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1 --$Revision: 96973 $
2 --**********************************************************************
3 --
4 -- NCBI Entrezgene
5 -- by James Ostell, 2001
6 --
7 -- Generic "Gene" object for Entrez Genes
8 -- This object is designed to incorporate a subset of information from
9 -- LocusLink and from records in Entrez Genomes to provide indexing,
10 -- linkage, and a useful summary report in Entrez for "Genes"
11 --
12 --**********************************************************************
13
14 NCBI-Entrezgene DEFINITIONS ::=
15 BEGIN
16
17 EXPORTS Entrezgene, Entrezgene-Set;
18
19 IMPORTS Gene-ref FROM NCBI-Gene
20 Prot-ref FROM NCBI-Protein
21 BioSource FROM NCBI-BioSource
22 RNA-ref FROM NCBI-RNA
23 Dbtag, Date FROM NCBI-General
24 Seq-loc FROM NCBI-Seqloc
25 Pub FROM NCBI-Pub;
26
27 --********************************************
28 -- Entrezgene is the "document" indexed in Entrez
29 -- and presented in the full display
30 -- It also contains the Entrez ID and date information
31 --*******************************************
32 Entrezgene ::= SEQUENCE {
33 track-info Gene-track OPTIONAL , -- not in submission, but in retrieval
34 type INTEGER { -- type of Gene
35 unknown (0) ,
36 tRNA (1) ,
37 rRNA (2) ,
38 snRNA (3) ,
39 scRNA (4) ,
40 snoRNA (5) ,
41 protein-coding (6) ,
42 pseudo (7) ,
43 transposon (8) ,
44 miscRNA (9) ,
45 other (255) } ,
46 source BioSource ,
47 gene Gene-ref , -- for locus-tag see note 3
48 prot Prot-ref OPTIONAL ,
49 rna RNA-ref OPTIONAL ,
50 summary VisibleString OPTIONAL , -- short summary
51 location SEQUENCE OF Maps OPTIONAL,
52 gene-source Gene-source OPTIONAL , -- NCBI source to Entrez
53 locus SEQUENCE OF Gene-commentary OPTIONAL , -- location of gene on chromosome (if known)
54 -- and all information about products
55 -- (mRNA, proteins and so on)
56 properties SEQUENCE OF Gene-commentary OPTIONAL ,
57 refgene SEQUENCE OF Gene-commentary OPTIONAL , -- NG for this?
58 homology SEQUENCE OF Gene-commentary OPTIONAL ,
59 comments SEQUENCE OF Gene-commentary OPTIONAL ,
60 unique-keys SEQUENCE OF Dbtag OPTIONAL , -- see note 3
61 xtra-index-terms SEQUENCE OF VisibleString OPTIONAL , -- see note 2
62 xtra-properties SEQUENCE OF Xtra-Terms OPTIONAL , -- see note 2
63 xtra-iq SEQUENCE OF Xtra-Terms OPTIONAL, -- see note 2
64 non-unique-keys SEQUENCE OF Dbtag OPTIONAL }
65
66 Entrezgene-Set ::= SET OF Entrezgene
67
68 Gene-track ::= SEQUENCE {
69 geneid INTEGER , -- required unique document id
70 status INTEGER {
71 live (0) ,
72 secondary (1) , -- synonym with merged
73 discontinued (2), -- 'deleted', still index and display to public
74 newentry (3) -- for GeneRif submission
75 } DEFAULT live ,
76 current-id SEQUENCE OF Dbtag OPTIONAL , -- see note 1 below
77 create-date Date , -- date created in Entrez
78 update-date Date , -- last date updated in Entrez
79 discontinue-date Date OPTIONAL } --
80
81 Gene-source ::= SEQUENCE {
82 src VisibleString , -- key to the source within NCBI locuslink, Ecoli, etc
83 src-int INTEGER OPTIONAL , -- eg. locuslink id
84 src-str1 VisibleString OPTIONAL , -- eg. chromosome1
85 src-str2 VisibleString OPTIONAL , -- see note 3
86 gene-display BOOLEAN DEFAULT FALSE , -- do we have a URL for gene display?
87 locus-display BOOLEAN DEFAULT FALSE , -- do we have a URL for map/locus display?
88 extra-terms BOOLEAN DEFAULT FALSE } -- do we have a URL for extra indexing terms?
