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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 :     </object>
8 :    
9 :     <object label="Phyla">
10 :     <scalar label="name" type="CHAR(250)" />
11 :     <object label="Domain" type="Domain" />
12 :     </object>
13 : bartels 1.2
14 : bartels 1.1 <object label="Class">
15 :     <scalar label="name" type="CHAR(250)" />
16 :     <object label="Phyla" type="Phyla" />
17 :     </object>
18 :    
19 : bartels 1.2 <object label="GOrder">
20 : bartels 1.1 <scalar label="name" type="CHAR(250)" />
21 :     <object label="Class" type="Class" />
22 :     </object>
23 :    
24 :     <object label="Family">
25 :     <scalar label="name" type="CHAR(250)" />
26 : bartels 1.2 <object label="GOrder" type="GOrder" />
27 : bartels 1.1 </object>
28 :    
29 :     <object label="Genus">
30 :     <scalar label="name" type="CHAR(250)" />
31 :     <object label="Family" type="Family" />
32 : bartels 1.2 <scalar label="form" type="INT"/>
33 :     </object>
34 :    
35 :     <object label="Species">
36 :     <scalar label="name" type="CHAR(250)" />
37 :     <object label="Genus" type="Genus" />
38 : bartels 1.5 <object label="ScientificSpecies" type="Species" />
39 : bartels 1.6 <scalar label="userflag1" type="INT" />
40 :     <scalar label="userflag2" type="INT" />
41 :     <scalar label="userflag3" type="INT" />
42 :     <scalar label="userflag4" type="INT" />
43 : bartels 1.8 <scalar label="computedscore" type="INT" />
44 :     <scalar label="score" type="INT" />
45 : bartels 1.1 </object>
46 :    
47 : bartels 1.4 <object label="Note">
48 :     <scalar label="user" type="CHAR(250)" />
49 :     <scalar label="description" type="CHAR(250)" />
50 :     <scalar label="timestamp" type="INT" />
51 :     <scalar label="voting" type="INT" />
52 : bartels 1.5 <scalar label="confidence" type="INT" />
53 :     <object label="Strain" type="Genome" />
54 : bartels 1.7 <object label="Species" type="Species" />
55 : bartels 1.9 <scalar label="taxid" type="INT" />
56 : bartels 1.4 </object>
57 :    
58 :     <object label="STScluster">
59 :     <scalar label="number" type="INT" />
60 :     <scalar label="seqrepresentation" type="INT" />
61 :     </object>
62 :    
63 :     <object label="Genome">
64 :     <scalar label="name" type="CHAR(250)" />
65 : bartels 1.8 es-> <object label="STScluster" type="STScluster" />
66 : bartels 1.4 <scalar label="STSvalue" type="FLOAT" />
67 :     <object label="Species" type="Species" />
68 : bartels 1.5 <scalar label="typeStrain" type="INT" />
69 :     <array>
70 :     <scalar label="strainAliases" type="CHAR(250)" />
71 :     </array>
72 : bartels 1.4 <scalar label="gramStain" type="CHAR(125)" />
73 :     <scalar label="taxid" type="CHAR(16)" />
74 :     <scalar label="ncNumber" type="CHAR(125)" />
75 :     <scalar label="ncbiNumber" type="INT" />
76 :     <scalar label="CMRAlias" type="CHAR(125)" />
77 :     <scalar label="CMRID" type="INT" />
78 : bartels 1.9 <scalar label="goldstamp" type="CHAR(125)" />
79 : bartels 1.4 <scalar label="carbon" type="CHAR(250)" />
80 :     <scalar label="chromosomeType" type="CHAR(250)" />
81 :     <scalar label="desease" type="INT" />
82 :     <scalar label="energy" type="CHAR(250)" />
83 :     <scalar label="oxygen" type="CHAR(250)" />
84 :     <scalar label="obligate" type="CHAR(125)" />
85 :     <scalar label="doubleTimeMins" type="INT" />
86 :     <scalar label="pH" type="FLOAT" />
87 :     <scalar label="temperature" type="INT" />
88 :     <scalar label="habitat" type="CHAR(250)" />
89 :     <scalar label="extremophile" type="CHAR(250)" />
