[Bio] / GBBergeyDB / GBBergeyDB.xml Repository:
ViewVC logotype

Diff of /GBBergeyDB/GBBergeyDB.xml

Parent Directory Parent Directory | Revision Log Revision Log | View Patch Patch

revision 1.2, Wed Jan 17 13:42:44 2007 UTC revision 1.17, Wed Mar 21 00:25:18 2007 UTC
# Line 4  Line 4 
4    
5  <object label="Domain">  <object label="Domain">
6    <scalar label="name" type="CHAR(250)" />    <scalar label="name" type="CHAR(250)" />
7      <scalar label="taxDOI" type="INT" />
8  </object>  </object>
9    
10  <object label="Phyla">  <object label="Phyla">
11    <scalar label="name" type="CHAR(250)" />    <scalar label="name" type="CHAR(250)" />
12    <object label="Domain" type="Domain" />    <object label="Domain" type="Domain" />
13      <scalar label="taxDOI" type="INT" />
14  </object>  </object>
15    
16  <object label="Class">  <object label="Class">
17    <scalar label="name" type="CHAR(250)" />    <scalar label="name" type="CHAR(250)" />
18    <object label="Phyla" type="Phyla" />    <object label="Phyla" type="Phyla" />
19      <scalar label="taxDOI" type="INT" />
20  </object>  </object>
21    
22  <object label="GOrder">  <object label="GOrder">
23    <scalar label="name" type="CHAR(250)" />    <scalar label="name" type="CHAR(250)" />
24    <object label="Class" type="Class" />    <object label="Class" type="Class" />
25      <scalar label="taxDOI" type="INT" />
26  </object>  </object>
27    
28  <object label="Family">  <object label="Family">
29    <scalar label="name" type="CHAR(250)" />    <scalar label="name" type="CHAR(250)" />
30    <object label="GOrder" type="GOrder" />    <object label="GOrder" type="GOrder" />
31      <scalar label="taxDOI" type="INT" />
32  </object>  </object>
33    
34  <object label="Genus">  <object label="Genus">
35    <scalar label="name" type="CHAR(250)" />    <scalar label="name" type="CHAR(250)" />
36    <object label="Family" type="Family" />    <object label="Family" type="Family" />
37    <scalar label="form" type="INT"/>    <scalar label="form" type="INT"/>
38      <scalar label="taxDOI" type="INT" />
39  </object>  </object>
40    
41  <object label="Species">  <object label="Species">
42    <scalar label="name" type="CHAR(250)" />    <scalar label="name" type="CHAR(250)" />
43    <object label="Genus" type="Genus" />    <object label="Genus" type="Genus" />
44      <object label="ScientificSpecies" type="Species" />
45      <scalar label="userflag1" type="INT" />
46      <scalar label="userflag2" type="INT" />
47      <scalar label="userflag3" type="INT" />
48      <scalar label="userflag4" type="INT" />
49      <scalar label="computedscore" type="INT" />
50      <scalar label="score" type="INT" />
51      <scalar label="taxid" type="INT" />
52      <scalar label="taxDOI" type="INT" />
53    </object>
54    
55    <object label="Note">
56      <scalar label="user" type="CHAR(250)" />
57      <scalar label="description" type="CHAR(250)" />
58      <scalar label="timestamp" type="INT" />
59      <scalar label="voting" type="INT" />
60      <scalar label="confidence" type="INT" />
61      <object label="Strain" type="Genome" />
62      <object label="Species" type="Species" />
63    </object>
64    
65    <object label="STScluster">
66      <scalar label="number" type="INT" />
67      <scalar label="seqrepresentation" type="INT" />
68      <object label="representative" type="Genome" />
69      <scalar label="score" type="FLOAT" />
70  </object>  </object>
71    
72    <object label="Genome">    <object label="Genome">
73      <scalar label="name" type="CHAR(250)" />      <scalar label="name" type="CHAR(250)" />
74      <object label="Genus" type="Genus" />    <object label="STScluster" type="STScluster" />
75      <scalar label="STSvalue" type="FLOAT" />
76      <object label="Species" type="Species" />      <object label="Species" type="Species" />
77      <scalar label="strain" type="CHAR(125)" />    <scalar label="typeStrain" type="INT" />
78      <scalar label="sixTeenS" type="TEXT" />
79      <array>
80        <scalar label="strainAliases" type="CHAR(250)" />
81      </array>
82      <scalar label="gramStain" type="CHAR(125)" />      <scalar label="gramStain" type="CHAR(125)" />
83      <scalar label="taxid" type="CHAR(16)" />      <scalar label="taxid" type="CHAR(16)" />
84      <scalar label="figid" type="CHAR(16)" />
