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--$Revision: 1.31 $
--**********************************************************************
--
-- 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"
--
--**********************************************************************
NCBI-Entrezgene DEFINITIONS ::=
BEGIN
EXPORTS Entrezgene, Entrezgene-Set, Gene-track, Gene-commentary;
IMPORTS 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
--*******************************************
Entrezgene ::= SEQUENCE {
track-info Gene-track OPTIONAL , -- not in submission, but in retrieval
type INTEGER { -- type of Gene
unknown (0) ,
tRNA (1) ,
rRNA (2) ,
snRNA (3) ,
scRNA (4) ,
snoRNA (5) ,
protein-coding (6) ,
pseudo (7) ,
transposon (8) ,
miscRNA (9) ,
ncRNA (10) ,
other (255) } ,
source BioSource ,
gene Gene-ref , -- for locus-tag see note 3
prot Prot-ref OPTIONAL ,
rna RNA-ref OPTIONAL ,
summary VisibleString OPTIONAL , -- short summary
location SEQUENCE OF Maps OPTIONAL,
gene-source Gene-source OPTIONAL , -- NCBI source to Entrez
locus SEQUENCE OF Gene-commentary OPTIONAL , -- location of gene on chromosome (if known)
-- and all information about products
-- (mRNA, proteins and so on)
properties SEQUENCE OF Gene-commentary OPTIONAL ,
refgene SEQUENCE OF Gene-commentary OPTIONAL , -- NG for this?
homology SEQUENCE OF Gene-commentary OPTIONAL ,
comments SEQUENCE OF Gene-commentary OPTIONAL ,
unique-keys SEQUENCE OF Dbtag OPTIONAL , -- see note 3
xtra-index-terms SEQUENCE OF VisibleString OPTIONAL , -- see note 2
xtra-properties SEQUENCE OF Xtra-Terms OPTIONAL , -- see note 2
xtra-iq SEQUENCE OF Xtra-Terms OPTIONAL, -- see note 2
non-unique-keys SEQUENCE OF Dbtag OPTIONAL }
Entrezgene-Set ::= SET OF Entrezgene
Gene-track ::= SEQUENCE {
geneid INTEGER , -- required unique document id
status INTEGER {
live (0) ,
secondary (1) , -- synonym with merged
discontinued (2), -- 'deleted', still index and display to public
newentry (3) -- for GeneRif submission
} DEFAULT live ,
current-id SEQUENCE OF Dbtag OPTIONAL , -- see note 1 below
create-date Date , -- date created in Entrez
update-date Date , -- last date updated in Entrez
discontinue-date Date OPTIONAL } --
Gene-source ::= SEQUENCE {
src VisibleString , -- key to the source within NCBI locuslink, Ecoli, etc
src-int INTEGER OPTIONAL , -- eg. locuslink id
src-str1 VisibleString OPTIONAL , -- eg. chromosome1
src-str2 VisibleString OPTIONAL , -- see note 3
gene-display BOOLEAN DEFAULT FALSE , -- do we have a URL for gene display?
locus-display BOOLEAN DEFAULT FALSE , -- do we have a URL for map/locus display?
extra-terms BOOLEAN DEFAULT FALSE } -- do we have a URL for extra indexing terms?
Gene-commentary ::= SEQUENCE {
type INTEGER { -- type of Gene Commentary
genomic (1) ,
pre-RNA (2) ,
mRNA (3) ,
rRNA (4) ,
tRNA (5) ,
snRNA (6) ,
scRNA (7) ,
peptide (8) ,
other-genetic (9) ,
genomic-mRNA (10) ,
cRNA (11) ,
mature-peptide (12) ,
pre-protein (13) ,
miscRNA (14) ,
snoRNA (15) ,
property (16) , -- 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 (17), -- currently not used
generif (18), -- to include generif in the main blob
phenotype(19), -- to display phenotype information
complex (20), -- used (but not limited) to identify resulting
-- interaction complexes
compound (21), -- pubchem entities
ncRNA (22),
gene-group (23), -- for relationship sets (such as pseudogene / parent gene)
comment (254) ,
other (255) } ,
heading VisibleString OPTIONAL , -- appears above text
label VisibleString OPTIONAL , -- occurs to left of text
-- for protein and RNA types it is a name
-- for property type it is a property tag
text VisibleString OPTIONAL , -- block of text
-- for property type it is a property value
accession VisibleString OPTIONAL , -- accession for the gi in the seqloc, see note 3
version INTEGER OPTIONAL , -- version for the accession above
xtra-properties SEQUENCE OF Xtra-Terms OPTIONAL , -- see note 2
refs SEQUENCE OF Pub OPTIONAL , -- refs for this
source SEQUENCE OF Other-source OPTIONAL , -- links and refs
genomic-coords SEQUENCE OF Seq-loc OPTIONAL , -- referenced sequences in genomic coords
seqs SEQUENCE OF Seq-loc OPTIONAL , -- referenced sequences in non-genomic coords
products SEQUENCE OF Gene-commentary OPTIONAL ,
properties SEQUENCE OF Gene-commentary OPTIONAL ,
comment SEQUENCE OF Gene-commentary OPTIONAL ,
create-date Date OPTIONAL ,
update-date Date OPTIONAL }
Other-source ::= SEQUENCE {
src Dbtag OPTIONAL , -- key to non-ncbi source
pre-text VisibleString OPTIONAL , -- text before anchor
anchor VisibleString OPTIONAL , -- text to show as highlight
url VisibleString OPTIONAL , -- if present, use this URL not Dbtag and datbase
post-text VisibleString OPTIONAL } -- text after anchor
Maps::= SEQUENCE {
display-str VisibleString ,
method CHOICE {
proxy VisibleString , --url to non mapviewer mapviewing resource
map-type ENUMERATED { -- units used in display-str to query mapviewer
cyto (0) ,
bp (1) ,
cM (2) ,
cR (3) ,
min (4)}}}
Xtra-Terms ::= SEQUENCE { -- see note 2
tag VisibleString ,
value VisibleString }
END
--**********************************************************************
--
-- Comments, notes, etc.
--
-- 1) Ignored unless status = secondary. This is where gene_ids (db = "GeneID")
-- are placed toward which the interface will direct users. It is also
-- available for placing other source-db specific tags (i.e., db = "LocusID").
--
-- 2) These 'xtra' objects are for submitting data for Entrez indexing
-- that might not fit anywhere in the Entrezgene specification but
-- are considered by the data source submittor to be important.
-- xtra-index-terms is any string.
-- xtra-properties are tag/value pairs of properties/feilds as
-- defined in the Entrez database (i.e.: UNIGENE/Hs.74561)
-- xtra-iq are tag/value pairs of Entrez database/UID as defined
-- in the Entrezgene indexing code (i.e.: NUCLEOTIDE/20270626)
--
-- 3) Locus-tag and src-str2 are expected to be unique per organism (tax_id).
-- Protein accessions and the tag-value pairs in unique-keys
-- are expected to be unique over all organisms.
--**********************************************************************
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