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revision 1.1.1.1, Thu Jan 11 16:16:10 2007 UTC revision 1.18, Tue Mar 27 19:08:33 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="Order">  <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="Order" type="Order" />    <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"/>
38      <scalar label="taxDOI" type="INT" />
39  </object>  </object>
40    
41    <object label="Genome">  <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      <scalar label="strain" type="CHAR(125)" />    <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      <scalar label="litNum" type="INT" />
54      <scalar label="added" type="INT" />
55      <array>
56        <scalar label="litArray" type="CHAR(250)" />
57      </array>
58    </object>
59    
60    <object label="Note">
61      <scalar label="user" type="CHAR(250)" />
62      <scalar label="description" type="CHAR(250)" />
63      <scalar label="timestamp" type="INT" />
64      <scalar label="voting" type="INT" />
65      <scalar label="confidence" type="INT" />
66      <object label="Strain" type="Genome" />
67      <object label="Species" type="Species" />
68    </object>
69    
70    <object label="STScluster">
71      <scalar label="number" type="INT" />
72      <scalar label="seqrepresentation" type="INT" />
73      <object label="representative" type="Genome" />
74      <object label="representative2" type="Genome" />
75      <scalar label="score" type="FLOAT" />
76      <scalar label="litCount" type="INT" />
77    </object>
78    
79    <object label="Genome">
80      <scalar label="inList" type="INT" />
81      <scalar label="genBank" type="CHAR(250)" />
82      <scalar label="collectionStatus" type="CHAR(250)" />
83      <scalar label="JGIStatus" type="CHAR(250)" />
84      <scalar label="name" type="CHAR(250)" />
85      <scalar label="RDPID" type="INT" />
86      <scalar label="nameDOI" type="CHAR(250)" /> <!-- delete the nm. -->
87      <scalar label="taxonDOI" type="INT" /> <!-- delete the tx. -->
88      <scalar label="exemplarDOI" type="INT" /> <!-- delete the ex. -->
89      <scalar label="prokMSAid" type="INT" /> <!--coming from GreenGenes -->
90      <scalar label="prokMSAname" type="CHAR(250)" /> <!--coming from GreenGenes -->
91      <object label="STScluster" type="STScluster" />
92      <scalar label="STSvalue" type="FLOAT" />
93      <object label="Species" type="Species" />
94      <scalar label="typeStrain" type="INT" />
95      <scalar label="sixTeenS" type="TEXT" />
96      <array>
97        <scalar label="strainAliases" type="CHAR(250)" />
98      </array>
99      <scalar label="gramStain" type="CHAR(125)" />      <scalar label="gramStain" type="CHAR(125)" />
100      <scalar label="taxid" type="CHAR(16)" />      <scalar label="taxid" type="CHAR(16)" />
101      <scalar label="figid" type="CHAR(16)" />
102      <scalar label="ncNumber" type="CHAR(125)" />      <scalar label="ncNumber" type="CHAR(125)" />
103      <scalar label="ncbiNumber" type="INT" />      <scalar label="ncbiNumber" type="INT" />
104      <scalar label="CMRAlias" type="CHAR(125)" />      <scalar label="CMRAlias" type="CHAR(125)" />
105      <scalar label="CMRID" type="INT" />      <scalar label="CMRID" type="INT" />
106      <scalar label="goldstamp" type="CHAR(125)" />
107      <scalar label="carbon" type="CHAR(250)" />      <scalar label="carbon" type="CHAR(250)" />
108      <scalar label="chromosomeType" type="CHAR(250)" />      <scalar label="chromosomeType" type="CHAR(250)" />
     <object label="Contact" type="Contact" />  
     <object label="FundingOrganisation" type="Institution" />  
     <object label="GenomeDatabase" type="GenomeDatabase" />  
     <object label="Institution" type="Institution" />  
109      <scalar label="desease" type="INT" />      <scalar label="desease" type="INT" />
