192 lines
8.1 KiB
Groff
192 lines
8.1 KiB
Groff
--$Revision: 462996 $
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--**********************************************************************
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--
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-- NCBI Entrezgene
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-- by James Ostell, 2001
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--
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-- Generic "Gene" object for Entrez Genes
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-- This object is designed to incorporate a subset of information from
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-- LocusLink and from records in Entrez Genomes to provide indexing,
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-- linkage, and a useful summary report in Entrez for "Genes"
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--
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--**********************************************************************
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NCBI-Entrezgene DEFINITIONS ::=
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BEGIN
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EXPORTS Entrezgene, Entrezgene-Set, Gene-track, Gene-commentary;
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IMPORTS Gene-ref FROM NCBI-Gene
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Prot-ref FROM NCBI-Protein
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BioSource FROM NCBI-BioSource
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RNA-ref FROM NCBI-RNA
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Dbtag, Date FROM NCBI-General
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Seq-loc FROM NCBI-Seqloc
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Pub FROM NCBI-Pub;
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--********************************************
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-- Entrezgene is the "document" indexed in Entrez
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-- and presented in the full display
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-- It also contains the Entrez ID and date information
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--*******************************************
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Entrezgene ::= SEQUENCE {
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track-info Gene-track OPTIONAL , -- not in submission, but in retrieval
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type INTEGER { -- type of Gene
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unknown (0) ,
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tRNA (1) ,
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rRNA (2) ,
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snRNA (3) ,
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scRNA (4) ,
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snoRNA (5) ,
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protein-coding (6) ,
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pseudo (7) ,
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transposon (8) ,
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miscRNA (9) ,
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ncRNA (10) ,
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biological-region (11),
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other (255) } ,
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source BioSource ,
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gene Gene-ref , -- for locus-tag see note 3
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prot Prot-ref OPTIONAL ,
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rna RNA-ref OPTIONAL ,
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summary VisibleString OPTIONAL , -- short summary
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location SEQUENCE OF Maps OPTIONAL,
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gene-source Gene-source OPTIONAL , -- NCBI source to Entrez
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locus SEQUENCE OF Gene-commentary OPTIONAL , -- location of gene on chromosome (if known)
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-- and all information about products
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-- (mRNA, proteins and so on)
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properties SEQUENCE OF Gene-commentary OPTIONAL ,
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refgene SEQUENCE OF Gene-commentary OPTIONAL , -- NG for this?
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homology SEQUENCE OF Gene-commentary OPTIONAL ,
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comments SEQUENCE OF Gene-commentary OPTIONAL ,
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unique-keys SEQUENCE OF Dbtag OPTIONAL , -- see note 3
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xtra-index-terms SEQUENCE OF VisibleString OPTIONAL , -- see note 2
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xtra-properties SEQUENCE OF Xtra-Terms OPTIONAL , -- see note 2
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xtra-iq SEQUENCE OF Xtra-Terms OPTIONAL, -- see note 2
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non-unique-keys SEQUENCE OF Dbtag OPTIONAL }
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Entrezgene-Set ::= SET OF Entrezgene
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Gene-track ::= SEQUENCE {
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geneid INTEGER , -- required unique document id
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status INTEGER {
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live (0) ,
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secondary (1) , -- synonym with merged
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discontinued (2) -- 'deleted', still index and display to public
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} DEFAULT live ,
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current-id SEQUENCE OF Dbtag OPTIONAL , -- see note 1 below
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create-date Date , -- date created in Entrez
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update-date Date , -- last date updated in Entrez
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discontinue-date Date OPTIONAL } --
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Gene-source ::= SEQUENCE {
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src VisibleString , -- key to the source within NCBI locuslink, Ecoli, etc
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src-int INTEGER OPTIONAL , -- eg. locuslink id
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src-str1 VisibleString OPTIONAL , -- eg. chromosome1
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src-str2 VisibleString OPTIONAL , -- see note 3
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gene-display BOOLEAN DEFAULT FALSE , -- do we have a URL for gene display?
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locus-display BOOLEAN DEFAULT FALSE , -- do we have a URL for map/locus display?
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extra-terms BOOLEAN DEFAULT FALSE } -- do we have a URL for extra indexing terms?