90 :     <scalar label="shape" type="CHAR(125)" />
91 :     <scalar label="width" type="FLOAT" />
92 :     <scalar label="motile" type="CHAR(125)" />
93 :     <scalar label="numberChromosomes" type="INT" />
94 :     <scalar label="totalReplicons" type="INT" />
95 :     <scalar label="hxh" type="INT" />
96 :     <scalar label="sequencingStatus" type="CHAR(250)" />
97 :     <scalar label="orderOfPublication" type="INT" />
98 :     <scalar label="InBergey" type="INT" />
99 :     <scalar label="InGOLD" type="INT" />
100 :     <scalar label="InNCBI" type="INT" />
101 : bartels 1.5 <scalar label="InDSMZ" type="INT" />
102 :     <scalar label="InCCUG" type="INT" />
103 : bartels 1.10 <scalar label="InSEED" type="INT" />
104 : bartels 1.4 <scalar label="InGenomeData" type="INT" />
105 :     <scalar label="InSTS" type="INT" />
106 :     <!-- added from andi's schema from now on -->
107 :     <scalar label="genetic_code" type="CHAR(255)" /> <!-- Genetic code of an organism --> <!-- (describing translation and use of start codons) -->
108 :     <scalar label="estiGenomeSize" type="INT" />
109 :     <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 -->
110 :     <array>
111 :     <scalar label="addFeatures" type="CHAR(250)" />
112 :     </array>
113 :     </object>
114 : bartels 1.3
115 :     <object label="GenomeSequence">
116 :     <object label="Genome" type="Genome" mandatory="1" /> <!-- Organism a sequence belongs to -->
117 :     <scalar label="version" type="int" /> <!-- Version number of the sequence -->
118 :     <scalar label="project" type="CHAR(255)"/> <!-- Number of Genome project --> <!-- I'm not sure if it is always a number -->
119 :     <object label="Contact" type="Contact" />
120 :     <array>
121 :     <object label="FundingOrganisation" type="Institution" />
122 :     </array>
123 :     <array>
124 :     <object label="GenomeDatabase" type="GenomeDatabase" />
125 :     </array>
126 :     <array>
127 :     <object label="Institution" type="Institution" />
128 :     </array>
129 :     <scalar label="sequenceLength" type="INT"/> <!-- length of sequence -->
130 :     <scalar label="releaseDate" type="int"/> <!-- Release date of the sequence -->
131 :     <scalar label="sequenceQuality" type="CHAR(255)"/> <!-- Quality of the sequence calculated by Ross's tool -->
132 :     <object label="sequenceFile" type="GenomesDB::File"/> <!-- File the genome sequence is extracted from -->
133 :     <scalar label="sequenceSourceLink" type="CHAR(255)"/> <!-- URL of the site providing the sequence/genome file -->
134 :     <scalar label="sequenceChecksum" type="int"/>
135 :     <scalar label="type" type="char(50)"/> <!-- Is complete genome sequence or plasmid, ... -->
136 :     <scalar label="lastUpdate" type="char(255)"/>
137 :     <scalar label="seedID" type="VARCHAR(255)"/> <!-- ID of the sequence in the SEED -->
138 :     <scalar label="insertionDate" type="int"/> <!-- Date when the genome was loaded into the SEED-->
139 :     <scalar label="genecalling" type="char(255)"/> <!-- Name of gencaller or repository if no gencaller information is available -->
140 :     <object label="genecallingSop" type="SOP"/> <!-- Standard Operating Procedure for the gene calling-->
141 :     <scalar label="genecallingDate" type="int" /> <!-- Date of the genecalling -->
142 :     <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, ... -->
143 :     <scalar label="comment" type="CHAR(255)"/> <!-- additional comment for the status, e.g. is required for describing the reasons of rejecting a sequence -->
144 :     <scalar label="noORFs" type="INT" />