89
90 Gene-commentary ::= SEQUENCE {
91 type INTEGER { -- type of Gene Commentary
92 genomic (1) ,
93 pre-RNA (2) ,
94 mRNA (3) ,
95 rRNA (4) ,
96 tRNA (5) ,
97 snRNA (6) ,
98 scRNA (7) ,
99 peptide (8) ,
100 other-genetic (9) ,
101 genomic-mRNA (10) ,
102 cRNA (11) ,
103 mature-peptide (12) ,
104 pre-protein (13) ,
105 miscRNA (14) ,
106 snoRNA (15) ,
107 property (16) , -- used to display tag/value pair
108 -- for this type label is used as property tag, text is used as property value,
109 -- other fields are not used.
110 reference (17), -- currently not used
111 generif (18), -- to include generif in the main blob
112 phenotype(19), -- to display phenotype information
113 complex (20), -- used (but not limited) to identify resulting
114 -- interaction complexes
115 compound (21), -- pubchem entities
116 comment (254) ,
117 other (255) } ,
118 heading VisibleString OPTIONAL , -- appears above text
119 label VisibleString OPTIONAL , -- occurs to left of text
120 -- for protein and RNA types it is a name
121 -- for property type it is a property tag
122 text VisibleString OPTIONAL , -- block of text
123 -- for property type it is a property value
124 accession VisibleString OPTIONAL , -- accession for the gi in the seqloc, see note 3
125 version INTEGER OPTIONAL , -- version for the accession above
126 xtra-properties SEQUENCE OF Xtra-Terms OPTIONAL , -- see note 2
127 refs SEQUENCE OF Pub OPTIONAL , -- refs for this
128 source SEQUENCE OF Other-source OPTIONAL , -- links and refs
129 genomic-coords SEQUENCE OF Seq-loc OPTIONAL , -- referenced sequences in genomic coords
130 seqs SEQUENCE OF Seq-loc OPTIONAL , -- referenced sequences in non-genomic coords
131 products SEQUENCE OF Gene-commentary OPTIONAL ,
132 properties SEQUENCE OF Gene-commentary OPTIONAL ,
133 comment SEQUENCE OF Gene-commentary OPTIONAL ,
134 create-date Date OPTIONAL ,
135 update-date Date OPTIONAL }
136
137 Other-source ::= SEQUENCE {
138 src Dbtag OPTIONAL , -- key to non-ncbi source
139 pre-text VisibleString OPTIONAL , -- text before anchor
140 anchor VisibleString OPTIONAL , -- text to show as highlight
141 url VisibleString OPTIONAL , -- if present, use this URL not Dbtag and datbase
142 post-text VisibleString OPTIONAL } -- text after anchor
143
144
145 Maps::= SEQUENCE {
146 display-str VisibleString ,
147 method CHOICE {
148 proxy VisibleString , --url to non mapviewer mapviewing resource
149 map-type ENUMERATED { -- units used in display-str to query mapviewer
150 cyto (0) ,
151 bp (1) ,
152 cM (2) ,
153 cR (3) ,
154 min (4)}}}
155
156 Xtra-Terms ::= SEQUENCE { -- see note 2
157 tag VisibleString ,
158 value VisibleString }
159
160 END
161
162 --**********************************************************************
163 --
164 -- Comments, notes, etc.
165 --
166 -- 1) Ignored unless status = secondary. This is where gene_ids (db = "GeneID")
167 -- are placed toward which the interface will direct users. It is also
168 -- available for placing other source-db specific tags (i.e., db = "LocusID").
169 --
170 -- 2) These 'xtra' objects are for submitting data for Entrez indexing
171 -- that might not fit anywhere in the Entrezgene specification but
172 -- are considered by the data source submittor to be important.
173 -- xtra-index-terms is any string.
174 -- xtra-properties are tag/value pairs of properties/feilds as
175 -- defined in the Entrez database (i.e.: UNIGENE/Hs.74561)
176 -- xtra-iq are tag/value pairs of Entrez database/UID as defined
177 -- in the Entrezgene indexing code (i.e.: NUCLEOTIDE/20270626)
178 --
179 -- 3) Locus-tag and src-str2 are expected to be unique per organism (tax_id).
180 -- Protein accessions and the tag-value pairs in unique-keys
181 -- are expected to be unique over all organisms.
182 --**********************************************************************
183
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