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Gene-commentary ::= SEQUENCE {
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type INTEGER { -- type of Gene Commentary
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genomic (1) ,
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pre-RNA (2) ,
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mRNA (3) ,
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rRNA (4) ,
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tRNA (5) ,
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snRNA (6) ,
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scRNA (7) ,
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peptide (8) ,
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other-genetic (9) ,
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genomic-mRNA (10) ,
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cRNA (11) ,
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mature-peptide (12) ,
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pre-protein (13) ,
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miscRNA (14) ,
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snoRNA (15) ,
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property (16) , -- used to display tag/value pair
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-- for this type label is used as property tag, text is used as property value,
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-- other fields are not used.
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reference (17), -- currently not used
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generif (18), -- to include generif in the main blob
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phenotype(19), -- to display phenotype information
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complex (20), -- used (but not limited) to identify resulting
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-- interaction complexes
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compound (21), -- pubchem entities
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ncRNA (22),
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gene-group (23), -- for relationship sets (such as pseudogene / parent gene)
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assembly (24), -- for full assembly accession
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assembly-unit (25), -- for the assembly unit corresponding to the refseq
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comment (254) ,
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other (255) } ,
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heading VisibleString OPTIONAL , -- appears above text
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label VisibleString OPTIONAL , -- occurs to left of text
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-- for protein and RNA types it is a name
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-- for property type it is a property tag
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text VisibleString OPTIONAL , -- block of text
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-- for property type it is a property value
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accession VisibleString OPTIONAL , -- accession for the gi in the seqloc, see note 3
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version INTEGER OPTIONAL , -- version for the accession above
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xtra-properties SEQUENCE OF Xtra-Terms OPTIONAL , -- see note 2
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refs SEQUENCE OF Pub OPTIONAL , -- refs for this
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source SEQUENCE OF Other-source OPTIONAL , -- links and refs
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genomic-coords SEQUENCE OF Seq-loc OPTIONAL , -- referenced sequences in genomic coords
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seqs SEQUENCE OF Seq-loc OPTIONAL , -- referenced sequences in non-genomic coords
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products SEQUENCE OF Gene-commentary OPTIONAL ,
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properties SEQUENCE OF Gene-commentary OPTIONAL ,
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comment SEQUENCE OF Gene-commentary OPTIONAL ,
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create-date Date OPTIONAL ,
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update-date Date OPTIONAL ,
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rna RNA-ref OPTIONAL }
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Other-source ::= SEQUENCE {
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src Dbtag OPTIONAL , -- key to non-ncbi source
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pre-text VisibleString OPTIONAL , -- text before anchor
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anchor VisibleString OPTIONAL , -- text to show as highlight
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url VisibleString OPTIONAL , -- if present, use this URL not Dbtag and datbase
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post-text VisibleString OPTIONAL } -- text after anchor
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Maps::= SEQUENCE {
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display-str VisibleString ,
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method CHOICE {
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proxy VisibleString , --url to non mapviewer mapviewing resource
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map-type ENUMERATED { -- units used in display-str to query mapviewer
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cyto (0) ,
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bp (1) ,
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cM (2) ,
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cR (3) ,
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min (4)}}}
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Xtra-Terms ::= SEQUENCE { -- see note 2
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tag VisibleString ,
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value VisibleString }
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END
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--**********************************************************************
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--
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-- Comments, notes, etc.
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--
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-- 1) Ignored unless status = secondary. This is where gene_ids (db = "GeneID")
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-- are placed toward which the interface will direct users. It is also
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-- available for placing other source-db specific tags (i.e., db = "LocusID").
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--
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-- 2) These 'xtra' objects are for submitting data for Entrez indexing
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-- that might not fit anywhere in the Entrezgene specification but
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-- are considered by the data source submittor to be important.
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-- xtra-index-terms is any string.
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-- xtra-properties are tag/value pairs of properties/feilds as
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-- defined in the Entrez database (i.e.: UNIGENE/Hs.74561)
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-- xtra-iq are tag/value pairs of Entrez database/UID as defined
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-- in the Entrezgene indexing code (i.e.: NUCLEOTIDE/20270626)
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--
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-- 3) Locus-tag and src-str2 are expected to be unique per organism (tax_id).
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-- Protein accessions and the tag-value pairs in unique-keys
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-- are expected to be unique over all organisms.
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--**********************************************************************
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