110      <scalar label="energie" type="CHAR(250)" />    <scalar label="energy" type="CHAR(250)" />
111      <scalar label="oxygen" type="CHAR(250)" />      <scalar label="oxygen" type="CHAR(250)" />
112      <scalar label="obligate" type="CHAR(125)" />      <scalar label="obligate" type="CHAR(125)" />
113      <scalar label="doubleTimeMins" type="INT" />      <scalar label="doubleTimeMins" type="INT" />
# Line 58  Line 117 
117      <scalar label="extremophile" type="CHAR(250)" />      <scalar label="extremophile" type="CHAR(250)" />
118      <scalar label="shape" type="CHAR(125)" />      <scalar label="shape" type="CHAR(125)" />
119      <scalar label="width" type="FLOAT" />      <scalar label="width" type="FLOAT" />
     <scalar label="genomeSize" type="INT" />  
     <scalar label="noORFs" type="INT" />  
120      <scalar label="motile" type="CHAR(125)" />      <scalar label="motile" type="CHAR(125)" />
121      <scalar label="numberChromosomes" type="INT" />      <scalar label="numberChromosomes" type="INT" />
122      <scalar label="totalReplicons" type="INT" />      <scalar label="totalReplicons" type="INT" />
123      <scalar label="100X100" type="INT" />    <scalar label="hxh" type="INT" />
124      <scalar label="sequencingStatus" type="CHAR(250)" />      <scalar label="sequencingStatus" type="CHAR(250)" />
125      <scalar label="orderOfPublication" type="INT" />      <scalar label="orderOfPublication" type="INT" />
126      <scalar label="publication" type="Publication" />    <scalar label="InBergey" type="INT" />
127      <scalar label="InGOLD" type="INT" />
128      <scalar label="InNCBI" type="INT" />
129      <scalar label="InDSMZ" type="INT" />
130      <scalar label="InCCUG" type="INT" />
131      <scalar label="InSEED" type="INT" />
132      <scalar label="InGenomeData" type="INT" />
133      <scalar label="InSTS" type="INT" />
134      <!-- added from andi's schema from now on -->
135      <scalar label="genetic_code" type="CHAR(255)" /> <!-- Genetic code of an organism --> <!--  (describing translation and use of start codons) -->
136      <scalar label="estiGenomeSize" type="INT" />
137      <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 -->
138      <array>
139        <scalar label="addFeatures" type="CHAR(250)" />
140      </array>
141    </object>
142    
143    <object label="GenomeSequence">
144        <object label="Genome" type="Genome" mandatory="1" /> <!--  Organism a sequence belongs to -->
145        <scalar label="version" type="int" /> <!-- Version number of the sequence -->
146        <scalar label="project" type="CHAR(255)"/> <!-- Number of Genome project --> <!-- I'm not sure if it is always a number -->
147        <object label="Contact" type="Contact" />
148        <array>
149          <object label="FundingOrganisation" type="Institution" />
150        </array>
151        <array>
152          <object label="GenomeDatabase" type="GenomeDatabase" />
153        </array>
154        <array>
155          <object label="Institution" type="Institution" />
156        </array>
157        <scalar label="sequenceLength" type="INT"/> <!-- length of sequence -->
158        <scalar label="releaseDate" type="int"/> <!-- Release date of the sequence -->
159        <scalar label="sequenceQuality" type="CHAR(255)"/> <!-- Quality of the sequence calculated by Ross's tool -->
160        <object label="sequenceFile" type="GenomesDB::File"/> <!-- File the genome sequence is extracted from -->
161        <scalar label="sequenceSourceLink" type="CHAR(255)"/> <!-- URL of the site providing the sequence/genome file  -->
162        <scalar label="sequenceChecksum" type="int"/>
163        <scalar label="type" type="char(50)"/> <!-- Is complete genome sequence or plasmid, ... -->
164        <scalar label="lastUpdate" type="char(255)"/>
165        <scalar label="seedID" type="VARCHAR(255)"/> <!-- ID of the sequence in the SEED -->
