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revision 1.2, Wed Jan 17 13:42:44 2007 UTC revision 1.13, Wed Feb 21 17:11:00 2007 UTC
# Line 35  Line 35 
35  <object label="Species">  <object label="Species">
36    <scalar label="name" type="CHAR(250)" />    <scalar label="name" type="CHAR(250)" />
37    <object label="Genus" type="Genus" />    <object label="Genus" type="Genus" />
38      <object label="ScientificSpecies" type="Species" />
39      <scalar label="userflag1" type="INT" />
40      <scalar label="userflag2" type="INT" />
41      <scalar label="userflag3" type="INT" />
42      <scalar label="userflag4" type="INT" />
43      <scalar label="computedscore" type="INT" />
44      <scalar label="score" type="INT" />
45      <scalar label="taxid" type="INT" />
46    </object>
47    
48    <object label="Note">
49      <scalar label="user" type="CHAR(250)" />
50      <scalar label="description" type="CHAR(250)" />
51      <scalar label="timestamp" type="INT" />
52      <scalar label="voting" type="INT" />
53      <scalar label="confidence" type="INT" />
54      <object label="Strain" type="Genome" />
55      <object label="Species" type="Species" />
56    </object>
57    
58    <object label="STScluster">
59      <scalar label="number" type="INT" />
60      <scalar label="seqrepresentation" type="INT" />
61  </object>  </object>
62    
63    <object label="Genome">    <object label="Genome">
64      <scalar label="name" type="CHAR(250)" />      <scalar label="name" type="CHAR(250)" />
65      <object label="Genus" type="Genus" />    <object label="STScluster" type="STScluster" />
66      <scalar label="STSvalue" type="FLOAT" />
67      <object label="Species" type="Species" />      <object label="Species" type="Species" />
68      <scalar label="strain" type="CHAR(125)" />    <scalar label="typeStrain" type="INT" />
69      <array>
70        <scalar label="strainAliases" type="CHAR(250)" />
71      </array>
72      <scalar label="gramStain" type="CHAR(125)" />      <scalar label="gramStain" type="CHAR(125)" />
73      <scalar label="taxid" type="CHAR(16)" />      <scalar label="taxid" type="CHAR(16)" />
74      <scalar label="figid" type="CHAR(16)" />
75      <scalar label="ncNumber" type="CHAR(125)" />      <scalar label="ncNumber" type="CHAR(125)" />
76      <scalar label="ncbiNumber" type="INT" />      <scalar label="ncbiNumber" type="INT" />
77      <scalar label="CMRAlias" type="CHAR(125)" />      <scalar label="CMRAlias" type="CHAR(125)" />
78      <scalar label="CMRID" type="INT" />      <scalar label="CMRID" type="INT" />
79      <scalar label="goldstamp" type="CHAR(125)" />
80      <scalar label="carbon" type="CHAR(250)" />      <scalar label="carbon" type="CHAR(250)" />
81      <scalar label="chromosomeType" type="CHAR(250)" />      <scalar label="chromosomeType" type="CHAR(250)" />
     <object label="Contact" type="Contact" />  
     <array>  
       <object label="FundingOrganisation" type="Institution" />  
     </array>  
     <array>  
       <object label="GenomeDatabase" type="GenomeDatabase" />  
     </array>  
     <array>  
       <object label="Institution" type="Institution" />  
     </array>  
82      <scalar label="desease" type="INT" />      <scalar label="desease" type="INT" />
83      <scalar label="energy" type="CHAR(250)" />      <scalar label="energy" type="CHAR(250)" />
84      <scalar label="oxygen" type="CHAR(250)" />      <scalar label="oxygen" type="CHAR(250)" />
# Line 71  Line 90 
90      <scalar label="extremophile" type="CHAR(250)" />      <scalar label="extremophile" type="CHAR(250)" />
91      <scalar label="shape" type="CHAR(125)" />      <scalar label="shape" type="CHAR(125)" />
92      <scalar label="width" type="FLOAT" />      <scalar label="width" type="FLOAT" />
     <scalar label="genomeSize" type="INT" />  
     <scalar label="noORFs" type="INT" />  
93      <scalar label="motile" type="CHAR(125)" />      <scalar label="motile" type="CHAR(125)" />
94      <scalar label="numberChromosomes" type="INT" />      <scalar label="numberChromosomes" type="INT" />
95      <scalar label="totalReplicons" type="INT" />      <scalar label="totalReplicons" type="INT" />
96      <scalar label="hxh" type="INT" />      <scalar label="hxh" type="INT" />
97      <scalar label="sequencingStatus" type="CHAR(250)" />      <scalar label="sequencingStatus" type="CHAR(250)" />
98      <scalar label="orderOfPublication" type="INT" />      <scalar label="orderOfPublication" type="INT" />
99      <object label="Publication" type="Publication" />    <scalar label="InBergey" type="INT" />
100      <scalar label="InGOLD" type="INT" />
101      <scalar label="InNCBI" type="INT" />
102      <scalar label="InDSMZ" type="INT" />
103      <scalar label="InCCUG" type="INT" />
104      <scalar label="InSEED" type="INT" />
105      <scalar label="InGenomeData" type="INT" />
106      <scalar label="InSTS" type="INT" />
107      <!-- added from andi's schema from now on -->
108      <scalar label="genetic_code" type="CHAR(255)" /> <!-- Genetic code of an organism --> <!--  (describing translation and use of start codons) -->
109      <scalar label="estiGenomeSize" type="INT" />
110      <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 -->
111      <array>      <array>