85      <scalar label="ncNumber" type="CHAR(125)" />      <scalar label="ncNumber" type="CHAR(125)" />
86      <scalar label="ncbiNumber" type="INT" />      <scalar label="ncbiNumber" type="INT" />
87      <scalar label="CMRAlias" type="CHAR(125)" />      <scalar label="CMRAlias" type="CHAR(125)" />
88      <scalar label="CMRID" type="INT" />      <scalar label="CMRID" type="INT" />
89      <scalar label="goldstamp" type="CHAR(125)" />
90      <scalar label="carbon" type="CHAR(250)" />      <scalar label="carbon" type="CHAR(250)" />
91      <scalar label="chromosomeType" type="CHAR(250)" />      <scalar label="chromosomeType" type="CHAR(250)" />
     <object label="Contact" type="Contact" />  
     <array>  
       <object label="FundingOrganisation" type="Institution" />  
     </array>  
     <array>  
       <object label="GenomeDatabase" type="GenomeDatabase" />  
     </array>  
     <array>  
       <object label="Institution" type="Institution" />  
     </array>  
92      <scalar label="desease" type="INT" />      <scalar label="desease" type="INT" />
93      <scalar label="energy" type="CHAR(250)" />      <scalar label="energy" type="CHAR(250)" />
94      <scalar label="oxygen" type="CHAR(250)" />      <scalar label="oxygen" type="CHAR(250)" />
# Line 71  Line 100 
100      <scalar label="extremophile" type="CHAR(250)" />      <scalar label="extremophile" type="CHAR(250)" />
101      <scalar label="shape" type="CHAR(125)" />      <scalar label="shape" type="CHAR(125)" />
102      <scalar label="width" type="FLOAT" />      <scalar label="width" type="FLOAT" />
     <scalar label="genomeSize" type="INT" />  
     <scalar label="noORFs" type="INT" />  
103      <scalar label="motile" type="CHAR(125)" />      <scalar label="motile" type="CHAR(125)" />
104      <scalar label="numberChromosomes" type="INT" />      <scalar label="numberChromosomes" type="INT" />
105      <scalar label="totalReplicons" type="INT" />      <scalar label="totalReplicons" type="INT" />
106      <scalar label="hxh" type="INT" />      <scalar label="hxh" type="INT" />
107      <scalar label="sequencingStatus" type="CHAR(250)" />      <scalar label="sequencingStatus" type="CHAR(250)" />
108      <scalar label="orderOfPublication" type="INT" />      <scalar label="orderOfPublication" type="INT" />
109      <object label="Publication" type="Publication" />    <scalar label="InBergey" type="INT" />
110      <scalar label="InGOLD" type="INT" />
111      <scalar label="InNCBI" type="INT" />
112      <scalar label="InDSMZ" type="INT" />
113      <scalar label="InCCUG" type="INT" />
114      <scalar label="InSEED" type="INT" />
115      <scalar label="InGenomeData" type="INT" />
116      <scalar label="InSTS" type="INT" />
117      <!-- added from andi's schema from now on -->
118      <scalar label="genetic_code" type="CHAR(255)" /> <!-- Genetic code of an organism --> <!--  (describing translation and use of start codons) -->
119      <scalar label="estiGenomeSize" type="INT" />
120      <scalar label="cultivationStatus" type="CHAR(255)" /> <!-- Flag for the procedure of cultivating an organism, it can be e.g. easy, hard, mediumm, slow ... --> <!-- Flags have to be discussed -->
121      <array>      <array>
122        <scalar label="addFeatures" type="CHAR(250)" />        <scalar label="addFeatures" type="CHAR(250)" />
123      </array>      </array>
124    </object>    </object>
125    
126    <object label="GenomeSequence">
127        <object label="Genome" type="Genome" mandatory="1" /> <!--  Organism a sequence belongs to -->
128        <scalar label="version" type="int" /> <!-- Version number of the sequence -->
129        <scalar label="project" type="CHAR(255)"/> <!-- Number of Genome project --> <!-- I'm not sure if it is always a number -->
130        <object label="Contact" type="Contact" />
131        <array>
132          <object label="FundingOrganisation" type="Institution" />
133        </array>
134        <array>
135          <object label="GenomeDatabase" type="GenomeDatabase" />
136        </array>
137        <array>
138          <object label="Institution" type="Institution" />
139        </array>
140        <scalar label="sequenceLength" type="INT"/> <!-- length of sequence -->
141        <scalar label="releaseDate" type="int"/> <!-- Release date of the sequence -->