145 :     <object label="Publication" type="Publication" />
146 :     </object>
147 :    
148 :    
149 : bartels 1.4 <object label="GenomeAlias">
150 :     <scalar label="name" type="CHAR(250)" />
151 :     <scalar label="scientificName" type="CHAR(250)" />
152 : bartels 1.9 <scalar label="taxid" type="INT" />
153 :     <scalar label="ident" type="INT" />
154 :     <scalar label="aliasType" type="CHAR(250)" />
155 : bartels 1.4 </object>
156 :    
157 : bartels 1.1 <object label="Publication">
158 :     <scalar label="pubmed" type="INT" />
159 :     <scalar label="url" type="CHAR(250)" />
160 :     <scalar label="year" type="INT" />
161 :     <scalar label="journal" type="CHAR(250)" />
162 :     <scalar label="number" type="INT" />
163 :     <scalar label="pages" type="CHAR(250)" />
164 :     </object>
165 :    
166 : bartels 1.2 <object label="Institution">
167 : bartels 1.1 <scalar label="name" type="CHAR(250)" />
168 :     <scalar label="url" type="CHAR(250)" />
169 :     </object>
170 :    
171 :     <object label="GenomeDatabase">
172 :     <scalar label="name" type="CHAR(250)" />
173 :     <scalar label="url" type="CHAR(250)" />
174 :     </object>
175 :    
176 :     <object label="Contact">
177 :     <scalar label="name" type="CHAR(250)" />
178 :     <scalar label="url" type="CHAR(250)" />
179 :     <scalar label="email" type="CHAR(250)" />
180 :     </object>
181 :    
182 :     <object label="GenomeFeatures">
183 :     <scalar label="name" type="CHAR(250)" />
184 :     <scalar label="value" type="CHAR(250)" />
185 :     </object>
186 :    
187 : bartels 1.3 <object label="SOP">
188 :     <scalar label="name" type="CHAR(50)"/> <!-- Name (Unique ID) of a given SOP -->
189 :     <scalar label="date" type="DATE"/> <!-- Date of changes/updates or creation in the SOP -->
190 :     <scalar label="url" type="CHAR(255)"/> <!-- where to find the SOP -->
191 :     <scalar label="note" type="TEXT"/>
192 :     <index>
193 :     <attribute label="name"/>
194 :     <attribute label="date"/>
195 :     </index>
196 :     </object>
197 :    
198 :     <object label="SequenceLog">
199 :     <object label="sequence" type="GenomesDB::GenomeSequence"/> <!-- Sequence for that an event occured -->
200 :     <scalar label="event" type="CHAR(255)"/> <!-- Event during the sequencing process, e.g. Start, Finished, ... -->
201 :     <scalar label="note" type="CHAR(255)"/> <!-- Detailed describtion of the event -->
202 :     <scalar label="date" type="int"/> <!-- Date of the event -->
203 :     <object label="organism" type="GenomesDB::Organism"/>
204 :     </object>
205 :    
206 :     <object label="File">
207 :     <scalar label="name" type="VARCHAR(255)" mandatory="1" /> <!-- File name -->
208 :     <scalar label="path" type="VARCHAR(255)" mandatory="1" /> <!-- Local path to the file -->
209 :     <scalar label="file_type" type="VARCHAR(25)" /> <!-- Describing type or format of the file, e.g. is fasta, embl or genbank -->
210 :     <scalar label="sequence_type" type="CHAR(25)" /> <!-- Can be DNA or AA , a file should either contain only DNA or AA sequences-->
211 :     <scalar label="creation_time" type="int" mandatory="1" /> <!-- Date and time of the creation of the file -->
212 :     <scalar label="uid" type="text" /> <!-- User id of the file -->
213 :     <index>
214 :     <attribute label="name" />
215 :     <attribute label="path" />
216 :     <attribute label="creation_time"/>
217 :     </index>
218 :     </object>
219 :    
220 : bartels 1.1 </project_space>

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