NCBI C++ Toolkit Cross Reference

C++/src/objects/entrezgene/entrezgene.dump

  1 M,14,entrezgene.asn:NCBI-Entrezgene
  2 --$Revision: 158545 $ 
  3 --********************************************************************** 
  4 -- 
  5 --  NCBI Entrezgene 
  6 --  by James Ostell, 2001 
  7 --   
  8 --  Generic "Gene" object for Entrez Genes 
  9 --    This object is designed to incorporate a subset of information from 
 10 --    LocusLink and from records in Entrez Genomes to provide indexing, 
 11 --    linkage, and a useful summary report in Entrez for "Genes" 
 12 -- 
 13 --********************************************************************** 
 14   T,32,NCBI-Entrezgene:Entrezgene
 15   T,67,NCBI-Entrezgene:Entrezgene-Set
 16   T,69,NCBI-Entrezgene:Gene-track
 17   T,82,NCBI-Entrezgene:Gene-source
 18   T,91,NCBI-Entrezgene:Gene-commentary
 19   T,141,NCBI-Entrezgene:Other-source
 20   T,149,NCBI-Entrezgene:Maps
 21   T,160,NCBI-Entrezgene:Xtra-Terms
 22 
 23 T,32,Entrezgene,SEQUENCE
 24 --******************************************** 
 25 -- Entrezgene is the "document" indexed in Entrez 
 26 --  and presented in the full display 
 27 -- It also contains the Entrez ID and date information 
 28 --******************************************* 
 29   F,33,Entrezgene:track-info,/Gene-track,OPTIONAL
 30   -- not in submission, but in retrieval 
 31   F,34,Entrezgene:type,INTEGER
 32   -- type of Gene
 33     V,35,Entrezgene:type:unknown,0
 34     V,36,Entrezgene:type:tRNA,1
 35     V,37,Entrezgene:type:rRNA,2
 36     V,38,Entrezgene:type:snRNA,3
 37     V,39,Entrezgene:type:scRNA,4
 38     V,40,Entrezgene:type:snoRNA,5
 39     V,41,Entrezgene:type:protein-coding,6
 40     V,42,Entrezgene:type:pseudo,7
 41     V,43,Entrezgene:type:transposon,8
 42     V,44,Entrezgene:type:miscRNA,9
 43     V,45,Entrezgene:type:ncRNA,10
 44     V,46,Entrezgene:type:other,255
 45   F,47,Entrezgene:source,/BioSource
 46   F,48,Entrezgene:gene,/Gene-ref
 47   -- for locus-tag see note 3
 48   F,49,Entrezgene:prot,/Prot-ref,OPTIONAL
 49   F,50,Entrezgene:rna,/RNA-ref,OPTIONAL
 50   F,51,Entrezgene:summary,VisibleString,OPTIONAL
 51   -- short summary 
 52   F,52,Entrezgene:location,SEQUENCE /Maps,OPTIONAL
 53   F,53,Entrezgene:gene-source,/Gene-source,OPTIONAL
 54   -- NCBI source to Entrez 
 55   F,54,Entrezgene:locus,SEQUENCE /Gene-commentary,OPTIONAL
 56   -- location of gene on chromosome (if known)
 57   -- and all information about products
 58   -- (mRNA, proteins and so on)
 59   F,57,Entrezgene:properties,SEQUENCE /Gene-commentary,OPTIONAL
 60   F,58,Entrezgene:refgene,SEQUENCE /Gene-commentary,OPTIONAL
 61   -- NG for this? 
 62   F,59,Entrezgene:homology,SEQUENCE /Gene-commentary,OPTIONAL
 63   F,60,Entrezgene:comments,SEQUENCE /Gene-commentary,OPTIONAL
 64   F,61,Entrezgene:unique-keys,SEQUENCE /Dbtag,OPTIONAL
 65   -- see note 3
 66   F,62,Entrezgene:xtra-index-terms,SEQUENCE VisibleString,OPTIONAL
 67   -- see note 2
 68   F,63,Entrezgene:xtra-properties,SEQUENCE /Xtra-Terms,OPTIONAL
 69   -- see note 2
 70   F,64,Entrezgene:xtra-iq,SEQUENCE /Xtra-Terms,OPTIONAL
 71   -- see note 2
 72   F,65,Entrezgene:non-unique-keys,SEQUENCE /Dbtag,OPTIONAL
 73 
 74 T,67,Entrezgene-Set,SET /Entrezgene
 75 
 76 T,69,Gene-track,SEQUENCE
 77   F,70,Gene-track:geneid,INTEGER
 78   -- required unique document id 
 79   F,71,Gene-track:status,INTEGER,DEFAULT,live
 80     V,72,Gene-track:status:live,0
 81     V,73,Gene-track:status:secondary,1
 82     -- synonym with merged
 83     V,74,Gene-track:status:discontinued,2
 84     -- 'deleted', still index and display to public
 85     V,75,Gene-track:status:newentry,3
 86     --  for GeneRif submission
 87   F,77,Gene-track:current-id,SEQUENCE /Dbtag,OPTIONAL
 88   -- see note 1 below
 89   F,78,Gene-track:create-date,/Date
 90   -- date created in Entrez 
 91   F,79,Gene-track:update-date,/Date
 92   -- last date updated in Entrez 
 93   F,80,Gene-track:discontinue-date,/Date,OPTIONAL
 94   --
 95 
 96 T,82,Gene-source,SEQUENCE
 97   F,83,Gene-source:src,VisibleString
 98   -- key to the source within NCBI locuslink, Ecoli, etc 
 99   F,84,Gene-source:src-int,INTEGER,OPTIONAL
100   -- eg. locuslink id 
101   F,85,Gene-source:src-str1,VisibleString,OPTIONAL
102   -- eg. chromosome1 
103   F,86,Gene-source:src-str2,VisibleString,OPTIONAL
104   -- see note 3
105   F,87,Gene-source:gene-display,BOOLEAN,DEFAULT,FALSE
106   -- do we have a URL for gene display? 
