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Annotation of /GBBergeyDB/GBBergeyDB.xml

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Revision 1.6 - (view) (download) (as text)

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

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