snoRNA |
protein-coding |
pseudo |
transposon |
miscRNA |
ncRNA |
other
) #IMPLIED >
<!ELEMENT Entrezgene_source (BioSource)>
<!-- for locus-tag see note 3 -->
<!ELEMENT Entrezgene_gene (Gene-ref)>
<!ELEMENT Entrezgene_prot (Prot-ref)>
<!ELEMENT Entrezgene_rna (RNA-ref)>
<!-- short summary -->
<!ELEMENT Entrezgene_summary (#PCDATA)>
<!ELEMENT Entrezgene_location (Maps*)>
<!-- NCBI source to Entrez -->
<!ELEMENT Entrezgene_gene-source (Gene-source)>
<!--
location of gene on chromosome (if known)
and all information about products
(mRNA, proteins and so on)
-->
<!ELEMENT Entrezgene_locus (Gene-commentary*)>
<!ELEMENT Entrezgene_properties (Gene-commentary*)>
<!-- NG for this? -->
<!ELEMENT Entrezgene_refgene (Gene-commentary*)>
<!ELEMENT Entrezgene_homology (Gene-commentary*)>
<!ELEMENT Entrezgene_comments (Gene-commentary*)>
<!-- see note 3 -->
<!ELEMENT Entrezgene_unique-keys (Dbtag*)>
<!-- see note 2 -->
<!ELEMENT Entrezgene_xtra-index-terms (Entrezgene_xtra-index-terms_E*)>
<!ELEMENT Entrezgene_xtra-index-terms_E (#PCDATA)>
<!-- see note 2 -->
<!ELEMENT Entrezgene_xtra-properties (Xtra-Terms*)>
<!-- see note 2 -->
<!ELEMENT Entrezgene_xtra-iq (Xtra-Terms*)>
<!ELEMENT Entrezgene_non-unique-keys (Dbtag*)>
<!ELEMENT Entrezgene-Set (Entrezgene*)>
<!ELEMENT Gene-track (
Gene-track_geneid,
Gene-track_status?,
Gene-track_current-id?,
Gene-track_create-date,
Gene-track_update-date,
Gene-track_discontinue-date?)>
<!-- required unique document id -->
<!ELEMENT Gene-track_geneid (%INTEGER;)>
<!ELEMENT Gene-track_status (%INTEGER;)>
<!--
secondary - synonym with merged
discontinued - 'deleted', still index and display to public
newentry - for GeneRif submission (DEPRECATED)
-->
<!ATTLIST Gene-track_status value (
live |
secondary |
discontinued |
newentry
) #IMPLIED >
<!-- see note 1 below -->
<!ELEMENT Gene-track_current-id (Dbtag*)>
<!-- date created in Entrez -->
<!ELEMENT Gene-track_create-date (Date)>
<!-- last date updated in Entrez -->
<!ELEMENT Gene-track_update-date (Date)>
<!-- -->
<!ELEMENT Gene-track_discontinue-date (Date)>
<!ELEMENT Gene-source (
Gene-source_src,
Gene-source_src-int?,
Gene-source_src-str1?,
Gene-source_src-str2?,
Gene-source_gene-display?,
Gene-source_locus-display?,
Gene-source_extra-terms?)>
<!-- key to the source within NCBI locuslink, Ecoli, etc -->
<!ELEMENT Gene-source_src (#PCDATA)>
<!-- eg. locuslink id -->
<!ELEMENT Gene-source_src-int (%INTEGER;)>
<!-- eg. chromosome1 -->
<!ELEMENT Gene-source_src-str1 (#PCDATA)>
<!-- see note 3 -->
<!ELEMENT Gene-source_src-str2 (#PCDATA)>
<!-- do we have a URL for gene display? -->
<!ELEMENT Gene-source_gene-display EMPTY>
<!ATTLIST Gene-source_gene-display value ( true | false ) "false" >
<!-- do we have a URL for map/locus display? -->
<!ELEMENT Gene-source_locus-display EMPTY>
<!ATTLIST Gene-source_locus-display value ( true | false ) "false" >
<!-- do we have a URL for extra indexing terms? -->
<!ELEMENT Gene-source_extra-terms EMPTY>
<!ATTLIST Gene-source_extra-terms value ( true | false ) "false" >
<!ELEMENT Gene-commentary (
Gene-commentary_type,
Gene-commentary_heading?,
Gene-commentary_label?,
Gene-commentary_text?,
Gene-commentary_accession?,
Gene-commentary_version?,
Gene-commentary_xtra-properties?,
Gene-commentary_refs?,
Gene-commentary_source?,
Gene-commentary_genomic-coords?,
Gene-commentary_seqs?,
Gene-commentary_products?,
Gene-commentary_properties?,
Gene-commentary_comment?,
Gene-commentary_create-date?,
Gene-commentary_update-date?)>
<!-- type of Gene Commentary -->
<!ELEMENT Gene-commentary_type (%INTEGER;)>
<!--
property - used to display tag/value pair
for this type label is used as property tag, text is used as property value,
other fields are not used.
