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Annotation of /GBBergeyDB/GBBergeyDB.xml

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Revision 1.3 - (view) (download) (as text)

1 : bartels 1.1 <?xml version="1.0" encoding="UTF-8"?>
2 :    
3 : bartels 1.3 <project_space label="GBergeyDB" 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 1.1 </object>
39 :    
40 :     <object label="Genome">
41 :     <scalar label="name" type="CHAR(250)" />
42 :     <object label="Genus" type="Genus" />
43 : bartels 1.2 <object label="Species" type="Species" />
44 : bartels 1.1 <scalar label="strain" type="CHAR(125)" />
45 :     <scalar label="gramStain" type="CHAR(125)" />
46 :     <scalar label="taxid" type="CHAR(16)" />
47 :     <scalar label="ncNumber" type="CHAR(125)" />
48 :     <scalar label="ncbiNumber" type="INT" />
49 :     <scalar label="CMRAlias" type="CHAR(125)" />
50 :     <scalar label="CMRID" type="INT" />
51 :     <scalar label="carbon" type="CHAR(250)" />
52 :     <scalar label="chromosomeType" type="CHAR(250)" />
53 : bartels 1.3 <!--
54 : bartels 1.1 <object label="Contact" type="Contact" />
55 : bartels 1.2 <array>
56 :     <object label="FundingOrganisation" type="Institution" />
57 :     </array>
58 :     <array>
59 :     <object label="GenomeDatabase" type="GenomeDatabase" />
60 :     </array>
61 :     <array>
62 :     <object label="Institution" type="Institution" />
63 :     </array>
64 : bartels 1.3 -->
65 : bartels 1.1 <scalar label="desease" type="INT" />
66 : bartels 1.2 <scalar label="energy" type="CHAR(250)" />
67 : bartels 1.1 <scalar label="oxygen" type="CHAR(250)" />
68 :     <scalar label="obligate" type="CHAR(125)" />
69 :     <scalar label="doubleTimeMins" type="INT" />
70 :     <scalar label="pH" type="FLOAT" />
71 :     <scalar label="temperature" type="INT" />
72 :     <scalar label="habitat" type="CHAR(250)" />
73 :     <scalar label="extremophile" type="CHAR(250)" />
74 :     <scalar label="shape" type="CHAR(125)" />
75 :     <scalar label="width" type="FLOAT" />
76 : bartels 1.3 <!-- <scalar label="genomeSize" type="INT" /> -->
77 :     <!-- <scalar label="noORFs" type="INT" /> -->
78 : bartels 1.1 <scalar label="motile" type="CHAR(125)" />
79 :     <scalar label="numberChromosomes" type="INT" />
80 :     <scalar label="totalReplicons" type="INT" />
81 : bartels 1.2 <scalar label="hxh" type="INT" />
82 : bartels 1.1 <scalar label="sequencingStatus" type="CHAR(250)" />
83 :     <scalar label="orderOfPublication" type="INT" />
84 : bartels 1.3 <!-- <object label="Publication" type="Publication" /> -->
85 : bartels 1.2 <array>
86 :     <scalar label="addFeatures" type="CHAR(250)" />
87 :     </array>
88 : bartels 1.3 <!-- added from andi's schema from now on -->
89 :     <scalar label="genetic_code" type="CHAR(255)" /> <!-- Genetic code of an organism --> <!-- (describing translation and use of start codons) -->
90 :     <scalar label="estiGenomeSize" type="INT" />
91 :     <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 -->
92 : bartels 1.1 </object>
93 :    
94 : bartels 1.3
95 :     <object label="GenomeSequence">
96 :     <object label="Genome" type="Genome" mandatory="1" /> <!-- Organism a sequence belongs to -->
97 :     <scalar label="version" type="int" /> <!-- Version number of the sequence -->
98 :     <scalar label="project" type="CHAR(255)"/> <!-- Number of Genome project --> <!-- I'm not sure if it is always a number -->
99 :     <object label="Contact" type="Contact" />
100 :     <array>
101 :     <object label="FundingOrganisation" type="Institution" />
102 :     </array>
103 :     <array>
104 :     <object label="GenomeDatabase" type="GenomeDatabase" />
105 :     </array>
106 :     <array>
107 :     <object label="Institution" type="Institution" />
108 :     </array>
109 :     <scalar label="sequenceLength" type="INT"/> <!-- length of sequence -->
110 :     <scalar label="releaseDate" type="int"/> <!-- Release date of the sequence -->
111 :     <scalar label="sequenceQuality" type="CHAR(255)"/> <!-- Quality of the sequence calculated by Ross's tool -->
112 :     <object label="sequenceFile" type="GenomesDB::File"/> <!-- File the genome sequence is extracted from -->
113 :     <scalar label="sequenceSourceLink" type="CHAR(255)"/> <!-- URL of the site providing the sequence/genome file -->
