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Annotation of /GBBergeyDB/GBBergeyDB.xml

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1 : bartels 1.1 <?xml version="1.0" encoding="UTF-8"?>
2 :    
3 : bartels 1.4 <project_space label="GBBergeyDB" superspace="GenDB">
4 : bartels 1.1
5 :     <object label="Domain">
6 :     <scalar label="name" type="CHAR(250)" />
7 : bartels 1.17 <scalar label="taxDOI" type="INT" />
8 : bartels 1.1 </object>
9 :    
10 :     <object label="Phyla">
11 :     <scalar label="name" type="CHAR(250)" />
12 :     <object label="Domain" type="Domain" />
13 : bartels 1.17 <scalar label="taxDOI" type="INT" />
14 : bartels 1.1 </object>
15 : bartels 1.2
16 : bartels 1.1 <object label="Class">
17 :     <scalar label="name" type="CHAR(250)" />
18 :     <object label="Phyla" type="Phyla" />
19 : bartels 1.17 <scalar label="taxDOI" type="INT" />
20 : bartels 1.1 </object>
21 :    
22 : bartels 1.2 <object label="GOrder">
23 : bartels 1.1 <scalar label="name" type="CHAR(250)" />
24 :     <object label="Class" type="Class" />
25 : bartels 1.17 <scalar label="taxDOI" type="INT" />
26 : bartels 1.1 </object>
27 :    
28 :     <object label="Family">
29 :     <scalar label="name" type="CHAR(250)" />
30 : bartels 1.2 <object label="GOrder" type="GOrder" />
31 : bartels 1.17 <scalar label="taxDOI" type="INT" />
32 : bartels 1.1 </object>
33 :    
34 :     <object label="Genus">
35 :     <scalar label="name" type="CHAR(250)" />
36 :     <object label="Family" type="Family" />
37 : bartels 1.2 <scalar label="form" type="INT"/>
38 : bartels 1.17 <scalar label="taxDOI" type="INT" />
39 : bartels 1.2 </object>
40 :    
41 :     <object label="Species">
42 :     <scalar label="name" type="CHAR(250)" />
43 :     <object label="Genus" type="Genus" />
44 : bartels 1.5 <object label="ScientificSpecies" type="Species" />
45 : bartels 1.6 <scalar label="userflag1" type="INT" />
46 :     <scalar label="userflag2" type="INT" />
47 :     <scalar label="userflag3" type="INT" />
48 :     <scalar label="userflag4" type="INT" />
49 : bartels 1.8 <scalar label="computedscore" type="INT" />
50 :     <scalar label="score" type="INT" />
51 : bartels 1.11 <scalar label="taxid" type="INT" />
52 : bartels 1.17 <scalar label="taxDOI" type="INT" />
53 : bartels 1.18 <scalar label="litNum" type="INT" />
54 :     <scalar label="added" type="INT" />
55 :     <array>
56 :     <scalar label="litArray" type="CHAR(250)" />
57 :     </array>
58 : bartels 1.1 </object>
59 :    
60 : bartels 1.4 <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 : bartels 1.5 <scalar label="confidence" type="INT" />
66 :     <object label="Strain" type="Genome" />
67 : bartels 1.7 <object label="Species" type="Species" />
68 : bartels 1.4 </object>
69 :    
70 :     <object label="STScluster">
71 :     <scalar label="number" type="INT" />
72 :     <scalar label="seqrepresentation" type="INT" />
73 : bartels 1.15 <object label="representative" type="Genome" />
74 : bartels 1.18 <object label="representative2" type="Genome" />
75 : bartels 1.16 <scalar label="score" type="FLOAT" />
76 : bartels 1.18 <scalar label="litCount" type="INT" />
77 : bartels 1.4 </object>
78 :    
79 :     <object label="Genome">
80 : bartels 1.18 <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 : bartels 1.13 <object label="STScluster" type="STScluster" />
92 : bartels 1.4 <scalar label="STSvalue" type="FLOAT" />
93 :     <object label="Species" type="Species" />
94 : bartels 1.5 <scalar label="typeStrain" type="INT" />
95 : bartels 1.14 <scalar label="sixTeenS" type="TEXT" />
96 : bartels 1.5 <array>