reference - currently not used
generif - to include generif in the main blob
phenotype - to display phenotype information
complex - used (but not limited) to identify resulting
interaction complexes
compound - pubchem entities
gene-group - for relationship sets (such as pseudogene / parent gene)
-->
<!ATTLIST Gene-commentary_type value (
genomic |
pre-RNA |
mRNA |
rRNA |
tRNA |
snRNA |
scRNA |
peptide |
other-genetic |
genomic-mRNA |
cRNA |
mature-peptide |
pre-protein |
miscRNA |
snoRNA |
property |
reference |
generif |
phenotype |
complex |
compound |
ncRNA |
gene-group |
comment |
other
) #IMPLIED >
<!-- appears above text -->
<!ELEMENT Gene-commentary_heading (#PCDATA)>
<!--
occurs to left of text
for protein and RNA types it is a name
for property type it is a property tag
-->
<!ELEMENT Gene-commentary_label (#PCDATA)>
<!--
block of text
for property type it is a property value
-->
<!ELEMENT Gene-commentary_text (#PCDATA)>
<!-- accession for the gi in the seqloc, see note 3 -->
<!ELEMENT Gene-commentary_accession (#PCDATA)>
<!-- version for the accession above -->
<!ELEMENT Gene-commentary_version (%INTEGER;)>
<!-- see note 2 -->
<!ELEMENT Gene-commentary_xtra-properties (Xtra-Terms*)>
<!-- refs for this -->
<!ELEMENT Gene-commentary_refs (Pub*)>
<!-- links and refs -->
<!ELEMENT Gene-commentary_source (Other-source*)>
<!-- referenced sequences in genomic coords -->
<!ELEMENT Gene-commentary_genomic-coords (Seq-loc*)>
<!-- referenced sequences in non-genomic coords -->
<!ELEMENT Gene-commentary_seqs (Seq-loc*)>
<!ELEMENT Gene-commentary_products (Gene-commentary*)>
<!ELEMENT Gene-commentary_properties (Gene-commentary*)>
<!ELEMENT Gene-commentary_comment (Gene-commentary*)>
<!ELEMENT Gene-commentary_create-date (Date)>
<!ELEMENT Gene-commentary_update-date (Date)>
<!ELEMENT Other-source (
Other-source_src?,
Other-source_pre-text?,
Other-source_anchor?,
Other-source_url?,
Other-source_post-text?)>
<!-- key to non-ncbi source -->
<!ELEMENT Other-source_src (Dbtag)>
<!-- text before anchor -->
<!ELEMENT Other-source_pre-text (#PCDATA)>
<!-- text to show as highlight -->
<!ELEMENT Other-source_anchor (#PCDATA)>
<!-- if present, use this URL not Dbtag and datbase -->
<!ELEMENT Other-source_url (#PCDATA)>
<!-- text after anchor -->
<!ELEMENT Other-source_post-text (#PCDATA)>
<!ELEMENT Maps (
Maps_display-str,
Maps_method)>
<!ELEMENT Maps_display-str (#PCDATA)>
<!ELEMENT Maps_method (
Maps_method_proxy |
Maps_method_map-type)>
<!--url to non mapviewer mapviewing resource -->
<!ELEMENT Maps_method_proxy (#PCDATA)>
<!-- units used in display-str to query mapviewer -->
<!ELEMENT Maps_method_map-type %ENUM;>
<!ATTLIST Maps_method_map-type value (
cyto |
bp |
cM |
cR |
min
) #REQUIRED >
<!-- see note 2 -->
<!ELEMENT Xtra-Terms (
Xtra-Terms_tag,
Xtra-Terms_value)>
<!ELEMENT Xtra-Terms_tag (#PCDATA)>
<!ELEMENT Xtra-Terms_value (#PCDATA)>
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