114 :     <scalar label="sequenceChecksum" type="int"/>
115 :     <scalar label="type" type="char(50)"/> <!-- Is complete genome sequence or plasmid, ... -->
116 :     <scalar label="lastUpdate" type="char(255)"/>
117 :     <scalar label="seedID" type="VARCHAR(255)"/> <!-- ID of the sequence in the SEED -->
118 :     <scalar label="insertionDate" type="int"/> <!-- Date when the genome was loaded into the SEED-->
119 :     <scalar label="genecalling" type="char(255)"/> <!-- Name of gencaller or repository if no gencaller information is available -->
120 :     <object label="genecallingSop" type="SOP"/> <!-- Standard Operating Procedure for the gene calling-->
121 :     <scalar label="genecallingDate" type="int" /> <!-- Date of the genecalling -->
122 :     <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, ... -->
123 :     <scalar label="comment" type="CHAR(255)"/> <!-- additional comment for the status, e.g. is required for describing the reasons of rejecting a sequence -->
124 :     <scalar label="noORFs" type="INT" />
125 :     <object label="Publication" type="Publication" />
126 :     </object>
127 :    
128 :    
129 : bartels 1.1 <object label="Publication">
130 :     <scalar label="pubmed" type="INT" />
131 :     <scalar label="url" type="CHAR(250)" />
132 :     <scalar label="year" type="INT" />
133 :     <scalar label="journal" type="CHAR(250)" />
134 :     <scalar label="number" type="INT" />
135 :     <scalar label="pages" type="CHAR(250)" />
136 :     </object>
137 :    
138 : bartels 1.2 <object label="Institution">
139 : bartels 1.1 <scalar label="name" type="CHAR(250)" />
140 :     <scalar label="url" type="CHAR(250)" />
141 :     </object>
142 :    
143 :     <object label="GenomeDatabase">
144 :     <scalar label="name" type="CHAR(250)" />
145 :     <scalar label="url" type="CHAR(250)" />
146 :     </object>
147 :    
148 :     <object label="Contact">
149 :     <scalar label="name" type="CHAR(250)" />
150 :     <scalar label="url" type="CHAR(250)" />
151 :     <scalar label="email" type="CHAR(250)" />
152 :     </object>
153 :    
154 :     <object label="GenomeFeatures">
155 :     <scalar label="name" type="CHAR(250)" />
156 :     <scalar label="value" type="CHAR(250)" />
157 :     </object>
158 :    
159 : bartels 1.3 <object label="SOP">
160 :     <scalar label="name" type="CHAR(50)"/> <!-- Name (Unique ID) of a given SOP -->
161 :     <scalar label="date" type="DATE"/> <!-- Date of changes/updates or creation in the SOP -->
162 :     <scalar label="url" type="CHAR(255)"/> <!-- where to find the SOP -->
163 :     <scalar label="note" type="TEXT"/>
164 :     <index>
165 :     <attribute label="name"/>
166 :     <attribute label="date"/>
167 :     </index>
168 :     </object>
169 :    
170 :     <object label="SequenceLog">
171 :     <object label="sequence" type="GenomesDB::GenomeSequence"/> <!-- Sequence for that an event occured -->
172 :     <scalar label="event" type="CHAR(255)"/> <!-- Event during the sequencing process, e.g. Start, Finished, ... -->
173 :     <scalar label="note" type="CHAR(255)"/> <!-- Detailed describtion of the event -->
174 :     <scalar label="date" type="int"/> <!-- Date of the event -->
175 :     <object label="organism" type="GenomesDB::Organism"/>
176 :     </object>
177 :    
178 :     <object label="File">
179 :     <scalar label="name" type="VARCHAR(255)" mandatory="1" /> <!-- File name -->
180 :     <scalar label="path" type="VARCHAR(255)" mandatory="1" /> <!-- Local path to the file -->
181 :     <scalar label="file_type" type="VARCHAR(25)" /> <!-- Describing type or format of the file, e.g. is fasta, embl or genbank -->
182 :     <scalar label="sequence_type" type="CHAR(25)" /> <!-- Can be DNA or AA , a file should either contain only DNA or AA sequences-->
183 :     <scalar label="creation_time" type="int" mandatory="1" /> <!-- Date and time of the creation of the file -->
184 :     <scalar label="uid" type="text" /> <!-- User id of the file -->
185 :     <index>
186 :     <attribute label="name" />
187 :     <attribute label="path" />
188 :     <attribute label="creation_time"/>
189 :     </index>
190 :     </object>
191 :    
192 : bartels 1.1 </project_space>

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