112        <scalar label="addFeatures" type="CHAR(250)" />        <scalar label="addFeatures" type="CHAR(250)" />
113      </array>      </array>
114    </object>    </object>
115    
116    <object label="GenomeSequence">
117        <object label="Genome" type="Genome" mandatory="1" /> <!--  Organism a sequence belongs to -->
118        <scalar label="version" type="int" /> <!-- Version number of the sequence -->
119        <scalar label="project" type="CHAR(255)"/> <!-- Number of Genome project --> <!-- I'm not sure if it is always a number -->
120        <object label="Contact" type="Contact" />
121        <array>
122          <object label="FundingOrganisation" type="Institution" />
123        </array>
124        <array>
125          <object label="GenomeDatabase" type="GenomeDatabase" />
126        </array>
127        <array>
128          <object label="Institution" type="Institution" />
129        </array>
130        <scalar label="sequenceLength" type="INT"/> <!-- length of sequence -->
131        <scalar label="releaseDate" type="int"/> <!-- Release date of the sequence -->
132        <scalar label="sequenceQuality" type="CHAR(255)"/> <!-- Quality of the sequence calculated by Ross's tool -->
133        <object label="sequenceFile" type="GenomesDB::File"/> <!-- File the genome sequence is extracted from -->
134        <scalar label="sequenceSourceLink" type="CHAR(255)"/> <!-- URL of the site providing the sequence/genome file  -->
135        <scalar label="sequenceChecksum" type="int"/>
136        <scalar label="type" type="char(50)"/> <!-- Is complete genome sequence or plasmid, ... -->
137        <scalar label="lastUpdate" type="char(255)"/>
138        <scalar label="seedID" type="VARCHAR(255)"/> <!-- ID of the sequence in the SEED -->
139        <scalar label="insertionDate" type="int"/> <!-- Date when the genome was loaded into the SEED-->
140        <scalar label="genecalling" type="char(255)"/> <!-- Name of gencaller or repository if no gencaller information is available -->
141        <object label="genecallingSop" type="SOP"/> <!-- Standard Operating Procedure for the gene calling-->
142        <scalar label="genecallingDate" type="int" /> <!-- Date of the genecalling -->
143        <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, ... -->
144        <scalar label="comment" type="CHAR(255)"/> <!-- additional comment for the status, e.g. is required for describing the reasons of rejecting a sequence -->
145        <scalar label="noORFs" type="INT" />
146        <object label="Publication" type="Publication" />
147    </object>
148    
149    
150    <object label="GenomeAlias">
151      <scalar label="name" type="CHAR(250)" />
152      <scalar label="scientificName" type="CHAR(250)" />
153      <scalar label="taxid" type="INT" />
154      <scalar label="ident" type="INT" />
155      <scalar label="aliasType" type="CHAR(250)" />
156    </object>
157    
158  <object label="Publication">  <object label="Publication">
159    <scalar label="pubmed" type="INT" />    <scalar label="pubmed" type="INT" />
160    <scalar label="url" type="CHAR(250)" />    <scalar label="url" type="CHAR(250)" />
# Line 115  Line 185 
185    <scalar label="value" type="CHAR(250)" />    <scalar label="value" type="CHAR(250)" />
186  </object>  </object>
187    
188    <object label="SOP">
189      <scalar label="name" type="CHAR(50)"/> <!-- Name (Unique ID) of a given SOP -->
190      <scalar label="date" type="DATE"/> <!-- Date of changes/updates or creation in the SOP -->
191      <scalar label="url" type="CHAR(255)"/> <!-- where to find the SOP -->
192      <scalar label="note" type="TEXT"/>
193      <index>
194          <attribute label="name"/>
195          <attribute label="date"/>
196      </index>
197    </object>
198    
199    <object label="SequenceLog">
200      <object label="sequence" type="GenomesDB::GenomeSequence"/> <!-- Sequence for that an event occured -->
201      <scalar label="event" type="CHAR(255)"/> <!-- Event during the sequencing process, e.g. Start, Finished, ... -->
202      <scalar label="note" type="CHAR(255)"/> <!-- Detailed describtion of the event -->
203      <scalar label="date" type="int"/> <!-- Date of the event -->
204      <object label="organism" type="GenomesDB::Organism"/>
205    </object>
206    
207    <object label="File">
208      <scalar label="name" type="VARCHAR(255)" mandatory="1" /> <!-- File name -->
209      <scalar label="path" type="VARCHAR(255)" mandatory="1" /> <!-- Local path to the file -->
210      <scalar label="file_type" type="VARCHAR(25)" /> <!-- Describing type or format of the file, e.g. is fasta, embl or genbank -->
211      <scalar label="sequence_type" type="CHAR(25)" /> <!-- Can be DNA or AA , a file should either contain only DNA or AA sequences-->
212      <scalar label="creation_time" type="int" mandatory="1" /> <!-- Date and time of the creation of the file -->
213      <scalar label="uid" type="text" /> <!-- User id of the file -->
214      <index>
215        <attribute label="name" />
216        <attribute label="path" />
217        <attribute label="creation_time"/>
218      </index>
219    </object>
220    
221  </project_space>  </project_space>

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