entrezgene.asn
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上传日期:2007-06-13
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- --$Revision: 1000.3 $
- --**********************************************************************
- --
- -- 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;
-
- 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) ,
- 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 }
-
- 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
-
- 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
- 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.
- --**********************************************************************