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1 --$Revision: 1.31 $
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, Gene-track, Gene-commentary;
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 ncRNA (10) ,
46 other (255) } ,
47 source BioSource ,
48 gene Gene-ref , -- for locus-tag see note 3
49 prot Prot-ref OPTIONAL ,
50 rna RNA-ref OPTIONAL ,
51 summary VisibleString OPTIONAL , -- short summary
52 location SEQUENCE OF Maps OPTIONAL,
53 gene-source Gene-source OPTIONAL , -- NCBI source to Entrez
54 locus SEQUENCE OF Gene-commentary OPTIONAL , -- location of gene on chromosome (if known)
55 -- and all information about products
56 -- (mRNA, proteins and so on)
57 properties SEQUENCE OF Gene-commentary OPTIONAL ,
58 refgene SEQUENCE OF Gene-commentary OPTIONAL , -- NG for this?
59 homology SEQUENCE OF Gene-commentary OPTIONAL ,
60 comments SEQUENCE OF Gene-commentary OPTIONAL ,
61 unique-keys SEQUENCE OF Dbtag OPTIONAL , -- see note 3
62 xtra-index-terms SEQUENCE OF VisibleString OPTIONAL , -- see note 2
63 xtra-properties SEQUENCE OF Xtra-Terms OPTIONAL , -- see note 2
64 xtra-iq SEQUENCE OF Xtra-Terms OPTIONAL, -- see note 2
65 non-unique-keys SEQUENCE OF Dbtag OPTIONAL }
66
67 Entrezgene-Set ::= SET OF Entrezgene
68
69 Gene-track ::= SEQUENCE {
70 geneid INTEGER , -- required unique document id
71 status INTEGER {
72 live (0) ,
73 secondary (1) , -- synonym with merged
74 discontinued (2), -- 'deleted', still index and display to public
75 newentry (3) -- for GeneRif submission
76 } DEFAULT live ,
77 current-id SEQUENCE OF Dbtag OPTIONAL , -- see note 1 below
78 create-date Date , -- date created in Entrez
79 update-date Date , -- last date updated in Entrez
80 discontinue-date Date OPTIONAL } --
81
82 Gene-source ::= SEQUENCE {
83 src VisibleString , -- key to the source within NCBI locuslink, Ecoli, etc
84 src-int INTEGER OPTIONAL , -- eg. locuslink id
85 src-str1 VisibleString OPTIONAL , -- eg. chromosome1
86 src-str2 VisibleString OPTIONAL , -- see note 3
87 gene-display BOOLEAN DEFAULT FALSE , -- do we have a URL for gene display?
88 locus-display BOOLEAN DEFAULT FALSE , -- do we have a URL for map/locus display?
89 extra-terms BOOLEAN DEFAULT FALSE } -- do we have a URL for extra indexing terms?
90
91 Gene-commentary ::= SEQUENCE {
92 type INTEGER { -- type of Gene Commentary
93 genomic (1) ,
94 pre-RNA (2) ,
95 mRNA (3) ,
96 rRNA (4) ,
97 tRNA (5) ,
98 snRNA (6) ,
99 scRNA (7) ,
100 peptide (8) ,
101 other-genetic (9) ,
102 genomic-mRNA (10) ,
103 cRNA (11) ,
104 mature-peptide (12) ,
105 pre-protein (13) ,
106 miscRNA (14) ,
107 snoRNA (15) ,
108 property (16) , -- used to display tag/value pair
109 -- for this type label is used as property tag, text is used as property value,
110 -- other fields are not used.
111 reference (17), -- currently not used
112 generif (18), -- to include generif in the main blob
113 phenotype(19), -- to display phenotype information
114 complex (20), -- used (but not limited) to identify resulting
115 -- interaction complexes
116 compound (21), -- pubchem entities
117
118 ncRNA (22),
119 gene-group (23), -- for relationship sets (such as pseudogene / parent gene)
120 comment (254) ,
121 other (255) } ,
122 heading VisibleString OPTIONAL , -- appears above text
123 label VisibleString OPTIONAL , -- occurs to left of text
124 -- for protein and RNA types it is a name
125 -- for property type it is a property tag
126 text VisibleString OPTIONAL , -- block of text
127 -- for property type it is a property value
128 accession VisibleString OPTIONAL , -- accession for the gi in the seqloc, see note 3
129 version INTEGER OPTIONAL , -- version for the accession above
130 xtra-properties SEQUENCE OF Xtra-Terms OPTIONAL , -- see note 2
131 refs SEQUENCE OF Pub OPTIONAL , -- refs for this
132 source SEQUENCE OF Other-source OPTIONAL , -- links and refs
133 genomic-coords SEQUENCE OF Seq-loc OPTIONAL , -- referenced sequences in genomic coords
134 seqs SEQUENCE OF Seq-loc OPTIONAL , -- referenced sequences in non-genomic coords
135 products SEQUENCE OF Gene-commentary OPTIONAL ,
136 properties SEQUENCE OF Gene-commentary OPTIONAL ,
137 comment SEQUENCE OF Gene-commentary OPTIONAL ,
138 create-date Date OPTIONAL ,
139 update-date Date OPTIONAL }
140
141 Other-source ::= SEQUENCE {
142 src Dbtag OPTIONAL , -- key to non-ncbi source
143 pre-text VisibleString OPTIONAL , -- text before anchor
144 anchor VisibleString OPTIONAL , -- text to show as highlight
145 url VisibleString OPTIONAL , -- if present, use this URL not Dbtag and datbase
146 post-text VisibleString OPTIONAL } -- text after anchor
147
148
149 Maps::= SEQUENCE {
150 display-str VisibleString ,
151 method CHOICE {
152 proxy VisibleString , --url to non mapviewer mapviewing resource
153 map-type ENUMERATED { -- units used in display-str to query mapviewer
154 cyto (0) ,
155 bp (1) ,
156 cM (2) ,
157 cR (3) ,
158 min (4)}}}
159
160 Xtra-Terms ::= SEQUENCE { -- see note 2
161 tag VisibleString ,
162 value VisibleString }
163
164 END
165
166 --**********************************************************************
167 --
168 -- Comments, notes, etc.
169 --
170 -- 1) Ignored unless status = secondary. This is where gene_ids (db = "GeneID")
171 -- are placed toward which the interface will direct users. It is also
172 -- available for placing other source-db specific tags (i.e., db = "LocusID").
173 --
174 -- 2) These 'xtra' objects are for submitting data for Entrez indexing
175 -- that might not fit anywhere in the Entrezgene specification but
176 -- are considered by the data source submittor to be important.
177 -- xtra-index-terms is any string.
178 -- xtra-properties are tag/value pairs of properties/feilds as
179 -- defined in the Entrez database (i.e.: UNIGENE/Hs.74561)
180 -- xtra-iq are tag/value pairs of Entrez database/UID as defined
181 -- in the Entrezgene indexing code (i.e.: NUCLEOTIDE/20270626)
182 --
183 -- 3) Locus-tag and src-str2 are expected to be unique per organism (tax_id).
184 -- Protein accessions and the tag-value pairs in unique-keys
185 -- are expected to be unique over all organisms.
186 --**********************************************************************
187
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