142        <scalar label="sequenceQuality" type="CHAR(255)"/> <!-- Quality of the sequence calculated by Ross's tool -->
143        <object label="sequenceFile" type="GenomesDB::File"/> <!-- File the genome sequence is extracted from -->
144        <scalar label="sequenceSourceLink" type="CHAR(255)"/> <!-- URL of the site providing the sequence/genome file  -->
145        <scalar label="sequenceChecksum" type="int"/>
146        <scalar label="type" type="char(50)"/> <!-- Is complete genome sequence or plasmid, ... -->
147        <scalar label="lastUpdate" type="char(255)"/>
148        <scalar label="seedID" type="VARCHAR(255)"/> <!-- ID of the sequence in the SEED -->
149        <scalar label="insertionDate" type="int"/> <!-- Date when the genome was loaded into the SEED-->
150        <scalar label="genecalling" type="char(255)"/> <!-- Name of gencaller or repository if no gencaller information is available -->
151        <object label="genecallingSop" type="SOP"/> <!-- Standard Operating Procedure for the gene calling-->
152        <scalar label="genecallingDate" type="int" /> <!-- Date of the genecalling -->
153        <scalar label="seedStatus" type="CHAR(50)"/> <!-- Status of the genome sequence describing the relation to the SEED, e.g. is new, is in seed or rejected, ... -->
154        <scalar label="comment" type="CHAR(255)"/> <!-- additional comment for the status, e.g. is required for describing the reasons of rejecting a sequence -->
155        <scalar label="noORFs" type="INT" />
156        <object label="Publication" type="Publication" />
157    </object>
158    
159    
160    <object label="GenomeAlias">
161      <scalar label="name" type="CHAR(250)" />
162      <scalar label="scientificName" type="CHAR(250)" />
163      <scalar label="taxid" type="INT" />
164      <scalar label="ident" type="INT" />
165      <scalar label="aliasType" type="CHAR(250)" />
166    </object>
167    
168  <object label="Publication">  <object label="Publication">
169    <scalar label="pubmed" type="INT" />    <scalar label="pubmed" type="INT" />
170    <scalar label="url" type="CHAR(250)" />    <scalar label="url" type="CHAR(250)" />
# Line 115  Line 195 
195    <scalar label="value" type="CHAR(250)" />    <scalar label="value" type="CHAR(250)" />
196  </object>  </object>
197    
198    <object label="SOP">
199      <scalar label="name" type="CHAR(50)"/> <!-- Name (Unique ID) of a given SOP -->
200      <scalar label="date" type="DATE"/> <!-- Date of changes/updates or creation in the SOP -->
201      <scalar label="url" type="CHAR(255)"/> <!-- where to find the SOP -->
202      <scalar label="note" type="TEXT"/>
203      <index>
204          <attribute label="name"/>
205          <attribute label="date"/>
206      </index>
207    </object>
208    
209    <object label="SequenceLog">
210      <object label="sequence" type="GenomesDB::GenomeSequence"/> <!-- Sequence for that an event occured -->
211      <scalar label="event" type="CHAR(255)"/> <!-- Event during the sequencing process, e.g. Start, Finished, ... -->
212      <scalar label="note" type="CHAR(255)"/> <!-- Detailed describtion of the event -->
213      <scalar label="date" type="int"/> <!-- Date of the event -->
214      <object label="organism" type="GenomesDB::Organism"/>
215    </object>
216    
217    <object label="File">
218      <scalar label="name" type="VARCHAR(255)" mandatory="1" /> <!-- File name -->
219      <scalar label="path" type="VARCHAR(255)" mandatory="1" /> <!-- Local path to the file -->
220      <scalar label="file_type" type="VARCHAR(25)" /> <!-- Describing type or format of the file, e.g. is fasta, embl or genbank -->
221      <scalar label="sequence_type" type="CHAR(25)" /> <!-- Can be DNA or AA , a file should either contain only DNA or AA sequences-->
222      <scalar label="creation_time" type="int" mandatory="1" /> <!-- Date and time of the creation of the file -->
223      <scalar label="uid" type="text" /> <!-- User id of the file -->
224      <index>
225        <attribute label="name" />
226        <attribute label="path" />
227        <attribute label="creation_time"/>
228      </index>
229    </object>
230    
231  </project_space>  </project_space>

Legend:
Removed from v.1.2  
changed lines
  Added in v.1.17

MCS Webmaster
ViewVC Help
Powered by ViewVC 1.0.3