166        <scalar label="insertionDate" type="int"/> <!-- Date when the genome was loaded into the SEED-->
167        <scalar label="genecalling" type="char(255)"/> <!-- Name of gencaller or repository if no gencaller information is available -->
168        <object label="genecallingSop" type="SOP"/> <!-- Standard Operating Procedure for the gene calling-->
169        <scalar label="genecallingDate" type="int" /> <!-- Date of the genecalling -->
170        <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, ... -->
171        <scalar label="comment" type="CHAR(255)"/> <!-- additional comment for the status, e.g. is required for describing the reasons of rejecting a sequence -->
172        <scalar label="noORFs" type="INT" />
173        <object label="Publication" type="Publication" />
174    </object>
175    
176    
177    <object label="GenomeAlias">
178      <scalar label="name" type="CHAR(250)" />
179      <scalar label="scientificName" type="CHAR(250)" />
180      <scalar label="taxid" type="INT" />
181      <scalar label="ident" type="INT" />
182      <scalar label="aliasType" type="CHAR(250)" />
183    </object>    </object>
184    
185  <object label="Publication">  <object label="Publication">
# Line 78  Line 191 
191    <scalar label="pages" type="CHAR(250)" />    <scalar label="pages" type="CHAR(250)" />
192  </object>  </object>
193    
194  <object label="Institiution">  <object label="Institution">
195    <scalar label="name" type="CHAR(250)" />    <scalar label="name" type="CHAR(250)" />
196    <scalar label="url" type="CHAR(250)" />    <scalar label="url" type="CHAR(250)" />
197  </object>  </object>
# Line 97  Line 210 
210  <object label="GenomeFeatures">  <object label="GenomeFeatures">
211    <scalar label="name" type="CHAR(250)" />    <scalar label="name" type="CHAR(250)" />
212    <scalar label="value" type="CHAR(250)" />    <scalar label="value" type="CHAR(250)" />
213    <object label="Genome" type="Genome" />  </object>
214    
215    <object label="SOP">
216      <scalar label="name" type="CHAR(50)"/> <!-- Name (Unique ID) of a given SOP -->
217      <scalar label="date" type="DATE"/> <!-- Date of changes/updates or creation in the SOP -->
218      <scalar label="url" type="CHAR(255)"/> <!-- where to find the SOP -->
219      <scalar label="note" type="TEXT"/>
220      <index>
221          <attribute label="name"/>
222          <attribute label="date"/>
223      </index>
224    </object>
225    
226    <object label="SequenceLog">
227      <object label="sequence" type="GenomesDB::GenomeSequence"/> <!-- Sequence for that an event occured -->
228      <scalar label="event" type="CHAR(255)"/> <!-- Event during the sequencing process, e.g. Start, Finished, ... -->
229      <scalar label="note" type="CHAR(255)"/> <!-- Detailed describtion of the event -->
230      <scalar label="date" type="int"/> <!-- Date of the event -->
231      <object label="organism" type="GenomesDB::Organism"/>
232    </object>
233    
234    <object label="File">
235      <scalar label="name" type="VARCHAR(255)" mandatory="1" /> <!-- File name -->
236      <scalar label="path" type="VARCHAR(255)" mandatory="1" /> <!-- Local path to the file -->
237      <scalar label="file_type" type="VARCHAR(25)" /> <!-- Describing type or format of the file, e.g. is fasta, embl or genbank -->
238      <scalar label="sequence_type" type="CHAR(25)" /> <!-- Can be DNA or AA , a file should either contain only DNA or AA sequences-->
239      <scalar label="creation_time" type="int" mandatory="1" /> <!-- Date and time of the creation of the file -->
240      <scalar label="uid" type="text" /> <!-- User id of the file -->
241      <index>
242        <attribute label="name" />
243        <attribute label="path" />
244        <attribute label="creation_time"/>
245      </index>
246  </object>  </object>
247    
248  </project_space>  </project_space>
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