97 :     <scalar label="strainAliases" type="CHAR(250)" />
98 :     </array>
99 : bartels 1.4 <scalar label="gramStain" type="CHAR(125)" />
100 :     <scalar label="taxid" type="CHAR(16)" />
101 : bartels 1.13 <scalar label="figid" type="CHAR(16)" />
102 : bartels 1.4 <scalar label="ncNumber" type="CHAR(125)" />
103 :     <scalar label="ncbiNumber" type="INT" />
104 :     <scalar label="CMRAlias" type="CHAR(125)" />
105 :     <scalar label="CMRID" type="INT" />
106 : bartels 1.9 <scalar label="goldstamp" type="CHAR(125)" />
107 : bartels 1.4 <scalar label="carbon" type="CHAR(250)" />
108 :     <scalar label="chromosomeType" type="CHAR(250)" />
109 :     <scalar label="desease" type="INT" />
110 :     <scalar label="energy" type="CHAR(250)" />
111 :     <scalar label="oxygen" type="CHAR(250)" />
112 :     <scalar label="obligate" type="CHAR(125)" />
113 :     <scalar label="doubleTimeMins" type="INT" />
114 :     <scalar label="pH" type="FLOAT" />
115 :     <scalar label="temperature" type="INT" />
116 :     <scalar label="habitat" type="CHAR(250)" />
117 :     <scalar label="extremophile" type="CHAR(250)" />
118 :     <scalar label="shape" type="CHAR(125)" />
119 :     <scalar label="width" type="FLOAT" />
120 :     <scalar label="motile" type="CHAR(125)" />
121 :     <scalar label="numberChromosomes" type="INT" />
122 :     <scalar label="totalReplicons" type="INT" />
123 :     <scalar label="hxh" type="INT" />
124 :     <scalar label="sequencingStatus" type="CHAR(250)" />
125 :     <scalar label="orderOfPublication" type="INT" />
126 :     <scalar label="InBergey" type="INT" />
127 :     <scalar label="InGOLD" type="INT" />
128 :     <scalar label="InNCBI" type="INT" />
129 : bartels 1.5 <scalar label="InDSMZ" type="INT" />
130 :     <scalar label="InCCUG" type="INT" />
131 : bartels 1.10 <scalar label="InSEED" type="INT" />
132 : bartels 1.4 <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 : bartels 1.3
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 : bartels 1.4 <object label="GenomeAlias">
178 :     <scalar label="name" type="CHAR(250)" />
179 :     <scalar label="scientificName" type="CHAR(250)" />
180 : bartels 1.9 <scalar label="taxid" type="INT" />
181 :     <scalar label="ident" type="INT" />
182 :     <scalar label="aliasType" type="CHAR(250)" />
183 : bartels 1.4 </object>
184 :    
185 : bartels 1.1 <object label="Publication">
186 :     <scalar label="pubmed" type="INT" />
187 :     <scalar label="url" type="CHAR(250)" />
188 :     <scalar label="year" type="INT" />
189 :     <scalar label="journal" type="CHAR(250)" />
190 :     <scalar label="number" type="INT" />
191 :     <scalar label="pages" type="CHAR(250)" />
192 :     </object>
193 :    
194 : bartels 1.2 <object label="Institution">
195 : bartels 1.1 <scalar label="name" type="CHAR(250)" />
196 :     <scalar label="url" type="CHAR(250)" />
197 :     </object>
198 :    
199 :     <object label="GenomeDatabase">
200 :     <scalar label="name" type="CHAR(250)" />
201 :     <scalar label="url" type="CHAR(250)" />
202 :     </object>
203 :    
204 :     <object label="Contact">
205 :     <scalar label="name" type="CHAR(250)" />
206 :     <scalar label="url" type="CHAR(250)" />
207 :     <scalar label="email" type="CHAR(250)" />
208 :     </object>
209 :    
210 :     <object label="GenomeFeatures">
211 :     <scalar label="name" type="CHAR(250)" />
212 :     <scalar label="value" type="CHAR(250)" />
213 :     </object>
214 :    
215 : bartels 1.3 <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>
247 :    
248 : bartels 1.1 </project_space>

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