107   F,88,Gene-source:locus-display,BOOLEAN,DEFAULT,FALSE
108   -- do we have a URL for map/locus display? 
109   F,89,Gene-source:extra-terms,BOOLEAN,DEFAULT,FALSE
110   -- do we have a URL for extra indexing terms? 
111 
112 T,91,Gene-commentary,SEQUENCE
113   F,92,Gene-commentary:type,INTEGER
114   -- type of Gene Commentary
115     V,93,Gene-commentary:type:genomic,1
116     V,94,Gene-commentary:type:pre-RNA,2
117     V,95,Gene-commentary:type:mRNA,3
118     V,96,Gene-commentary:type:rRNA,4
119     V,97,Gene-commentary:type:tRNA,5
120     V,98,Gene-commentary:type:snRNA,6
121     V,99,Gene-commentary:type:scRNA,7
122     V,100,Gene-commentary:type:peptide,8
123     V,101,Gene-commentary:type:other-genetic,9
124     V,102,Gene-commentary:type:genomic-mRNA,10
125     V,103,Gene-commentary:type:cRNA,11
126     V,104,Gene-commentary:type:mature-peptide,12
127     V,105,Gene-commentary:type:pre-protein,13
128     V,106,Gene-commentary:type:miscRNA,14
129     V,107,Gene-commentary:type:snoRNA,15
130     V,108,Gene-commentary:type:property,16
131     -- used to display tag/value pair
132     -- for this type label is used as property tag, text is used as property value, 
133     -- other fields are not used.
134     V,111,Gene-commentary:type:reference,17
135     -- currently not used             
136     V,112,Gene-commentary:type:generif,18
137     -- to include generif in the main blob             
138     V,113,Gene-commentary:type:phenotype,19
139     -- to display phenotype information
140     V,114,Gene-commentary:type:complex,20
141     -- used (but not limited) to identify resulting 
142     -- interaction complexes
143     V,116,Gene-commentary:type:compound,21
144     -- pubchem entities
145     V,118,Gene-commentary:type:ncRNA,22
146     V,119,Gene-commentary:type:gene-group,23
147     -- for relationship sets (such as pseudogene / parent gene)
148     V,120,Gene-commentary:type:comment,254
149     V,121,Gene-commentary:type:other,255
150   F,122,Gene-commentary:heading,VisibleString,OPTIONAL
151   -- appears above text 
152   F,123,Gene-commentary:label,VisibleString,OPTIONAL
153   -- occurs to left of text
154   -- for protein and RNA types it is a name
155   -- for property type it is a property tag  
156   F,126,Gene-commentary:text,VisibleString,OPTIONAL
157   -- block of text 
158   -- for property type it is a property value  
159   F,128,Gene-commentary:accession,VisibleString,OPTIONAL
160   -- accession for the gi in the seqloc, see note 3
161   F,129,Gene-commentary:version,INTEGER,OPTIONAL
162   -- version for the accession above
163   F,130,Gene-commentary:xtra-properties,SEQUENCE /Xtra-Terms,OPTIONAL
164   -- see note 2
165   F,131,Gene-commentary:refs,SEQUENCE /Pub,OPTIONAL
166   -- refs for this 
167   F,132,Gene-commentary:source,SEQUENCE /Other-source,OPTIONAL
168   -- links and refs 
169   F,133,Gene-commentary:genomic-coords,SEQUENCE /Seq-loc,OPTIONAL
170   -- referenced sequences in genomic coords
171   F,134,Gene-commentary:seqs,SEQUENCE /Seq-loc,OPTIONAL
172   -- referenced sequences in non-genomic coords
173   F,135,Gene-commentary:products,SEQUENCE /Gene-commentary,OPTIONAL
174   F,136,Gene-commentary:properties,SEQUENCE /Gene-commentary,OPTIONAL
175   F,137,Gene-commentary:comment,SEQUENCE /Gene-commentary,OPTIONAL
176   F,138,Gene-commentary:create-date,/Date,OPTIONAL
177   F,139,Gene-commentary:update-date,/Date,OPTIONAL
178 
179 T,141,Other-source,SEQUENCE
180   F,142,Other-source:src,/Dbtag,OPTIONAL
181   -- key to non-ncbi source 
182   F,143,Other-source:pre-text,VisibleString,OPTIONAL
183   -- text before anchor 
184   F,144,Other-source:anchor,VisibleString,OPTIONAL
185   -- text to show as highlight 
186   F,145,Other-source:url,VisibleString,OPTIONAL
187   -- if present, use this URL not Dbtag and datbase 
188   F,146,Other-source:post-text,VisibleString,OPTIONAL
189   -- text after anchor 
190 
191 T,149,Maps,SEQUENCE
192   F,150,Maps:display-str,VisibleString
193   F,151,Maps:method,CHOICE
194     F,152,Maps:method:proxy,VisibleString
195     --url to non mapviewer mapviewing resource
196     F,153,Maps:method:map-type,ENUMERATED
197     -- units used in display-str to query mapviewer 
198       V,154,Maps:method:map-type:cyto,0
199       V,155,Maps:method:map-type:bp,1
200       V,156,Maps:method:map-type:cM,2
201       V,157,Maps:method:map-type:cR,3
202       V,158,Maps:method:map-type:min,4
203 
204 T,160,Xtra-Terms,SEQUENCE
205 -- see note 2
206   F,161,Xtra-Terms:tag,VisibleString
207   F,162,Xtra-Terms:value,VisibleString
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